Multiple sequence alignment - TraesCS5A01G018000

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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 TraesCS5A01G018000 chr5A 100.000 2708 0 0 1 2708 14229125 14226418 0.000000e+00 5001.0
1 TraesCS5A01G018000 chr5A 88.555 699 77 1 979 1677 14194185 14193490 0.000000e+00 845.0
2 TraesCS5A01G018000 chr5B 89.571 1189 59 36 731 1908 15187270 15186136 0.000000e+00 1448.0
3 TraesCS5A01G018000 chr5B 91.969 1021 62 13 762 1776 15053969 15054975 0.000000e+00 1413.0
4 TraesCS5A01G018000 chr5B 90.476 798 67 6 984 1776 15125742 15126535 0.000000e+00 1044.0
5 TraesCS5A01G018000 chr5B 88.445 701 77 2 979 1678 15005855 15005158 0.000000e+00 843.0
6 TraesCS5A01G018000 chr5B 92.095 506 23 8 2206 2708 15077157 15077648 0.000000e+00 697.0
7 TraesCS5A01G018000 chr5B 88.998 509 25 19 2204 2708 15182642 15182161 3.860000e-168 601.0
8 TraesCS5A01G018000 chr5B 94.203 345 17 3 1433 1776 15076598 15076940 8.590000e-145 523.0
9 TraesCS5A01G018000 chr5B 91.935 372 19 4 2340 2708 15186012 15185649 6.690000e-141 510.0
10 TraesCS5A01G018000 chr5B 89.600 125 7 5 1757 1880 15182887 15182768 1.300000e-33 154.0
11 TraesCS5A01G018000 chr5B 90.909 99 5 2 1862 1959 15076977 15077072 2.190000e-26 130.0
12 TraesCS5A01G018000 chr5B 95.946 74 3 0 1808 1881 15054969 15055042 1.320000e-23 121.0
13 TraesCS5A01G018000 chr5B 94.366 71 4 0 1811 1881 15126536 15126606 2.850000e-20 110.0
14 TraesCS5A01G018000 chr5B 95.556 45 2 0 2017 2061 15077067 15077111 3.740000e-09 73.1
15 TraesCS5A01G018000 chr2D 88.049 728 62 14 1 721 527436191 527435482 0.000000e+00 839.0
16 TraesCS5A01G018000 chr2D 86.621 725 84 13 1 721 576968437 576969152 0.000000e+00 789.0
17 TraesCS5A01G018000 chr2D 86.327 490 42 14 1 489 27639680 27639215 6.690000e-141 510.0
18 TraesCS5A01G018000 chr2D 93.662 142 8 1 2062 2202 505645782 505645923 7.600000e-51 211.0
19 TraesCS5A01G018000 chr2D 91.729 133 10 1 2062 2193 505791686 505791818 1.660000e-42 183.0
20 TraesCS5A01G018000 chr2D 86.429 140 15 4 2064 2201 498231153 498231290 1.680000e-32 150.0
21 TraesCS5A01G018000 chr7B 88.663 688 75 1 990 1677 685479126 685478442 0.000000e+00 835.0
22 TraesCS5A01G018000 chr1D 87.690 723 71 16 1 721 277331187 277330481 0.000000e+00 826.0
23 TraesCS5A01G018000 chr1D 89.466 655 65 4 68 721 102508858 102508207 0.000000e+00 824.0
24 TraesCS5A01G018000 chr7D 88.671 662 72 2 60 721 130254404 130255062 0.000000e+00 804.0
25 TraesCS5A01G018000 chr7D 79.622 476 74 17 1 472 465947970 465948426 1.210000e-83 320.0
26 TraesCS5A01G018000 chr3D 86.621 725 84 13 1 721 397103843 397103128 0.000000e+00 789.0
27 TraesCS5A01G018000 chr3D 86.639 726 79 16 1 721 581322476 581321764 0.000000e+00 787.0
28 TraesCS5A01G018000 chr3A 86.307 723 81 14 1 721 686687233 686687939 0.000000e+00 771.0
29 TraesCS5A01G018000 chr5D 86.092 719 87 10 1 718 304760589 304761295 0.000000e+00 761.0
30 TraesCS5A01G018000 chr4B 84.966 725 84 15 1 721 24514486 24513783 0.000000e+00 712.0
31 TraesCS5A01G018000 chr4B 84.211 133 21 0 1545 1677 12492320 12492188 2.190000e-26 130.0
32 TraesCS5A01G018000 chr1A 93.007 143 9 1 2062 2203 13488863 13489005 9.830000e-50 207.0
33 TraesCS5A01G018000 chr2A 91.791 134 8 3 2062 2194 650205359 650205490 1.660000e-42 183.0
34 TraesCS5A01G018000 chr2A 84.496 129 18 2 2067 2193 118462652 118462524 2.830000e-25 126.0
35 TraesCS5A01G018000 chr2A 83.088 136 19 4 2068 2200 118460415 118460281 1.320000e-23 121.0
36 TraesCS5A01G018000 chr1B 89.437 142 12 3 2062 2201 484377279 484377419 2.770000e-40 176.0
37 TraesCS5A01G018000 chr1B 98.113 53 1 0 1 53 555285791 555285739 2.870000e-15 93.5
38 TraesCS5A01G018000 chr3B 88.652 141 15 1 2062 2201 779140058 779140198 1.290000e-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 TraesCS5A01G018000 chr5A 14226418 14229125 2707 True 5001.000 5001 100.00000 1 2708 1 chr5A.!!$R2 2707
1 TraesCS5A01G018000 chr5A 14193490 14194185 695 True 845.000 845 88.55500 979 1677 1 chr5A.!!$R1 698
2 TraesCS5A01G018000 chr5B 15005158 15005855 697 True 843.000 843 88.44500 979 1678 1 chr5B.!!$R1 699
3 TraesCS5A01G018000 chr5B 15053969 15055042 1073 False 767.000 1413 93.95750 762 1881 2 chr5B.!!$F1 1119
4 TraesCS5A01G018000 chr5B 15182161 15187270 5109 True 678.250 1448 90.02600 731 2708 4 chr5B.!!$R2 1977
5 TraesCS5A01G018000 chr5B 15125742 15126606 864 False 577.000 1044 92.42100 984 1881 2 chr5B.!!$F3 897
