Multiple sequence alignment - TraesCS2A01G059200

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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 TraesCS2A01G059200 chr2A 100.000 5951 0 0 1 5951 25105690 25099740 0.000000e+00 10990
1 TraesCS2A01G059200 chr2A 84.931 2953 351 49 2046 4944 25027337 25030249 0.000000e+00 2902
2 TraesCS2A01G059200 chr2A 83.554 906 96 26 965 1848 25026337 25027211 0.000000e+00 798
3 TraesCS2A01G059200 chr2A 81.353 606 65 27 129 705 25025429 25026015 3.270000e-122 449
4 TraesCS2A01G059200 chr2A 100.000 95 0 0 5857 5951 24909138 24909232 6.130000e-40 176
5 TraesCS2A01G059200 chr2A 97.297 74 1 1 5856 5928 15088400 15088473 2.250000e-24 124
6 TraesCS2A01G059200 chr2D 95.283 2989 128 5 1963 4945 23486100 23489081 0.000000e+00 4726
7 TraesCS2A01G059200 chr2D 93.699 1825 91 6 34 1849 23484261 23486070 0.000000e+00 2712
8 TraesCS2A01G059200 chr2D 96.857 891 28 0 4966 5856 23490446 23491336 0.000000e+00 1491
9 TraesCS2A01G059200 chr2D 70.511 1743 425 73 3144 4843 528323163 528324859 7.550000e-74 289
10 TraesCS2A01G059200 chr2D 70.494 688 171 22 3449 4120 647804831 647804160 3.770000e-22 117
11 TraesCS2A01G059200 chr3A 78.132 439 86 7 998 1434 681560238 681560668 2.730000e-68 270
12 TraesCS2A01G059200 chr3A 76.484 438 86 6 998 1434 681521951 681522372 7.760000e-54 222
13 TraesCS2A01G059200 chr3A 87.879 99 5 5 5854 5946 601366753 601366850 6.310000e-20 110
14 TraesCS2A01G059200 chr7D 72.632 855 189 34 3931 4770 36495739 36494915 2.140000e-59 241
15 TraesCS2A01G059200 chr7D 89.583 96 7 2 5857 5951 75277511 75277418 1.050000e-22 119
16 TraesCS2A01G059200 chr1B 76.376 436 93 10 1001 1434 632018299 632017872 6.000000e-55 226
17 TraesCS2A01G059200 chr5D 89.796 98 6 4 5855 5951 95802510 95802416 8.100000e-24 122
18 TraesCS2A01G059200 chr7B 89.474 95 5 5 5859 5951 24046242 24046151 1.360000e-21 115
19 TraesCS2A01G059200 chr5A 94.521 73 4 0 5853 5925 487760140 487760212 4.870000e-21 113
20 TraesCS2A01G059200 chr6A 93.421 76 4 1 5854 5928 592484911 592484986 1.750000e-20 111
21 TraesCS2A01G059200 chr7A 87.368 95 8 4 5858 5951 450418724 450418815 8.160000e-19 106


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 TraesCS2A01G059200 chr2A 25099740 25105690 5950 True 10990.000000 10990 100.000000 1 5951 1 chr2A.!!$R1 5950
1 TraesCS2A01G059200 chr2A 25025429 25030249 4820 False 1383.000000 2902 83.279333 129 4944 3 chr2A.!!$F3 4815
2 TraesCS2A01G059200 chr2D 23484261 23491336 7075 False 2976.333333 4726 95.279667 34 5856 3 chr2D.!!$F2 5822
3 TraesCS2A01G059200 chr2D 528323163 528324859 1696 False 289.000000 289 70.511000 3144 4843 1 chr2D.!!$F1 1699
4 TraesCS2A01G059200 chr7D 36494915 36495739 824 True 241.000000 241 72.632000 3931 4770 1 chr7D.!!$R1 839

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
505 524 0.913934 TCCTACCATCCTTGCCAGCA 60.914 55.000 0.00 0.0 0.00 4.41 F
1484 1602 0.108472 TCATCGTCTCAAGCTGCTGG 60.108 55.000 1.35 0.0 0.00 4.85 F
1956 2086 0.035458 AAGGTGAGGTGAAGCCGAAG 59.965 55.000 0.00 0.0 43.70 3.79 F
1963 2093 0.178068 GGTGAAGCCGAAGATGCCTA 59.822 55.000 0.00 0.0 0.00 3.93 F
2260 2399 0.250338 GGAAACAGGCGAGTCCAACT 60.250 55.000 0.00 0.0 37.29 3.16 F
2262 2401 0.250338 AAACAGGCGAGTCCAACTCC 60.250 55.000 1.69 0.0 42.12 3.85 F
2544 2701 0.870313 AGGAGATATCAGGGGAGGCA 59.130 55.000 5.32 0.0 0.00 4.75 F
3201 3370 1.003812 CCACCGGGAGAACCAATAACA 59.996 52.381 6.32 0.0 40.22 2.41 F
4617 4816 2.161609 CGTGCTTCCCAAATTACACTCC 59.838 50.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1966 0.040603 GCTGTTTCTGCTGCTCACAC 60.041 55.000 0.00 0.00 0.00 3.82 R
2385 2524 1.002430 TCTTTGATGTGAGCCTCGCTT 59.998 47.619 6.84 0.00 39.88 4.68 R
2965 3131 1.057275 TTGGTGTACAGCAGACCCCA 61.057 55.000 25.27 11.07 39.95 4.96 R
3108 3274 1.379044 GCCAGGTGCACAGCCTAAT 60.379 57.895 20.43 0.00 40.77 1.73 R
3276 3445 1.718280 GTAGAATCCCCGGGATGTCT 58.282 55.000 26.32 22.46 42.27 3.41 R
3361 3530 2.337359 TAGCTCCTGTTGGGGTTAGT 57.663 50.000 0.00 0.00 35.83 2.24 R
4323 4501 0.392706 TGGCTCGAAGCAACTTCTCA 59.607 50.000 5.85 0.00 44.75 3.27 R
4893 5113 0.036010 ATCCACTCTCGGTGCTTTGG 60.036 55.000 0.00 0.00 44.08 3.28 R
5928 7492 0.038709 CTATGGGCTAGCTGCGAGTC 60.039 60.000 15.72 8.74 44.05 3.36 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
24 25 7.671495 AATCTTGGCAATTTAAAATCACCAC 57.329 32.000 0.00 0.00 0.00 4.16
25 26 6.166984 TCTTGGCAATTTAAAATCACCACA 57.833 33.333 0.00 0.00 0.00 4.17
26 27 6.767456 TCTTGGCAATTTAAAATCACCACAT 58.233 32.000 0.00 0.00 0.00 3.21
27 28 6.649973 TCTTGGCAATTTAAAATCACCACATG 59.350 34.615 0.00 0.00 0.00 3.21
28 29 5.862845 TGGCAATTTAAAATCACCACATGT 58.137 33.333 0.00 0.00 0.00 3.21
29 30 5.699915 TGGCAATTTAAAATCACCACATGTG 59.300 36.000 19.31 19.31 46.88 3.21
76 77 1.298859 CGTCTGGTGTAGCAAAGCCC 61.299 60.000 0.00 0.00 0.00 5.19
93 94 2.117156 CCAGCCATGCCTACTGTGC 61.117 63.158 0.00 0.00 0.00 4.57
99 100 1.661341 CATGCCTACTGTGCTTCCTC 58.339 55.000 0.00 0.00 0.00 3.71
105 106 3.683847 GCCTACTGTGCTTCCTCATGAAT 60.684 47.826 0.00 0.00 31.06 2.57
114 115 8.662781 TGTGCTTCCTCATGAATAGTAAATAC 57.337 34.615 0.00 0.00 31.06 1.89
115 116 7.715249 TGTGCTTCCTCATGAATAGTAAATACC 59.285 37.037 0.00 0.00 31.06 2.73
277 278 2.038820 CCCACAAGTTCATTTTGCCCAT 59.961 45.455 0.00 0.00 0.00 4.00
