Multiple sequence alignment - TraesCS2A01G378800

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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 TraesCS2A01G378800 chr2A 100.000 2531 0 0 1 2531 621516971 621514441 0.000000e+00 4674
1 TraesCS2A01G378800 chr2D 90.102 1859 102 26 1 1821 478697786 478699600 0.000000e+00 2338
2 TraesCS2A01G378800 chr2B 92.806 1126 57 8 641 1758 561259747 561258638 0.000000e+00 1609
3 TraesCS2A01G378800 chr2B 88.336 643 43 7 3 617 561260382 561259744 0.000000e+00 743
4 TraesCS2A01G378800 chr4D 88.806 536 52 7 1997 2531 495347361 495346833 0.000000e+00 651
5 TraesCS2A01G378800 chr7D 89.494 514 46 8 2022 2531 529829903 529829394 0.000000e+00 643
6 TraesCS2A01G378800 chr7D 88.224 518 53 5 2020 2531 12601076 12600561 1.660000e-171 612
7 TraesCS2A01G378800 chr7D 88.304 513 49 8 2022 2531 236814227 236813723 2.790000e-169 604
8 TraesCS2A01G378800 chr7D 87.938 514 59 3 2020 2531 567606752 567606240 1.000000e-168 603
9 TraesCS2A01G378800 chr6D 87.570 539 52 10 1997 2531 319356324 319356851 5.990000e-171 610
10 TraesCS2A01G378800 chr1D 87.061 541 58 7 1997 2531 49886074 49885540 3.600000e-168 601
11 TraesCS2A01G378800 chr1D 86.667 540 62 8 1997 2531 420371421 420370887 7.800000e-165 590
12 TraesCS2A01G378800 chr1A 86.606 545 60 9 1994 2531 568152980 568153518 7.800000e-165 590


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 TraesCS2A01G378800 chr2A 621514441 621516971 2530 True 4674 4674 100.000 1 2531 1 chr2A.!!$R1 2530
1 TraesCS2A01G378800 chr2D 478697786 478699600 1814 False 2338 2338 90.102 1 1821 1 chr2D.!!$F1 1820
2 TraesCS2A01G378800 chr2B 561258638 561260382 1744 True 1176 1609 90.571 3 1758 2 chr2B.!!$R1 1755
3 TraesCS2A01G378800 chr4D 495346833 495347361 528 True 651 651 88.806 1997 2531 1 chr4D.!!$R1 534
4 TraesCS2A01G378800 chr7D 529829394 529829903 509 True 643 643 89.494 2022 2531 1 chr7D.!!$R3 509
5 TraesCS2A01G378800 chr7D 12600561 12601076 515 True 612 612 88.224 2020 2531 1 chr7D.!!$R1 511
6 TraesCS2A01G378800 chr7D 236813723 236814227 504 True 604 604 88.304 2022 2531 1 chr7D.!!$R2 509
7 TraesCS2A01G378800 chr7D 567606240 567606752 512 True 603 603 87.938 2020 2531 1 chr7D.!!$R4 511
8 TraesCS2A01G378800 chr6D 319356324 319356851 527 False 610 610 87.570 1997 2531 1 chr6D.!!$F1 534
9 TraesCS2A01G378800 chr1D 49885540 49886074 534 True 601 601 87.061 1997 2531 1 chr1D.!!$R1 534
10 TraesCS2A01G378800 chr1D 420370887 420371421 534 True 590 590 86.667 1997 2531 1 chr1D.!!$R2 534
11 TraesCS2A01G378800 chr1A 568152980 568153518 538 False 590 590 86.606 1994 2531 1 chr1A.!!$F1 537

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
680 709 0.254178 AGCTGGAATGCCGTCTTGAT 59.746 50.0 0.0 0.0 36.79 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1962 0.037697 CGACACCGGTGAGAAATGGA 60.038 55.0 40.21 0.0 0.0 3.41 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
29 30 3.796178 TCTTCAAACAACATTCTTTGCGC 59.204 39.130 0.00 0.00 0.00 6.09
113 114 4.421479 AAGTGCGCTCTCGTCCGG 62.421 66.667 13.07 0.00 38.14 5.14
134 138 3.304190 GGTACAAACTTACAACCCGCAAG 60.304 47.826 0.00 0.00 0.00 4.01
139 143 0.889186 CTTACAACCCGCAAGCCACT 60.889 55.000 0.00 0.00 0.00 4.00
160 164 3.870633 ACTCCTCCAGAATTACACGAC 57.129 47.619 0.00 0.00 0.00 4.34
201 205 2.182825 CAACGCGTAATCTAGCTTCGT 58.817 47.619 14.46 0.00 0.00 3.85
324 329 1.446272 CCGTTCTCCAGCGTCTTCC 60.446 63.158 0.00 0.00 0.00 3.46
398 427 5.901853 TGGGACATGCATGGGATTATTTTAA 59.098 36.000 29.41 0.98 0.00 1.52
400 429 7.072202 TGGGACATGCATGGGATTATTTTAATT 59.928 33.333 29.41 3.99 0.00 1.40
408 437 8.764287 GCATGGGATTATTTTAATTTTTCTCGG 58.236 33.333 0.00 0.00 0.00 4.63
409 438 8.764287 CATGGGATTATTTTAATTTTTCTCGGC 58.236 33.333 0.00 0.00 0.00 5.54
410 439 6.975772 TGGGATTATTTTAATTTTTCTCGGCG 59.024 34.615 0.00 0.00 0.00 6.46