6 TraesCS5A01G018000 chr5B 15076598 15077648 1050 False 355.775 697 93.19075 1433 2708 4 chr5B.!!$F2 1275
7 TraesCS5A01G018000 chr2D 527435482 527436191 709 True 839.000 839 88.04900 1 721 1 chr2D.!!$R2 720
8 TraesCS5A01G018000 chr2D 576968437 576969152 715 False 789.000 789 86.62100 1 721 1 chr2D.!!$F4 720
9 TraesCS5A01G018000 chr7B 685478442 685479126 684 True 835.000 835 88.66300 990 1677 1 chr7B.!!$R1 687
10 TraesCS5A01G018000 chr1D 277330481 277331187 706 True 826.000 826 87.69000 1 721 1 chr1D.!!$R2 720
11 TraesCS5A01G018000 chr1D 102508207 102508858 651 True 824.000 824 89.46600 68 721 1 chr1D.!!$R1 653
12 TraesCS5A01G018000 chr7D 130254404 130255062 658 False 804.000 804 88.67100 60 721 1 chr7D.!!$F1 661
13 TraesCS5A01G018000 chr3D 397103128 397103843 715 True 789.000 789 86.62100 1 721 1 chr3D.!!$R1 720
14 TraesCS5A01G018000 chr3D 581321764 581322476 712 True 787.000 787 86.63900 1 721 1 chr3D.!!$R2 720
15 TraesCS5A01G018000 chr3A 686687233 686687939 706 False 771.000 771 86.30700 1 721 1 chr3A.!!$F1 720
16 TraesCS5A01G018000 chr5D 304760589 304761295 706 False 761.000 761 86.09200 1 718 1 chr5D.!!$F1 717
17 TraesCS5A01G018000 chr4B 24513783 24514486 703 True 712.000 712 84.96600 1 721 1 chr4B.!!$R2 720

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
725 748 0.32121 TGGCGTGTGTCTGTTATGGG 60.321 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2519 5875 0.250234 CCATCGTGGATGTCTGTGGT 59.75 55.0 5.03 0.0 40.96 4.16 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
39 41 3.041365 CTCCTCCCTCCCTCCCAT 58.959 66.667 0.00 0.00 0.00 4.00
88 100 1.381872 AGGGAGGCTCGTAGCACAT 60.382 57.895 8.69 0.00 44.75 3.21
90 102 0.969894 GGGAGGCTCGTAGCACATAT 59.030 55.000 8.69 0.00 44.75 1.78
148 164 1.066286 CGTTTACACCCCCGGTCATAA 60.066 52.381 0.00 0.00 31.02 1.90
170 186 3.396260 TTTGTAGTGCTTAGGCGAAGT 57.604 42.857 9.14 0.00 42.25 3.01
189 206 1.137872 GTCCTGCGGAGATCACTTCAT 59.862 52.381 5.10 0.00 29.39 2.57
264 281 0.324614 TGCTGGATCAAGAAGGCGAA 59.675 50.000 0.00 0.00 0.00 4.70
268 285 1.839994 TGGATCAAGAAGGCGAAGGAT 59.160 47.619 0.00 0.00 0.00 3.24
277 294 1.079405 GGCGAAGGATGTCACCGAA 60.079 57.895 0.00 0.00 34.73 4.30
287 304 1.149361 TGTCACCGAACTGAACGTGC 61.149 55.000 0.00 0.00 0.00 5.34
288 305 1.142097 TCACCGAACTGAACGTGCA 59.858 52.632 0.00 0.00 0.00 4.57
293 310 1.920574 CCGAACTGAACGTGCATAGAG 59.079 52.381 0.00 0.00 0.00 2.43
342 360 1.942677 TCGGTTGAAGCACGAAGAAA 58.057 45.000 0.00 0.00 33.21 2.52
397 415 2.818432 CGCTTATGGTCTACGAGGGTAT 59.182 50.000 0.00 0.00 0.00 2.73
418 438 2.258109 GTAGACACACTCTCCCCCTTT 58.742 52.381 0.00 0.00 0.00 3.11
491 513 4.686191 TGTTTTCCATGCAACATTTCCT 57.314 36.364 0.00 0.00 0.00 3.36
581 603 6.040504 TGAACGGTGATAGTCATACTGCTTAT 59.959 38.462 0.00 0.00 0.00 1.73
585 607 6.294231 CGGTGATAGTCATACTGCTTATCACT 60.294 42.308 17.41 0.00 40.95 3.41
616 638 2.102070 TTGAATCGGCGGTATTGTGT 57.898 45.000 7.21 0.00 0.00 3.72
626 648 2.267426 CGGTATTGTGTGATGAAGCGA 58.733 47.619 0.00 0.00 0.00 4.93
657 679 2.235155 ACCTTACATGTCCACGCACATA 59.765 45.455 0.00 0.00 35.10 2.29
680 703 4.355925 GGTTCCACCGACTGACAC 57.644 61.111 0.00 0.00 0.00 3.67
681 704 1.301479 GGTTCCACCGACTGACACC 60.301 63.158 0.00 0.00 0.00 4.16
685 708 1.125093 TCCACCGACTGACACCCAAT 61.125 55.000 0.00 0.00 0.00 3.16
688 711 2.551287 CCACCGACTGACACCCAATTTA 60.551 50.000 0.00 0.00 0.00 1.40
699 722 8.320617 ACTGACACCCAATTTATTTTGCATAAT 58.679 29.630 7.55 7.55 0.00 1.28
701 724 8.316946 TGACACCCAATTTATTTTGCATAATGA 58.683 29.630 12.07 1.64 0.00 2.57
711 734 0.466007 TGCATAATGATGGCTGGCGT 60.466 50.000 0.00 0.00 33.26 5.68
721 744 1.301401 GGCTGGCGTGTGTCTGTTA 60.301 57.895 0.00 0.00 0.00 2.41
722 745 0.673644 GGCTGGCGTGTGTCTGTTAT 60.674 55.000 0.00 0.00 0.00 1.89
723 746 0.443869 GCTGGCGTGTGTCTGTTATG 59.556 55.000 0.00 0.00 0.00 1.90
724 747 1.078709 CTGGCGTGTGTCTGTTATGG 58.921 55.000 0.00 0.00 0.00 2.74
725 748 0.321210 TGGCGTGTGTCTGTTATGGG 60.321 55.000 0.00 0.00 0.00 4.00
726 749 0.321298 GGCGTGTGTCTGTTATGGGT 60.321 55.000 0.00 0.00 0.00 4.51
727 750 0.796312 GCGTGTGTCTGTTATGGGTG 59.204 55.000 0.00 0.00 0.00 4.61
728 751 1.438651 CGTGTGTCTGTTATGGGTGG 58.561 55.000 0.00 0.00 0.00 4.61
729 752 1.165270 GTGTGTCTGTTATGGGTGGC 58.835 55.000 0.00 0.00 0.00 5.01
730 753 0.321210 TGTGTCTGTTATGGGTGGCG 60.321 55.000 0.00 0.00 0.00 5.69
