Multiple sequence alignment - TraesCS6A01G345700

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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 TraesCS6A01G345700 chr6A 100.000 1736 0 0 856 2591 579130546 579132281 0.000000e+00 3206.0
1 TraesCS6A01G345700 chr6A 100.000 385 0 0 1 385 579129691 579130075 0.000000e+00 712.0
2 TraesCS6A01G345700 chr7D 94.155 941 53 1 921 1861 64682576 64681638 0.000000e+00 1432.0
3 TraesCS6A01G345700 chr7D 94.814 887 36 7 923 1807 313716711 313717589 0.000000e+00 1375.0
4 TraesCS6A01G345700 chr4D 95.618 890 37 1 975 1864 92671310 92670423 0.000000e+00 1426.0
5 TraesCS6A01G345700 chr4D 92.691 301 16 6 86 383 92671988 92671691 1.840000e-116 429.0
6 TraesCS6A01G345700 chr5D 93.233 931 47 4 947 1864 287811387 287810460 0.000000e+00 1356.0
7 TraesCS6A01G345700 chr5D 93.311 299 18 2 82 379 287812153 287811856 8.510000e-120 440.0
8 TraesCS6A01G345700 chr5D 91.438 292 23 2 86 375 497306140 497305849 1.440000e-107 399.0
9 TraesCS6A01G345700 chr5D 92.364 275 20 1 88 361 53755586 53755860 8.690000e-105 390.0
10 TraesCS6A01G345700 chr3A 92.971 939 47 4 926 1864 79335264 79334345 0.000000e+00 1351.0
11 TraesCS6A01G345700 chr3D 93.151 876 50 4 989 1864 426936964 426936099 0.000000e+00 1277.0
12 TraesCS6A01G345700 chr3D 93.023 301 19 2 86 385 545071961 545071662 3.060000e-119 438.0
13 TraesCS6A01G345700 chr3D 90.635 299 19 2 88 377 601117363 601117065 3.130000e-104 388.0
14 TraesCS6A01G345700 chrUn 91.123 935 63 7 939 1864 105428129 105427206 0.000000e+00 1249.0
15 TraesCS6A01G345700 chr2A 92.177 882 67 1 982 1863 78622711 78623590 0.000000e+00 1245.0
16 TraesCS6A01G345700 chr2A 90.789 152 14 0 1714 1865 646854066 646854217 1.220000e-48 204.0
17 TraesCS6A01G345700 chr1A 89.148 986 84 12 886 1861 478632682 478633654 0.000000e+00 1206.0
18 TraesCS6A01G345700 chr6D 88.845 762 54 8 1861 2591 432926264 432927025 0.000000e+00 907.0
19 TraesCS6A01G345700 chr6D 93.333 90 6 0 1 90 432926179 432926268 1.620000e-27 134.0
20 TraesCS6A01G345700 chr6B 92.097 329 26 0 2260 2588 653693710 653694038 5.050000e-127 464.0
21 TraesCS6A01G345700 chr6B 86.732 407 36 5 1869 2268 653860982 653861377 1.100000e-118 436.0
22 TraesCS6A01G345700 chr6B 92.754 276 20 0 86 361 38933300 38933575 1.440000e-107 399.0
23 TraesCS6A01G345700 chr6B 92.222 90 7 0 1 90 653859442 653859531 7.530000e-26 128.0
24 TraesCS6A01G345700 chr6B 97.059 34 1 0 2260 2293 23348566 23348599 1.000000e-04 58.4
25 TraesCS6A01G345700 chr4B 93.091 275 18 1 88 361 577064128 577063854 4.020000e-108 401.0
26 TraesCS6A01G345700 chr3B 91.958 286 21 2 86 369 794530649 794530934 1.440000e-107 399.0
27 TraesCS6A01G345700 chr5A 97.059 34 1 0 2260 2293 512839570 512839537 1.000000e-04 58.4


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 TraesCS6A01G345700 chr6A 579129691 579132281 2590 False 1959.0 3206 100.0000 1 2591 2 chr6A.!!$F1 2590
1 TraesCS6A01G345700 chr7D 64681638 64682576 938 True 1432.0 1432 94.1550 921 1861 1 chr7D.!!$R1 940
2 TraesCS6A01G345700 chr7D 313716711 313717589 878 False 1375.0 1375 94.8140 923 1807 1 chr7D.!!$F1 884
3 TraesCS6A01G345700 chr4D 92670423 92671988 1565 True 927.5 1426 94.1545 86 1864 2 chr4D.!!$R1 1778
4 TraesCS6A01G345700 chr5D 287810460 287812153 1693 True 898.0 1356 93.2720 82 1864 2 chr5D.!!$R2 1782
5 TraesCS6A01G345700 chr3A 79334345 79335264 919 True 1351.0 1351 92.9710 926 1864 1 chr3A.!!$R1 938
6 TraesCS6A01G345700 chr3D 426936099 426936964 865 True 1277.0 1277 93.1510 989 1864 1 chr3D.!!$R1 875
7 TraesCS6A01G345700 chrUn 105427206 105428129 923 True 1249.0 1249 91.1230 939 1864 1 chrUn.!!$R1 925
8 TraesCS6A01G345700 chr2A 78622711 78623590 879 False 1245.0 1245 92.1770 982 1863 1 chr2A.!!$F1 881
9 TraesCS6A01G345700 chr1A 478632682 478633654 972 False 1206.0 1206 89.1480 886 1861 1 chr1A.!!$F1 975
10 TraesCS6A01G345700 chr6D 432926179 432927025 846 False 520.5 907 91.0890 1 2591 2 chr6D.!!$F1 2590
11 TraesCS6A01G345700 chr6B 653859442 653861377 1935 False 282.0 436 89.4770 1 2268 2 chr6B.!!$F4 2267

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
151 152 1.568504 TGGACCGTCTGAGGCTAAAT 58.431 50.0 0.0 0.0 33.69 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 3636 0.034186 CCCCATCTGCAGTAGCCAAA 60.034 55.0 14.67 0.0 41.13 3.28 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
151 152 1.568504 TGGACCGTCTGAGGCTAAAT 58.431 50.000 0.00 0.00 33.69 1.40
161 162 1.757118 TGAGGCTAAATACGCAGCTCT 59.243 47.619 0.00 0.00 37.91 4.09
164 165 4.039245 TGAGGCTAAATACGCAGCTCTAAT 59.961 41.667 0.00 0.00 37.91 1.73
198 200 4.813346 AAAAAGATGGACCGCGGT 57.187 50.000 34.89 34.89 0.00 5.68
1068 1445 1.527370 GCAGAAGCCCTCCGGTAAT 59.473 57.895 0.00 0.00 33.58 1.89
1320 1888 2.340078 GTCAGTGCTGGCGAGACA 59.660 61.111 0.00 0.00 0.00 3.41
1332 1933 1.747367 CGAGACAGACGAGGAGGCT 60.747 63.158 0.00 0.00 40.36 4.58
1378 2628 2.035312 AGTACGTCCAGGCCGAGT 59.965 61.111 0.00 0.00 0.00 4.18
1391 2642 2.240667 AGGCCGAGTTGGAGTACTACTA 59.759 50.000 6.66 0.00 42.00 1.82
1750 3355 2.229784 GGAGTTGCTCTTTTGGACCATG 59.770 50.000 0.00 0.00 0.00 3.66
1868 3486 7.465353 TCTATTGGAGATGCTCTTAGATGAG 57.535 40.000 0.00 0.00 37.16 2.90
1869 3487 7.237255 TCTATTGGAGATGCTCTTAGATGAGA 58.763 38.462 0.00 0.00 36.23 3.27