364 365 4.240096 CAGCAATCAAAGTCATTCCCAAC 58.760 43.478 0.00 0.00 0.00 3.77
365 366 3.057315 AGCAATCAAAGTCATTCCCAACG 60.057 43.478 0.00 0.00 0.00 4.10
436 451 1.985895 ACCTGAAGTAAAGGGTCTGGG 59.014 52.381 0.00 0.00 39.30 4.45
505 524 0.913934 TCCTACCATCCTTGCCAGCA 60.914 55.000 0.00 0.00 0.00 4.41
518 537 4.339872 TTGCCAGCACAAGAAAATGAAT 57.660 36.364 0.00 0.00 0.00 2.57
520 539 2.997986 GCCAGCACAAGAAAATGAATGG 59.002 45.455 0.00 0.00 0.00 3.16
522 541 2.997986 CAGCACAAGAAAATGAATGGGC 59.002 45.455 0.00 0.00 42.46 5.36
580 607 1.126846 CTTTTGTCACGTCATCTCGCC 59.873 52.381 0.00 0.00 0.00 5.54
603 630 1.090052 CGAGATTGTCCGGCCCTTTC 61.090 60.000 0.00 0.00 0.00 2.62
803 897 4.464069 AGAAGACAAACTAGCTAGGCAG 57.536 45.455 24.35 14.84 0.00 4.85
867 968 4.445452 AAGTTTAGGTGCATGCTTGATG 57.555 40.909 20.33 0.00 34.84 3.07
943 1052 3.581332 TCTCGGTTGACCCTTTACTTCAT 59.419 43.478 0.00 0.00 0.00 2.57
949 1058 3.826524 TGACCCTTTACTTCATGCACAA 58.173 40.909 0.00 0.00 0.00 3.33
1116 1234 3.052262 TCATCAAGGAGGAGATGGAGAGT 60.052 47.826 0.00 0.00 41.45 3.24
1190 1308 4.357947 GCACGACGAGCAGGTCCA 62.358 66.667 12.54 0.00 33.30 4.02
1260 1378 2.439883 GACCTCTACCTCCGGCGT 60.440 66.667 6.01 0.00 0.00 5.68
1434 1552 2.043752 TACGGCGTGGAGATCCCA 60.044 61.111 24.86 0.00 44.25 4.37
1445 1563 0.397254 GAGATCCCACGGAAGGAGGA 60.397 60.000 0.00 0.00 40.13 3.71
1453 1571 4.475135 GGAAGGAGGAGGCGGCAC 62.475 72.222 13.08 4.32 0.00 5.01
1467 1585 2.281484 GCACCTTTGCCCTCGTCA 60.281 61.111 0.00 0.00 43.66 4.35
1484 1602 0.108472 TCATCGTCTCAAGCTGCTGG 60.108 55.000 1.35 0.00 0.00 4.85
1487 1605 1.744368 CGTCTCAAGCTGCTGGCAT 60.744 57.895 1.35 0.00 44.79 4.40
1506 1636 5.369404 TGGCATAGAATACAAGGAGGATGAA 59.631 40.000 0.00 0.00 0.00 2.57
1524 1654 5.700373 GGATGAAGACTATCAGATTCAAGCC 59.300 44.000 0.00 0.00 35.47 4.35
1528 1658 1.486310 ACTATCAGATTCAAGCCGCCA 59.514 47.619 0.00 0.00 0.00 5.69
1572 1702 1.470112 GCTCTAGAACCTCGCCTTGTC 60.470 57.143 0.00 0.00 0.00 3.18
1592 1722 1.174783 GAGGAGTACTGTGCCGAGAA 58.825 55.000 0.00 0.00 0.00 2.87
1593 1723 1.133407 GAGGAGTACTGTGCCGAGAAG 59.867 57.143 0.00 0.00 0.00 2.85
1594 1724 0.458716 GGAGTACTGTGCCGAGAAGC 60.459 60.000 0.00 0.00 0.00 3.86
1595 1725 0.528470 GAGTACTGTGCCGAGAAGCT 59.472 55.000 0.00 0.00 0.00 3.74
1596 1726 1.743958 GAGTACTGTGCCGAGAAGCTA 59.256 52.381 0.00 0.00 0.00 3.32
1597 1727 1.746220 AGTACTGTGCCGAGAAGCTAG 59.254 52.381 0.00 0.00 0.00 3.42
1598 1728 1.473278 GTACTGTGCCGAGAAGCTAGT 59.527 52.381 0.00 0.00 35.83 2.57
1599 1729 0.528470 ACTGTGCCGAGAAGCTAGTC 59.472 55.000 0.00 0.00 0.00 2.59
1600 1730 0.524392 CTGTGCCGAGAAGCTAGTCG 60.524 60.000 10.05 10.05 35.91 4.18
1601 1731 0.958876 TGTGCCGAGAAGCTAGTCGA 60.959 55.000 17.01 0.00 38.50 4.20
1602 1732 0.248296 GTGCCGAGAAGCTAGTCGAG 60.248 60.000 17.01 9.49 38.50 4.04
1603 1733 0.392595 TGCCGAGAAGCTAGTCGAGA 60.393 55.000 17.01 2.74 38.50 4.04
1606 1736 2.011222 CCGAGAAGCTAGTCGAGAAGT 58.989 52.381 17.01 0.00 38.50 3.01
1645 1775 1.013596 GCAAGCCAAAACCAACAACC 58.986 50.000 0.00 0.00 0.00 3.77
1698 1828 1.507141 CGGATGATACAAAGGGCGCC 61.507 60.000 21.18 21.18 0.00 6.53
1701 1831 3.583086 GATACAAAGGGCGCCGGC 61.583 66.667 22.54 19.07 38.90 6.13
1755 1885 2.855370 CAAAAACTTTAAGCGCACGGTT 59.145 40.909 11.47 12.42 39.33 4.44
1764 1894 2.330041 CGCACGGTTTGGGTCAAC 59.670 61.111 0.00 0.00 33.41 3.18
1774 1904 2.047179 GGGTCAACCTCTCGGCAC 60.047 66.667 0.00 0.00 35.85 5.01
1797 1927 1.565759 CACTTCCCATGGGATCTTCCA 59.434 52.381 34.21 17.12 44.74 3.53
1809 1939 2.633488 GATCTTCCACTGTTACCCAGC 58.367 52.381 0.00 0.00 45.68 4.85
1831 1961 3.497763 CGAGATCCTCTCCTACATCCTGT 60.498 52.174 0.00 0.00 40.34 4.00
1836 1966 4.991776 TCCTCTCCTACATCCTGTATGAG 58.008 47.826 11.22 11.22 42.89 2.90
1839 1969 5.130705 TCTCCTACATCCTGTATGAGTGT 57.869 43.478 14.91 0.00 42.45 3.55
1840 1970 4.889995 TCTCCTACATCCTGTATGAGTGTG 59.110 45.833 14.91 0.00 42.45 3.82
1841 1971 4.867086 TCCTACATCCTGTATGAGTGTGA 58.133 43.478 0.00 0.00 39.07 3.58
1842 1972 4.889995 TCCTACATCCTGTATGAGTGTGAG 59.110 45.833 0.00 0.00 39.07 3.51
1843 1973 3.533606 ACATCCTGTATGAGTGTGAGC 57.466 47.619 0.00 0.00 39.07 4.26
1844 1974 2.833943 ACATCCTGTATGAGTGTGAGCA 59.166 45.455 0.00 0.00 39.07 4.26
1845 1975 3.118847 ACATCCTGTATGAGTGTGAGCAG 60.119 47.826 0.00 0.00 39.07 4.24
1846 1976 1.205655 TCCTGTATGAGTGTGAGCAGC 59.794 52.381 0.00 0.00 0.00 5.25
1847 1977 1.066645 CCTGTATGAGTGTGAGCAGCA 60.067 52.381 0.00 0.00 0.00 4.41
1848 1978 2.269172 CTGTATGAGTGTGAGCAGCAG 58.731 52.381 0.00 0.00 0.00 4.24
1849 1979 1.895131 TGTATGAGTGTGAGCAGCAGA 59.105 47.619 0.00 0.00 0.00 4.26
1850 1980 2.299867 TGTATGAGTGTGAGCAGCAGAA 59.700 45.455 0.00 0.00 0.00 3.02
1851 1981 2.556144 ATGAGTGTGAGCAGCAGAAA 57.444 45.000 0.00 0.00 0.00 2.52
1852 1982 1.586422 TGAGTGTGAGCAGCAGAAAC 58.414 50.000 0.00 0.00 0.00 2.78
1853 1983 1.134431 TGAGTGTGAGCAGCAGAAACA 60.134 47.619 0.00 0.00 0.00 2.83
1854 1984 1.530293 GAGTGTGAGCAGCAGAAACAG 59.470 52.381 0.00 0.00 0.00 3.16
1855 1985 0.040603 GTGTGAGCAGCAGAAACAGC 60.041 55.000 0.00 0.00 0.00 4.40
1856 1986 0.464193 TGTGAGCAGCAGAAACAGCA 60.464 50.000 0.00 0.00 0.00 4.41
1857 1987 0.879765 GTGAGCAGCAGAAACAGCAT 59.120 50.000 0.00 0.00 0.00 3.79
1858 1988 0.879090 TGAGCAGCAGAAACAGCATG 59.121 50.000 0.00 0.00 46.00 4.06