731 754 0.321298 GTGTCTGTTATGGGTGGCGT 60.321 55.000 0.00 0.00 0.00 5.68
732 755 0.398696 TGTCTGTTATGGGTGGCGTT 59.601 50.000 0.00 0.00 0.00 4.84
733 756 1.202830 TGTCTGTTATGGGTGGCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
734 757 1.883926 GTCTGTTATGGGTGGCGTTTT 59.116 47.619 0.00 0.00 0.00 2.43
735 758 2.295070 GTCTGTTATGGGTGGCGTTTTT 59.705 45.455 0.00 0.00 0.00 1.94
770 793 5.276395 CGCTATTGTTTCTGGTAGTGATTCG 60.276 44.000 0.00 0.00 0.00 3.34
798 821 1.278127 TGGCCTTCTAGCACCTTACAC 59.722 52.381 3.32 0.00 0.00 2.90
805 828 7.039223 GGCCTTCTAGCACCTTACACTATAATA 60.039 40.741 0.00 0.00 0.00 0.98
806 829 7.813627 GCCTTCTAGCACCTTACACTATAATAC 59.186 40.741 0.00 0.00 0.00 1.89
807 830 8.021973 CCTTCTAGCACCTTACACTATAATACG 58.978 40.741 0.00 0.00 0.00 3.06
808 831 8.455903 TTCTAGCACCTTACACTATAATACGT 57.544 34.615 0.00 0.00 0.00 3.57
809 832 9.559732 TTCTAGCACCTTACACTATAATACGTA 57.440 33.333 0.00 0.00 0.00 3.57
810 833 9.730705 TCTAGCACCTTACACTATAATACGTAT 57.269 33.333 1.14 1.14 0.00 3.06
852 878 0.821301 TGCAGCCGTGGAAAATGTCA 60.821 50.000 0.00 0.00 0.00 3.58
937 972 3.900941 GCAATAAATACCTCCATTGCCG 58.099 45.455 6.83 0.00 44.71 5.69
956 992 2.518349 ACACCGCCAAACCACCAG 60.518 61.111 0.00 0.00 0.00 4.00
1027 1064 4.813526 CTCGCGTCGTCCACCTCG 62.814 72.222 5.77 0.00 0.00 4.63
1095 1135 3.041940 GTGGTGAACCGGTGCTCG 61.042 66.667 15.35 0.00 39.43 5.03
1176 1216 3.057548 CAGCTCAACATGCCCGCA 61.058 61.111 0.00 0.00 0.00 5.69
1254 1294 4.408821 GGCCACTGCATCACCGGA 62.409 66.667 9.46 0.00 40.13 5.14
1449 1489 2.662596 GCCGTGGACATCACCAGA 59.337 61.111 0.00 0.00 43.23 3.86
1638 1678 1.669115 CCAGACCAGCACCTTCACG 60.669 63.158 0.00 0.00 0.00 4.35
1671 1711 1.825474 ACCAACTACCAGATCGTCCTG 59.175 52.381 0.00 0.00 0.00 3.86
1716 1756 5.011533 GCACATGGATCAGTAAGTAGAGGAT 59.988 44.000 0.00 0.00 0.00 3.24
1720 1760 7.952930 ACATGGATCAGTAAGTAGAGGATGTAT 59.047 37.037 0.00 0.00 0.00 2.29
1738 1781 8.165397 AGGATGTATTACTCCTAGTAGTCTTCC 58.835 40.741 11.06 0.00 40.15 3.46
1739 1782 8.165397 GGATGTATTACTCCTAGTAGTCTTCCT 58.835 40.741 0.00 0.00 31.47 3.36
1771 1814 3.480505 TGATCATCCATCATTCTGCGT 57.519 42.857 0.00 0.00 36.51 5.24
1772 1815 3.135994 TGATCATCCATCATTCTGCGTG 58.864 45.455 0.00 0.00 36.51 5.34
1773 1816 2.696989 TCATCCATCATTCTGCGTGT 57.303 45.000 0.00 0.00 0.00 4.49
1774 1817 2.282407 TCATCCATCATTCTGCGTGTG 58.718 47.619 0.00 0.00 0.00 3.82
1775 1818 1.019673 ATCCATCATTCTGCGTGTGC 58.980 50.000 0.00 0.00 43.20 4.57
1776 1819 1.026182 TCCATCATTCTGCGTGTGCC 61.026 55.000 0.00 0.00 41.78 5.01
1777 1820 1.430632 CATCATTCTGCGTGTGCCC 59.569 57.895 0.00 0.00 41.78 5.36
1778 1821 1.002257 ATCATTCTGCGTGTGCCCA 60.002 52.632 0.00 0.00 41.78 5.36
1779 1822 0.394762 ATCATTCTGCGTGTGCCCAT 60.395 50.000 0.00 0.00 41.78 4.00
1780 1823 0.251634 TCATTCTGCGTGTGCCCATA 59.748 50.000 0.00 0.00 41.78 2.74
1781 1824 1.134128 TCATTCTGCGTGTGCCCATAT 60.134 47.619 0.00 0.00 41.78 1.78
1782 1825 1.677576 CATTCTGCGTGTGCCCATATT 59.322 47.619 0.00 0.00 41.78 1.28
1783 1826 2.700722 TTCTGCGTGTGCCCATATTA 57.299 45.000 0.00 0.00 41.78 0.98
1784 1827 2.928801 TCTGCGTGTGCCCATATTAT 57.071 45.000 0.00 0.00 41.78 1.28
1785 1828 4.344359 TTCTGCGTGTGCCCATATTATA 57.656 40.909 0.00 0.00 41.78 0.98
1786 1829 4.551702 TCTGCGTGTGCCCATATTATAT 57.448 40.909 0.00 0.00 41.78 0.86
1787 1830 5.669164 TCTGCGTGTGCCCATATTATATA 57.331 39.130 0.00 0.00 41.78 0.86
1788 1831 5.416083 TCTGCGTGTGCCCATATTATATAC 58.584 41.667 0.00 0.00 41.78 1.47
1789 1832 5.186992 TCTGCGTGTGCCCATATTATATACT 59.813 40.000 0.00 0.00 41.78 2.12
1790 1833 5.416083 TGCGTGTGCCCATATTATATACTC 58.584 41.667 0.00 0.00 41.78 2.59
1791 1834 4.809426 GCGTGTGCCCATATTATATACTCC 59.191 45.833 0.00 0.00 33.98 3.85
1792 1835 5.041287 CGTGTGCCCATATTATATACTCCG 58.959 45.833 0.00 0.00 0.00 4.63
1793 1836 5.393787 CGTGTGCCCATATTATATACTCCGT 60.394 44.000 0.00 0.00 0.00 4.69
1794 1837 6.183360 CGTGTGCCCATATTATATACTCCGTA 60.183 42.308 0.00 0.00 0.00 4.02
1795 1838 7.469594 CGTGTGCCCATATTATATACTCCGTAT 60.470 40.741 0.00 0.00 33.05 3.06
1796 1839 8.853126 GTGTGCCCATATTATATACTCCGTATA 58.147 37.037 0.00 0.00 35.77 1.47
1797 1840 9.596308 TGTGCCCATATTATATACTCCGTATAT 57.404 33.333 10.38 10.38 42.26 0.86
1953 2018 7.337689 GCCATGAATATTGCTACATCTATGGAA 59.662 37.037 0.00 0.00 34.70 3.53
1954 2019 9.234827 CCATGAATATTGCTACATCTATGGAAA 57.765 33.333 0.00 0.00 34.70 3.13