457 486 4.519540 ACTGACAAGTGTGTTTTGCTTT 57.480 36.364 0.00 0.00 38.41 3.51
572 601 5.184096 TCTCTGTTCTGTTCGCTTAATCTCT 59.816 40.000 0.00 0.00 0.00 3.10
579 608 7.757097 TCTGTTCGCTTAATCTCTGTAATTC 57.243 36.000 0.00 0.00 0.00 2.17
613 642 6.240894 TCACTTCTAGAAACAGCATCCATTT 58.759 36.000 6.63 0.00 0.00 2.32
614 643 6.372659 TCACTTCTAGAAACAGCATCCATTTC 59.627 38.462 6.63 0.00 33.40 2.17
615 644 6.373774 CACTTCTAGAAACAGCATCCATTTCT 59.626 38.462 6.63 4.11 43.39 2.52
616 645 6.597280 ACTTCTAGAAACAGCATCCATTTCTC 59.403 38.462 6.63 0.00 40.85 2.87
617 646 6.305272 TCTAGAAACAGCATCCATTTCTCT 57.695 37.500 1.92 0.00 40.85 3.10
618 647 6.715280 TCTAGAAACAGCATCCATTTCTCTT 58.285 36.000 1.92 0.00 40.85 2.85
619 648 7.851228 TCTAGAAACAGCATCCATTTCTCTTA 58.149 34.615 1.92 0.00 40.85 2.10
620 649 8.489489 TCTAGAAACAGCATCCATTTCTCTTAT 58.511 33.333 1.92 0.00 40.85 1.73
621 650 7.330900 AGAAACAGCATCCATTTCTCTTATG 57.669 36.000 0.00 0.00 38.04 1.90
622 651 6.888632 AGAAACAGCATCCATTTCTCTTATGT 59.111 34.615 0.00 0.00 38.04 2.29
623 652 7.395489 AGAAACAGCATCCATTTCTCTTATGTT 59.605 33.333 0.00 0.00 38.04 2.71
624 653 7.472334 AACAGCATCCATTTCTCTTATGTTT 57.528 32.000 0.00 0.00 0.00 2.83
625 654 7.472334 ACAGCATCCATTTCTCTTATGTTTT 57.528 32.000 0.00 0.00 0.00 2.43
626 655 7.542025 ACAGCATCCATTTCTCTTATGTTTTC 58.458 34.615 0.00 0.00 0.00 2.29
627 656 7.395489 ACAGCATCCATTTCTCTTATGTTTTCT 59.605 33.333 0.00 0.00 0.00 2.52
628 657 7.914346 CAGCATCCATTTCTCTTATGTTTTCTC 59.086 37.037 0.00 0.00 0.00 2.87
629 658 6.909357 GCATCCATTTCTCTTATGTTTTCTCG 59.091 38.462 0.00 0.00 0.00 4.04
630 659 7.414540 GCATCCATTTCTCTTATGTTTTCTCGT 60.415 37.037 0.00 0.00 0.00 4.18
631 660 7.596749 TCCATTTCTCTTATGTTTTCTCGTC 57.403 36.000 0.00 0.00 0.00 4.20
632 661 6.310467 TCCATTTCTCTTATGTTTTCTCGTCG 59.690 38.462 0.00 0.00 0.00 5.12
633 662 6.090898 CCATTTCTCTTATGTTTTCTCGTCGT 59.909 38.462 0.00 0.00 0.00 4.34
634 663 6.686130 TTTCTCTTATGTTTTCTCGTCGTC 57.314 37.500 0.00 0.00 0.00 4.20
635 664 5.624344 TCTCTTATGTTTTCTCGTCGTCT 57.376 39.130 0.00 0.00 0.00 4.18
636 665 5.629097 TCTCTTATGTTTTCTCGTCGTCTC 58.371 41.667 0.00 0.00 0.00 3.36
637 666 5.180680 TCTCTTATGTTTTCTCGTCGTCTCA 59.819 40.000 0.00 0.00 0.00 3.27
638 667 5.152097 TCTTATGTTTTCTCGTCGTCTCAC 58.848 41.667 0.00 0.00 0.00 3.51
639 668 2.129823 TGTTTTCTCGTCGTCTCACC 57.870 50.000 0.00 0.00 0.00 4.02
649 678 1.210413 CGTCTCACCTCTCACACCG 59.790 63.158 0.00 0.00 0.00 4.94
671 700 1.005294 CGTGCAAACAGCTGGAATGC 61.005 55.000 24.93 24.93 45.94 3.56
673 702 1.444895 GCAAACAGCTGGAATGCCG 60.445 57.895 22.60 5.55 41.15 5.69
680 709 0.254178 AGCTGGAATGCCGTCTTGAT 59.746 50.000 0.00 0.00 36.79 2.57
720 749 7.365741 TCTTCTTCAGAATTTCAGAAATGCAC 58.634 34.615 15.31 7.89 33.01 4.57
725 754 6.913170 TCAGAATTTCAGAAATGCACCTAAC 58.087 36.000 15.31 0.00 0.00 2.34
747 776 2.048222 GCGTGTCTAGCACCAGCA 60.048 61.111 10.44 0.00 44.97 4.41
748 777 2.383527 GCGTGTCTAGCACCAGCAC 61.384 63.158 10.44 0.00 44.97 4.40
749 778 1.006220 CGTGTCTAGCACCAGCACA 60.006 57.895 10.44 0.00 44.97 4.57
750 779 0.599991 CGTGTCTAGCACCAGCACAA 60.600 55.000 10.44 0.00 44.97 3.33
751 780 1.813513 GTGTCTAGCACCAGCACAAT 58.186 50.000 6.14 0.00 45.49 2.71
769 798 3.243267 ACAATAAACGGTGCAACAAGTCC 60.243 43.478 0.98 0.00 39.98 3.85
809 838 3.045601 TGCTTCTCAGGCTCACTAAAC 57.954 47.619 0.00 0.00 0.00 2.01
865 894 5.771666 ACTGTGACACCAATGATTTTCATCT 59.228 36.000 2.45 0.00 35.76 2.90
898 927 7.222872 TCTCTACTACGCTAGCTATAAAAGGT 58.777 38.462 13.93 2.97 39.81 3.50
1012 1041 3.959478 GACCGCATGGACGAAGATA 57.041 52.632 0.00 0.00 39.21 1.98
1038 1067 4.081030 CGCTGCAGCACCAAGACG 62.081 66.667 36.03 15.08 42.21 4.18
1100 1129 5.654650 CAGACTACCTCAAGTACCTCTTCAT 59.345 44.000 0.00 0.00 33.63 2.57
1170 1199 0.543410 TCTCCTCCTACCACGGCAAA 60.543 55.000 0.00 0.00 0.00 3.68
1253 1282 3.717294 CAACAGCCCTAGCCCCGT 61.717 66.667 0.00 0.00 41.25 5.28