1859 1989 1.162698 GAGCAGCAGAAACAGCATGA 58.837 50.000 0.00 0.00 39.69 3.07
1860 1990 1.130749 GAGCAGCAGAAACAGCATGAG 59.869 52.381 0.00 0.00 39.69 2.90
1861 1991 0.170561 GCAGCAGAAACAGCATGAGG 59.829 55.000 0.00 0.00 39.69 3.86
1862 1992 1.817357 CAGCAGAAACAGCATGAGGA 58.183 50.000 0.00 0.00 39.69 3.71
1863 1993 2.366533 CAGCAGAAACAGCATGAGGAT 58.633 47.619 0.00 0.00 39.69 3.24
1864 1994 2.097629 CAGCAGAAACAGCATGAGGATG 59.902 50.000 0.00 0.00 39.69 3.51
1865 1995 2.026542 AGCAGAAACAGCATGAGGATGA 60.027 45.455 0.00 0.00 39.69 2.92
1866 1996 2.355132 GCAGAAACAGCATGAGGATGAG 59.645 50.000 0.00 0.00 39.69 2.90
1867 1997 2.355132 CAGAAACAGCATGAGGATGAGC 59.645 50.000 0.00 0.00 39.69 4.26
1868 1998 2.026542 AGAAACAGCATGAGGATGAGCA 60.027 45.455 0.00 0.00 39.69 4.26
1869 1999 2.039818 AACAGCATGAGGATGAGCAG 57.960 50.000 0.00 0.00 39.69 4.24
1870 2000 0.464013 ACAGCATGAGGATGAGCAGC 60.464 55.000 0.00 0.00 39.69 5.25
1871 2001 0.463833 CAGCATGAGGATGAGCAGCA 60.464 55.000 0.00 0.00 39.69 4.41
1872 2002 0.179043 AGCATGAGGATGAGCAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
1873 2003 0.179054 GCATGAGGATGAGCAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1874 2004 1.746171 GCATGAGGATGAGCAGCAGAA 60.746 52.381 0.00 0.00 0.00 3.02
1875 2005 2.640184 CATGAGGATGAGCAGCAGAAA 58.360 47.619 0.00 0.00 0.00 2.52
1876 2006 2.105006 TGAGGATGAGCAGCAGAAAC 57.895 50.000 0.00 0.00 0.00 2.78
1877 2007 1.348696 TGAGGATGAGCAGCAGAAACA 59.651 47.619 0.00 0.00 0.00 2.83
1878 2008 2.008329 GAGGATGAGCAGCAGAAACAG 58.992 52.381 0.00 0.00 0.00 3.16
1879 2009 0.450983 GGATGAGCAGCAGAAACAGC 59.549 55.000 0.00 0.00 0.00 4.40
1880 2010 1.162698 GATGAGCAGCAGAAACAGCA 58.837 50.000 0.00 0.00 0.00 4.41
1881 2011 1.743958 GATGAGCAGCAGAAACAGCAT 59.256 47.619 0.00 0.00 0.00 3.79
1882 2012 0.879090 TGAGCAGCAGAAACAGCATG 59.121 50.000 0.00 0.00 46.00 4.06
1883 2013 1.162698 GAGCAGCAGAAACAGCATGA 58.837 50.000 0.00 0.00 39.69 3.07
1884 2014 1.130749 GAGCAGCAGAAACAGCATGAG 59.869 52.381 0.00 0.00 39.69 2.90
1885 2015 0.170561 GCAGCAGAAACAGCATGAGG 59.829 55.000 0.00 0.00 39.69 3.86
1886 2016 1.817357 CAGCAGAAACAGCATGAGGA 58.183 50.000 0.00 0.00 39.69 3.71
1887 2017 2.366533 CAGCAGAAACAGCATGAGGAT 58.633 47.619 0.00 0.00 39.69 3.24
1888 2018 2.097629 CAGCAGAAACAGCATGAGGATG 59.902 50.000 0.00 0.00 39.69 3.51
1889 2019 2.026542 AGCAGAAACAGCATGAGGATGA 60.027 45.455 0.00 0.00 39.69 2.92
1890 2020 2.355132 GCAGAAACAGCATGAGGATGAG 59.645 50.000 0.00 0.00 39.69 2.90
1891 2021 2.355132 CAGAAACAGCATGAGGATGAGC 59.645 50.000 0.00 0.00 39.69 4.26
1892 2022 2.026542 AGAAACAGCATGAGGATGAGCA 60.027 45.455 0.00 0.00 39.69 4.26
1893 2023 2.039818 AACAGCATGAGGATGAGCAG 57.960 50.000 0.00 0.00 39.69 4.24
1894 2024 0.464013 ACAGCATGAGGATGAGCAGC 60.464 55.000 0.00 0.00 39.69 5.25
1895 2025 0.463833 CAGCATGAGGATGAGCAGCA 60.464 55.000 0.00 0.00 39.69 4.41
1896 2026 0.179043 AGCATGAGGATGAGCAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
1897 2027 0.179054 GCATGAGGATGAGCAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1898 2028 1.746171 GCATGAGGATGAGCAGCAGAA 60.746 52.381 0.00 0.00 0.00 3.02
1899 2029 2.640184 CATGAGGATGAGCAGCAGAAA 58.360 47.619 0.00 0.00 0.00 2.52
1900 2030 2.105006 TGAGGATGAGCAGCAGAAAC 57.895 50.000 0.00 0.00 0.00 2.78
1901 2031 1.348696 TGAGGATGAGCAGCAGAAACA 59.651 47.619 0.00 0.00 0.00 2.83
1902 2032 2.008329 GAGGATGAGCAGCAGAAACAG 58.992 52.381 0.00 0.00 0.00 3.16
1903 2033 0.450983 GGATGAGCAGCAGAAACAGC 59.549 55.000 0.00 0.00 0.00 4.40
1904 2034 1.162698 GATGAGCAGCAGAAACAGCA 58.837 50.000 0.00 0.00 0.00 4.41
1905 2035 1.743958 GATGAGCAGCAGAAACAGCAT 59.256 47.619 0.00 0.00 0.00 3.79
1906 2036 0.879090 TGAGCAGCAGAAACAGCATG 59.121 50.000 0.00 0.00 46.00 4.06
1907 2037 1.162698 GAGCAGCAGAAACAGCATGA 58.837 50.000 0.00 0.00 39.69 3.07
1908 2038 1.130749 GAGCAGCAGAAACAGCATGAG 59.869 52.381 0.00 0.00 39.69 2.90
1909 2039 0.170561 GCAGCAGAAACAGCATGAGG 59.829 55.000 0.00 0.00 39.69 3.86
1910 2040 1.817357 CAGCAGAAACAGCATGAGGA 58.183 50.000 0.00 0.00 39.69 3.71
1921 2051 0.179054 GCATGAGGATGAGCAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1935 2065 2.328099 GCAGAAAGTCACAGGCGGG 61.328 63.158 0.00 0.00 0.00 6.13
1941 2071 4.643387 GTCACAGGCGGGCAAGGT 62.643 66.667 3.78 0.00 0.00 3.50
1950 2080 1.672356 CGGGCAAGGTGAGGTGAAG 60.672 63.158 0.00 0.00 0.00 3.02
1951 2081 1.973812 GGGCAAGGTGAGGTGAAGC 60.974 63.158 0.00 0.00 0.00 3.86
1952 2082 1.973812 GGCAAGGTGAGGTGAAGCC 60.974 63.158 0.00 0.00 37.58 4.35
1954 2084 1.371183 CAAGGTGAGGTGAAGCCGA 59.629 57.895 0.00 0.00 43.70 5.54
1955 2085 0.250295 CAAGGTGAGGTGAAGCCGAA 60.250 55.000 0.00 0.00 43.70 4.30
1956 2086 0.035458 AAGGTGAGGTGAAGCCGAAG 59.965 55.000 0.00 0.00 43.70 3.79
1957 2087 0.832135 AGGTGAGGTGAAGCCGAAGA 60.832 55.000 0.00 0.00 43.70 2.87
1958 2088 0.250513 GGTGAGGTGAAGCCGAAGAT 59.749 55.000 0.00 0.00 43.70 2.40
1960 2090 0.391661 TGAGGTGAAGCCGAAGATGC 60.392 55.000 0.00 0.00 43.70 3.91
1961 2091 1.078143 AGGTGAAGCCGAAGATGCC 60.078 57.895 0.00 0.00 43.70 4.40
1962 2092 1.078143 GGTGAAGCCGAAGATGCCT 60.078 57.895 0.00 0.00 0.00 4.75
1963 2093 0.178068 GGTGAAGCCGAAGATGCCTA 59.822 55.000 0.00 0.00 0.00 3.93
1964 2094 1.202698 GGTGAAGCCGAAGATGCCTAT 60.203 52.381 0.00 0.00 0.00 2.57