1964 2029 8.826710 TGCTACATCTATGGAAAATTTCTTACG 58.173 33.333 5.65 0.00 0.00 3.18
1965 2030 7.798982 GCTACATCTATGGAAAATTTCTTACGC 59.201 37.037 5.65 0.00 0.00 4.42
1966 2031 7.624360 ACATCTATGGAAAATTTCTTACGCA 57.376 32.000 5.65 0.00 0.00 5.24
1967 2032 7.472543 ACATCTATGGAAAATTTCTTACGCAC 58.527 34.615 5.65 0.00 0.00 5.34
1968 2033 7.120579 ACATCTATGGAAAATTTCTTACGCACA 59.879 33.333 5.65 0.00 0.00 4.57
1969 2034 7.072177 TCTATGGAAAATTTCTTACGCACAG 57.928 36.000 5.65 0.00 0.00 3.66
1970 2035 5.957842 ATGGAAAATTTCTTACGCACAGA 57.042 34.783 5.65 0.00 0.00 3.41
1971 2036 5.759506 TGGAAAATTTCTTACGCACAGAA 57.240 34.783 5.65 0.00 0.00 3.02
1972 2037 6.325919 TGGAAAATTTCTTACGCACAGAAT 57.674 33.333 5.65 0.00 30.26 2.40
1973 2038 6.744112 TGGAAAATTTCTTACGCACAGAATT 58.256 32.000 5.65 0.00 30.26 2.17
1974 2039 6.861055 TGGAAAATTTCTTACGCACAGAATTC 59.139 34.615 5.65 0.00 30.26 2.17
1975 2040 6.308041 GGAAAATTTCTTACGCACAGAATTCC 59.692 38.462 5.65 6.82 33.16 3.01
1976 2041 4.965119 ATTTCTTACGCACAGAATTCCC 57.035 40.909 0.65 0.00 30.26 3.97
1977 2042 3.695830 TTCTTACGCACAGAATTCCCT 57.304 42.857 0.65 0.00 0.00 4.20
1978 2043 2.972625 TCTTACGCACAGAATTCCCTG 58.027 47.619 0.65 0.00 39.93 4.45
1979 2044 2.565391 TCTTACGCACAGAATTCCCTGA 59.435 45.455 0.65 0.00 37.59 3.86
1980 2045 3.007506 TCTTACGCACAGAATTCCCTGAA 59.992 43.478 0.65 0.00 37.59 3.02
1981 2046 2.496899 ACGCACAGAATTCCCTGAAT 57.503 45.000 0.65 0.00 37.59 2.57
1982 2047 2.086869 ACGCACAGAATTCCCTGAATG 58.913 47.619 0.65 0.00 37.59 2.67
1983 2048 2.290260 ACGCACAGAATTCCCTGAATGA 60.290 45.455 0.65 0.00 37.59 2.57
1984 2049 2.353889 CGCACAGAATTCCCTGAATGAG 59.646 50.000 0.65 0.00 37.59 2.90
1985 2050 2.686915 GCACAGAATTCCCTGAATGAGG 59.313 50.000 0.65 0.00 42.38 3.86
1986 2051 3.875369 GCACAGAATTCCCTGAATGAGGT 60.875 47.826 0.65 0.00 40.87 3.85
1987 2052 3.693085 CACAGAATTCCCTGAATGAGGTG 59.307 47.826 0.65 0.00 40.87 4.00
1988 2053 3.331889 ACAGAATTCCCTGAATGAGGTGT 59.668 43.478 0.65 0.00 40.87 4.16
1989 2054 4.202609 ACAGAATTCCCTGAATGAGGTGTT 60.203 41.667 0.65 0.00 40.87 3.32
1990 2055 4.768968 CAGAATTCCCTGAATGAGGTGTTT 59.231 41.667 0.65 0.00 40.87 2.83
1991 2056 4.768968 AGAATTCCCTGAATGAGGTGTTTG 59.231 41.667 0.65 0.00 40.87 2.93
1992 2057 3.874383 TTCCCTGAATGAGGTGTTTGA 57.126 42.857 0.00 0.00 40.87 2.69
1993 2058 3.140325 TCCCTGAATGAGGTGTTTGAC 57.860 47.619 0.00 0.00 40.87 3.18
1994 2059 2.711009 TCCCTGAATGAGGTGTTTGACT 59.289 45.455 0.00 0.00 40.87 3.41
1995 2060 3.077359 CCCTGAATGAGGTGTTTGACTC 58.923 50.000 0.00 0.00 40.87 3.36
1996 2061 3.496692 CCCTGAATGAGGTGTTTGACTCA 60.497 47.826 0.00 0.00 46.62 3.41
2003 2068 5.545063 TGAGGTGTTTGACTCATAGTGAA 57.455 39.130 0.00 0.00 38.71 3.18
2004 2069 5.924356 TGAGGTGTTTGACTCATAGTGAAA 58.076 37.500 0.00 0.00 38.71 2.69
2005 2070 5.991606 TGAGGTGTTTGACTCATAGTGAAAG 59.008 40.000 0.00 0.00 38.71 2.62
2006 2071 6.174720 AGGTGTTTGACTCATAGTGAAAGA 57.825 37.500 0.00 0.00 32.21 2.52
2007 2072 6.226787 AGGTGTTTGACTCATAGTGAAAGAG 58.773 40.000 0.00 0.00 32.21 2.85
2008 2073 6.042093 AGGTGTTTGACTCATAGTGAAAGAGA 59.958 38.462 0.00 0.00 32.21 3.10
2009 2074 6.706270 GGTGTTTGACTCATAGTGAAAGAGAA 59.294 38.462 0.00 0.00 32.21 2.87
2010 2075 7.226720 GGTGTTTGACTCATAGTGAAAGAGAAA 59.773 37.037 0.00 0.00 32.21 2.52
2011 2076 8.612619 GTGTTTGACTCATAGTGAAAGAGAAAA 58.387 33.333 0.00 0.00 32.21 2.29
2012 2077 9.173021 TGTTTGACTCATAGTGAAAGAGAAAAA 57.827 29.630 0.00 0.00 32.21 1.94
2061 2126 5.426833 ACATCCTCTTTGCTTACTCCTGTAT 59.573 40.000 0.00 0.00 0.00 2.29
2062 2127 5.599999 TCCTCTTTGCTTACTCCTGTATC 57.400 43.478 0.00 0.00 0.00 2.24
2063 2128 5.023452 TCCTCTTTGCTTACTCCTGTATCA 58.977 41.667 0.00 0.00 0.00 2.15
2065 2130 6.839134 TCCTCTTTGCTTACTCCTGTATCATA 59.161 38.462 0.00 0.00 0.00 2.15
2071 2136 5.047021 TGCTTACTCCTGTATCATAGGCATC 60.047 44.000 0.00 0.00 35.23 3.91
2072 2137 5.644977 TTACTCCTGTATCATAGGCATCG 57.355 43.478 0.00 0.00 35.23 3.84
2073 2138 2.828520 ACTCCTGTATCATAGGCATCGG 59.171 50.000 0.00 0.00 35.23 4.18
2074 2139 2.167281 CTCCTGTATCATAGGCATCGGG 59.833 54.545 0.00 0.00 35.23 5.14
2076 2141 1.902508 CTGTATCATAGGCATCGGGGT 59.097 52.381 0.00 0.00 0.00 4.95
2077 2142 1.899814 TGTATCATAGGCATCGGGGTC 59.100 52.381 0.00 0.00 0.00 4.46
2078 2143 1.899814 GTATCATAGGCATCGGGGTCA 59.100 52.381 0.00 0.00 0.00 4.02
2079 2144 0.979665 ATCATAGGCATCGGGGTCAG 59.020 55.000 0.00 0.00 0.00 3.51