1870 3488 6.938698 ATTGGAGATGCTCTTAGATGAGAT 57.061 37.500 0.00 0.00 36.23 2.75
1871 3489 5.725325 TGGAGATGCTCTTAGATGAGATG 57.275 43.478 0.00 0.00 36.23 2.90
1872 3490 4.021280 TGGAGATGCTCTTAGATGAGATGC 60.021 45.833 0.00 0.00 36.23 3.91
1873 3491 4.021280 GGAGATGCTCTTAGATGAGATGCA 60.021 45.833 0.00 0.00 36.23 3.96
1874 3492 5.511031 GGAGATGCTCTTAGATGAGATGCAA 60.511 44.000 0.00 0.00 35.24 4.08
1875 3493 5.926663 AGATGCTCTTAGATGAGATGCAAA 58.073 37.500 0.00 0.00 35.24 3.68
1876 3494 6.535540 AGATGCTCTTAGATGAGATGCAAAT 58.464 36.000 0.00 0.00 35.24 2.32
1877 3495 7.677892 AGATGCTCTTAGATGAGATGCAAATA 58.322 34.615 0.00 0.00 35.24 1.40
1878 3496 8.322828 AGATGCTCTTAGATGAGATGCAAATAT 58.677 33.333 0.00 0.00 35.24 1.28
1879 3497 9.597170 GATGCTCTTAGATGAGATGCAAATATA 57.403 33.333 0.00 0.00 35.24 0.86
1881 3499 9.597170 TGCTCTTAGATGAGATGCAAATATATC 57.403 33.333 0.00 0.00 36.23 1.63
1882 3500 8.754096 GCTCTTAGATGAGATGCAAATATATCG 58.246 37.037 0.00 0.00 36.23 2.92
1883 3501 9.800433 CTCTTAGATGAGATGCAAATATATCGT 57.200 33.333 0.00 0.00 36.23 3.73
1884 3502 9.794685 TCTTAGATGAGATGCAAATATATCGTC 57.205 33.333 0.00 0.00 35.54 4.20
1885 3503 8.932945 TTAGATGAGATGCAAATATATCGTCC 57.067 34.615 0.00 0.00 35.79 4.79
1886 3504 6.344500 AGATGAGATGCAAATATATCGTCCC 58.656 40.000 0.00 0.00 35.79 4.46
1887 3505 5.745312 TGAGATGCAAATATATCGTCCCT 57.255 39.130 0.00 0.00 0.00 4.20
1888 3506 5.482006 TGAGATGCAAATATATCGTCCCTG 58.518 41.667 0.00 0.00 0.00 4.45
1889 3507 5.012046 TGAGATGCAAATATATCGTCCCTGT 59.988 40.000 0.00 0.00 0.00 4.00
1890 3508 5.869579 AGATGCAAATATATCGTCCCTGTT 58.130 37.500 0.00 0.00 0.00 3.16
1891 3509 5.702670 AGATGCAAATATATCGTCCCTGTTG 59.297 40.000 0.00 0.00 0.00 3.33
1892 3510 3.563808 TGCAAATATATCGTCCCTGTTGC 59.436 43.478 7.30 7.30 40.33 4.17
1893 3511 3.815401 GCAAATATATCGTCCCTGTTGCT 59.185 43.478 7.08 0.00 37.67 3.91
1894 3512 4.083802 GCAAATATATCGTCCCTGTTGCTC 60.084 45.833 7.08 0.00 37.67 4.26
1895 3513 3.963428 ATATATCGTCCCTGTTGCTCC 57.037 47.619 0.00 0.00 0.00 4.70
1896 3514 0.389391 ATATCGTCCCTGTTGCTCCG 59.611 55.000 0.00 0.00 0.00 4.63
1897 3515 2.292794 TATCGTCCCTGTTGCTCCGC 62.293 60.000 0.00 0.00 0.00 5.54
1898 3516 4.379243 CGTCCCTGTTGCTCCGCT 62.379 66.667 0.00 0.00 0.00 5.52
1899 3517 2.978824 GTCCCTGTTGCTCCGCTA 59.021 61.111 0.00 0.00 0.00 4.26
1900 3518 1.295423 GTCCCTGTTGCTCCGCTAA 59.705 57.895 0.00 0.00 0.00 3.09
1901 3519 1.019805 GTCCCTGTTGCTCCGCTAAC 61.020 60.000 0.00 0.00 0.00 2.34
1902 3520 1.192146 TCCCTGTTGCTCCGCTAACT 61.192 55.000 0.00 0.00 0.00 2.24
1903 3521 0.321653 CCCTGTTGCTCCGCTAACTT 60.322 55.000 0.00 0.00 0.00 2.66
1904 3522 0.798776 CCTGTTGCTCCGCTAACTTG 59.201 55.000 0.00 0.00 0.00 3.16
1905 3523 1.512926 CTGTTGCTCCGCTAACTTGT 58.487 50.000 0.00 0.00 0.00 3.16
1906 3524 1.461127 CTGTTGCTCCGCTAACTTGTC 59.539 52.381 0.00 0.00 0.00 3.18
1907 3525 1.202592 TGTTGCTCCGCTAACTTGTCA 60.203 47.619 0.00 0.00 0.00 3.58
1908 3526 1.194772 GTTGCTCCGCTAACTTGTCAC 59.805 52.381 0.00 0.00 0.00 3.67
1909 3527 0.320421 TGCTCCGCTAACTTGTCACC 60.320 55.000 0.00 0.00 0.00 4.02
1910 3528 0.320421 GCTCCGCTAACTTGTCACCA 60.320 55.000 0.00 0.00 0.00 4.17
1911 3529 1.429463 CTCCGCTAACTTGTCACCAC 58.571 55.000 0.00 0.00 0.00 4.16
1912 3530 1.000955 CTCCGCTAACTTGTCACCACT 59.999 52.381 0.00 0.00 0.00 4.00
1913 3531 1.414919 TCCGCTAACTTGTCACCACTT 59.585 47.619 0.00 0.00 0.00 3.16
1914 3532 1.798813 CCGCTAACTTGTCACCACTTC 59.201 52.381 0.00 0.00 0.00 3.01
1915 3533 1.455786 CGCTAACTTGTCACCACTTCG 59.544 52.381 0.00 0.00 0.00 3.79
1916 3534 2.480845 GCTAACTTGTCACCACTTCGT 58.519 47.619 0.00 0.00 0.00 3.85
1917 3535 2.221055 GCTAACTTGTCACCACTTCGTG 59.779 50.000 0.00 0.00 34.93 4.35
1918 3536 2.396590 AACTTGTCACCACTTCGTGT 57.603 45.000 0.00 0.00 35.18 4.49
1919 3537 2.396590 ACTTGTCACCACTTCGTGTT 57.603 45.000 0.00 0.00 35.18 3.32
1920 3538 2.006888 ACTTGTCACCACTTCGTGTTG 58.993 47.619 0.00 0.00 35.18 3.33
1921 3539 0.730265 TTGTCACCACTTCGTGTTGC 59.270 50.000 0.00 0.00 35.18 4.17
1922 3540 0.391793 TGTCACCACTTCGTGTTGCA 60.392 50.000 0.00 0.00 35.18 4.08
1923 3541 0.027586 GTCACCACTTCGTGTTGCAC 59.972 55.000 0.00 0.00 35.18 4.57
1924 3542 1.092921 TCACCACTTCGTGTTGCACC 61.093 55.000 0.00 0.00 35.18 5.01
1925 3543 1.095228 CACCACTTCGTGTTGCACCT 61.095 55.000 0.00 0.00 0.00 4.00
1926 3544 0.393808 ACCACTTCGTGTTGCACCTT 60.394 50.000 0.00 0.00 0.00 3.50
1927 3545 1.134340 ACCACTTCGTGTTGCACCTTA 60.134 47.619 0.00 0.00 0.00 2.69
1928 3546 2.151202 CCACTTCGTGTTGCACCTTAT 58.849 47.619 0.00 0.00 0.00 1.73
1929 3547 2.159627 CCACTTCGTGTTGCACCTTATC 59.840 50.000 0.00 0.00 0.00 1.75
1930 3548 3.067106 CACTTCGTGTTGCACCTTATCT 58.933 45.455 0.00 0.00 0.00 1.98
1931 3549 3.498397 CACTTCGTGTTGCACCTTATCTT 59.502 43.478 0.00 0.00 0.00 2.40
1932 3550 4.688879 CACTTCGTGTTGCACCTTATCTTA 59.311 41.667 0.00 0.00 0.00 2.10
1933 3551 4.689345 ACTTCGTGTTGCACCTTATCTTAC 59.311 41.667 0.00 0.00 0.00 2.34
1934 3552 3.592059 TCGTGTTGCACCTTATCTTACC 58.408 45.455 0.00 0.00 0.00 2.85
1935 3553 3.259876 TCGTGTTGCACCTTATCTTACCT 59.740 43.478 0.00 0.00 0.00 3.08
1936 3554 3.617263 CGTGTTGCACCTTATCTTACCTC 59.383 47.826 0.00 0.00 0.00 3.85
1937 3555 4.620803 CGTGTTGCACCTTATCTTACCTCT 60.621 45.833 0.00 0.00 0.00 3.69
1938 3556 5.246307 GTGTTGCACCTTATCTTACCTCTT 58.754 41.667 0.00 0.00 0.00 2.85