1291 1320 1.668294 CTCCACTCACGGCTGAAGT 59.332 57.895 0.00 0.00 0.00 3.01
1428 1457 1.847798 ATGGGTTGGCCTGCTACGAA 61.848 55.000 3.32 0.00 34.45 3.85
1506 1535 1.302832 CAGGGCGCAGAACTTTCCT 60.303 57.895 10.83 0.00 0.00 3.36
1518 1547 1.770294 ACTTTCCTCCGGTTTTGCAA 58.230 45.000 0.00 0.00 0.00 4.08
1571 1607 2.334653 CTGAGAGATCGAGGGCGC 59.665 66.667 0.00 0.00 37.46 6.53
1679 1716 8.854979 TTTTGATTTCTACATGAGTGTTTGTG 57.145 30.769 0.00 0.00 39.77 3.33
1804 1851 4.755123 TCACTTTCTTTTGGCTAGTGCTAC 59.245 41.667 0.00 0.00 36.91 3.58
1807 1854 1.066430 TCTTTTGGCTAGTGCTACCCG 60.066 52.381 0.00 0.00 39.59 5.28
1808 1855 0.688487 TTTTGGCTAGTGCTACCCGT 59.312 50.000 0.00 0.00 39.59 5.28
1810 1857 1.940883 TTGGCTAGTGCTACCCGTCG 61.941 60.000 0.00 0.00 39.59 5.12
1855 1902 3.717712 GCATCGAGCGATTTACAGC 57.282 52.632 2.12 0.00 31.62 4.40
1856 1903 0.233332 GCATCGAGCGATTTACAGCC 59.767 55.000 2.12 0.00 31.62 4.85
1857 1904 0.504384 CATCGAGCGATTTACAGCCG 59.496 55.000 2.12 0.00 31.62 5.52
1863 1910 2.456000 CGATTTACAGCCGCACACT 58.544 52.632 0.00 0.00 0.00 3.55
1864 1911 0.095245 CGATTTACAGCCGCACACTG 59.905 55.000 0.00 0.00 41.08 3.66
1865 1912 0.447801 GATTTACAGCCGCACACTGG 59.552 55.000 0.00 0.00 39.55 4.00
1872 1919 2.666862 CCGCACACTGGCCGTAAA 60.667 61.111 0.00 0.00 0.00 2.01
1873 1920 2.255172 CCGCACACTGGCCGTAAAA 61.255 57.895 0.00 0.00 0.00 1.52
1874 1921 1.206578 CGCACACTGGCCGTAAAAG 59.793 57.895 0.00 0.00 0.00 2.27
1875 1922 1.081442 GCACACTGGCCGTAAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
1876 1923 1.791103 GCACACTGGCCGTAAAAGCA 61.791 55.000 0.00 0.00 0.00 3.91
1877 1924 0.040425 CACACTGGCCGTAAAAGCAC 60.040 55.000 0.00 0.00 0.00 4.40
1878 1925 1.170290 ACACTGGCCGTAAAAGCACC 61.170 55.000 0.00 0.00 0.00 5.01
1879 1926 1.964373 ACTGGCCGTAAAAGCACCG 60.964 57.895 0.00 0.00 0.00 4.94
1880 1927 3.322706 CTGGCCGTAAAAGCACCGC 62.323 63.158 0.00 0.00 0.00 5.68
1881 1928 4.111016 GGCCGTAAAAGCACCGCC 62.111 66.667 0.00 0.00 36.02 6.13
1882 1929 4.111016 GCCGTAAAAGCACCGCCC 62.111 66.667 0.00 0.00 0.00 6.13
1883 1930 3.795342 CCGTAAAAGCACCGCCCG 61.795 66.667 0.00 0.00 0.00 6.13
1884 1931 3.795342 CGTAAAAGCACCGCCCGG 61.795 66.667 4.96 4.96 42.03 5.73
1885 1932 4.111016 GTAAAAGCACCGCCCGGC 62.111 66.667 6.63 0.00 39.32 6.13
1913 1960 4.933064 CCTCGCCGCCATCGTCTC 62.933 72.222 0.00 0.00 0.00 3.36
1914 1961 4.933064 CTCGCCGCCATCGTCTCC 62.933 72.222 0.00 0.00 0.00 3.71
1916 1963 4.933064 CGCCGCCATCGTCTCCTC 62.933 72.222 0.00 0.00 0.00 3.71
1917 1964 4.593864 GCCGCCATCGTCTCCTCC 62.594 72.222 0.00 0.00 0.00 4.30
1918 1965 3.147595 CCGCCATCGTCTCCTCCA 61.148 66.667 0.00 0.00 0.00 3.86
1919 1966 2.502492 CCGCCATCGTCTCCTCCAT 61.502 63.158 0.00 0.00 0.00 3.41
1920 1967 1.443407 CGCCATCGTCTCCTCCATT 59.557 57.895 0.00 0.00 0.00 3.16
1921 1968 0.179073 CGCCATCGTCTCCTCCATTT 60.179 55.000 0.00 0.00 0.00 2.32
1922 1969 1.587547 GCCATCGTCTCCTCCATTTC 58.412 55.000 0.00 0.00 0.00 2.17
1923 1970 1.139853 GCCATCGTCTCCTCCATTTCT 59.860 52.381 0.00 0.00 0.00 2.52
1924 1971 2.804933 GCCATCGTCTCCTCCATTTCTC 60.805 54.545 0.00 0.00 0.00 2.87
1925 1972 2.432146 CCATCGTCTCCTCCATTTCTCA 59.568 50.000 0.00 0.00 0.00 3.27
1926 1973 3.452474 CATCGTCTCCTCCATTTCTCAC 58.548 50.000 0.00 0.00 0.00 3.51
1927 1974 1.825474 TCGTCTCCTCCATTTCTCACC 59.175 52.381 0.00 0.00 0.00 4.02
1928 1975 1.469940 CGTCTCCTCCATTTCTCACCG 60.470 57.143 0.00 0.00 0.00 4.94
1929 1976 1.134670 GTCTCCTCCATTTCTCACCGG 60.135 57.143 0.00 0.00 0.00 5.28
1930 1977 0.905357 CTCCTCCATTTCTCACCGGT 59.095 55.000 0.00 0.00 0.00 5.28
1931 1978 0.613260 TCCTCCATTTCTCACCGGTG 59.387 55.000 29.26 29.26 0.00 4.94
1932 1979 0.324943 CCTCCATTTCTCACCGGTGT 59.675 55.000 32.74 11.90 0.00 4.16
1933 1980 1.676014 CCTCCATTTCTCACCGGTGTC 60.676 57.143 32.74 0.00 0.00 3.67
1934 1981 0.037697 TCCATTTCTCACCGGTGTCG 60.038 55.000 32.74 23.98 0.00 4.35