2080 2145 0.398522 TCATAGGCATCGGGGTCAGT 60.399 55.000 0.00 0.00 0.00 3.41
2081 2146 0.469917 CATAGGCATCGGGGTCAGTT 59.530 55.000 0.00 0.00 0.00 3.16
2082 2147 0.469917 ATAGGCATCGGGGTCAGTTG 59.530 55.000 0.00 0.00 0.00 3.16
2083 2148 0.616395 TAGGCATCGGGGTCAGTTGA 60.616 55.000 0.00 0.00 0.00 3.18
2084 2149 1.745489 GGCATCGGGGTCAGTTGAC 60.745 63.158 3.67 3.67 44.04 3.18
2097 2162 4.475944 GTCAGTTGACCCAATGAATTTCG 58.524 43.478 0.72 0.00 39.07 3.46
2098 2163 4.215399 GTCAGTTGACCCAATGAATTTCGA 59.785 41.667 0.72 0.00 39.07 3.71
2100 2165 5.300539 TCAGTTGACCCAATGAATTTCGAAA 59.699 36.000 13.91 13.91 0.00 3.46
2106 2171 7.441017 TGACCCAATGAATTTCGAAAATCTTT 58.559 30.769 22.80 19.76 0.00 2.52
2107 2172 7.598493 TGACCCAATGAATTTCGAAAATCTTTC 59.402 33.333 22.80 17.67 0.00 2.62
2108 2173 6.873605 ACCCAATGAATTTCGAAAATCTTTCC 59.126 34.615 22.80 1.80 0.00 3.13
2111 2176 8.250332 CCAATGAATTTCGAAAATCTTTCCCTA 58.750 33.333 22.80 5.21 0.00 3.53
2115 2180 9.855021 TGAATTTCGAAAATCTTTCCCTAATTC 57.145 29.630 22.80 13.83 0.00 2.17
2116 2181 9.855021 GAATTTCGAAAATCTTTCCCTAATTCA 57.145 29.630 15.66 0.00 31.82 2.57
2117 2182 9.860898 AATTTCGAAAATCTTTCCCTAATTCAG 57.139 29.630 15.66 0.00 0.00 3.02
2118 2183 7.996098 TTCGAAAATCTTTCCCTAATTCAGT 57.004 32.000 0.00 0.00 0.00 3.41
2119 2184 7.377766 TCGAAAATCTTTCCCTAATTCAGTG 57.622 36.000 0.00 0.00 0.00 3.66
2120 2185 6.030228 CGAAAATCTTTCCCTAATTCAGTGC 58.970 40.000 0.00 0.00 0.00 4.40
2121 2186 6.127897 CGAAAATCTTTCCCTAATTCAGTGCT 60.128 38.462 0.00 0.00 0.00 4.40
2123 2507 7.872113 AAATCTTTCCCTAATTCAGTGCTAG 57.128 36.000 0.00 0.00 0.00 3.42
2127 2511 4.737855 TCCCTAATTCAGTGCTAGTCAC 57.262 45.455 8.67 8.67 45.98 3.67
2143 2527 9.250624 GTGCTAGTCACTAACATTTATAGAAGG 57.749 37.037 9.26 0.00 42.38 3.46
2151 2535 9.057089 CACTAACATTTATAGAAGGATGAACCC 57.943 37.037 0.00 0.00 40.05 4.11
2155 3038 7.056635 ACATTTATAGAAGGATGAACCCACTG 58.943 38.462 0.00 0.00 40.05 3.66
2159 3042 0.706433 AAGGATGAACCCACTGCCAT 59.294 50.000 0.00 0.00 40.05 4.40
2161 3044 2.138542 AGGATGAACCCACTGCCATAT 58.861 47.619 0.00 0.00 40.05 1.78
2163 3046 3.073062 AGGATGAACCCACTGCCATATAC 59.927 47.826 0.00 0.00 40.05 1.47
2164 3047 3.181445 GGATGAACCCACTGCCATATACA 60.181 47.826 0.00 0.00 0.00 2.29
2169 3052 2.106511 ACCCACTGCCATATACATGACC 59.893 50.000 0.00 0.00 33.67 4.02
2174 3057 3.009473 ACTGCCATATACATGACCCCATC 59.991 47.826 0.00 0.00 33.67 3.51
2176 3059 3.397282 TGCCATATACATGACCCCATCAA 59.603 43.478 0.00 0.00 41.93 2.57
2177 3060 4.141065 TGCCATATACATGACCCCATCAAA 60.141 41.667 0.00 0.00 41.93 2.69
2178 3061 4.218417 GCCATATACATGACCCCATCAAAC 59.782 45.833 0.00 0.00 41.93 2.93
2179 3062 5.384336 CCATATACATGACCCCATCAAACA 58.616 41.667 0.00 0.00 41.93 2.83
2180 3063 6.012113 CCATATACATGACCCCATCAAACAT 58.988 40.000 0.00 0.00 41.93 2.71
2219 5573 3.557595 CCTGCTCATTCCGTAGATCAAAC 59.442 47.826 0.00 0.00 0.00 2.93
2315 5669 0.041312 CGTTTAGCCGCATATGCACC 60.041 55.000 26.52 16.12 42.21 5.01
2325 5679 4.816392 CCGCATATGCACCTACTATTACA 58.184 43.478 26.52 0.00 42.21 2.41
2368 5724 3.562343 ACATGCTCCTAGTCTAGACGA 57.438 47.619 17.07 11.32 36.20 4.20
2387 5743 9.295214 CTAGACGAATCACAATATATCATGTCC 57.705 37.037 0.00 0.00 0.00 4.02
2390 5746 9.639601 GACGAATCACAATATATCATGTCCTTA 57.360 33.333 0.00 0.00 0.00 2.69
2421 5777 4.260375 CGCACTTCATCTCTTTTTATCCGG 60.260 45.833 0.00 0.00 0.00 5.14
2614 5972 3.738282 CCTTTTCTCTCTCGACACAACTG 59.262 47.826 0.00 0.00 0.00 3.16
2620 5978 4.155099 TCTCTCTCGACACAACTGAAGATC 59.845 45.833 0.00 0.00 0.00 2.75
2621 5979 3.821033 TCTCTCGACACAACTGAAGATCA 59.179 43.478 0.00 0.00 0.00 2.92
2686 6045 6.658188 AGAGTCATTAATAGCTAGGACCAC 57.342 41.667 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 7.013834 TCCCCACACACACACATATATATAGA 58.986 38.462 0.00 0.00 0.00 1.98
74 86 2.587522 TCTGATATGTGCTACGAGCCT 58.412 47.619 0.00 0.00 41.51 4.58
78 90 6.515832 ACAATTGATCTGATATGTGCTACGA 58.484 36.000 13.59 0.00 0.00 3.43
80 92 8.226448 GCTAACAATTGATCTGATATGTGCTAC 58.774 37.037 13.59 0.00 0.00 3.58
88 100 5.523552 CACACGGCTAACAATTGATCTGATA 59.476 40.000 13.59 0.00 0.00 2.15
90 102 3.684305 CACACGGCTAACAATTGATCTGA 59.316 43.478 13.59 0.00 0.00 3.27
124 139 1.193462 ACCGGGGGTGTAAACGATGA 61.193 55.000 6.32 0.00 32.98 2.92
148 164 4.324267 ACTTCGCCTAAGCACTACAAAAT 58.676 39.130 0.00 0.00 38.93 1.82