1939 3557 5.351740 GTGTTGCACCTTATCTTACCTCTTC 59.648 44.000 0.00 0.00 0.00 2.87
1940 3558 5.012664 TGTTGCACCTTATCTTACCTCTTCA 59.987 40.000 0.00 0.00 0.00 3.02
1941 3559 5.957771 TGCACCTTATCTTACCTCTTCAT 57.042 39.130 0.00 0.00 0.00 2.57
1942 3560 5.674525 TGCACCTTATCTTACCTCTTCATG 58.325 41.667 0.00 0.00 0.00 3.07
1943 3561 5.059833 GCACCTTATCTTACCTCTTCATGG 58.940 45.833 0.00 0.00 0.00 3.66
1944 3562 5.615289 CACCTTATCTTACCTCTTCATGGG 58.385 45.833 0.00 0.00 0.00 4.00
1945 3563 4.660771 ACCTTATCTTACCTCTTCATGGGG 59.339 45.833 0.00 0.00 0.00 4.96
1946 3564 4.907875 CCTTATCTTACCTCTTCATGGGGA 59.092 45.833 0.00 0.00 0.00 4.81
1947 3565 5.012561 CCTTATCTTACCTCTTCATGGGGAG 59.987 48.000 8.29 8.29 0.00 4.30
1948 3566 3.776731 TCTTACCTCTTCATGGGGAGA 57.223 47.619 14.45 5.99 0.00 3.71
1949 3567 4.286813 TCTTACCTCTTCATGGGGAGAT 57.713 45.455 14.45 3.46 0.00 2.75
1950 3568 4.635473 TCTTACCTCTTCATGGGGAGATT 58.365 43.478 14.45 6.40 0.00 2.40
1951 3569 5.039645 TCTTACCTCTTCATGGGGAGATTT 58.960 41.667 14.45 4.60 0.00 2.17
1952 3570 3.941704 ACCTCTTCATGGGGAGATTTC 57.058 47.619 14.45 0.00 0.00 2.17
1953 3571 3.468850 ACCTCTTCATGGGGAGATTTCT 58.531 45.455 14.45 0.00 0.00 2.52
1954 3572 3.457749 ACCTCTTCATGGGGAGATTTCTC 59.542 47.826 14.45 0.00 42.14 2.87
1955 3573 3.457380 CCTCTTCATGGGGAGATTTCTCA 59.543 47.826 14.45 0.00 44.60 3.27
1956 3574 4.444591 CCTCTTCATGGGGAGATTTCTCAG 60.445 50.000 14.45 0.00 44.60 3.35
1957 3575 4.107072 TCTTCATGGGGAGATTTCTCAGT 58.893 43.478 9.65 0.00 44.60 3.41
1958 3576 4.163078 TCTTCATGGGGAGATTTCTCAGTC 59.837 45.833 9.65 0.00 44.60 3.51
1959 3577 3.453868 TCATGGGGAGATTTCTCAGTCA 58.546 45.455 9.65 4.96 44.60 3.41
1960 3578 3.198635 TCATGGGGAGATTTCTCAGTCAC 59.801 47.826 9.65 0.00 44.60 3.67
1961 3579 2.907892 TGGGGAGATTTCTCAGTCACT 58.092 47.619 9.65 0.00 44.60 3.41
1962 3580 2.834549 TGGGGAGATTTCTCAGTCACTC 59.165 50.000 9.65 0.00 44.60 3.51
1963 3581 2.169561 GGGGAGATTTCTCAGTCACTCC 59.830 54.545 9.65 0.00 44.60 3.85
1964 3582 3.103742 GGGAGATTTCTCAGTCACTCCT 58.896 50.000 9.65 0.00 44.60 3.69
1965 3583 3.517500 GGGAGATTTCTCAGTCACTCCTT 59.482 47.826 9.65 0.00 44.60 3.36
1966 3584 4.019771 GGGAGATTTCTCAGTCACTCCTTT 60.020 45.833 9.65 0.00 44.60 3.11
1967 3585 5.175127 GGAGATTTCTCAGTCACTCCTTTC 58.825 45.833 9.65 0.00 44.60 2.62
1968 3586 5.046663 GGAGATTTCTCAGTCACTCCTTTCT 60.047 44.000 9.65 0.00 44.60 2.52
1969 3587 6.036577 AGATTTCTCAGTCACTCCTTTCTC 57.963 41.667 0.00 0.00 0.00 2.87
1970 3588 5.779771 AGATTTCTCAGTCACTCCTTTCTCT 59.220 40.000 0.00 0.00 0.00 3.10
1971 3589 5.461032 TTTCTCAGTCACTCCTTTCTCTC 57.539 43.478 0.00 0.00 0.00 3.20
1972 3590 4.105754 TCTCAGTCACTCCTTTCTCTCA 57.894 45.455 0.00 0.00 0.00 3.27
1973 3591 3.823873 TCTCAGTCACTCCTTTCTCTCAC 59.176 47.826 0.00 0.00 0.00 3.51
1974 3592 3.566351 TCAGTCACTCCTTTCTCTCACA 58.434 45.455 0.00 0.00 0.00 3.58
1975 3593 3.319405 TCAGTCACTCCTTTCTCTCACAC 59.681 47.826 0.00 0.00 0.00 3.82
1976 3594 3.068732 CAGTCACTCCTTTCTCTCACACA 59.931 47.826 0.00 0.00 0.00 3.72
1977 3595 3.068873 AGTCACTCCTTTCTCTCACACAC 59.931 47.826 0.00 0.00 0.00 3.82
1978 3596 2.034685 TCACTCCTTTCTCTCACACACG 59.965 50.000 0.00 0.00 0.00 4.49
1979 3597 2.034685 CACTCCTTTCTCTCACACACGA 59.965 50.000 0.00 0.00 0.00 4.35
1980 3598 2.034812 ACTCCTTTCTCTCACACACGAC 59.965 50.000 0.00 0.00 0.00 4.34
1981 3599 1.001706 TCCTTTCTCTCACACACGACG 60.002 52.381 0.00 0.00 0.00 5.12
1982 3600 0.778815 CTTTCTCTCACACACGACGC 59.221 55.000 0.00 0.00 0.00 5.19
1983 3601 0.101579 TTTCTCTCACACACGACGCA 59.898 50.000 0.00 0.00 0.00 5.24
1984 3602 0.313987 TTCTCTCACACACGACGCAT 59.686 50.000 0.00 0.00 0.00 4.73
1985 3603 0.109735 TCTCTCACACACGACGCATC 60.110 55.000 0.00 0.00 0.00 3.91
1986 3604 0.109551 CTCTCACACACGACGCATCT 60.110 55.000 0.00 0.00 0.00 2.90
1987 3605 0.313987 TCTCACACACGACGCATCTT 59.686 50.000 0.00 0.00 0.00 2.40
1988 3606 1.139989 CTCACACACGACGCATCTTT 58.860 50.000 0.00 0.00 0.00 2.52
1989 3607 2.030628 TCTCACACACGACGCATCTTTA 60.031 45.455 0.00 0.00 0.00 1.85
1990 3608 2.923655 CTCACACACGACGCATCTTTAT 59.076 45.455 0.00 0.00 0.00 1.40
1991 3609 2.921121 TCACACACGACGCATCTTTATC 59.079 45.455 0.00 0.00 0.00 1.75
1992 3610 2.923655 CACACACGACGCATCTTTATCT 59.076 45.455 0.00 0.00 0.00 1.98
1993 3611 3.367932 CACACACGACGCATCTTTATCTT 59.632 43.478 0.00 0.00 0.00 2.40
1994 3612 3.367932 ACACACGACGCATCTTTATCTTG 59.632 43.478 0.00 0.00 0.00 3.02
1995 3613 2.348666 ACACGACGCATCTTTATCTTGC 59.651 45.455 0.00 0.00 0.00 4.01
2003 3621 5.476752 GCATCTTTATCTTGCGTTCTTCT 57.523 39.130 0.00 0.00 0.00 2.85
2004 3622 5.497273 GCATCTTTATCTTGCGTTCTTCTC 58.503 41.667 0.00 0.00 0.00 2.87
2005 3623 5.503194 GCATCTTTATCTTGCGTTCTTCTCC 60.503 44.000 0.00 0.00 0.00 3.71
2006 3624 4.504858 TCTTTATCTTGCGTTCTTCTCCC 58.495 43.478 0.00 0.00 0.00 4.30
2007 3625 2.981859 TATCTTGCGTTCTTCTCCCC 57.018 50.000 0.00 0.00 0.00 4.81
2008 3626 0.984230 ATCTTGCGTTCTTCTCCCCA 59.016 50.000 0.00 0.00 0.00 4.96
2009 3627 0.034896 TCTTGCGTTCTTCTCCCCAC 59.965 55.000 0.00 0.00 0.00 4.61
2010 3628 0.955919 CTTGCGTTCTTCTCCCCACC 60.956 60.000 0.00 0.00 0.00 4.61
2011 3629 2.046217 GCGTTCTTCTCCCCACCC 60.046 66.667 0.00 0.00 0.00 4.61
2012 3630 2.890766 GCGTTCTTCTCCCCACCCA 61.891 63.158 0.00 0.00 0.00 4.51
2013 3631 1.003718 CGTTCTTCTCCCCACCCAC 60.004 63.158 0.00 0.00 0.00 4.61