1967 2097 2.147150 GAAGCCGAAGATGCCTATTCC 58.853 52.381 0.00 0.00 0.00 3.01
1969 2099 1.771255 AGCCGAAGATGCCTATTCCTT 59.229 47.619 0.00 0.00 0.00 3.36
1993 2126 4.581409 GGGAAGGTTACAGTTACAAAGCAA 59.419 41.667 0.00 0.00 0.00 3.91
2000 2133 3.131396 ACAGTTACAAAGCAAGACTCCG 58.869 45.455 0.00 0.00 0.00 4.63
2041 2174 7.581213 ATGTTTAATTATGGAGAAATCCGCA 57.419 32.000 0.00 0.00 0.00 5.69
2043 2176 7.479980 TGTTTAATTATGGAGAAATCCGCAAG 58.520 34.615 0.00 0.00 0.00 4.01
2044 2177 4.574599 AATTATGGAGAAATCCGCAAGC 57.425 40.909 0.00 0.00 0.00 4.01
2055 2188 1.660167 TCCGCAAGCAGATTGATGAG 58.340 50.000 1.54 0.00 41.83 2.90
2258 2397 1.833606 TGGAAACAGGCGAGTCCAA 59.166 52.632 0.00 0.00 37.22 3.53
2259 2398 0.534203 TGGAAACAGGCGAGTCCAAC 60.534 55.000 0.00 0.00 37.22 3.77
2260 2399 0.250338 GGAAACAGGCGAGTCCAACT 60.250 55.000 0.00 0.00 37.29 3.16
2261 2400 1.149148 GAAACAGGCGAGTCCAACTC 58.851 55.000 0.00 0.00 41.71 3.01
2262 2401 0.250338 AAACAGGCGAGTCCAACTCC 60.250 55.000 1.69 0.00 42.12 3.85
2263 2402 1.407656 AACAGGCGAGTCCAACTCCA 61.408 55.000 1.69 0.00 42.12 3.86
2544 2701 0.870313 AGGAGATATCAGGGGAGGCA 59.130 55.000 5.32 0.00 0.00 4.75
2547 2704 2.050144 GAGATATCAGGGGAGGCAACA 58.950 52.381 5.32 0.00 41.41 3.33
2847 3013 2.877786 TGCTGTCATCGAAGAAGCAAAA 59.122 40.909 18.45 3.57 43.58 2.44
2912 3078 2.011947 TGATGTTGCTGCTGCTATCAC 58.988 47.619 17.00 8.60 40.48 3.06
3009 3175 6.091555 AGGGATAGTGGATAAGATTAAGCCA 58.908 40.000 0.00 0.00 0.00 4.75
3016 3182 4.404394 TGGATAAGATTAAGCCACGTCTGA 59.596 41.667 0.00 0.00 0.00 3.27
3063 3229 5.583854 CCTCCAAGATGACAAAGACTATGTG 59.416 44.000 0.00 0.00 0.00 3.21
3069 3235 4.607293 TGACAAAGACTATGTGTCAGCT 57.393 40.909 10.83 0.00 45.02 4.24
3105 3271 3.823304 AGGAGTCCAGAAATGCTTTGAAC 59.177 43.478 12.86 0.00 0.00 3.18
3108 3274 4.985538 AGTCCAGAAATGCTTTGAACCTA 58.014 39.130 0.00 0.00 0.00 3.08
3157 3323 1.013596 TGTGTCCACAAAGAACAGCG 58.986 50.000 0.00 0.00 38.56 5.18
3201 3370 1.003812 CCACCGGGAGAACCAATAACA 59.996 52.381 6.32 0.00 40.22 2.41
3228 3397 5.194432 TCTCTAGTTGGACTCTACCATGAC 58.806 45.833 0.00 0.00 39.82 3.06
3276 3445 4.754618 CGGATGATTAATGGAAATGACGGA 59.245 41.667 0.00 0.00 0.00 4.69
3345 3514 5.944599 ACATGAGTTCTGCATGAAGATCTTT 59.055 36.000 14.41 4.55 44.49 2.52
3347 3516 5.311265 TGAGTTCTGCATGAAGATCTTTGT 58.689 37.500 14.41 0.00 35.01 2.83
3361 3530 7.877612 TGAAGATCTTTGTGTATGCTCTTTACA 59.122 33.333 9.87 0.00 0.00 2.41
3393 3562 3.580458 ACAGGAGCTATGAAGAACTGTGT 59.420 43.478 5.45 0.00 33.80 3.72
3413 3582 5.586243 TGTGTAAGCTAAATGAAGATCTGGC 59.414 40.000 0.00 0.00 0.00 4.85
3429 3598 3.190878 GCTCCCGCCAAGACATTG 58.809 61.111 0.00 0.00 36.09 2.82
3588 3760 3.741388 CGGAGGGGTTGATAACTAAGCAG 60.741 52.174 0.00 0.00 0.00 4.24
3643 3815 6.481644 GCAATGTTTTGACACCCTGATTAAAA 59.518 34.615 0.00 0.00 34.60 1.52
3644 3816 7.011857 GCAATGTTTTGACACCCTGATTAAAAA 59.988 33.333 0.00 0.00 34.60 1.94
4213 4391 8.873144 AGATTGAGAAAATGGAAAATTTGGAGA 58.127 29.630 0.00 0.00 0.00 3.71
4246 4424 3.743017 GGGCTTCAGGGGATGGCA 61.743 66.667 0.00 0.00 43.12 4.92
4291 4469 3.774766 TCTATGGCAACTAAGGAAGCTCA 59.225 43.478 0.00 0.00 37.61 4.26
4292 4470 2.949177 TGGCAACTAAGGAAGCTCAA 57.051 45.000 0.00 0.00 37.61 3.02
4323 4501 3.071023 TCGAAGACAGGAACAATCACCTT 59.929 43.478 0.00 0.00 33.91 3.50
4362 4540 4.770795 CCATCGGAGACCTAAAAGATTGT 58.229 43.478 0.00 0.00 42.51 2.71
4395 4573 9.170890 TCCCTTTCAATCACTATATCCTACAAT 57.829 33.333 0.00 0.00 0.00 2.71
4433 4611 2.928757 CTCTCTCCAACAAAGAGATGCG 59.071 50.000 3.49 0.00 46.11 4.73
4617 4816 2.161609 CGTGCTTCCCAAATTACACTCC 59.838 50.000 0.00 0.00 0.00 3.85
4788 5008 4.482990 AGATTGTTTTGTCCTCCACCAAT 58.517 39.130 0.00 0.00 0.00 3.16
4812 5032 4.473477 AAGGTTTCTTAGTGGGATCGAG 57.527 45.455 0.00 0.00 0.00 4.04
4883 5103 8.624776 CCTACTTTCATTTTCTCAAGACAAAGT 58.375 33.333 0.00 0.00 0.00 2.66
4893 5113 6.274157 TCTCAAGACAAAGTATCTCCTGAC 57.726 41.667 0.00 0.00 0.00 3.51
4956 5176 4.371855 CGAAGCTACCTTGTGAGTATGA 57.628 45.455 0.00 0.00 0.00 2.15
4957 5177 4.938080 CGAAGCTACCTTGTGAGTATGAT 58.062 43.478 0.00 0.00 0.00 2.45
4958 5178 4.742167 CGAAGCTACCTTGTGAGTATGATG 59.258 45.833 0.00 0.00 0.00 3.07
4959 5179 5.665459 GAAGCTACCTTGTGAGTATGATGT 58.335 41.667 0.00 0.00 0.00 3.06
4961 5181 6.150396 AGCTACCTTGTGAGTATGATGTAC 57.850 41.667 0.00 0.00 0.00 2.90
4962 5182 5.656859 AGCTACCTTGTGAGTATGATGTACA 59.343 40.000 0.00 0.00 0.00 2.90
4964 5184 6.816640 GCTACCTTGTGAGTATGATGTACAAA 59.183 38.462 0.00 0.00 31.67 2.83
4965 5185 7.495934 GCTACCTTGTGAGTATGATGTACAAAT 59.504 37.037 0.00 0.00 31.67 2.32
4966 5186 7.849804 ACCTTGTGAGTATGATGTACAAATC 57.150 36.000 0.00 0.00 31.67 2.17
5009 6573 4.510167 AGGGAGATGTACAAATCCTTGG 57.490 45.455 22.29 0.00 36.82 3.61
5064 6628 8.883954 TCTCAATCAAGTCTTATGATGATGAC 57.116 34.615 0.00 0.00 37.58 3.06
5083 6647 2.427453 GACGAAGGCCATCTAGTCTTCA 59.573 50.000 5.01 0.00 36.39 3.02
5142 6706 0.539051 AGTGTCCTACCATCAGCAGC 59.461 55.000 0.00 0.00 0.00 5.25
5259 6823 2.027377 ACTGAAGGAGATTGAGTGCAGG 60.027 50.000 0.00 0.00 33.70 4.85
5292 6856 4.040217 GTGCCATATCAGGTGAGAAGAGAT 59.960 45.833 0.00 0.00 0.00 2.75
5293 6857 5.244851 GTGCCATATCAGGTGAGAAGAGATA 59.755 44.000 0.00 0.00 0.00 1.98
5294 6858 5.244851 TGCCATATCAGGTGAGAAGAGATAC 59.755 44.000 0.00 0.00 0.00 2.24