189 206 0.458260 CGGTATGGTGACGGTGATGA 59.542 55.000 0.00 0.00 0.00 2.92
219 236 4.121317 CGTCGAGGTAGTAGATGAGTTCT 58.879 47.826 0.00 0.00 38.57 3.01
264 281 1.336887 CGTTCAGTTCGGTGACATCCT 60.337 52.381 0.00 0.00 0.00 3.24
268 285 1.149361 GCACGTTCAGTTCGGTGACA 61.149 55.000 0.00 0.00 0.00 3.58
277 294 1.078759 GCGCTCTATGCACGTTCAGT 61.079 55.000 0.00 0.00 43.06 3.41
287 304 2.659897 GCACCTCCGCGCTCTATG 60.660 66.667 5.56 0.00 0.00 2.23
288 305 3.917760 GGCACCTCCGCGCTCTAT 61.918 66.667 5.56 0.00 0.00 1.98
342 360 3.079960 ACGCGATTGATGTAGTCGAAT 57.920 42.857 15.93 0.00 40.55 3.34
397 415 0.784495 AGGGGGAGAGTGTGTCTACA 59.216 55.000 0.00 0.00 37.99 2.74
418 438 2.102925 TCGATGGAGATGCATAGCAACA 59.897 45.455 0.00 0.00 43.62 3.33
558 580 4.737855 AAGCAGTATGACTATCACCGTT 57.262 40.909 0.00 0.00 39.69 4.44
559 581 5.535030 TGATAAGCAGTATGACTATCACCGT 59.465 40.000 0.00 0.00 39.69 4.83
581 603 7.483375 CGCCGATTCAAAATAAAACATTAGTGA 59.517 33.333 0.00 0.00 0.00 3.41
585 607 6.622549 ACCGCCGATTCAAAATAAAACATTA 58.377 32.000 0.00 0.00 0.00 1.90
591 613 6.030849 CACAATACCGCCGATTCAAAATAAA 58.969 36.000 0.00 0.00 0.00 1.40
601 623 1.138069 TCATCACACAATACCGCCGAT 59.862 47.619 0.00 0.00 0.00 4.18
616 638 2.577059 GTCCGGGTCGCTTCATCA 59.423 61.111 0.00 0.00 0.00 3.07
626 648 0.326927 CATGTAAGGTTGGTCCGGGT 59.673 55.000 0.00 0.00 41.99 5.28
680 703 7.446013 AGCCATCATTATGCAAAATAAATTGGG 59.554 33.333 0.00 0.00 0.00 4.12
681 704 8.286800 CAGCCATCATTATGCAAAATAAATTGG 58.713 33.333 0.00 0.00 0.00 3.16
685 708 5.759273 GCCAGCCATCATTATGCAAAATAAA 59.241 36.000 0.00 0.00 0.00 1.40
688 711 3.735591 GCCAGCCATCATTATGCAAAAT 58.264 40.909 0.00 0.00 0.00 1.82
699 722 2.358615 GACACACGCCAGCCATCA 60.359 61.111 0.00 0.00 0.00 3.07
701 724 2.359107 CAGACACACGCCAGCCAT 60.359 61.111 0.00 0.00 0.00 4.40
711 734 0.321210 CGCCACCCATAACAGACACA 60.321 55.000 0.00 0.00 0.00 3.72
736 759 7.708998 ACCAGAAACAATAGCGTTTAGAAAAA 58.291 30.769 0.00 0.00 39.17 1.94
737 760 7.266922 ACCAGAAACAATAGCGTTTAGAAAA 57.733 32.000 0.00 0.00 39.17 2.29
748 771 5.812642 AGCGAATCACTACCAGAAACAATAG 59.187 40.000 0.00 0.00 0.00 1.73
751 774 3.745975 CAGCGAATCACTACCAGAAACAA 59.254 43.478 0.00 0.00 0.00 2.83
770 793 1.134280 TGCTAGAAGGCCAGAATCAGC 60.134 52.381 5.01 6.32 0.00 4.26
833 859 0.821301 TGACATTTTCCACGGCTGCA 60.821 50.000 0.50 0.00 0.00 4.41
836 862 1.247567 CCTTGACATTTTCCACGGCT 58.752 50.000 0.00 0.00 0.00 5.52
903 933 0.810426 TTATTGCCGCGCGTCCATAA 60.810 50.000 29.95 20.54 0.00 1.90
937 972 4.279043 GGTGGTTTGGCGGTGTGC 62.279 66.667 0.00 0.00 45.38 4.57
956 992 1.638467 GTGATGCGGCGATTCTGAC 59.362 57.895 12.98 0.00 0.00 3.51
1018 1055 4.131088 GAGGGCGACGAGGTGGAC 62.131 72.222 0.00 0.00 0.00 4.02
1062 1102 2.125832 ACGGTTATGGTGGTCGCG 60.126 61.111 0.00 0.00 0.00 5.87
1095 1135 1.666872 GCCCGGCCATATCGTGTAC 60.667 63.158 2.24 0.00 0.00 2.90
1308 1348 3.760035 CCCAGCGTGTACTCGGCT 61.760 66.667 18.02 12.52 0.00 5.52
1359 1399 1.859080 GTATTGAAGCCGTCGATGACC 59.141 52.381 6.11 0.00 32.19 4.02
1638 1678 4.966787 TTGGTTCCGGCTGGGCAC 62.967 66.667 12.87 9.02 35.24 5.01
1716 1756 8.334522 AGAGGAAGACTACTAGGAGTAATACA 57.665 38.462 7.87 0.00 29.00 2.29
1720 1760 8.391305 AGTAAGAGGAAGACTACTAGGAGTAA 57.609 38.462 7.87 0.00 29.00 2.24
1759 1802 1.307355 TGGGCACACGCAGAATGATG 61.307 55.000 0.00 0.00 39.69 3.07
1766 1809 5.419542 AGTATATAATATGGGCACACGCAG 58.580 41.667 0.00 0.00 42.66 5.18
1767 1810 5.414789 AGTATATAATATGGGCACACGCA 57.585 39.130 0.00 0.00 43.66 5.24
1768 1811 4.809426 GGAGTATATAATATGGGCACACGC 59.191 45.833 0.00 0.00 37.44 5.34
1769 1812 5.041287 CGGAGTATATAATATGGGCACACG 58.959 45.833 0.00 0.00 0.00 4.49
1770 1813 5.974108 ACGGAGTATATAATATGGGCACAC 58.026 41.667 0.00 0.00 41.94 3.82
1803 1846 3.504127 ATGCACGCACGCACATATGTG 62.504 52.381 28.07 28.07 46.56 3.21
1804 1847 1.368345 ATGCACGCACGCACATATGT 61.368 50.000 1.41 1.41 46.56 2.29
1805 1848 0.926628 CATGCACGCACGCACATATG 60.927 55.000 0.00 0.00 46.56 1.78
1806 1849 1.352753 CATGCACGCACGCACATAT 59.647 52.632 0.00 0.00 46.56 1.78
1827 1892 4.465512 GCTGAATGGCACGCACCG 62.466 66.667 0.00 0.00 0.00 4.94
1918 1983 8.911965 TGTAGCAATATTCATGGCATAAAAAGA 58.088 29.630 0.00 0.00 32.99 2.52
1922 1987 8.640063 AGATGTAGCAATATTCATGGCATAAA 57.360 30.769 0.00 0.00 32.99 1.40
1927 1992 6.825213 TCCATAGATGTAGCAATATTCATGGC 59.175 38.462 0.00 0.00 31.35 4.40
1928 1993 8.797350 TTCCATAGATGTAGCAATATTCATGG 57.203 34.615 0.00 0.00 0.00 3.66