2014 3632 1.764571 CGTTCTTCTCCCCACCCACA 61.765 60.000 0.00 0.00 0.00 4.17
2015 3633 0.698818 GTTCTTCTCCCCACCCACAT 59.301 55.000 0.00 0.00 0.00 3.21
2016 3634 1.075536 GTTCTTCTCCCCACCCACATT 59.924 52.381 0.00 0.00 0.00 2.71
2017 3635 1.455822 TCTTCTCCCCACCCACATTT 58.544 50.000 0.00 0.00 0.00 2.32
2018 3636 1.786441 TCTTCTCCCCACCCACATTTT 59.214 47.619 0.00 0.00 0.00 1.82
2019 3637 2.178984 TCTTCTCCCCACCCACATTTTT 59.821 45.455 0.00 0.00 0.00 1.94
2036 3654 1.838112 TTTTGGCTACTGCAGATGGG 58.162 50.000 23.35 8.08 41.91 4.00
2037 3655 0.034186 TTTGGCTACTGCAGATGGGG 60.034 55.000 23.35 6.28 41.91 4.96
2038 3656 1.207488 TTGGCTACTGCAGATGGGGT 61.207 55.000 23.35 0.00 41.91 4.95
2039 3657 1.147153 GGCTACTGCAGATGGGGTC 59.853 63.158 23.35 2.92 41.91 4.46
2040 3658 1.626356 GGCTACTGCAGATGGGGTCA 61.626 60.000 23.35 0.00 41.91 4.02
2041 3659 0.462759 GCTACTGCAGATGGGGTCAC 60.463 60.000 23.35 0.00 39.41 3.67
2042 3660 1.198713 CTACTGCAGATGGGGTCACT 58.801 55.000 23.35 0.00 0.00 3.41
2043 3661 0.904649 TACTGCAGATGGGGTCACTG 59.095 55.000 23.35 0.00 35.14 3.66
2044 3662 1.077930 CTGCAGATGGGGTCACTGG 60.078 63.158 8.42 0.00 33.00 4.00
2045 3663 2.439156 GCAGATGGGGTCACTGGC 60.439 66.667 0.00 0.00 33.00 4.85
2046 3664 2.124983 CAGATGGGGTCACTGGCG 60.125 66.667 0.00 0.00 0.00 5.69
2047 3665 3.402681 AGATGGGGTCACTGGCGG 61.403 66.667 0.00 0.00 0.00 6.13
2063 3681 2.836360 GGCGATGGGGGACGACTA 60.836 66.667 0.00 0.00 34.48 2.59
2064 3682 2.416260 GCGATGGGGGACGACTAC 59.584 66.667 0.00 0.00 0.00 2.73
2065 3683 2.420568 GCGATGGGGGACGACTACA 61.421 63.158 0.00 0.00 0.00 2.74
2066 3684 1.734137 CGATGGGGGACGACTACAG 59.266 63.158 0.00 0.00 0.00 2.74
2067 3685 1.735376 CGATGGGGGACGACTACAGG 61.735 65.000 0.00 0.00 0.00 4.00
2068 3686 1.382695 ATGGGGGACGACTACAGGG 60.383 63.158 0.00 0.00 0.00 4.45
2069 3687 2.762875 GGGGGACGACTACAGGGG 60.763 72.222 0.00 0.00 0.00 4.79
2070 3688 2.762875 GGGGACGACTACAGGGGG 60.763 72.222 0.00 0.00 0.00 5.40
2071 3689 2.038490 GGGACGACTACAGGGGGT 59.962 66.667 0.00 0.00 0.00 4.95
2072 3690 2.356780 GGGACGACTACAGGGGGTG 61.357 68.421 0.00 0.00 0.00 4.61
2073 3691 1.608627 GGACGACTACAGGGGGTGT 60.609 63.158 0.00 0.00 43.86 4.16
2074 3692 1.190178 GGACGACTACAGGGGGTGTT 61.190 60.000 0.00 0.00 40.94 3.32
2075 3693 0.037605 GACGACTACAGGGGGTGTTG 60.038 60.000 0.00 0.00 40.94 3.33
2076 3694 0.761702 ACGACTACAGGGGGTGTTGT 60.762 55.000 0.00 0.00 46.26 3.32
2077 3695 0.320421 CGACTACAGGGGGTGTTGTG 60.320 60.000 0.00 0.00 44.02 3.33
2078 3696 1.053424 GACTACAGGGGGTGTTGTGA 58.947 55.000 0.00 0.00 44.02 3.58
2079 3697 1.002087 GACTACAGGGGGTGTTGTGAG 59.998 57.143 0.00 0.00 44.02 3.51
2080 3698 1.348064 CTACAGGGGGTGTTGTGAGA 58.652 55.000 0.00 0.00 40.94 3.27
2081 3699 1.002087 CTACAGGGGGTGTTGTGAGAC 59.998 57.143 0.00 0.00 40.94 3.36
2082 3700 1.073199 CAGGGGGTGTTGTGAGACC 59.927 63.158 0.00 0.00 38.46 3.85
2083 3701 1.385347 AGGGGGTGTTGTGAGACCA 60.385 57.895 0.00 0.00 40.91 4.02
2084 3702 1.228154 GGGGGTGTTGTGAGACCAC 60.228 63.158 0.00 0.00 41.82 4.16
2085 3703 1.228154 GGGGTGTTGTGAGACCACC 60.228 63.158 0.00 0.00 46.35 4.61
2087 3705 2.702847 GGTGTTGTGAGACCACCAC 58.297 57.895 3.28 0.00 46.33 4.16
2088 3706 0.818040 GGTGTTGTGAGACCACCACC 60.818 60.000 3.28 7.76 46.33 4.61
2089 3707 0.107410 GTGTTGTGAGACCACCACCA 60.107 55.000 0.00 0.00 42.53 4.17
2090 3708 0.621082 TGTTGTGAGACCACCACCAA 59.379 50.000 0.00 0.00 42.53 3.67
2091 3709 1.214175 TGTTGTGAGACCACCACCAAT 59.786 47.619 0.00 0.00 42.53 3.16
2092 3710 1.608590 GTTGTGAGACCACCACCAATG 59.391 52.381 0.00 0.00 42.53 2.82
2093 3711 0.537143 TGTGAGACCACCACCAATGC 60.537 55.000 0.00 0.00 42.53 3.56
2094 3712 1.074775 TGAGACCACCACCAATGCC 59.925 57.895 0.00 0.00 0.00 4.40
2095 3713 2.034066 AGACCACCACCAATGCCG 59.966 61.111 0.00 0.00 0.00 5.69
2096 3714 3.061848 GACCACCACCAATGCCGG 61.062 66.667 0.00 0.00 0.00 6.13
2100 3718 4.380945 ACCACCAATGCCGGCCAT 62.381 61.111 26.77 14.88 35.06 4.40
2101 3719 2.123939 CCACCAATGCCGGCCATA 60.124 61.111 26.77 5.45 32.67 2.74
2102 3720 2.195567 CCACCAATGCCGGCCATAG 61.196 63.158 26.77 13.22 32.67 2.23
2103 3721 1.453745 CACCAATGCCGGCCATAGT 60.454 57.895 26.77 13.95 32.67 2.12
2104 3722 1.453745 ACCAATGCCGGCCATAGTG 60.454 57.895 26.77 15.17 32.67 2.74
2105 3723 2.195567 CCAATGCCGGCCATAGTGG 61.196 63.158 26.77 20.71 41.55 4.00
2126 3744 3.730761 CACGAGCAGGGCAGCAAC 61.731 66.667 0.00 0.00 36.85 4.17
2127 3745 4.254709 ACGAGCAGGGCAGCAACA 62.255 61.111 0.00 0.00 36.85 3.33
2128 3746 3.730761 CGAGCAGGGCAGCAACAC 61.731 66.667 0.00 0.00 36.85 3.32
2129 3747 2.595463 GAGCAGGGCAGCAACACA 60.595 61.111 0.00 0.00 36.85 3.72
2130 3748 1.975407 GAGCAGGGCAGCAACACAT 60.975 57.895 0.00 0.00 36.85 3.21
2131 3749 2.209064 GAGCAGGGCAGCAACACATG 62.209 60.000 0.00 0.00 36.85 3.21
2143 3761 2.698803 CAACACATGCTACTGTAGGCA 58.301 47.619 16.09 13.88 42.80 4.75
2144 3762 3.073678 CAACACATGCTACTGTAGGCAA 58.926 45.455 16.09 1.85 41.90 4.52
2145 3763 2.699954 ACACATGCTACTGTAGGCAAC 58.300 47.619 16.09 0.64 41.90 4.17
2146 3764 1.660607 CACATGCTACTGTAGGCAACG 59.339 52.381 16.09 11.60 41.90 4.10
2147 3765 1.290203 CATGCTACTGTAGGCAACGG 58.710 55.000 16.09 5.99 41.90 4.44
2148 3766 0.178068 ATGCTACTGTAGGCAACGGG 59.822 55.000 16.09 0.00 41.90 5.28
2149 3767 0.901114 TGCTACTGTAGGCAACGGGA 60.901 55.000 16.09 0.00 46.39 5.14