5338 6902 3.127895 TGTTCTTACACACAAGCCACAAC 59.872 43.478 0.00 0.00 0.00 3.32
5361 6925 4.799564 ACAAGACCAAGCAAAAGAAACA 57.200 36.364 0.00 0.00 0.00 2.83
5394 6958 4.553330 AAAGGACGATGATACAAGGTGT 57.447 40.909 0.00 0.00 0.00 4.16
5539 7103 3.718434 TCCATTCATATCACTGCTTCCCT 59.282 43.478 0.00 0.00 0.00 4.20
5547 7111 0.250640 CACTGCTTCCCTGAACTGCT 60.251 55.000 0.00 0.00 0.00 4.24
5579 7143 1.168407 ATGCTATCCATGTGCGTGCC 61.168 55.000 0.00 0.00 31.48 5.01
5602 7166 5.163269 CCTGTCATGGTATCTCCTTCAATCA 60.163 44.000 0.00 0.00 37.07 2.57
5616 7180 4.275689 CCTTCAATCACTTGTGCTTGTGTA 59.724 41.667 14.34 4.39 35.82 2.90
5622 7186 3.944650 TCACTTGTGCTTGTGTACATGTT 59.055 39.130 2.30 0.00 42.13 2.71
5722 7286 4.330074 CGGAGGAACACTTGTATCAATGAC 59.670 45.833 0.00 0.00 0.00 3.06
5822 7386 6.516355 CGATTTCGTCATTGTGTTCTTGTAAG 59.484 38.462 0.00 0.00 34.11 2.34
5856 7420 3.543680 ATGCTATCCATATGCGTACCC 57.456 47.619 0.00 0.00 30.69 3.69
5857 7421 2.252714 TGCTATCCATATGCGTACCCA 58.747 47.619 0.00 0.00 0.00 4.51
5858 7422 2.233676 TGCTATCCATATGCGTACCCAG 59.766 50.000 0.00 0.00 0.00 4.45
5859 7423 2.418746 GCTATCCATATGCGTACCCAGG 60.419 54.545 0.00 0.00 0.00 4.45
5860 7424 0.984230 ATCCATATGCGTACCCAGGG 59.016 55.000 2.85 2.85 0.00 4.45
5861 7425 1.302511 CCATATGCGTACCCAGGGC 60.303 63.158 4.91 0.00 0.00 5.19
5862 7426 1.302511 CATATGCGTACCCAGGGCC 60.303 63.158 4.91 0.00 0.00 5.80
5863 7427 2.879233 ATATGCGTACCCAGGGCCG 61.879 63.158 4.91 9.83 0.00 6.13
5914 7478 4.522975 GGGCCCCCGAAATCCAGG 62.523 72.222 12.23 0.00 0.00 4.45
5919 7483 4.522975 CCCGAAATCCAGGGGCCC 62.523 72.222 17.12 17.12 43.90 5.80
5920 7484 4.522975 CCGAAATCCAGGGGCCCC 62.523 72.222 35.90 35.90 0.00 5.80
5922 7486 2.603580 GAAATCCAGGGGCCCCTC 59.396 66.667 42.42 25.19 46.28 4.30
5923 7487 3.029981 AAATCCAGGGGCCCCTCC 61.030 66.667 42.42 15.50 46.28 4.30
5936 7500 4.135153 CCTCCCACGGACTCGCAG 62.135 72.222 0.00 0.00 40.63 5.18
5937 7501 4.803426 CTCCCACGGACTCGCAGC 62.803 72.222 0.00 0.00 40.63 5.25
5939 7503 3.449227 CCCACGGACTCGCAGCTA 61.449 66.667 0.00 0.00 40.63 3.32
5940 7504 2.103143 CCACGGACTCGCAGCTAG 59.897 66.667 0.00 0.00 40.63 3.42
5941 7505 2.580867 CACGGACTCGCAGCTAGC 60.581 66.667 6.62 6.62 40.63 3.42
5942 7506 3.827898 ACGGACTCGCAGCTAGCC 61.828 66.667 12.13 0.00 41.38 3.93
5943 7507 4.577246 CGGACTCGCAGCTAGCCC 62.577 72.222 12.13 2.17 41.38 5.19
5944 7508 3.461773 GGACTCGCAGCTAGCCCA 61.462 66.667 12.13 0.00 41.38 5.36
5945 7509 2.801631 GGACTCGCAGCTAGCCCAT 61.802 63.158 12.13 0.00 41.38 4.00
5946 7510 1.464376 GGACTCGCAGCTAGCCCATA 61.464 60.000 12.13 0.00 41.38 2.74
5947 7511 0.038709 GACTCGCAGCTAGCCCATAG 60.039 60.000 12.13 7.14 41.38 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.222872 TGTGGTGATTTTAAATTGCCAAGATT 58.777 30.769 12.97 0.00 0.00 2.40
1 2 6.767456 TGTGGTGATTTTAAATTGCCAAGAT 58.233 32.000 12.97 0.00 0.00 2.40
2 3 6.166984 TGTGGTGATTTTAAATTGCCAAGA 57.833 33.333 12.97 4.22 0.00 3.02
3 4 6.427547 ACATGTGGTGATTTTAAATTGCCAAG 59.572 34.615 12.97 9.90 0.00 3.61
4 5 6.294473 ACATGTGGTGATTTTAAATTGCCAA 58.706 32.000 12.97 7.02 0.00 4.52
5 6 5.862845 ACATGTGGTGATTTTAAATTGCCA 58.137 33.333 0.00 9.08 0.00 4.92
22 23 0.240145 CTGCAACAGCTCCACATGTG 59.760 55.000 19.31 19.31 0.00 3.21
23 24 0.109153 TCTGCAACAGCTCCACATGT 59.891 50.000 0.00 0.00 0.00 3.21
24 25 0.803117 CTCTGCAACAGCTCCACATG 59.197 55.000 0.00 0.00 0.00 3.21
25 26 0.959372 GCTCTGCAACAGCTCCACAT 60.959 55.000 9.61 0.00 33.75 3.21
26 27 1.598962 GCTCTGCAACAGCTCCACA 60.599 57.895 9.61 0.00 33.75 4.17
27 28 1.575576 CTGCTCTGCAACAGCTCCAC 61.576 60.000 16.28 0.00 38.41 4.02
28 29 1.302271 CTGCTCTGCAACAGCTCCA 60.302 57.895 16.28 0.00 38.41 3.86
29 30 0.888285 AACTGCTCTGCAACAGCTCC 60.888 55.000 16.28 0.00 38.41 4.70
30 31 0.516439 GAACTGCTCTGCAACAGCTC 59.484 55.000 16.28 8.32 38.41 4.09
31 32 0.179037 TGAACTGCTCTGCAACAGCT 60.179 50.000 16.28 3.27 38.41 4.24
32 33 0.879765 ATGAACTGCTCTGCAACAGC 59.120 50.000 9.90 9.90 38.41 4.40
76 77 0.679002 AAGCACAGTAGGCATGGCTG 60.679 55.000 30.53 17.76 36.41 4.85
114 115 5.920903 AGGCATTCCATAAATCATGTTTGG 58.079 37.500 0.00 0.00 32.21 3.28
115 116 6.643770 GCTAGGCATTCCATAAATCATGTTTG 59.356 38.462 0.00 0.00 32.21 2.93
216 217 6.659668 ACAGTGCAAGTAGAACACTCTATAGA 59.340 38.462 1.69 1.69 42.59 1.98
250 251 4.448732 GCAAAATGAACTTGTGGGATGAAC 59.551 41.667 0.00 0.00 0.00 3.18
277 278 6.367374 TGAAGTTGTTATGGATGAGGTGTA 57.633 37.500 0.00 0.00 0.00 2.90
364 365 3.674528 ATCTATGGGAGATGCTGTTCG 57.325 47.619 0.00 0.00 43.71 3.95
436 451 4.036734 TGTTTCTTCAGTTCAGAACCATGC 59.963 41.667 9.85 0.00 29.70 4.06
505 524 4.154942 AGTCTGCCCATTCATTTTCTTGT 58.845 39.130 0.00 0.00 0.00 3.16
518 537 0.399091 ATGCCTAGCTAGTCTGCCCA 60.399 55.000 19.31 6.90 0.00 5.36
520 539 1.068194 CGTATGCCTAGCTAGTCTGCC 60.068 57.143 19.31 3.82 0.00 4.85
522 541 3.992260 AACGTATGCCTAGCTAGTCTG 57.008 47.619 19.31 5.62 0.00 3.51
591 618 1.376037 CTGACAGAAAGGGCCGGAC 60.376 63.158 5.05 0.00 0.00 4.79
867 968 5.252969 ACACATGACAATGCATTATGGTC 57.747 39.130 19.78 18.55 39.75 4.02
943 1052 7.403312 AGCTTATTGTATTATTGGTTGTGCA 57.597 32.000 0.00 0.00 0.00 4.57
949 1058 7.721399 AGCAAGCTAGCTTATTGTATTATTGGT 59.279 33.333 28.87 15.46 43.70 3.67