1938 2003 8.826710 CGTAAGAAATTTTCCATAGATGTAGCA 58.173 33.333 5.52 0.00 43.02 3.49
1939 2004 7.798982 GCGTAAGAAATTTTCCATAGATGTAGC 59.201 37.037 5.52 0.00 43.02 3.58
1940 2005 8.826710 TGCGTAAGAAATTTTCCATAGATGTAG 58.173 33.333 5.52 0.00 43.02 2.74
1941 2006 8.609176 GTGCGTAAGAAATTTTCCATAGATGTA 58.391 33.333 5.52 0.00 43.02 2.29
1942 2007 7.120579 TGTGCGTAAGAAATTTTCCATAGATGT 59.879 33.333 5.52 0.00 43.02 3.06
1953 2018 5.476945 AGGGAATTCTGTGCGTAAGAAATTT 59.523 36.000 5.23 0.00 37.22 1.82
1954 2019 5.010282 AGGGAATTCTGTGCGTAAGAAATT 58.990 37.500 5.23 0.00 37.22 1.82
1955 2020 4.396166 CAGGGAATTCTGTGCGTAAGAAAT 59.604 41.667 5.23 0.00 37.22 2.17
1956 2021 3.751175 CAGGGAATTCTGTGCGTAAGAAA 59.249 43.478 5.23 0.00 37.22 2.52
1957 2022 3.007506 TCAGGGAATTCTGTGCGTAAGAA 59.992 43.478 5.23 0.00 38.01 2.52
1958 2023 2.565391 TCAGGGAATTCTGTGCGTAAGA 59.435 45.455 5.23 0.00 36.27 2.10
1959 2024 2.972625 TCAGGGAATTCTGTGCGTAAG 58.027 47.619 5.23 0.00 36.25 2.34
1960 2025 3.410631 TTCAGGGAATTCTGTGCGTAA 57.589 42.857 5.23 0.00 36.25 3.18
1961 2026 3.055458 TCATTCAGGGAATTCTGTGCGTA 60.055 43.478 5.23 0.00 36.25 4.42
1962 2027 2.086869 CATTCAGGGAATTCTGTGCGT 58.913 47.619 5.23 0.00 36.25 5.24
1963 2028 2.353889 CTCATTCAGGGAATTCTGTGCG 59.646 50.000 5.23 0.00 36.25 5.34
1964 2029 2.686915 CCTCATTCAGGGAATTCTGTGC 59.313 50.000 5.23 0.00 38.91 4.57
1975 2040 4.330250 ATGAGTCAAACACCTCATTCAGG 58.670 43.478 0.00 0.00 44.03 3.86
1976 2041 6.091849 CACTATGAGTCAAACACCTCATTCAG 59.908 42.308 7.39 3.42 44.03 3.02
1977 2042 5.934043 CACTATGAGTCAAACACCTCATTCA 59.066 40.000 7.39 0.00 44.03 2.57
1978 2043 6.166279 TCACTATGAGTCAAACACCTCATTC 58.834 40.000 7.39 0.00 44.03 2.67
1979 2044 6.114187 TCACTATGAGTCAAACACCTCATT 57.886 37.500 7.39 0.00 44.03 2.57
1981 2046 5.545063 TTCACTATGAGTCAAACACCTCA 57.455 39.130 0.00 0.00 41.61 3.86
1982 2047 6.223852 TCTTTCACTATGAGTCAAACACCTC 58.776 40.000 0.00 0.00 0.00 3.85
1983 2048 6.042093 TCTCTTTCACTATGAGTCAAACACCT 59.958 38.462 0.00 0.00 31.64 4.00
1984 2049 6.223852 TCTCTTTCACTATGAGTCAAACACC 58.776 40.000 0.00 0.00 31.64 4.16
1985 2050 7.715265 TTCTCTTTCACTATGAGTCAAACAC 57.285 36.000 0.00 0.00 31.64 3.32
1986 2051 8.731275 TTTTCTCTTTCACTATGAGTCAAACA 57.269 30.769 0.00 0.00 31.64 2.83
2013 2078 9.802039 TGTAAGAGGGACTATGTTAAAATTGTT 57.198 29.630 0.00 0.00 41.55 2.83
2014 2079 9.975218 ATGTAAGAGGGACTATGTTAAAATTGT 57.025 29.630 0.00 0.00 41.55 2.71
2061 2126 0.398522 ACTGACCCCGATGCCTATGA 60.399 55.000 0.00 0.00 0.00 2.15
2062 2127 0.469917 AACTGACCCCGATGCCTATG 59.530 55.000 0.00 0.00 0.00 2.23
2063 2128 0.469917 CAACTGACCCCGATGCCTAT 59.530 55.000 0.00 0.00 0.00 2.57
2065 2130 1.918293 TCAACTGACCCCGATGCCT 60.918 57.895 0.00 0.00 0.00 4.75
2076 2141 4.393834 TCGAAATTCATTGGGTCAACTGA 58.606 39.130 0.00 0.00 0.00 3.41
2077 2142 4.764679 TCGAAATTCATTGGGTCAACTG 57.235 40.909 0.00 0.00 0.00 3.16
2078 2143 5.782893 TTTCGAAATTCATTGGGTCAACT 57.217 34.783 6.47 0.00 0.00 3.16
2079 2144 6.868339 AGATTTTCGAAATTCATTGGGTCAAC 59.132 34.615 26.12 3.56 0.00 3.18
2080 2145 6.991938 AGATTTTCGAAATTCATTGGGTCAA 58.008 32.000 26.12 4.45 0.00 3.18
2081 2146 6.588719 AGATTTTCGAAATTCATTGGGTCA 57.411 33.333 26.12 4.63 0.00 4.02
2082 2147 7.063426 GGAAAGATTTTCGAAATTCATTGGGTC 59.937 37.037 26.12 13.61 0.00 4.46
2083 2148 6.873605 GGAAAGATTTTCGAAATTCATTGGGT 59.126 34.615 26.12 8.99 0.00 4.51
2084 2149 6.313658 GGGAAAGATTTTCGAAATTCATTGGG 59.686 38.462 26.12 0.00 0.00 4.12
2085 2150 7.099120 AGGGAAAGATTTTCGAAATTCATTGG 58.901 34.615 26.12 0.00 0.00 3.16
2086 2151 9.638239 TTAGGGAAAGATTTTCGAAATTCATTG 57.362 29.630 26.12 0.00 0.00 2.82
2089 2154 9.855021 GAATTAGGGAAAGATTTTCGAAATTCA 57.145 29.630 26.12 8.99 0.00 2.57
2090 2155 9.855021 TGAATTAGGGAAAGATTTTCGAAATTC 57.145 29.630 20.05 20.05 0.00 2.17
2093 2158 8.296713 CACTGAATTAGGGAAAGATTTTCGAAA 58.703 33.333 6.47 6.47 0.00 3.46
2094 2159 7.574967 GCACTGAATTAGGGAAAGATTTTCGAA 60.575 37.037 0.00 0.00 0.00 3.71
2095 2160 6.128007 GCACTGAATTAGGGAAAGATTTTCGA 60.128 38.462 0.00 0.00 0.00 3.71
2096 2161 6.030228 GCACTGAATTAGGGAAAGATTTTCG 58.970 40.000 0.00 0.00 0.00 3.46
2097 2162 7.163001 AGCACTGAATTAGGGAAAGATTTTC 57.837 36.000 0.00 0.00 0.00 2.29
2098 2163 7.890655 ACTAGCACTGAATTAGGGAAAGATTTT 59.109 33.333 0.00 0.00 0.00 1.82
2100 2165 6.963322 ACTAGCACTGAATTAGGGAAAGATT 58.037 36.000 0.00 0.00 0.00 2.40