2150 3768 0.459759 GCTACTGTAGGCAACGGGAC 60.460 60.000 16.09 0.00 46.39 4.46
2151 3769 1.183549 CTACTGTAGGCAACGGGACT 58.816 55.000 6.95 0.00 46.39 3.85
2152 3770 1.549170 CTACTGTAGGCAACGGGACTT 59.451 52.381 6.95 0.00 46.39 3.01
2153 3771 0.034896 ACTGTAGGCAACGGGACTTG 59.965 55.000 2.71 0.00 46.39 3.16
2154 3772 0.320374 CTGTAGGCAACGGGACTTGA 59.680 55.000 0.00 0.00 46.39 3.02
2155 3773 0.759959 TGTAGGCAACGGGACTTGAA 59.240 50.000 0.00 0.00 46.39 2.69
2156 3774 1.141254 TGTAGGCAACGGGACTTGAAA 59.859 47.619 0.00 0.00 46.39 2.69
2157 3775 1.534163 GTAGGCAACGGGACTTGAAAC 59.466 52.381 0.00 0.00 46.39 2.78
2158 3776 0.822121 AGGCAACGGGACTTGAAACC 60.822 55.000 0.00 0.00 46.39 3.27
2159 3777 1.658114 GCAACGGGACTTGAAACCC 59.342 57.895 0.00 0.00 42.43 4.11
2160 3778 1.802337 GCAACGGGACTTGAAACCCC 61.802 60.000 0.00 0.00 42.86 4.95
2163 3781 2.035155 GGGACTTGAAACCCCGGG 59.965 66.667 15.80 15.80 40.19 5.73
2164 3782 2.837326 GGGACTTGAAACCCCGGGT 61.837 63.158 21.85 2.03 40.19 5.28
2166 3784 1.176619 GGACTTGAAACCCCGGGTTG 61.177 60.000 23.11 12.36 46.20 3.77
2167 3785 1.152631 ACTTGAAACCCCGGGTTGG 60.153 57.895 23.11 14.69 46.20 3.77
2168 3786 1.152631 CTTGAAACCCCGGGTTGGT 60.153 57.895 23.11 8.01 46.20 3.67
2169 3787 1.455959 TTGAAACCCCGGGTTGGTG 60.456 57.895 23.11 5.85 46.20 4.17
2170 3788 2.599281 GAAACCCCGGGTTGGTGG 60.599 66.667 23.11 4.98 46.20 4.61
2171 3789 4.227583 AAACCCCGGGTTGGTGGG 62.228 66.667 23.11 4.12 46.20 4.61
2178 3796 4.702274 GGGTTGGTGGGGCTGCAT 62.702 66.667 0.50 0.00 0.00 3.96
2179 3797 3.070576 GGTTGGTGGGGCTGCATC 61.071 66.667 0.50 0.00 0.00 3.91
2180 3798 3.070576 GTTGGTGGGGCTGCATCC 61.071 66.667 0.50 0.00 0.00 3.51
2181 3799 4.738998 TTGGTGGGGCTGCATCCG 62.739 66.667 0.50 0.00 0.00 4.18
2207 3825 3.593794 GGCCGACGACCGAGCTAT 61.594 66.667 0.00 0.00 41.76 2.97
2210 3828 0.240411 GCCGACGACCGAGCTATAAT 59.760 55.000 0.00 0.00 41.76 1.28
2220 3838 3.040990 CGAGCTATAATCGGTCGCTAG 57.959 52.381 0.00 0.00 43.88 3.42
2268 3886 1.200716 CGCAATGACAATGCTGGAACT 59.799 47.619 13.40 0.00 41.64 3.01
2270 3888 3.486375 CGCAATGACAATGCTGGAACTAG 60.486 47.826 13.40 0.00 41.64 2.57
2272 3890 3.641434 ATGACAATGCTGGAACTAGCT 57.359 42.857 11.06 0.00 44.01 3.32
2274 3892 3.754965 TGACAATGCTGGAACTAGCTTT 58.245 40.909 11.06 8.26 44.01 3.51
2295 3933 3.936902 TTTGTTTGCTACAGTCGACAC 57.063 42.857 19.50 4.85 38.19 3.67
2299 3937 2.706555 TTGCTACAGTCGACACAGAG 57.293 50.000 19.50 10.08 0.00 3.35
2391 4030 6.524101 ACAATTGACCACTAGTGTTTTTGT 57.476 33.333 21.18 17.66 27.51 2.83
2394 4033 5.968528 TTGACCACTAGTGTTTTTGTTGT 57.031 34.783 21.18 9.26 0.00 3.32
2428 4067 2.267426 GCTGAAACCAGCGTTTTGTTT 58.733 42.857 1.44 0.00 46.25 2.83
2431 4070 3.654414 TGAAACCAGCGTTTTGTTTTGT 58.346 36.364 0.00 0.00 42.34 2.83
2432 4071 4.058817 TGAAACCAGCGTTTTGTTTTGTT 58.941 34.783 0.00 0.00 42.34 2.83
2438 4077 3.677596 CAGCGTTTTGTTTTGTTGGAACT 59.322 39.130 0.00 0.00 0.00 3.01
2439 4078 3.677596 AGCGTTTTGTTTTGTTGGAACTG 59.322 39.130 0.00 0.00 0.00 3.16
2442 4081 3.971245 TTTGTTTTGTTGGAACTGGCT 57.029 38.095 0.00 0.00 0.00 4.75
2522 4161 2.812011 GGAAACGTCATTTGCTACCACT 59.188 45.455 0.00 0.00 35.81 4.00
2523 4162 3.998341 GGAAACGTCATTTGCTACCACTA 59.002 43.478 0.00 0.00 35.81 2.74
2530 4169 5.687730 CGTCATTTGCTACCACTATAGTCTG 59.312 44.000 1.26 0.00 0.00 3.51
2561 4202 6.742363 GCTGGAACCAGAATTTTTCAAAGGAT 60.742 38.462 22.96 0.00 46.30 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 2.547211 GACCGTCTATTAGAGCTGCGTA 59.453 50.000 0.00 0.00 0.00 4.42
186 187 3.140225 GAGGAGACCGCGGTCCATC 62.140 68.421 45.66 37.33 45.59 3.51
198 200 6.588756 GTGTTGTATTTTACATCACGAGGAGA 59.411 38.462 11.14 0.00 44.51 3.71
225 227 3.736213 GTGATGTATATTTGCATCGCGG 58.264 45.455 6.13 0.00 45.03 6.46
1320 1888 2.196925 CGCCATAGCCTCCTCGTCT 61.197 63.158 0.00 0.00 34.57 4.18
1378 2628 4.582869 TCACGCTTCTAGTAGTACTCCAA 58.417 43.478 5.96 0.04 0.00 3.53
1391 2642 2.164865 CTGCTCCACCTCACGCTTCT 62.165 60.000 0.00 0.00 0.00 2.85
1403 2686 1.823250 GCCCCTTCTTTTTCTGCTCCA 60.823 52.381 0.00 0.00 0.00 3.86
1674 3279 7.918536 TCTTGAAACGACATACTACTAGTCT 57.081 36.000 0.00 0.00 0.00 3.24
1796 3414 4.461431 ACCGAAGATGTAAAATTTGGACCC 59.539 41.667 0.00 0.00 32.63 4.46
1864 3482 6.111382 CAGGGACGATATATTTGCATCTCAT 58.889 40.000 0.00 0.00 0.00 2.90
1865 3483 5.012046 ACAGGGACGATATATTTGCATCTCA 59.988 40.000 0.00 0.00 0.00 3.27
1866 3484 5.482908 ACAGGGACGATATATTTGCATCTC 58.517 41.667 0.00 0.00 0.00 2.75
1867 3485 5.489792 ACAGGGACGATATATTTGCATCT 57.510 39.130 0.00 0.00 0.00 2.90
1868 3486 5.617751 GCAACAGGGACGATATATTTGCATC 60.618 44.000 8.81 0.00 38.36 3.91
1869 3487 4.216257 GCAACAGGGACGATATATTTGCAT 59.784 41.667 8.81 0.00 38.36 3.96
1870 3488 3.563808 GCAACAGGGACGATATATTTGCA 59.436 43.478 8.81 0.00 38.36 4.08
1871 3489 3.815401 AGCAACAGGGACGATATATTTGC 59.185 43.478 6.44 6.44 38.68 3.68
1872 3490 4.452455 GGAGCAACAGGGACGATATATTTG 59.548 45.833 0.00 0.00 0.00 2.32
1873 3491 4.642429 GGAGCAACAGGGACGATATATTT 58.358 43.478 0.00 0.00 0.00 1.40
1874 3492 3.306088 CGGAGCAACAGGGACGATATATT 60.306 47.826 0.00 0.00 0.00 1.28
1875 3493 2.231478 CGGAGCAACAGGGACGATATAT 59.769 50.000 0.00 0.00 0.00 0.86
1876 3494 1.611977 CGGAGCAACAGGGACGATATA 59.388 52.381 0.00 0.00 0.00 0.86
1877 3495 0.389391 CGGAGCAACAGGGACGATAT 59.611 55.000 0.00 0.00 0.00 1.63