1935 1982 0.320421 CCATTTCTCACCGGTGTCGT 60.320 55.000 32.74 13.69 33.95 4.34
1936 1983 0.790207 CATTTCTCACCGGTGTCGTG 59.210 55.000 32.74 20.42 33.95 4.35
1937 1984 0.949105 ATTTCTCACCGGTGTCGTGC 60.949 55.000 32.74 0.00 33.95 5.34
1938 1985 2.299503 TTTCTCACCGGTGTCGTGCA 62.300 55.000 32.74 12.78 33.95 4.57
1939 1986 2.048222 CTCACCGGTGTCGTGCAT 60.048 61.111 32.74 0.00 33.95 3.96
1940 1987 2.356913 TCACCGGTGTCGTGCATG 60.357 61.111 32.74 5.46 33.95 4.06
1941 1988 4.088762 CACCGGTGTCGTGCATGC 62.089 66.667 26.95 11.82 33.95 4.06
1942 1989 4.617520 ACCGGTGTCGTGCATGCA 62.618 61.111 18.46 18.46 33.95 3.96
1943 1990 3.792047 CCGGTGTCGTGCATGCAG 61.792 66.667 23.41 15.31 33.95 4.41
1944 1991 4.450122 CGGTGTCGTGCATGCAGC 62.450 66.667 23.41 14.84 45.96 5.25
1955 2002 4.025858 ATGCAGCAGCGTGTCCCT 62.026 61.111 0.00 0.00 46.23 4.20
1956 2003 4.994471 TGCAGCAGCGTGTCCCTG 62.994 66.667 0.00 0.00 46.23 4.45
1957 2004 4.996434 GCAGCAGCGTGTCCCTGT 62.996 66.667 0.00 0.00 32.93 4.00
1958 2005 3.046087 CAGCAGCGTGTCCCTGTG 61.046 66.667 0.00 0.00 32.93 3.66
1959 2006 4.320456 AGCAGCGTGTCCCTGTGG 62.320 66.667 0.00 0.00 32.93 4.17
1960 2007 4.626081 GCAGCGTGTCCCTGTGGT 62.626 66.667 0.00 0.00 32.93 4.16
1961 2008 2.111043 CAGCGTGTCCCTGTGGTT 59.889 61.111 0.00 0.00 0.00 3.67
1962 2009 2.111043 AGCGTGTCCCTGTGGTTG 59.889 61.111 0.00 0.00 0.00 3.77
1963 2010 3.660111 GCGTGTCCCTGTGGTTGC 61.660 66.667 0.00 0.00 0.00 4.17
1964 2011 2.203139 CGTGTCCCTGTGGTTGCA 60.203 61.111 0.00 0.00 0.00 4.08
1965 2012 2.253758 CGTGTCCCTGTGGTTGCAG 61.254 63.158 0.00 0.00 36.31 4.41
1966 2013 2.203337 TGTCCCTGTGGTTGCAGC 60.203 61.111 0.00 0.00 35.28 5.25
1967 2014 2.113986 GTCCCTGTGGTTGCAGCT 59.886 61.111 0.00 0.00 35.28 4.24
1968 2015 1.968540 GTCCCTGTGGTTGCAGCTC 60.969 63.158 0.00 0.00 35.28 4.09
1969 2016 2.674380 CCCTGTGGTTGCAGCTCC 60.674 66.667 0.00 0.00 35.28 4.70
1970 2017 2.674380 CCTGTGGTTGCAGCTCCC 60.674 66.667 0.00 0.00 35.28 4.30
1971 2018 2.674380 CTGTGGTTGCAGCTCCCC 60.674 66.667 0.00 0.00 0.00 4.81
1972 2019 4.641645 TGTGGTTGCAGCTCCCCG 62.642 66.667 0.00 0.00 0.00 5.73
1973 2020 4.643387 GTGGTTGCAGCTCCCCGT 62.643 66.667 0.00 0.00 0.00 5.28
1974 2021 4.329545 TGGTTGCAGCTCCCCGTC 62.330 66.667 0.00 0.00 0.00 4.79
1975 2022 4.329545 GGTTGCAGCTCCCCGTCA 62.330 66.667 0.00 0.00 0.00 4.35
1976 2023 3.050275 GTTGCAGCTCCCCGTCAC 61.050 66.667 0.00 0.00 0.00 3.67
1977 2024 4.680237 TTGCAGCTCCCCGTCACG 62.680 66.667 0.00 0.00 0.00 4.35
1980 2027 4.436998 CAGCTCCCCGTCACGACC 62.437 72.222 0.00 0.00 0.00 4.79
1983 2030 4.112341 CTCCCCGTCACGACCGTC 62.112 72.222 0.00 0.00 0.00 4.79
1989 2036 4.702081 GTCACGACCGTCGCAGCT 62.702 66.667 20.67 0.00 45.12 4.24
1990 2037 3.973516 TCACGACCGTCGCAGCTT 61.974 61.111 20.67 0.00 45.12 3.74
1991 2038 3.767230 CACGACCGTCGCAGCTTG 61.767 66.667 20.67 7.42 45.12 4.01
1992 2039 3.973516 ACGACCGTCGCAGCTTGA 61.974 61.111 20.67 0.00 45.12 3.02
2003 2050 1.201998 CGCAGCTTGAATGCACTAGTG 60.202 52.381 18.93 18.93 44.05 2.74
2014 2061 3.569194 TGCACTAGTGGAAAACAGGAA 57.431 42.857 23.95 0.00 0.00 3.36
2035 2082 1.076677 ACTAGTCCCGGTTTCAGAGGA 59.923 52.381 0.00 0.00 0.00 3.71
2036 2083 2.292323 ACTAGTCCCGGTTTCAGAGGAT 60.292 50.000 0.00 0.00 0.00 3.24
2132 2179 1.208165 AATCGGGACAGAAGGGGCTT 61.208 55.000 0.00 0.00 0.00 4.35
2174 2222 1.630878 CAGGCAGGAGGACCTTTAGTT 59.369 52.381 0.00 0.00 45.36 2.24
2175 2223 2.040412 CAGGCAGGAGGACCTTTAGTTT 59.960 50.000 0.00 0.00 45.36 2.66
2204 2252 0.394080 ACACCGACCGGAACCAAAAA 60.394 50.000 16.07 0.00 38.96 1.94
2216 2264 3.431486 GGAACCAAAAAGGCATTCACACA 60.431 43.478 0.00 0.00 43.14 3.72
2299 2349 6.010201 AGGGGATTTTGGAGGGTTAATTTAGA 60.010 38.462 0.00 0.00 0.00 2.10
2328 2380 8.972458 TTCATATTGTGTTGGCTAGCTAATAA 57.028 30.769 17.12 12.49 0.00 1.40
2412 2473 2.864946 CTCGACACGCTAGCTAGTAAGA 59.135 50.000 21.62 12.02 0.00 2.10