2106 2171 4.737855 GTGACTAGCACTGAATTAGGGA 57.262 45.455 9.26 0.00 44.27 4.20
2118 2183 9.197306 TCCTTCTATAAATGTTAGTGACTAGCA 57.803 33.333 11.52 11.52 32.24 3.49
2127 2511 9.057089 GTGGGTTCATCCTTCTATAAATGTTAG 57.943 37.037 0.00 0.00 36.25 2.34
2131 2515 6.016777 GCAGTGGGTTCATCCTTCTATAAATG 60.017 42.308 0.00 0.00 36.25 2.32
2133 2517 5.437060 GCAGTGGGTTCATCCTTCTATAAA 58.563 41.667 0.00 0.00 36.25 1.40
2134 2518 4.141482 GGCAGTGGGTTCATCCTTCTATAA 60.141 45.833 0.00 0.00 36.25 0.98
2140 2524 0.706433 ATGGCAGTGGGTTCATCCTT 59.294 50.000 0.00 0.00 36.25 3.36
2142 2526 2.664402 ATATGGCAGTGGGTTCATCC 57.336 50.000 0.00 0.00 0.00 3.51
2143 2527 4.085357 TGTATATGGCAGTGGGTTCATC 57.915 45.455 0.00 0.00 0.00 2.92
2149 2533 2.553028 GGGTCATGTATATGGCAGTGGG 60.553 54.545 6.39 0.00 40.72 4.61
2151 2535 2.106338 TGGGGTCATGTATATGGCAGTG 59.894 50.000 6.39 0.00 40.72 3.66
2155 3038 3.719268 TGATGGGGTCATGTATATGGC 57.281 47.619 0.00 0.00 38.20 4.40
2159 3042 7.969690 AAAATGTTTGATGGGGTCATGTATA 57.030 32.000 0.00 0.00 36.54 1.47
2161 3044 6.678568 AAAAATGTTTGATGGGGTCATGTA 57.321 33.333 0.00 0.00 36.54 2.29
2185 3068 4.040952 GGAATGAGCAGGGATAAAGCTAGA 59.959 45.833 0.00 0.00 39.02 2.43
2187 3070 3.244215 CGGAATGAGCAGGGATAAAGCTA 60.244 47.826 0.00 0.00 39.02 3.32
2192 3075 3.572642 TCTACGGAATGAGCAGGGATAA 58.427 45.455 0.00 0.00 0.00 1.75
2194 3077 2.088104 TCTACGGAATGAGCAGGGAT 57.912 50.000 0.00 0.00 0.00 3.85
2195 3078 1.964223 GATCTACGGAATGAGCAGGGA 59.036 52.381 0.00 0.00 0.00 4.20
2196 3079 1.688735 TGATCTACGGAATGAGCAGGG 59.311 52.381 0.00 0.00 0.00 4.45
2197 3080 3.459232 TTGATCTACGGAATGAGCAGG 57.541 47.619 0.00 0.00 30.15 4.85
2198 3081 3.557595 GGTTTGATCTACGGAATGAGCAG 59.442 47.826 0.00 0.00 30.15 4.24
2199 3082 3.531538 GGTTTGATCTACGGAATGAGCA 58.468 45.455 0.00 0.00 0.00 4.26
2200 3083 2.872858 GGGTTTGATCTACGGAATGAGC 59.127 50.000 0.00 0.00 0.00 4.26
2201 3084 4.137116 TGGGTTTGATCTACGGAATGAG 57.863 45.455 0.00 0.00 0.00 2.90
2219 5573 5.663795 GCACGAGCATGATTATATATGGG 57.336 43.478 0.00 0.00 41.58 4.00
2387 5743 9.994432 AAAGAGATGAAGTGCGATTAAATTAAG 57.006 29.630 0.00 0.00 0.00 1.85
2392 5748 9.988350 GATAAAAAGAGATGAAGTGCGATTAAA 57.012 29.630 0.00 0.00 0.00 1.52
2393 5749 8.612619 GGATAAAAAGAGATGAAGTGCGATTAA 58.387 33.333 0.00 0.00 0.00 1.40
2394 5750 7.042725 CGGATAAAAAGAGATGAAGTGCGATTA 60.043 37.037 0.00 0.00 0.00 1.75
2395 5751 6.238211 CGGATAAAAAGAGATGAAGTGCGATT 60.238 38.462 0.00 0.00 0.00 3.34
2396 5752 5.235186 CGGATAAAAAGAGATGAAGTGCGAT 59.765 40.000 0.00 0.00 0.00 4.58
2397 5753 4.566759 CGGATAAAAAGAGATGAAGTGCGA 59.433 41.667 0.00 0.00 0.00 5.10
2398 5754 4.260375 CCGGATAAAAAGAGATGAAGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
2399 5755 4.636206 ACCGGATAAAAAGAGATGAAGTGC 59.364 41.667 9.46 0.00 0.00 4.40
2400 5756 6.743575 AACCGGATAAAAAGAGATGAAGTG 57.256 37.500 9.46 0.00 0.00 3.16
2401 5757 6.940298 TCAAACCGGATAAAAAGAGATGAAGT 59.060 34.615 9.46 0.00 0.00 3.01
2402 5758 7.377766 TCAAACCGGATAAAAAGAGATGAAG 57.622 36.000 9.46 0.00 0.00 3.02
2514 5870 1.073025 TGGATGTCTGTGGTGCACC 59.927 57.895 29.67 29.67 32.73 5.01
2515 5871 1.568612 CGTGGATGTCTGTGGTGCAC 61.569 60.000 8.80 8.80 34.56 4.57
2516 5872 1.301637 CGTGGATGTCTGTGGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
2517 5873 0.391661 ATCGTGGATGTCTGTGGTGC 60.392 55.000 0.00 0.00 0.00 5.01
2518 5874 1.362768 CATCGTGGATGTCTGTGGTG 58.637 55.000 0.00 0.00 35.54 4.17
2519 5875 0.250234 CCATCGTGGATGTCTGTGGT 59.750 55.000 5.03 0.00 40.96 4.16
2520 5876 0.536724 TCCATCGTGGATGTCTGTGG 59.463 55.000 5.03 0.00 42.67 4.17
2542 5898 6.755206 TGTGGATAAGATAATTAGGTGACCG 58.245 40.000 0.00 0.00 0.00 4.79
2590 5948 1.686587 TGTGTCGAGAGAGAAAAGGCA 59.313 47.619 0.00 0.00 43.49 4.75
2591 5949 2.440539 TGTGTCGAGAGAGAAAAGGC 57.559 50.000 0.00 0.00 43.49 4.35
2592 5950 3.738282 CAGTTGTGTCGAGAGAGAAAAGG 59.262 47.826 0.00 0.00 43.49 3.11
2593 5951 4.611943 TCAGTTGTGTCGAGAGAGAAAAG 58.388 43.478 0.00 0.00 43.49 2.27
2598 5956 3.906014 TCTTCAGTTGTGTCGAGAGAG 57.094 47.619 0.00 0.00 43.49 3.20
2614 5972 2.100989 AGTGGTCCTACCGTGATCTTC 58.899 52.381 0.00 0.00 42.58 2.87
2620 5978 1.553706 AGGTTAGTGGTCCTACCGTG 58.446 55.000 0.00 0.00 42.58 4.94
2621 5979 1.897802 CAAGGTTAGTGGTCCTACCGT 59.102 52.381 0.00 0.00 42.58 4.83


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

AutoCloner maintained by Alex Coulton.