1878 3496 1.813859 CGGAGCAACAGGGACGATA 59.186 57.895 0.00 0.00 0.00 2.92
1879 3497 2.579201 CGGAGCAACAGGGACGAT 59.421 61.111 0.00 0.00 0.00 3.73
1892 3510 1.000955 AGTGGTGACAAGTTAGCGGAG 59.999 52.381 0.00 0.00 46.06 4.63
1893 3511 1.045407 AGTGGTGACAAGTTAGCGGA 58.955 50.000 0.00 0.00 46.06 5.54
1894 3512 1.798813 GAAGTGGTGACAAGTTAGCGG 59.201 52.381 0.00 0.00 46.06 5.52
1895 3513 1.455786 CGAAGTGGTGACAAGTTAGCG 59.544 52.381 0.00 0.00 46.06 4.26
1896 3514 2.480845 ACGAAGTGGTGACAAGTTAGC 58.519 47.619 0.00 0.00 46.06 3.09
1911 3529 4.092968 GGTAAGATAAGGTGCAACACGAAG 59.907 45.833 3.64 0.00 39.98 3.79
1912 3530 3.998341 GGTAAGATAAGGTGCAACACGAA 59.002 43.478 3.64 0.00 39.98 3.85
1913 3531 3.259876 AGGTAAGATAAGGTGCAACACGA 59.740 43.478 3.64 0.00 39.98 4.35
1914 3532 3.596214 AGGTAAGATAAGGTGCAACACG 58.404 45.455 3.64 0.00 39.98 4.49
1915 3533 4.833390 AGAGGTAAGATAAGGTGCAACAC 58.167 43.478 3.64 0.00 39.98 3.32
1916 3534 5.012664 TGAAGAGGTAAGATAAGGTGCAACA 59.987 40.000 3.64 0.00 39.98 3.33
1917 3535 5.488341 TGAAGAGGTAAGATAAGGTGCAAC 58.512 41.667 0.00 0.00 0.00 4.17
1918 3536 5.755409 TGAAGAGGTAAGATAAGGTGCAA 57.245 39.130 0.00 0.00 0.00 4.08
1919 3537 5.396772 CCATGAAGAGGTAAGATAAGGTGCA 60.397 44.000 0.00 0.00 0.00 4.57
1920 3538 5.059833 CCATGAAGAGGTAAGATAAGGTGC 58.940 45.833 0.00 0.00 0.00 5.01
1921 3539 5.455326 CCCCATGAAGAGGTAAGATAAGGTG 60.455 48.000 0.00 0.00 0.00 4.00
1922 3540 4.660771 CCCCATGAAGAGGTAAGATAAGGT 59.339 45.833 0.00 0.00 0.00 3.50
1923 3541 4.907875 TCCCCATGAAGAGGTAAGATAAGG 59.092 45.833 0.00 0.00 0.00 2.69
1924 3542 5.841237 TCTCCCCATGAAGAGGTAAGATAAG 59.159 44.000 10.84 0.00 0.00 1.73
1925 3543 5.788430 TCTCCCCATGAAGAGGTAAGATAA 58.212 41.667 10.84 0.00 0.00 1.75
1926 3544 5.418692 TCTCCCCATGAAGAGGTAAGATA 57.581 43.478 10.84 0.00 0.00 1.98
1927 3545 4.286813 TCTCCCCATGAAGAGGTAAGAT 57.713 45.455 10.84 0.00 0.00 2.40
1928 3546 3.776731 TCTCCCCATGAAGAGGTAAGA 57.223 47.619 10.84 0.00 0.00 2.10
1929 3547 5.131809 AGAAATCTCCCCATGAAGAGGTAAG 59.868 44.000 10.84 0.00 0.00 2.34
1930 3548 5.039645 AGAAATCTCCCCATGAAGAGGTAA 58.960 41.667 10.84 0.00 0.00 2.85
1931 3549 4.635473 AGAAATCTCCCCATGAAGAGGTA 58.365 43.478 10.84 0.00 0.00 3.08
1932 3550 3.457749 GAGAAATCTCCCCATGAAGAGGT 59.542 47.826 10.84 2.68 37.02 3.85
1933 3551 3.457380 TGAGAAATCTCCCCATGAAGAGG 59.543 47.826 7.91 0.00 42.20 3.69
1934 3552 4.163839 ACTGAGAAATCTCCCCATGAAGAG 59.836 45.833 7.91 0.00 42.20 2.85
1935 3553 4.107072 ACTGAGAAATCTCCCCATGAAGA 58.893 43.478 7.91 0.00 42.20 2.87
1936 3554 4.080695 TGACTGAGAAATCTCCCCATGAAG 60.081 45.833 7.91 0.01 42.20 3.02
1937 3555 3.845992 TGACTGAGAAATCTCCCCATGAA 59.154 43.478 7.91 0.00 42.20 2.57
1938 3556 3.198635 GTGACTGAGAAATCTCCCCATGA 59.801 47.826 7.91 0.00 42.20 3.07
1939 3557 3.199508 AGTGACTGAGAAATCTCCCCATG 59.800 47.826 7.91 0.00 42.20 3.66
1940 3558 3.454082 GAGTGACTGAGAAATCTCCCCAT 59.546 47.826 7.91 0.00 42.20 4.00
1941 3559 2.834549 GAGTGACTGAGAAATCTCCCCA 59.165 50.000 7.91 1.17 42.20 4.96
1942 3560 2.169561 GGAGTGACTGAGAAATCTCCCC 59.830 54.545 7.91 0.00 42.20 4.81
1943 3561 3.103742 AGGAGTGACTGAGAAATCTCCC 58.896 50.000 7.91 0.59 42.20 4.30
1944 3562 4.817318 AAGGAGTGACTGAGAAATCTCC 57.183 45.455 7.91 0.00 42.20 3.71
1945 3563 6.036577 AGAAAGGAGTGACTGAGAAATCTC 57.963 41.667 3.43 3.43 43.15 2.75
1946 3564 5.779771 AGAGAAAGGAGTGACTGAGAAATCT 59.220 40.000 0.00 0.00 0.00 2.40
1947 3565 6.036577 AGAGAAAGGAGTGACTGAGAAATC 57.963 41.667 0.00 0.00 0.00 2.17
1948 3566 5.541868 TGAGAGAAAGGAGTGACTGAGAAAT 59.458 40.000 0.00 0.00 0.00 2.17
1949 3567 4.895889 TGAGAGAAAGGAGTGACTGAGAAA 59.104 41.667 0.00 0.00 0.00 2.52
1950 3568 4.279671 GTGAGAGAAAGGAGTGACTGAGAA 59.720 45.833 0.00 0.00 0.00 2.87
1951 3569 3.823873 GTGAGAGAAAGGAGTGACTGAGA 59.176 47.826 0.00 0.00 0.00 3.27
1952 3570 3.571828 TGTGAGAGAAAGGAGTGACTGAG 59.428 47.826 0.00 0.00 0.00 3.35
1953 3571 3.319405 GTGTGAGAGAAAGGAGTGACTGA 59.681 47.826 0.00 0.00 0.00 3.41
1954 3572 3.068732 TGTGTGAGAGAAAGGAGTGACTG 59.931 47.826 0.00 0.00 0.00 3.51
1955 3573 3.068873 GTGTGTGAGAGAAAGGAGTGACT 59.931 47.826 0.00 0.00 0.00 3.41
1956 3574 3.385577 GTGTGTGAGAGAAAGGAGTGAC 58.614 50.000 0.00 0.00 0.00 3.67
1957 3575 2.034685 CGTGTGTGAGAGAAAGGAGTGA 59.965 50.000 0.00 0.00 0.00 3.41
1958 3576 2.034685 TCGTGTGTGAGAGAAAGGAGTG 59.965 50.000 0.00 0.00 0.00 3.51
1959 3577 2.034812 GTCGTGTGTGAGAGAAAGGAGT 59.965 50.000 0.00 0.00 0.00 3.85
1960 3578 2.667137 GTCGTGTGTGAGAGAAAGGAG 58.333 52.381 0.00 0.00 0.00 3.69
1961 3579 1.001706 CGTCGTGTGTGAGAGAAAGGA 60.002 52.381 0.00 0.00 0.00 3.36
1962 3580 1.409412 CGTCGTGTGTGAGAGAAAGG 58.591 55.000 0.00 0.00 0.00 3.11
1963 3581 0.778815 GCGTCGTGTGTGAGAGAAAG 59.221 55.000 0.00 0.00 0.00 2.62
1964 3582 0.101579 TGCGTCGTGTGTGAGAGAAA 59.898 50.000 0.00 0.00 0.00 2.52
1965 3583 0.313987 ATGCGTCGTGTGTGAGAGAA 59.686 50.000 0.00 0.00 0.00 2.87
1966 3584 0.109735 GATGCGTCGTGTGTGAGAGA 60.110 55.000 0.00 0.00 0.00 3.10
1967 3585 0.109551 AGATGCGTCGTGTGTGAGAG 60.110 55.000 0.00 0.00 0.00 3.20
1968 3586 0.313987 AAGATGCGTCGTGTGTGAGA 59.686 50.000 0.00 0.00 0.00 3.27
1969 3587 1.139989 AAAGATGCGTCGTGTGTGAG 58.860 50.000 0.00 0.00 0.00 3.51
1970 3588 2.425578 TAAAGATGCGTCGTGTGTGA 57.574 45.000 0.00 0.00 0.00 3.58
1971 3589 2.923655 AGATAAAGATGCGTCGTGTGTG 59.076 45.455 0.00 0.00 0.00 3.82