2418 2479 5.109903 ACACGCTAGCTAGTAAGAAAATGG 58.890 41.667 21.62 3.55 0.00 3.16
2443 2504 7.556275 GGAGGAACCATTAATTACACAAGATCA 59.444 37.037 0.00 0.00 38.79 2.92
2462 2523 9.152595 CAAGATCATCATGAACATATACAGAGG 57.847 37.037 0.00 0.00 0.00 3.69
2497 2562 1.669604 TCTCCGAGAGAATGGTCGAG 58.330 55.000 0.00 0.00 38.50 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.533535 CGCGCAAAGAATGTTGTTTGAA 59.466 40.909 16.60 0.00 42.16 2.69
10 11 2.115595 CGCGCAAAGAATGTTGTTTGA 58.884 42.857 16.60 0.00 42.16 2.69
29 30 2.349886 GCTAGTCAGGCTTGAATCAACG 59.650 50.000 0.70 0.00 34.49 4.10
94 95 2.569134 GGACGAGAGCGCACTTCT 59.431 61.111 11.47 3.06 42.48 2.85
113 114 3.850740 GCTTGCGGGTTGTAAGTTTGTAC 60.851 47.826 0.00 0.00 41.80 2.90
134 138 3.451178 TGTAATTCTGGAGGAGTAGTGGC 59.549 47.826 0.00 0.00 0.00 5.01
139 143 3.376234 CGTCGTGTAATTCTGGAGGAGTA 59.624 47.826 0.00 0.00 0.00 2.59
160 164 0.672401 ACGTGTGCTTTACCCCATCG 60.672 55.000 0.00 0.00 0.00 3.84
201 205 2.903547 GCTTGGTCTCGCCGCAAAA 61.904 57.895 0.00 0.00 41.21 2.44
283 288 3.553095 AAGACCAGGGTTCCGCAGC 62.553 63.158 0.00 0.00 0.00 5.25
284 289 1.376037 GAAGACCAGGGTTCCGCAG 60.376 63.158 0.00 0.00 0.00 5.18
285 290 1.841556 AGAAGACCAGGGTTCCGCA 60.842 57.895 0.00 0.00 0.00 5.69
286 291 1.376037 CAGAAGACCAGGGTTCCGC 60.376 63.158 0.00 0.00 0.00 5.54
287 292 1.296715 CCAGAAGACCAGGGTTCCG 59.703 63.158 0.00 0.00 0.00 4.30
288 293 1.002011 GCCAGAAGACCAGGGTTCC 60.002 63.158 0.00 0.00 0.00 3.62
324 329 5.017490 TGAGGAGTTACTCTTACTTGAGGG 58.983 45.833 12.41 0.00 38.32 4.30
398 427 1.315257 ATGCTGCCGCCGAGAAAAAT 61.315 50.000 0.00 0.00 34.43 1.82
400 429 2.359850 ATGCTGCCGCCGAGAAAA 60.360 55.556 0.00 0.00 34.43 2.29
408 437 3.818787 CCTTCACCATGCTGCCGC 61.819 66.667 0.00 0.00 0.00 6.53
409 438 1.526575 AAACCTTCACCATGCTGCCG 61.527 55.000 0.00 0.00 0.00 5.69
410 439 0.037975 CAAACCTTCACCATGCTGCC 60.038 55.000 0.00 0.00 0.00 4.85
457 486 4.038271 ACTCTCTCCATTTTTCATGCCA 57.962 40.909 0.00 0.00 0.00 4.92
494 523 0.606401 AGTTGTCTTGGCCATCACGG 60.606 55.000 6.09 0.00 38.11 4.94
579 608 7.540055 GCTGTTTCTAGAAGTGAAAAATGATGG 59.460 37.037 5.12 0.00 35.54 3.51
591 620 6.479884 AGAAATGGATGCTGTTTCTAGAAGT 58.520 36.000 13.53 0.00 39.63 3.01
613 642 5.180680 TGAGACGACGAGAAAACATAAGAGA 59.819 40.000 0.00 0.00 0.00 3.10
614 643 5.284188 GTGAGACGACGAGAAAACATAAGAG 59.716 44.000 0.00 0.00 0.00 2.85
615 644 5.152097 GTGAGACGACGAGAAAACATAAGA 58.848 41.667 0.00 0.00 0.00 2.10
616 645 4.323868 GGTGAGACGACGAGAAAACATAAG 59.676 45.833 0.00 0.00 0.00 1.73
617 646 4.022589 AGGTGAGACGACGAGAAAACATAA 60.023 41.667 0.00 0.00 0.00 1.90
618 647 3.504906 AGGTGAGACGACGAGAAAACATA 59.495 43.478 0.00 0.00 0.00 2.29
619 648 2.296471 AGGTGAGACGACGAGAAAACAT 59.704 45.455 0.00 0.00 0.00 2.71
620 649 1.679680 AGGTGAGACGACGAGAAAACA 59.320 47.619 0.00 0.00 0.00 2.83
621 650 2.030981 AGAGGTGAGACGACGAGAAAAC 60.031 50.000 0.00 0.00 0.00 2.43
622 651 2.225963 GAGAGGTGAGACGACGAGAAAA 59.774 50.000 0.00 0.00 0.00 2.29
623 652 1.805345 GAGAGGTGAGACGACGAGAAA 59.195 52.381 0.00 0.00 0.00 2.52
624 653 1.270678 TGAGAGGTGAGACGACGAGAA 60.271 52.381 0.00 0.00 0.00 2.87
625 654 0.320697 TGAGAGGTGAGACGACGAGA 59.679 55.000 0.00 0.00 0.00 4.04
626 655 0.444651 GTGAGAGGTGAGACGACGAG 59.555 60.000 0.00 0.00 0.00 4.18
627 656 0.250166 TGTGAGAGGTGAGACGACGA 60.250 55.000 0.00 0.00 0.00 4.20
628 657 0.110147 GTGTGAGAGGTGAGACGACG 60.110 60.000 0.00 0.00 0.00 5.12
629 658 0.241481 GGTGTGAGAGGTGAGACGAC 59.759 60.000 0.00 0.00 0.00 4.34
630 659 1.235281 CGGTGTGAGAGGTGAGACGA 61.235 60.000 0.00 0.00 0.00 4.20
631 660 1.210413 CGGTGTGAGAGGTGAGACG 59.790 63.158 0.00 0.00 0.00 4.18
632 661 1.199558 GTACGGTGTGAGAGGTGAGAC 59.800 57.143 0.00 0.00 0.00 3.36
633 662 1.531423 GTACGGTGTGAGAGGTGAGA 58.469 55.000 0.00 0.00 0.00 3.27
634 663 0.168348 CGTACGGTGTGAGAGGTGAG 59.832 60.000 7.57 0.00 0.00 3.51