1116 1234 0.107508 GCTCCAGGAAGCTGTGCATA 60.108 55.000 0.00 0.00 39.27 3.14
1190 1308 0.320771 GACCTGCTTCATCCACGTGT 60.321 55.000 15.65 0.00 0.00 4.49
1260 1378 2.043752 TAGACCGCCGGATCACCA 60.044 61.111 11.71 0.00 35.59 4.17
1305 1423 1.920325 CCAGGAAGCCCACCAGAGA 60.920 63.158 0.00 0.00 33.88 3.10
1411 1529 1.945354 ATCTCCACGCCGTACCACAG 61.945 60.000 0.00 0.00 0.00 3.66
1414 1532 2.420568 GGATCTCCACGCCGTACCA 61.421 63.158 0.00 0.00 35.64 3.25
1453 1571 1.079127 ACGATGACGAGGGCAAAGG 60.079 57.895 0.00 0.00 42.66 3.11
1461 1579 1.543614 CAGCTTGAGACGATGACGAG 58.456 55.000 0.00 0.00 42.66 4.18
1462 1580 0.456824 GCAGCTTGAGACGATGACGA 60.457 55.000 0.00 0.00 42.66 4.20
1467 1585 1.449246 GCCAGCAGCTTGAGACGAT 60.449 57.895 0.00 0.00 38.99 3.73
1484 1602 6.648725 GTCTTCATCCTCCTTGTATTCTATGC 59.351 42.308 0.00 0.00 0.00 3.14
1487 1605 9.303116 GATAGTCTTCATCCTCCTTGTATTCTA 57.697 37.037 0.00 0.00 0.00 2.10
1506 1636 2.224161 GGCGGCTTGAATCTGATAGTCT 60.224 50.000 0.00 0.00 0.00 3.24
1524 1654 2.106683 GGGATCAGAACCGTTGGCG 61.107 63.158 0.00 0.00 37.95 5.69
1572 1702 1.025113 TCTCGGCACAGTACTCCTCG 61.025 60.000 0.00 0.00 0.00 4.63
1592 1722 2.724454 TGGCTAACTTCTCGACTAGCT 58.276 47.619 0.00 0.00 37.51 3.32
1593 1723 3.119424 AGTTGGCTAACTTCTCGACTAGC 60.119 47.826 10.03 0.00 44.57 3.42
1594 1724 4.416620 CAGTTGGCTAACTTCTCGACTAG 58.583 47.826 13.44 0.00 44.57 2.57
1595 1725 3.192844 CCAGTTGGCTAACTTCTCGACTA 59.807 47.826 13.44 0.00 44.57 2.59
1596 1726 2.028930 CCAGTTGGCTAACTTCTCGACT 60.029 50.000 13.44 0.00 44.57 4.18
1597 1727 2.338500 CCAGTTGGCTAACTTCTCGAC 58.662 52.381 13.44 0.00 44.57 4.20
1598 1728 2.743636 CCAGTTGGCTAACTTCTCGA 57.256 50.000 13.44 0.00 44.57 4.04
1645 1775 4.888038 CAATGGATGCCATGGATATACG 57.112 45.455 18.40 0.00 44.40 3.06
1701 1831 2.421877 AAGAGTCCTGTGCGACGGTG 62.422 60.000 0.00 0.00 37.85 4.94
1713 1843 1.609072 GTGGCAAACCTCAAAGAGTCC 59.391 52.381 0.00 0.00 36.63 3.85
1737 1867 2.456010 CAAACCGTGCGCTTAAAGTTT 58.544 42.857 9.73 8.73 0.00 2.66
1831 1961 3.244181 TGTTTCTGCTGCTCACACTCATA 60.244 43.478 0.00 0.00 0.00 2.15
1836 1966 0.040603 GCTGTTTCTGCTGCTCACAC 60.041 55.000 0.00 0.00 0.00 3.82
1839 1969 0.879090 CATGCTGTTTCTGCTGCTCA 59.121 50.000 0.00 0.00 34.93 4.26
1840 1970 1.130749 CTCATGCTGTTTCTGCTGCTC 59.869 52.381 0.00 0.00 34.93 4.26
1841 1971 1.166129 CTCATGCTGTTTCTGCTGCT 58.834 50.000 0.00 0.00 34.93 4.24
1842 1972 0.170561 CCTCATGCTGTTTCTGCTGC 59.829 55.000 0.00 0.00 0.00 5.25
1843 1973 1.817357 TCCTCATGCTGTTTCTGCTG 58.183 50.000 0.00 0.00 0.00 4.41
1844 1974 2.026542 TCATCCTCATGCTGTTTCTGCT 60.027 45.455 0.00 0.00 0.00 4.24
1845 1975 2.355132 CTCATCCTCATGCTGTTTCTGC 59.645 50.000 0.00 0.00 0.00 4.26
1846 1976 2.355132 GCTCATCCTCATGCTGTTTCTG 59.645 50.000 0.00 0.00 0.00 3.02
1847 1977 2.026542 TGCTCATCCTCATGCTGTTTCT 60.027 45.455 0.00 0.00 0.00 2.52
1848 1978 2.355132 CTGCTCATCCTCATGCTGTTTC 59.645 50.000 0.00 0.00 0.00 2.78
1849 1979 2.366533 CTGCTCATCCTCATGCTGTTT 58.633 47.619 0.00 0.00 0.00 2.83
1850 1980 2.017623 GCTGCTCATCCTCATGCTGTT 61.018 52.381 0.00 0.00 0.00 3.16
1851 1981 0.464013 GCTGCTCATCCTCATGCTGT 60.464 55.000 0.00 0.00 0.00 4.40
1852 1982 0.463833 TGCTGCTCATCCTCATGCTG 60.464 55.000 0.00 0.00 0.00 4.41
1853 1983 0.179043 CTGCTGCTCATCCTCATGCT 60.179 55.000 0.00 0.00 0.00 3.79
1854 1984 0.179054 TCTGCTGCTCATCCTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
1855 1985 2.327200 TTCTGCTGCTCATCCTCATG 57.673 50.000 0.00 0.00 0.00 3.07
1856 1986 2.026542 TGTTTCTGCTGCTCATCCTCAT 60.027 45.455 0.00 0.00 0.00 2.90
1857 1987 1.348696 TGTTTCTGCTGCTCATCCTCA 59.651 47.619 0.00 0.00 0.00 3.86
1858 1988 2.008329 CTGTTTCTGCTGCTCATCCTC 58.992 52.381 0.00 0.00 0.00 3.71
1859 1989 1.949547 GCTGTTTCTGCTGCTCATCCT 60.950 52.381 0.00 0.00 0.00 3.24
1860 1990 0.450983 GCTGTTTCTGCTGCTCATCC 59.549 55.000 0.00 0.00 0.00 3.51
1861 1991 1.162698 TGCTGTTTCTGCTGCTCATC 58.837 50.000 0.00 0.00 34.93 2.92
1862 1992 1.472878 CATGCTGTTTCTGCTGCTCAT 59.527 47.619 0.00 0.00 34.93 2.90
1863 1993 0.879090 CATGCTGTTTCTGCTGCTCA 59.121 50.000 0.00 0.00 34.93 4.26
1864 1994 1.130749 CTCATGCTGTTTCTGCTGCTC 59.869 52.381 0.00 0.00 34.93 4.26
1865 1995 1.166129 CTCATGCTGTTTCTGCTGCT 58.834 50.000 0.00 0.00 34.93 4.24
1866 1996 0.170561 CCTCATGCTGTTTCTGCTGC 59.829 55.000 0.00 0.00 0.00 5.25
1867 1997 1.817357 TCCTCATGCTGTTTCTGCTG 58.183 50.000 0.00 0.00 0.00 4.41
1868 1998 2.026542 TCATCCTCATGCTGTTTCTGCT 60.027 45.455 0.00 0.00 0.00 4.24
1869 1999 2.355132 CTCATCCTCATGCTGTTTCTGC 59.645 50.000 0.00 0.00 0.00 4.26
1870 2000 2.355132 GCTCATCCTCATGCTGTTTCTG 59.645 50.000 0.00 0.00 0.00 3.02
1871 2001 2.026542 TGCTCATCCTCATGCTGTTTCT 60.027 45.455 0.00 0.00 0.00 2.52
1872 2002 2.355132 CTGCTCATCCTCATGCTGTTTC 59.645 50.000 0.00 0.00 0.00 2.78
1873 2003 2.366533 CTGCTCATCCTCATGCTGTTT 58.633 47.619 0.00 0.00 0.00 2.83
1874 2004 2.017623 GCTGCTCATCCTCATGCTGTT 61.018 52.381 0.00 0.00 0.00 3.16
1875 2005 0.464013 GCTGCTCATCCTCATGCTGT 60.464 55.000 0.00 0.00 0.00 4.40
1876 2006 0.463833 TGCTGCTCATCCTCATGCTG 60.464 55.000 0.00 0.00 0.00 4.41
1877 2007 0.179043 CTGCTGCTCATCCTCATGCT 60.179 55.000 0.00 0.00 0.00 3.79
1878 2008 0.179054 TCTGCTGCTCATCCTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
1879 2009 2.327200 TTCTGCTGCTCATCCTCATG 57.673 50.000 0.00 0.00 0.00 3.07