1972 3590 3.232213 AGATAAAGATGCGTCGTGTGT 57.768 42.857 0.00 0.00 0.00 3.72
1973 3591 3.782250 GCAAGATAAAGATGCGTCGTGTG 60.782 47.826 0.00 0.00 0.00 3.82
1974 3592 2.348666 GCAAGATAAAGATGCGTCGTGT 59.651 45.455 0.00 0.00 0.00 4.49
1975 3593 2.961436 GCAAGATAAAGATGCGTCGTG 58.039 47.619 0.00 0.00 0.00 4.35
1981 3599 5.476752 AGAAGAACGCAAGATAAAGATGC 57.523 39.130 0.00 0.00 43.62 3.91
1982 3600 5.007136 GGGAGAAGAACGCAAGATAAAGATG 59.993 44.000 0.00 0.00 43.62 2.90
1983 3601 5.119694 GGGAGAAGAACGCAAGATAAAGAT 58.880 41.667 0.00 0.00 43.62 2.40
1984 3602 4.504858 GGGAGAAGAACGCAAGATAAAGA 58.495 43.478 0.00 0.00 43.62 2.52
1985 3603 3.623510 GGGGAGAAGAACGCAAGATAAAG 59.376 47.826 0.00 0.00 43.62 1.85
1986 3604 3.008594 TGGGGAGAAGAACGCAAGATAAA 59.991 43.478 0.00 0.00 43.62 1.40
1987 3605 2.569853 TGGGGAGAAGAACGCAAGATAA 59.430 45.455 0.00 0.00 43.62 1.75
1988 3606 2.093658 GTGGGGAGAAGAACGCAAGATA 60.094 50.000 0.00 0.00 43.62 1.98
1989 3607 0.984230 TGGGGAGAAGAACGCAAGAT 59.016 50.000 0.00 0.00 43.62 2.40
1990 3608 0.034896 GTGGGGAGAAGAACGCAAGA 59.965 55.000 0.00 0.00 43.62 3.02
1992 3610 1.072505 GGTGGGGAGAAGAACGCAA 59.927 57.895 0.00 0.00 0.00 4.85
1993 3611 2.747686 GGTGGGGAGAAGAACGCA 59.252 61.111 0.00 0.00 0.00 5.24
1994 3612 2.046217 GGGTGGGGAGAAGAACGC 60.046 66.667 0.00 0.00 0.00 4.84
1995 3613 1.003718 GTGGGTGGGGAGAAGAACG 60.004 63.158 0.00 0.00 0.00 3.95
1996 3614 0.698818 ATGTGGGTGGGGAGAAGAAC 59.301 55.000 0.00 0.00 0.00 3.01
1997 3615 1.455822 AATGTGGGTGGGGAGAAGAA 58.544 50.000 0.00 0.00 0.00 2.52
1998 3616 1.455822 AAATGTGGGTGGGGAGAAGA 58.544 50.000 0.00 0.00 0.00 2.87
1999 3617 2.309136 AAAATGTGGGTGGGGAGAAG 57.691 50.000 0.00 0.00 0.00 2.85
2000 3618 2.785357 AAAAATGTGGGTGGGGAGAA 57.215 45.000 0.00 0.00 0.00 2.87
2016 3634 2.170166 CCCATCTGCAGTAGCCAAAAA 58.830 47.619 14.67 0.00 41.13 1.94
2017 3635 1.616725 CCCCATCTGCAGTAGCCAAAA 60.617 52.381 14.67 0.00 41.13 2.44
2018 3636 0.034186 CCCCATCTGCAGTAGCCAAA 60.034 55.000 14.67 0.00 41.13 3.28
2019 3637 1.207488 ACCCCATCTGCAGTAGCCAA 61.207 55.000 14.67 0.00 41.13 4.52
2020 3638 1.616327 ACCCCATCTGCAGTAGCCA 60.616 57.895 14.67 0.00 41.13 4.75
2021 3639 1.147153 GACCCCATCTGCAGTAGCC 59.853 63.158 14.67 0.00 41.13 3.93
2022 3640 0.462759 GTGACCCCATCTGCAGTAGC 60.463 60.000 14.67 0.00 42.57 3.58
2023 3641 1.134580 CAGTGACCCCATCTGCAGTAG 60.135 57.143 14.67 7.39 0.00 2.57
2024 3642 0.904649 CAGTGACCCCATCTGCAGTA 59.095 55.000 14.67 0.48 0.00 2.74
2025 3643 1.681666 CAGTGACCCCATCTGCAGT 59.318 57.895 14.67 0.00 0.00 4.40
2026 3644 1.077930 CCAGTGACCCCATCTGCAG 60.078 63.158 7.63 7.63 0.00 4.41
2027 3645 3.080641 CCAGTGACCCCATCTGCA 58.919 61.111 0.00 0.00 0.00 4.41
2028 3646 2.439156 GCCAGTGACCCCATCTGC 60.439 66.667 0.00 0.00 0.00 4.26
2029 3647 2.124983 CGCCAGTGACCCCATCTG 60.125 66.667 0.00 0.00 0.00 2.90
2030 3648 3.402681 CCGCCAGTGACCCCATCT 61.403 66.667 0.00 0.00 0.00 2.90
2046 3664 2.836360 TAGTCGTCCCCCATCGCC 60.836 66.667 0.00 0.00 0.00 5.54
2047 3665 2.351336 CTGTAGTCGTCCCCCATCGC 62.351 65.000 0.00 0.00 0.00 4.58
2048 3666 1.734137 CTGTAGTCGTCCCCCATCG 59.266 63.158 0.00 0.00 0.00 3.84
2049 3667 1.400530 CCCTGTAGTCGTCCCCCATC 61.401 65.000 0.00 0.00 0.00 3.51
2050 3668 1.382695 CCCTGTAGTCGTCCCCCAT 60.383 63.158 0.00 0.00 0.00 4.00
2051 3669 2.038329 CCCTGTAGTCGTCCCCCA 59.962 66.667 0.00 0.00 0.00 4.96
2052 3670 2.762875 CCCCTGTAGTCGTCCCCC 60.763 72.222 0.00 0.00 0.00 5.40
2053 3671 2.762875 CCCCCTGTAGTCGTCCCC 60.763 72.222 0.00 0.00 0.00 4.81
2054 3672 2.038490 ACCCCCTGTAGTCGTCCC 59.962 66.667 0.00 0.00 0.00 4.46
2055 3673 1.190178 AACACCCCCTGTAGTCGTCC 61.190 60.000 0.00 0.00 30.51 4.79
2056 3674 0.037605 CAACACCCCCTGTAGTCGTC 60.038 60.000 0.00 0.00 30.51 4.20
2057 3675 0.761702 ACAACACCCCCTGTAGTCGT 60.762 55.000 0.00 0.00 30.51 4.34
2058 3676 0.320421 CACAACACCCCCTGTAGTCG 60.320 60.000 0.00 0.00 30.51 4.18
2059 3677 1.002087 CTCACAACACCCCCTGTAGTC 59.998 57.143 0.00 0.00 30.51 2.59
2060 3678 1.056660 CTCACAACACCCCCTGTAGT 58.943 55.000 0.00 0.00 30.51 2.73
2061 3679 1.002087 GTCTCACAACACCCCCTGTAG 59.998 57.143 0.00 0.00 30.51 2.74
2062 3680 1.053424 GTCTCACAACACCCCCTGTA 58.947 55.000 0.00 0.00 30.51 2.74
2063 3681 1.705997 GGTCTCACAACACCCCCTGT 61.706 60.000 0.00 0.00 32.89 4.00
2064 3682 1.073199 GGTCTCACAACACCCCCTG 59.927 63.158 0.00 0.00 0.00 4.45
2065 3683 1.385347 TGGTCTCACAACACCCCCT 60.385 57.895 0.00 0.00 0.00 4.79
2066 3684 1.228154 GTGGTCTCACAACACCCCC 60.228 63.158 0.00 0.00 43.13 5.40
2067 3685 1.228154 GGTGGTCTCACAACACCCC 60.228 63.158 0.00 0.00 46.90 4.95
2068 3686 4.475527 GGTGGTCTCACAACACCC 57.524 61.111 0.00 0.00 46.90 4.61
2071 3689 0.621082 TTGGTGGTGGTCTCACAACA 59.379 50.000 6.40 0.00 46.95 3.33
2072 3690 1.608590 CATTGGTGGTGGTCTCACAAC 59.391 52.381 0.00 0.00 44.97 3.32
2073 3691 1.979855 CATTGGTGGTGGTCTCACAA 58.020 50.000 0.00 0.00 45.32 3.33
2074 3692 0.537143 GCATTGGTGGTGGTCTCACA 60.537 55.000 0.00 0.00 45.32 3.58
2075 3693 1.244019 GGCATTGGTGGTGGTCTCAC 61.244 60.000 0.00 0.00 42.91 3.51
2076 3694 1.074775 GGCATTGGTGGTGGTCTCA 59.925 57.895 0.00 0.00 0.00 3.27
2077 3695 2.040544 CGGCATTGGTGGTGGTCTC 61.041 63.158 0.00 0.00 0.00 3.36
2078 3696 2.034066 CGGCATTGGTGGTGGTCT 59.966 61.111 0.00 0.00 0.00 3.85
2079 3697 3.061848 CCGGCATTGGTGGTGGTC 61.062 66.667 0.00 0.00 0.00 4.02