635 664 0.535780 ACGTACGGTGTGAGAGGTGA 60.536 55.000 21.06 0.00 0.00 4.02
636 665 0.386858 CACGTACGGTGTGAGAGGTG 60.387 60.000 21.06 0.21 41.89 4.00
637 666 1.954528 CACGTACGGTGTGAGAGGT 59.045 57.895 21.06 0.00 41.89 3.85
638 667 4.861883 CACGTACGGTGTGAGAGG 57.138 61.111 21.06 0.00 41.89 3.69
649 678 0.941542 TTCCAGCTGTTTGCACGTAC 59.058 50.000 13.81 0.00 45.94 3.67
661 690 0.254178 ATCAAGACGGCATTCCAGCT 59.746 50.000 0.00 0.00 34.17 4.24
671 700 5.897377 AAAAACCTCCATAATCAAGACGG 57.103 39.130 0.00 0.00 0.00 4.79
696 725 6.585322 GGTGCATTTCTGAAATTCTGAAGAAG 59.415 38.462 12.74 9.67 36.07 2.85
702 731 6.917533 AGTTAGGTGCATTTCTGAAATTCTG 58.082 36.000 12.74 5.49 0.00 3.02
710 739 3.425359 CGCTCAAGTTAGGTGCATTTCTG 60.425 47.826 0.00 0.00 0.00 3.02
720 749 2.094700 TGCTAGACACGCTCAAGTTAGG 60.095 50.000 0.00 0.00 0.00 2.69
747 776 3.243267 GGACTTGTTGCACCGTTTATTGT 60.243 43.478 0.00 0.00 0.00 2.71
748 777 3.243234 TGGACTTGTTGCACCGTTTATTG 60.243 43.478 0.00 0.00 0.00 1.90
749 778 2.952978 TGGACTTGTTGCACCGTTTATT 59.047 40.909 0.00 0.00 0.00 1.40
750 779 2.552315 CTGGACTTGTTGCACCGTTTAT 59.448 45.455 0.00 0.00 0.00 1.40
751 780 1.944024 CTGGACTTGTTGCACCGTTTA 59.056 47.619 0.00 0.00 0.00 2.01
769 798 3.829948 CAAGCACAAATTAGCTGGACTG 58.170 45.455 0.00 0.00 41.70 3.51
809 838 2.194201 TTCGGGGCAAGAAAGGTTAG 57.806 50.000 0.00 0.00 0.00 2.34
865 894 5.713389 AGCTAGCGTAGTAGAGATAGAGAGA 59.287 44.000 9.55 0.00 0.00 3.10
997 1026 2.989840 GGAATCTATCTTCGTCCATGCG 59.010 50.000 0.00 0.00 0.00 4.73
1150 1179 0.970937 TTGCCGTGGTAGGAGGAGAG 60.971 60.000 0.00 0.00 0.00 3.20
1170 1199 2.896801 CGGCAGACGCTTGTTGCTT 61.897 57.895 0.00 0.00 40.11 3.91
1278 1307 2.046892 CCCCACTTCAGCCGTGAG 60.047 66.667 0.00 0.00 34.35 3.51
1428 1457 1.115930 AGTCCACGTCAGGCTCAAGT 61.116 55.000 0.00 0.00 0.00 3.16
1506 1535 2.887889 CGAGCGTTGCAAAACCGGA 61.888 57.895 9.46 0.00 0.00 5.14
1591 1627 3.349022 AGAACGTACTCCTCTCCTCTTG 58.651 50.000 0.00 0.00 0.00 3.02
1775 1819 8.458843 GCACTAGCCAAAAGAAAGTGATAATTA 58.541 33.333 5.03 0.00 39.93 1.40
1777 1821 6.660949 AGCACTAGCCAAAAGAAAGTGATAAT 59.339 34.615 5.03 0.00 43.56 1.28
1780 1824 4.401925 AGCACTAGCCAAAAGAAAGTGAT 58.598 39.130 5.03 0.00 43.56 3.06
1782 1826 4.083271 GGTAGCACTAGCCAAAAGAAAGTG 60.083 45.833 0.00 0.00 43.56 3.16
1783 1827 4.072839 GGTAGCACTAGCCAAAAGAAAGT 58.927 43.478 0.00 0.00 43.56 2.66
1784 1828 4.686839 GGTAGCACTAGCCAAAAGAAAG 57.313 45.455 0.00 0.00 43.56 2.62
1834 1881 0.930310 TGTAAATCGCTCGATGCTGC 59.070 50.000 5.47 0.00 40.11 5.25
1835 1882 1.070975 GCTGTAAATCGCTCGATGCTG 60.071 52.381 5.47 5.29 40.11 4.41
1836 1883 1.212616 GCTGTAAATCGCTCGATGCT 58.787 50.000 5.47 0.00 40.11 3.79
1837 1884 0.233332 GGCTGTAAATCGCTCGATGC 59.767 55.000 5.47 4.51 34.70 3.91
1838 1885 0.504384 CGGCTGTAAATCGCTCGATG 59.496 55.000 5.47 0.00 34.70 3.84
1839 1886 1.215655 GCGGCTGTAAATCGCTCGAT 61.216 55.000 0.00 0.00 45.16 3.59
1840 1887 1.876714 GCGGCTGTAAATCGCTCGA 60.877 57.895 0.00 0.00 45.16 4.04
1841 1888 2.621000 GCGGCTGTAAATCGCTCG 59.379 61.111 0.00 0.00 45.16 5.03
1845 1892 0.095245 CAGTGTGCGGCTGTAAATCG 59.905 55.000 0.00 0.00 0.00 3.34
1846 1893 0.447801 CCAGTGTGCGGCTGTAAATC 59.552 55.000 0.00 0.00 32.41 2.17
1847 1894 1.586154 GCCAGTGTGCGGCTGTAAAT 61.586 55.000 0.00 0.00 46.56 1.40
1848 1895 2.258013 GCCAGTGTGCGGCTGTAAA 61.258 57.895 0.00 0.00 46.56 2.01
1849 1896 2.668212 GCCAGTGTGCGGCTGTAA 60.668 61.111 0.00 0.00 46.56 2.41
1855 1902 2.182614 CTTTTACGGCCAGTGTGCGG 62.183 60.000 2.24 8.81 37.56 5.69
1856 1903 1.206578 CTTTTACGGCCAGTGTGCG 59.793 57.895 2.24 0.00 0.00 5.34
1857 1904 1.081442 GCTTTTACGGCCAGTGTGC 60.081 57.895 2.24 0.00 0.00 4.57
1858 1905 0.040425 GTGCTTTTACGGCCAGTGTG 60.040 55.000 2.24 0.00 0.00 3.82
1859 1906 1.170290 GGTGCTTTTACGGCCAGTGT 61.170 55.000 2.24 0.00 0.00 3.55
1860 1907 1.579429 GGTGCTTTTACGGCCAGTG 59.421 57.895 2.24 0.00 0.00 3.66