1880 2010 2.026542 TGTTTCTGCTGCTCATCCTCAT 60.027 45.455 0.00 0.00 0.00 2.90
1881 2011 1.348696 TGTTTCTGCTGCTCATCCTCA 59.651 47.619 0.00 0.00 0.00 3.86
1882 2012 2.008329 CTGTTTCTGCTGCTCATCCTC 58.992 52.381 0.00 0.00 0.00 3.71
1883 2013 1.949547 GCTGTTTCTGCTGCTCATCCT 60.950 52.381 0.00 0.00 0.00 3.24
1884 2014 0.450983 GCTGTTTCTGCTGCTCATCC 59.549 55.000 0.00 0.00 0.00 3.51
1885 2015 1.162698 TGCTGTTTCTGCTGCTCATC 58.837 50.000 0.00 0.00 34.93 2.92
1886 2016 1.472878 CATGCTGTTTCTGCTGCTCAT 59.527 47.619 0.00 0.00 34.93 2.90
1887 2017 0.879090 CATGCTGTTTCTGCTGCTCA 59.121 50.000 0.00 0.00 34.93 4.26
1888 2018 1.130749 CTCATGCTGTTTCTGCTGCTC 59.869 52.381 0.00 0.00 34.93 4.26
1889 2019 1.166129 CTCATGCTGTTTCTGCTGCT 58.834 50.000 0.00 0.00 34.93 4.24
1890 2020 0.170561 CCTCATGCTGTTTCTGCTGC 59.829 55.000 0.00 0.00 0.00 5.25
1891 2021 1.817357 TCCTCATGCTGTTTCTGCTG 58.183 50.000 0.00 0.00 0.00 4.41
1892 2022 2.026542 TCATCCTCATGCTGTTTCTGCT 60.027 45.455 0.00 0.00 0.00 4.24
1893 2023 2.355132 CTCATCCTCATGCTGTTTCTGC 59.645 50.000 0.00 0.00 0.00 4.26
1894 2024 2.355132 GCTCATCCTCATGCTGTTTCTG 59.645 50.000 0.00 0.00 0.00 3.02
1895 2025 2.026542 TGCTCATCCTCATGCTGTTTCT 60.027 45.455 0.00 0.00 0.00 2.52
1896 2026 2.355132 CTGCTCATCCTCATGCTGTTTC 59.645 50.000 0.00 0.00 0.00 2.78
1897 2027 2.366533 CTGCTCATCCTCATGCTGTTT 58.633 47.619 0.00 0.00 0.00 2.83
1898 2028 2.017623 GCTGCTCATCCTCATGCTGTT 61.018 52.381 0.00 0.00 0.00 3.16
1899 2029 0.464013 GCTGCTCATCCTCATGCTGT 60.464 55.000 0.00 0.00 0.00 4.40
1900 2030 0.463833 TGCTGCTCATCCTCATGCTG 60.464 55.000 0.00 0.00 0.00 4.41
1901 2031 0.179043 CTGCTGCTCATCCTCATGCT 60.179 55.000 0.00 0.00 0.00 3.79
1902 2032 0.179054 TCTGCTGCTCATCCTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
1903 2033 2.327200 TTCTGCTGCTCATCCTCATG 57.673 50.000 0.00 0.00 0.00 3.07
1904 2034 2.239150 ACTTTCTGCTGCTCATCCTCAT 59.761 45.455 0.00 0.00 0.00 2.90
1905 2035 1.627329 ACTTTCTGCTGCTCATCCTCA 59.373 47.619 0.00 0.00 0.00 3.86
1906 2036 2.278854 GACTTTCTGCTGCTCATCCTC 58.721 52.381 0.00 0.00 0.00 3.71
1907 2037 1.627329 TGACTTTCTGCTGCTCATCCT 59.373 47.619 0.00 0.00 0.00 3.24
1908 2038 1.736681 GTGACTTTCTGCTGCTCATCC 59.263 52.381 0.00 0.00 0.00 3.51
1909 2039 2.415857 CTGTGACTTTCTGCTGCTCATC 59.584 50.000 0.00 0.00 0.00 2.92
1910 2040 2.424557 CTGTGACTTTCTGCTGCTCAT 58.575 47.619 0.00 0.00 0.00 2.90
1921 2051 1.898574 CTTGCCCGCCTGTGACTTT 60.899 57.895 0.00 0.00 0.00 2.66
1935 2065 2.328099 CGGCTTCACCTCACCTTGC 61.328 63.158 0.00 0.00 35.61 4.01
1941 2071 0.391661 GCATCTTCGGCTTCACCTCA 60.392 55.000 0.00 0.00 35.61 3.86
1950 2080 1.876156 CAAGGAATAGGCATCTTCGGC 59.124 52.381 0.00 0.00 0.00 5.54
1951 2081 2.498167 CCAAGGAATAGGCATCTTCGG 58.502 52.381 0.00 0.00 0.00 4.30
1952 2082 2.104792 TCCCAAGGAATAGGCATCTTCG 59.895 50.000 0.00 0.00 0.00 3.79
1954 2084 4.176120 CTTCCCAAGGAATAGGCATCTT 57.824 45.455 0.00 0.00 41.23 2.40
1955 2085 3.872459 CTTCCCAAGGAATAGGCATCT 57.128 47.619 0.00 0.00 41.23 2.90
1967 2097 5.278315 GCTTTGTAACTGTAACCTTCCCAAG 60.278 44.000 0.00 0.00 0.00 3.61
1969 2099 4.139038 GCTTTGTAACTGTAACCTTCCCA 58.861 43.478 0.00 0.00 0.00 4.37
1993 2126 3.614092 TCAGTATTTCGTACCGGAGTCT 58.386 45.455 9.46 0.00 33.58 3.24
2016 2149 8.684386 TGCGGATTTCTCCATAATTAAACATA 57.316 30.769 0.00 0.00 42.19 2.29
2020 2153 6.096141 TGCTTGCGGATTTCTCCATAATTAAA 59.904 34.615 0.00 0.00 42.19 1.52
2041 2174 5.124645 GTTCCTGATCTCATCAATCTGCTT 58.875 41.667 0.00 0.00 39.11 3.91
2043 2176 4.449131 TGTTCCTGATCTCATCAATCTGC 58.551 43.478 0.00 0.00 39.11 4.26
2044 2177 5.527951 CCTTGTTCCTGATCTCATCAATCTG 59.472 44.000 0.00 0.00 39.11 2.90
2055 2188 3.594603 TCTCGAACCTTGTTCCTGATC 57.405 47.619 1.66 0.00 0.00 2.92
2183 2316 1.124477 CCCCTCTGAGGATAGTGGCC 61.124 65.000 25.18 0.00 37.67 5.36
2258 2397 3.454082 GAGATGAATCTGGGTCTTGGAGT 59.546 47.826 0.00 0.00 37.25 3.85
2259 2398 3.492309 CGAGATGAATCTGGGTCTTGGAG 60.492 52.174 0.00 0.00 37.25 3.86
2260 2399 2.432146 CGAGATGAATCTGGGTCTTGGA 59.568 50.000 0.00 0.00 37.25 3.53
2261 2400 2.432146 TCGAGATGAATCTGGGTCTTGG 59.568 50.000 0.00 0.00 37.25 3.61
2262 2401 3.808466 TCGAGATGAATCTGGGTCTTG 57.192 47.619 0.00 0.00 37.25 3.02
2263 2402 6.678568 ATTATCGAGATGAATCTGGGTCTT 57.321 37.500 0.00 0.00 37.25 3.01
2385 2524 1.002430 TCTTTGATGTGAGCCTCGCTT 59.998 47.619 6.84 0.00 39.88 4.68
2544 2701 3.292936 GCAGCAGCAGCACCTGTT 61.293 61.111 4.63 0.00 45.49 3.16
2547 2704 2.401699 TAACAGCAGCAGCAGCACCT 62.402 55.000 12.92 0.00 45.49 4.00
2847 3013 8.435982 CCTGATACTATTCCCTTCATCTTTTCT 58.564 37.037 0.00 0.00 0.00 2.52
2912 3078 4.262164 CCAGGGTTTCTTTGATGGTTTCAG 60.262 45.833 0.00 0.00 35.27 3.02
2965 3131 1.057275 TTGGTGTACAGCAGACCCCA 61.057 55.000 25.27 11.07 39.95 4.96
3009 3175 5.701290 CAGGGTCTTCTTATTTTTCAGACGT 59.299 40.000 0.00 0.00 35.65 4.34
3016 3182 9.634021 GAGGATAATCAGGGTCTTCTTATTTTT 57.366 33.333 0.00 0.00 0.00 1.94
3063 3229 1.450312 CCACCGGGATTCAGCTGAC 60.450 63.158 18.03 5.76 35.59 3.51
3088 3254 6.603201 CCTAATAGGTTCAAAGCATTTCTGGA 59.397 38.462 0.00 0.00 35.03 3.86
3105 3271 1.475751 CCAGGTGCACAGCCTAATAGG 60.476 57.143 20.43 0.99 38.80 2.57
3108 3274 1.379044 GCCAGGTGCACAGCCTAAT 60.379 57.895 20.43 0.00 40.77 1.73
3157 3323 6.092670 GGATAGCAAAAATCTTTGGCCTTTTC 59.907 38.462 3.32 0.00 41.96 2.29