2083 3701 2.909457 CTATGGCCGGCATTGGTGGT 62.909 60.000 30.85 6.56 0.00 4.16
2084 3702 2.123939 TATGGCCGGCATTGGTGG 60.124 61.111 30.85 0.00 0.00 4.61
2085 3703 1.453745 ACTATGGCCGGCATTGGTG 60.454 57.895 30.85 14.81 0.00 4.17
2086 3704 1.453745 CACTATGGCCGGCATTGGT 60.454 57.895 30.85 19.51 0.00 3.67
2087 3705 2.195567 CCACTATGGCCGGCATTGG 61.196 63.158 30.85 21.10 0.00 3.16
2088 3706 3.435590 CCACTATGGCCGGCATTG 58.564 61.111 30.85 21.03 0.00 2.82
2097 3715 2.586079 CTCGTGGCGCCACTATGG 60.586 66.667 46.04 34.16 44.16 2.74
2098 3716 3.264897 GCTCGTGGCGCCACTATG 61.265 66.667 46.04 35.96 44.16 2.23
2099 3717 3.723235 CTGCTCGTGGCGCCACTAT 62.723 63.158 46.04 0.00 44.16 2.12
2100 3718 4.435436 CTGCTCGTGGCGCCACTA 62.435 66.667 46.04 38.20 44.16 2.74
2109 3727 3.730761 GTTGCTGCCCTGCTCGTG 61.731 66.667 0.00 0.00 0.00 4.35
2110 3728 4.254709 TGTTGCTGCCCTGCTCGT 62.255 61.111 0.00 0.00 0.00 4.18
2111 3729 3.730761 GTGTTGCTGCCCTGCTCG 61.731 66.667 0.00 0.00 0.00 5.03
2112 3730 1.975407 ATGTGTTGCTGCCCTGCTC 60.975 57.895 0.00 0.00 0.00 4.26
2113 3731 2.116772 ATGTGTTGCTGCCCTGCT 59.883 55.556 0.00 0.00 0.00 4.24
2114 3732 2.260434 CATGTGTTGCTGCCCTGC 59.740 61.111 0.00 0.00 0.00 4.85
2123 3741 2.698803 TGCCTACAGTAGCATGTGTTG 58.301 47.619 1.50 0.00 34.56 3.33
2124 3742 3.074412 GTTGCCTACAGTAGCATGTGTT 58.926 45.455 1.50 0.00 39.11 3.32
2125 3743 2.699954 GTTGCCTACAGTAGCATGTGT 58.300 47.619 1.50 0.00 39.11 3.72
2126 3744 1.660607 CGTTGCCTACAGTAGCATGTG 59.339 52.381 1.50 0.00 39.11 3.21
2127 3745 1.405526 CCGTTGCCTACAGTAGCATGT 60.406 52.381 1.50 0.00 39.11 3.21
2128 3746 1.290203 CCGTTGCCTACAGTAGCATG 58.710 55.000 1.50 0.00 39.11 4.06
2129 3747 0.178068 CCCGTTGCCTACAGTAGCAT 59.822 55.000 1.50 0.00 39.11 3.79
2130 3748 0.901114 TCCCGTTGCCTACAGTAGCA 60.901 55.000 1.50 1.66 37.18 3.49
2131 3749 0.459759 GTCCCGTTGCCTACAGTAGC 60.460 60.000 1.50 0.00 0.00 3.58
2132 3750 1.183549 AGTCCCGTTGCCTACAGTAG 58.816 55.000 0.00 0.00 0.00 2.57
2133 3751 1.274167 CAAGTCCCGTTGCCTACAGTA 59.726 52.381 0.00 0.00 0.00 2.74
2134 3752 0.034896 CAAGTCCCGTTGCCTACAGT 59.965 55.000 0.00 0.00 0.00 3.55
2135 3753 0.320374 TCAAGTCCCGTTGCCTACAG 59.680 55.000 0.00 0.00 0.00 2.74
2136 3754 0.759959 TTCAAGTCCCGTTGCCTACA 59.240 50.000 0.00 0.00 0.00 2.74
2137 3755 1.534163 GTTTCAAGTCCCGTTGCCTAC 59.466 52.381 0.00 0.00 0.00 3.18
2138 3756 1.543871 GGTTTCAAGTCCCGTTGCCTA 60.544 52.381 0.00 0.00 0.00 3.93
2139 3757 0.822121 GGTTTCAAGTCCCGTTGCCT 60.822 55.000 0.00 0.00 0.00 4.75
2140 3758 1.658114 GGTTTCAAGTCCCGTTGCC 59.342 57.895 0.00 0.00 0.00 4.52
2141 3759 1.658114 GGGTTTCAAGTCCCGTTGC 59.342 57.895 0.00 0.00 33.97 4.17
2142 3760 2.337361 GGGGTTTCAAGTCCCGTTG 58.663 57.895 0.00 0.00 44.27 4.10
2143 3761 4.914128 GGGGTTTCAAGTCCCGTT 57.086 55.556 0.00 0.00 44.27 4.44
2146 3764 2.035155 CCCGGGGTTTCAAGTCCC 59.965 66.667 14.71 0.00 42.73 4.46
2147 3765 1.152138 AACCCGGGGTTTCAAGTCC 59.848 57.895 25.84 0.00 44.33 3.85
2148 3766 1.176619 CCAACCCGGGGTTTCAAGTC 61.177 60.000 28.73 0.00 44.33 3.01
2149 3767 1.152631 CCAACCCGGGGTTTCAAGT 60.153 57.895 28.73 4.08 44.33 3.16
2150 3768 1.152631 ACCAACCCGGGGTTTCAAG 60.153 57.895 28.73 18.73 44.33 3.02
2151 3769 1.455959 CACCAACCCGGGGTTTCAA 60.456 57.895 28.73 0.00 44.33 2.69
2152 3770 2.196229 CACCAACCCGGGGTTTCA 59.804 61.111 28.73 0.00 44.33 2.69
2153 3771 2.599281 CCACCAACCCGGGGTTTC 60.599 66.667 28.73 0.00 44.33 2.78
2154 3772 4.227583 CCCACCAACCCGGGGTTT 62.228 66.667 28.73 13.16 44.33 3.27
2161 3779 4.702274 ATGCAGCCCCACCAACCC 62.702 66.667 0.00 0.00 0.00 4.11
2162 3780 3.070576 GATGCAGCCCCACCAACC 61.071 66.667 0.00 0.00 0.00 3.77
2163 3781 3.070576 GGATGCAGCCCCACCAAC 61.071 66.667 10.76 0.00 0.00 3.77
2164 3782 4.738998 CGGATGCAGCCCCACCAA 62.739 66.667 16.93 0.00 0.00 3.67
2190 3808 1.789078 TTATAGCTCGGTCGTCGGCC 61.789 60.000 5.59 5.59 39.77 6.13
2191 3809 0.240411 ATTATAGCTCGGTCGTCGGC 59.760 55.000 0.00 0.00 39.77 5.54
2192 3810 1.463693 CGATTATAGCTCGGTCGTCGG 60.464 57.143 0.00 0.00 39.77 4.79
2193 3811 1.866982 CGATTATAGCTCGGTCGTCG 58.133 55.000 0.00 0.00 40.90 5.12
2200 3818 2.415857 ACTAGCGACCGATTATAGCTCG 59.584 50.000 0.00 0.00 39.14 5.03
2207 3825 1.466856 ACCACACTAGCGACCGATTA 58.533 50.000 0.00 0.00 0.00 1.75
2210 3828 1.287815 CAACCACACTAGCGACCGA 59.712 57.895 0.00 0.00 0.00 4.69
2274 3892 3.685272 TGTGTCGACTGTAGCAAACAAAA 59.315 39.130 17.92 0.00 37.74 2.44
2288 3926 4.748102 TCATAACCAAAACTCTGTGTCGAC 59.252 41.667 9.11 9.11 0.00 4.20
2290 3928 4.988540 TCTCATAACCAAAACTCTGTGTCG 59.011 41.667 0.00 0.00 0.00 4.35
2338 3976 4.953940 AAAAGCCACTTCCAGCAAAATA 57.046 36.364 0.00 0.00 0.00 1.40
2473 4112 3.819564 ATAGTCTCAGCGGCACAATTA 57.180 42.857 1.45 0.00 0.00 1.40
2475 4114 2.698855 AATAGTCTCAGCGGCACAAT 57.301 45.000 1.45 0.00 0.00 2.71
2487 4126 4.819630 TGACGTTTCCAGCAAAAATAGTCT 59.180 37.500 0.00 0.00 32.37 3.24
2522 4161 5.626142 TGGTTCCAGCAAAAACAGACTATA 58.374 37.500 0.00 0.00 0.00 1.31
2523 4162 4.469657 TGGTTCCAGCAAAAACAGACTAT 58.530 39.130 0.00 0.00 0.00 2.12
2530 4169 6.093357 TGAAAAATTCTGGTTCCAGCAAAAAC 59.907 34.615 13.44 4.12 34.33 2.43
2561 4202 1.669760 GCGTCATTGTCCCGTTGGA 60.670 57.895 0.00 0.00 38.75 3.53


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

AutoCloner maintained by Alex Coulton.