1861 1908 1.964373 CGGTGCTTTTACGGCCAGT 60.964 57.895 2.24 4.29 0.00 4.00
1862 1909 2.867472 CGGTGCTTTTACGGCCAG 59.133 61.111 2.24 0.00 0.00 4.85
1863 1910 3.358707 GCGGTGCTTTTACGGCCA 61.359 61.111 2.24 0.00 39.95 5.36
1866 1913 3.795342 CGGGCGGTGCTTTTACGG 61.795 66.667 0.00 0.00 0.00 4.02
1867 1914 3.795342 CCGGGCGGTGCTTTTACG 61.795 66.667 0.00 0.00 0.00 3.18
1868 1915 4.111016 GCCGGGCGGTGCTTTTAC 62.111 66.667 1.81 0.00 37.65 2.01
1901 1948 2.032860 AATGGAGGAGACGATGGCGG 62.033 60.000 0.00 0.00 43.17 6.13
1902 1949 0.179073 AAATGGAGGAGACGATGGCG 60.179 55.000 0.00 0.00 44.79 5.69
1903 1950 1.139853 AGAAATGGAGGAGACGATGGC 59.860 52.381 0.00 0.00 0.00 4.40
1904 1951 2.432146 TGAGAAATGGAGGAGACGATGG 59.568 50.000 0.00 0.00 0.00 3.51
1905 1952 3.452474 GTGAGAAATGGAGGAGACGATG 58.548 50.000 0.00 0.00 0.00 3.84
1906 1953 2.432510 GGTGAGAAATGGAGGAGACGAT 59.567 50.000 0.00 0.00 0.00 3.73
1907 1954 1.825474 GGTGAGAAATGGAGGAGACGA 59.175 52.381 0.00 0.00 0.00 4.20
1908 1955 1.469940 CGGTGAGAAATGGAGGAGACG 60.470 57.143 0.00 0.00 0.00 4.18
1909 1956 1.134670 CCGGTGAGAAATGGAGGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
1910 1957 1.195115 CCGGTGAGAAATGGAGGAGA 58.805 55.000 0.00 0.00 0.00 3.71
1911 1958 0.905357 ACCGGTGAGAAATGGAGGAG 59.095 55.000 6.12 0.00 0.00 3.69
1912 1959 0.613260 CACCGGTGAGAAATGGAGGA 59.387 55.000 31.31 0.00 0.00 3.71
1913 1960 0.324943 ACACCGGTGAGAAATGGAGG 59.675 55.000 40.21 10.24 0.00 4.30
1914 1961 1.726853 GACACCGGTGAGAAATGGAG 58.273 55.000 40.21 10.82 0.00 3.86
1915 1962 0.037697 CGACACCGGTGAGAAATGGA 60.038 55.000 40.21 0.00 0.00 3.41
1916 1963 0.320421 ACGACACCGGTGAGAAATGG 60.320 55.000 40.21 20.75 40.78 3.16
1917 1964 0.790207 CACGACACCGGTGAGAAATG 59.210 55.000 40.21 23.99 40.78 2.32
1918 1965 0.949105 GCACGACACCGGTGAGAAAT 60.949 55.000 40.21 18.59 40.78 2.17
1919 1966 1.593209 GCACGACACCGGTGAGAAA 60.593 57.895 40.21 0.00 40.78 2.52
1920 1967 2.028484 GCACGACACCGGTGAGAA 59.972 61.111 40.21 0.00 40.78 2.87
1921 1968 2.570284 ATGCACGACACCGGTGAGA 61.570 57.895 40.21 17.41 40.78 3.27
1922 1969 2.048222 ATGCACGACACCGGTGAG 60.048 61.111 40.21 31.55 40.78 3.51
1923 1970 2.356913 CATGCACGACACCGGTGA 60.357 61.111 40.21 18.00 40.78 4.02
1924 1971 4.088762 GCATGCACGACACCGGTG 62.089 66.667 32.83 32.83 40.78 4.94
1925 1972 4.617520 TGCATGCACGACACCGGT 62.618 61.111 18.46 0.00 40.78 5.28
1926 1973 3.792047 CTGCATGCACGACACCGG 61.792 66.667 18.46 0.00 40.78 5.28
1927 1974 4.450122 GCTGCATGCACGACACCG 62.450 66.667 18.46 6.37 42.31 4.94
1936 1983 4.471726 GGACACGCTGCTGCATGC 62.472 66.667 11.82 11.82 35.58 4.06
1937 1984 3.807538 GGGACACGCTGCTGCATG 61.808 66.667 16.29 13.34 38.47 4.06
1938 1985 4.025858 AGGGACACGCTGCTGCAT 62.026 61.111 16.29 0.00 39.64 3.96
1939 1986 4.994471 CAGGGACACGCTGCTGCA 62.994 66.667 16.29 0.88 37.59 4.41
1940 1987 4.996434 ACAGGGACACGCTGCTGC 62.996 66.667 14.04 5.34 46.25 5.25
1941 1988 3.046087 CACAGGGACACGCTGCTG 61.046 66.667 14.04 8.93 46.25 4.41
1942 1989 4.320456 CCACAGGGACACGCTGCT 62.320 66.667 14.04 1.76 46.25 4.24
1943 1990 4.626081 ACCACAGGGACACGCTGC 62.626 66.667 14.04 0.00 46.25 5.25
1945 1992 2.111043 CAACCACAGGGACACGCT 59.889 61.111 0.00 0.00 38.05 5.07
1946 1993 3.660111 GCAACCACAGGGACACGC 61.660 66.667 0.00 0.00 38.05 5.34
1947 1994 2.203139 TGCAACCACAGGGACACG 60.203 61.111 0.00 0.00 38.05 4.49
1948 1995 2.555547 GCTGCAACCACAGGGACAC 61.556 63.158 0.00 0.00 38.16 3.67
1949 1996 2.203337 GCTGCAACCACAGGGACA 60.203 61.111 0.00 0.00 38.16 4.02
1950 1997 1.968540 GAGCTGCAACCACAGGGAC 60.969 63.158 1.02 0.00 38.16 4.46
1951 1998 2.431683 GAGCTGCAACCACAGGGA 59.568 61.111 1.02 0.00 38.16 4.20
1952 1999 2.674380 GGAGCTGCAACCACAGGG 60.674 66.667 0.00 0.00 38.16 4.45
1953 2000 2.674380 GGGAGCTGCAACCACAGG 60.674 66.667 7.79 0.00 38.16 4.00
1954 2001 2.674380 GGGGAGCTGCAACCACAG 60.674 66.667 7.79 0.00 40.80 3.66