3201 3370 5.580998 TGGTAGAGTCCAACTAGAGAACAT 58.419 41.667 0.00 0.00 34.24 2.71
3260 3429 5.123227 GGATGTCTCCGTCATTTCCATTAA 58.877 41.667 0.00 0.00 0.00 1.40
3276 3445 1.718280 GTAGAATCCCCGGGATGTCT 58.282 55.000 26.32 22.46 42.27 3.41
3285 3454 3.877508 CCAAGATTTCACGTAGAATCCCC 59.122 47.826 15.52 0.00 35.83 4.81
3288 3457 3.938963 TGGCCAAGATTTCACGTAGAATC 59.061 43.478 0.61 12.67 35.83 2.52
3347 3516 4.532916 TGGGGTTAGTGTAAAGAGCATACA 59.467 41.667 0.00 0.00 0.00 2.29
3361 3530 2.337359 TAGCTCCTGTTGGGGTTAGT 57.663 50.000 0.00 0.00 35.83 2.24
3393 3562 5.455326 GGGAGCCAGATCTTCATTTAGCTTA 60.455 44.000 0.00 0.00 0.00 3.09
3413 3582 3.909662 CCAATGTCTTGGCGGGAG 58.090 61.111 0.00 0.00 45.28 4.30
3429 3598 6.936900 TGATCATATTCTTAGCTTTACTGCCC 59.063 38.462 0.00 0.00 0.00 5.36
3588 3760 3.958860 ACTGCAGTGGCCCAGTCC 61.959 66.667 20.97 0.00 37.77 3.85
4213 4391 5.263599 TGAAGCCCTGACATTTGACAATAT 58.736 37.500 0.00 0.00 0.00 1.28
4246 4424 8.133024 AGATGTCTTATCTCTTTCAACTCACT 57.867 34.615 0.00 0.00 0.00 3.41
4291 4469 4.819105 TCCTGTCTTCGATAACCACATT 57.181 40.909 0.00 0.00 0.00 2.71
4292 4470 4.020573 TGTTCCTGTCTTCGATAACCACAT 60.021 41.667 0.00 0.00 0.00 3.21
4323 4501 0.392706 TGGCTCGAAGCAACTTCTCA 59.607 50.000 5.85 0.00 44.75 3.27
4347 4525 5.046231 GGACTGGAGACAATCTTTTAGGTCT 60.046 44.000 0.00 0.00 42.90 3.85
4362 4540 3.251484 AGTGATTGAAAGGGACTGGAGA 58.749 45.455 0.00 0.00 40.86 3.71
4433 4611 5.305585 TGGGACTTTGTCTTAACAGATCAC 58.694 41.667 0.00 0.00 36.57 3.06
4617 4816 1.845266 CATTGGATCGGAGTCTGACG 58.155 55.000 3.08 0.00 0.00 4.35
4761 4981 4.821805 GTGGAGGACAAAACAATCTTCTCA 59.178 41.667 0.00 0.00 0.00 3.27
4788 5008 7.064866 TCTCGATCCCACTAAGAAACCTTATA 58.935 38.462 0.00 0.00 0.00 0.98
4883 5103 1.207089 CGGTGCTTTGGTCAGGAGATA 59.793 52.381 0.00 0.00 0.00 1.98
4893 5113 0.036010 ATCCACTCTCGGTGCTTTGG 60.036 55.000 0.00 0.00 44.08 3.28
4945 5165 7.882791 ACAAGGATTTGTACATCATACTCACAA 59.117 33.333 0.00 0.00 45.45 3.33
4946 5166 7.334171 CACAAGGATTTGTACATCATACTCACA 59.666 37.037 0.00 0.00 45.53 3.58
4948 5168 7.619965 TCACAAGGATTTGTACATCATACTCA 58.380 34.615 0.00 0.00 45.53 3.41
4951 5171 9.547753 AGTATCACAAGGATTTGTACATCATAC 57.452 33.333 0.00 0.00 45.53 2.39
4952 5172 9.764363 GAGTATCACAAGGATTTGTACATCATA 57.236 33.333 0.00 0.00 45.53 2.15
4953 5173 8.267183 TGAGTATCACAAGGATTTGTACATCAT 58.733 33.333 0.00 0.00 45.53 2.45
4954 5174 7.619965 TGAGTATCACAAGGATTTGTACATCA 58.380 34.615 0.00 0.00 45.53 3.07
5064 6628 3.190874 GTTGAAGACTAGATGGCCTTCG 58.809 50.000 12.65 2.81 38.20 3.79
5083 6647 6.550854 TCAAGATTTGGGAACTCATCTTTGTT 59.449 34.615 0.00 0.00 37.57 2.83
5215 6779 1.135315 CGGAAGGTTGTCAATGCCATG 60.135 52.381 0.00 0.00 0.00 3.66
5216 6780 1.176527 CGGAAGGTTGTCAATGCCAT 58.823 50.000 0.00 0.00 0.00 4.40
5259 6823 0.179018 GATATGGCACCTGGTCACCC 60.179 60.000 11.86 6.81 31.00 4.61
5271 6835 4.888326 ATCTCTTCTCACCTGATATGGC 57.112 45.455 0.00 0.00 0.00 4.40
5292 6856 2.393557 GGCTTTATGCGCTGCAGTA 58.606 52.632 16.64 2.57 43.65 2.74
5293 6857 3.190878 GGCTTTATGCGCTGCAGT 58.809 55.556 16.64 0.00 43.65 4.40
5338 6902 4.928615 TGTTTCTTTTGCTTGGTCTTGTTG 59.071 37.500 0.00 0.00 0.00 3.33
5394 6958 1.377202 GAAGCGGGAGATTGGTGCA 60.377 57.895 0.00 0.00 39.41 4.57
5434 6998 7.031975 GCCGATTCTTCATCTTTCTTTTCAAT 58.968 34.615 0.00 0.00 0.00 2.57
5445 7009 0.531532 CCAGCGCCGATTCTTCATCT 60.532 55.000 2.29 0.00 0.00 2.90
5539 7103 0.395586 ACAAACAGGCCAGCAGTTCA 60.396 50.000 5.01 0.00 0.00 3.18
5579 7143 5.757320 GTGATTGAAGGAGATACCATGACAG 59.243 44.000 0.00 0.00 42.04 3.51
5602 7166 4.157656 ACAAACATGTACACAAGCACAAGT 59.842 37.500 0.00 0.00 0.00 3.16
5722 7286 2.240493 ACTCCTCACACCAGTTTTCG 57.760 50.000 0.00 0.00 0.00 3.46
5781 7345 0.667487 ATCGCTTGACACGTCACAGG 60.667 55.000 0.00 0.00 39.66 4.00
5790 7354 2.805671 ACAATGACGAAATCGCTTGACA 59.194 40.909 15.61 5.51 44.43 3.58
5822 7386 4.020218 TGGATAGCATACTTACATCAGCCC 60.020 45.833 0.00 0.00 0.00 5.19
5897 7461 4.522975 CCTGGATTTCGGGGGCCC 62.523 72.222 15.76 15.76 38.27 5.80
5902 7466 4.522975 GGGCCCCTGGATTTCGGG 62.523 72.222 12.23 0.00 41.69 5.14
5903 7467 4.522975 GGGGCCCCTGGATTTCGG 62.523 72.222 35.49 0.00 0.00 4.30
5904 7468 3.420482 AGGGGCCCCTGGATTTCG 61.420 66.667 43.96 0.00 46.22 3.46
5919 7483 4.135153 CTGCGAGTCCGTGGGAGG 62.135 72.222 0.00 0.00 38.24 4.30
5920 7484 4.803426 GCTGCGAGTCCGTGGGAG 62.803 72.222 0.00 0.00 38.24 4.30
5921 7485 3.931190 TAGCTGCGAGTCCGTGGGA 62.931 63.158 0.00 0.00 38.24 4.37
5922 7486 3.417275 CTAGCTGCGAGTCCGTGGG 62.417 68.421 0.00 0.00 38.24 4.61
5923 7487 2.103143 CTAGCTGCGAGTCCGTGG 59.897 66.667 0.00 0.00 38.24 4.94
5924 7488 2.580867 GCTAGCTGCGAGTCCGTG 60.581 66.667 7.70 0.00 38.24 4.94
5925 7489 3.827898 GGCTAGCTGCGAGTCCGT 61.828 66.667 15.72 0.00 44.05 4.69
5926 7490 4.577246 GGGCTAGCTGCGAGTCCG 62.577 72.222 17.46 0.00 44.05 4.79
5927 7491 1.464376 TATGGGCTAGCTGCGAGTCC 61.464 60.000 24.10 24.10 44.05 3.85
5928 7492 0.038709 CTATGGGCTAGCTGCGAGTC 60.039 60.000 15.72 8.74 44.05 3.36
5929 7493 2.045280 CTATGGGCTAGCTGCGAGT 58.955 57.895 15.72 0.00 44.05 4.18
5930 7494 4.983628 CTATGGGCTAGCTGCGAG 57.016 61.111 15.72 5.33 44.05 5.03


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

AutoCloner maintained by Alex Coulton.