1955 2002 4.641645 CGGGGAGCTGCAACCACA 62.642 66.667 7.79 0.00 0.00 4.17
1956 2003 4.643387 ACGGGGAGCTGCAACCAC 62.643 66.667 7.79 11.85 0.00 4.16
1957 2004 4.329545 GACGGGGAGCTGCAACCA 62.330 66.667 7.79 0.00 0.00 3.67
1958 2005 4.329545 TGACGGGGAGCTGCAACC 62.330 66.667 7.79 4.81 0.00 3.77
1959 2006 3.050275 GTGACGGGGAGCTGCAAC 61.050 66.667 7.79 0.00 0.00 4.17
1960 2007 4.680237 CGTGACGGGGAGCTGCAA 62.680 66.667 7.79 0.00 0.00 4.08
1963 2010 4.436998 GGTCGTGACGGGGAGCTG 62.437 72.222 4.70 0.00 0.00 4.24
1966 2013 4.112341 GACGGTCGTGACGGGGAG 62.112 72.222 4.70 0.00 36.16 4.30
1972 2019 4.702081 AGCTGCGACGGTCGTGAC 62.702 66.667 28.75 18.53 42.81 3.67
1973 2020 3.973516 AAGCTGCGACGGTCGTGA 61.974 61.111 28.75 16.31 42.81 4.35
1974 2021 3.767230 CAAGCTGCGACGGTCGTG 61.767 66.667 28.75 22.19 42.81 4.35
1975 2022 2.765250 ATTCAAGCTGCGACGGTCGT 62.765 55.000 28.75 8.89 42.81 4.34
1976 2023 2.094659 ATTCAAGCTGCGACGGTCG 61.095 57.895 25.18 25.18 43.89 4.79
1977 2024 1.421485 CATTCAAGCTGCGACGGTC 59.579 57.895 0.00 0.00 0.00 4.79
1978 2025 2.680913 GCATTCAAGCTGCGACGGT 61.681 57.895 0.00 0.00 0.00 4.83
1979 2026 2.099062 GCATTCAAGCTGCGACGG 59.901 61.111 0.00 0.00 0.00 4.79
1980 2027 1.510623 GTGCATTCAAGCTGCGACG 60.511 57.895 0.00 0.00 42.62 5.12
1981 2028 1.061711 CTAGTGCATTCAAGCTGCGAC 59.938 52.381 0.00 0.00 42.62 5.19
1982 2029 1.338105 ACTAGTGCATTCAAGCTGCGA 60.338 47.619 0.00 0.00 42.62 5.10
1983 2030 1.081892 ACTAGTGCATTCAAGCTGCG 58.918 50.000 0.00 0.00 42.62 5.18
1984 2031 1.131883 CCACTAGTGCATTCAAGCTGC 59.868 52.381 17.86 0.00 40.10 5.25
1985 2032 2.703416 TCCACTAGTGCATTCAAGCTG 58.297 47.619 17.86 0.00 34.99 4.24
1986 2033 3.423539 TTCCACTAGTGCATTCAAGCT 57.576 42.857 17.86 0.00 34.99 3.74
1987 2034 4.229876 GTTTTCCACTAGTGCATTCAAGC 58.770 43.478 17.86 3.62 0.00 4.01
1988 2035 5.437289 TGTTTTCCACTAGTGCATTCAAG 57.563 39.130 17.86 2.03 0.00 3.02
1989 2036 4.278170 CCTGTTTTCCACTAGTGCATTCAA 59.722 41.667 17.86 2.61 0.00 2.69
1990 2037 3.820467 CCTGTTTTCCACTAGTGCATTCA 59.180 43.478 17.86 10.64 0.00 2.57
1991 2038 4.072131 TCCTGTTTTCCACTAGTGCATTC 58.928 43.478 17.86 6.82 0.00 2.67
1992 2039 4.098914 TCCTGTTTTCCACTAGTGCATT 57.901 40.909 17.86 0.00 0.00 3.56
2003 2050 3.072211 CGGGACTAGTTTCCTGTTTTCC 58.928 50.000 12.47 0.00 37.28 3.13
2014 2061 1.900486 CCTCTGAAACCGGGACTAGTT 59.100 52.381 6.32 0.00 0.00 2.24
2035 2082 4.576879 GTTCCGGAACCAGAACTAAAGAT 58.423 43.478 33.02 0.00 39.42 2.40
2036 2083 3.999046 GTTCCGGAACCAGAACTAAAGA 58.001 45.455 33.02 0.00 39.42 2.52
2052 2099 0.322648 ACCTTTTAGTCCCGGTTCCG 59.677 55.000 0.00 4.08 0.00 4.30
2115 2162 2.203938 AAGCCCCTTCTGTCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
2190 2238 0.966179 ATGCCTTTTTGGTTCCGGTC 59.034 50.000 0.00 0.00 38.35 4.79
2196 2244 3.902881 TGTGTGAATGCCTTTTTGGTT 57.097 38.095 0.00 0.00 38.35 3.67
2204 2252 1.460504 CTGCTGATGTGTGAATGCCT 58.539 50.000 0.00 0.00 0.00 4.75
2216 2264 1.077644 CCTTCTGCCAGCTGCTGAT 60.078 57.895 30.10 0.00 45.84 2.90
2299 2349 6.125029 AGCTAGCCAACACAATATGAAATCT 58.875 36.000 12.13 0.00 0.00 2.40
2316 2368 5.986741 GGTCACTTCTCTTTATTAGCTAGCC 59.013 44.000 12.13 0.00 0.00 3.93
2350 2406 0.179137 CTAGCATCGACCAAGCACGA 60.179 55.000 0.00 0.00 42.49 4.35
2386 2447 0.961358 AGCTAGCGTGTCGAGGTCTT 60.961 55.000 9.55 0.00 0.00 3.01
2390 2451 1.579698 TACTAGCTAGCGTGTCGAGG 58.420 55.000 20.91 0.00 0.00 4.63
2418 2479 8.506168 TGATCTTGTGTAATTAATGGTTCCTC 57.494 34.615 0.00 0.00 0.00 3.71
2443 2504 7.290948 TCACTTCCCTCTGTATATGTTCATGAT 59.709 37.037 0.00 0.00 0.00 2.45
2462 2523 2.094442 CGGAGAAAGAGAGGTCACTTCC 60.094 54.545 0.00 0.00 0.00 3.46
2489 2554 2.032030 CGAAAACTTGTTGCTCGACCAT 60.032 45.455 10.73 0.00 0.00 3.55
2497 2562 7.168637 TCGGATAGATATACGAAAACTTGTTGC 59.831 37.037 4.69 0.00 45.29 4.17


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

AutoCloner maintained by Alex Coulton.