Multiple sequence alignment - TraesCS2A01G566900

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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 TraesCS2A01G566900 chr2A 100.000 2222 0 0 1 2222 765851485 765849264 0.000000e+00 4104
1 TraesCS2A01G566900 chr2A 96.306 1949 62 5 1 1943 48258085 48260029 0.000000e+00 3192
2 TraesCS2A01G566900 chr2A 95.823 407 14 3 1539 1943 48259195 48259600 0.000000e+00 654
3 TraesCS2A01G566900 chr2A 92.636 258 19 0 1965 2222 714000912 714001169 2.690000e-99 372
4 TraesCS2A01G566900 chr3A 96.870 1949 55 3 1 1943 684743936 684745884 0.000000e+00 3256
5 TraesCS2A01G566900 chr3A 95.466 1544 65 2 1 1540 459623250 459621708 0.000000e+00 2459
6 TraesCS2A01G566900 chr3A 95.084 1546 68 4 4 1541 11605922 11604377 0.000000e+00 2427
7 TraesCS2A01G566900 chr3A 94.955 1546 70 4 4 1541 11599034 11597489 0.000000e+00 2416
8 TraesCS2A01G566900 chr3A 92.248 258 20 0 1965 2222 658313005 658313262 1.250000e-97 366
9 TraesCS2A01G566900 chr4B 96.768 1949 57 3 1 1943 604142980 604144928 0.000000e+00 3245
10 TraesCS2A01G566900 chr4B 95.593 1543 63 2 1 1539 85985492 85987033 0.000000e+00 2468
11 TraesCS2A01G566900 chr4B 96.069 407 14 2 1539 1943 604144093 604144499 0.000000e+00 662
12 TraesCS2A01G566900 chr4B 92.636 258 17 2 1965 2222 508522510 508522765 9.690000e-99 370
13 TraesCS2A01G566900 chr6A 96.619 1952 60 3 1 1946 531392493 531390542 0.000000e+00 3234
14 TraesCS2A01G566900 chr6A 95.854 410 15 2 1539 1946 531391380 531390971 0.000000e+00 662
15 TraesCS2A01G566900 chr6A 92.636 258 17 2 1965 2222 592442969 592442714 9.690000e-99 370
16 TraesCS2A01G566900 chr6A 92.248 258 19 1 1965 2222 513105402 513105658 4.510000e-97 364
17 TraesCS2A01G566900 chr5A 95.023 1547 71 2 1 1541 23905554 23904008 0.000000e+00 2425
18 TraesCS2A01G566900 chr5B 95.610 410 16 2 1539 1946 492815826 492815417 0.000000e+00 656
19 TraesCS2A01G566900 chr5B 92.248 258 18 2 1965 2222 660346559 660346304 4.510000e-97 364
20 TraesCS2A01G566900 chr3B 95.599 409 16 2 1537 1943 572677095 572677503 0.000000e+00 654
21 TraesCS2A01G566900 chr3B 92.636 258 17 2 1965 2222 636770580 636770325 9.690000e-99 370
22 TraesCS2A01G566900 chr2B 92.636 258 17 2 1965 2222 77778056 77777801 9.690000e-99 370
23 TraesCS2A01G566900 chr4A 92.248 258 19 1 1965 2222 721824331 721824587 4.510000e-97 364


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 TraesCS2A01G566900 chr2A 765849264 765851485 2221 True 4104.0 4104 100.0000 1 2222 1 chr2A.!!$R1 2221
1 TraesCS2A01G566900 chr2A 48258085 48260029 1944 False 1923.0 3192 96.0645 1 1943 2 chr2A.!!$F2 1942
2 TraesCS2A01G566900 chr3A 684743936 684745884 1948 False 3256.0 3256 96.8700 1 1943 1 chr3A.!!$F2 1942
3 TraesCS2A01G566900 chr3A 459621708 459623250 1542 True 2459.0 2459 95.4660 1 1540 1 chr3A.!!$R3 1539
4 TraesCS2A01G566900 chr3A 11604377 11605922 1545 True 2427.0 2427 95.0840 4 1541 1 chr3A.!!$R2 1537
5 TraesCS2A01G566900 chr3A 11597489 11599034 1545 True 2416.0 2416 94.9550 4 1541 1 chr3A.!!$R1 1537
6 TraesCS2A01G566900 chr4B 85985492 85987033 1541 False 2468.0 2468 95.5930 1 1539 1 chr4B.!!$F1 1538
7 TraesCS2A01G566900 chr4B 604142980 604144928 1948 False 1953.5 3245 96.4185 1 1943 2 chr4B.!!$F3 1942
8 TraesCS2A01G566900 chr6A 531390542 531392493 1951 True 1948.0 3234 96.2365 1 1946 2 chr6A.!!$R2 1945
9 TraesCS2A01G566900 chr5A 23904008 23905554 1546 True 2425.0 2425 95.0230 1 1541 1 chr5A.!!$R1 1540

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
666 671 2.197465 AGGGGATGGTGTTACCTCTTC 58.803 52.381 0.0 0.0 39.58 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2158 0.099436 GCTTGCTAATTGACCAGGCG 59.901 55.0 0.0 0.0 0.0 5.52 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
42 43 7.918562 GCCTTAAACAACATGTCTTCAAGTTTA 59.081 33.333 0.00 5.84 34.00 2.01
592 597 5.242838 CACCTTAATTCCAGGTAAAGCAACA 59.757 40.000 8.59 0.00 43.30 3.33
638 643 8.911965 TGATCAAATAGCACAAATAAGGCAATA 58.088 29.630 0.00 0.00 0.00 1.90
666 671 2.197465 AGGGGATGGTGTTACCTCTTC 58.803 52.381 0.00 0.00 39.58 2.87
730 735 3.426695 CCAAAGAAGCCGACATGAACATC 60.427 47.826 0.00 0.00 0.00 3.06
962 972 3.016736 CCCACTGAACAGACACTTTGTT 58.983 45.455 8.87 0.00 41.21 2.83
1033 1043 2.673200 GGAGAGCATGCCCTGGACA 61.673 63.158 15.66 0.00 0.00 4.02
1047 1057 1.208052 CTGGACATGGATGGAGTCGTT 59.792 52.381 0.00 0.00 33.18 3.85
1049 1059 1.207089 GGACATGGATGGAGTCGTTGA 59.793 52.381 0.00 0.00 33.18 3.18
1125 1135 1.202722 GGTGTGTTCCCGGAGAAAGAA 60.203 52.381 0.73 0.00 35.85 2.52
1286 1297 5.378230 AGGATGGATGCACTCTGATTTAA 57.622 39.130 0.00 0.00 0.00 1.52
1605 1617 4.429522 TGCATGATGGCGGCAGGT 62.430 61.111 19.29 0.00 36.28 4.00
1838 1851 4.488126 GCTAAGTGCACACAGAAAATGA 57.512 40.909 21.04 0.00 42.31 2.57
1914 1927 5.105269 TGGTATTGGATCTGTGTACGCTTTA 60.105 40.000 8.10 0.00 0.00 1.85
1943 1956 6.811665 GGTGTGCTTAAAGAAGTTCTTGTTTT 59.188 34.615 18.70 5.88 36.71 2.43
1946 1959 9.515020 TGTGCTTAAAGAAGTTCTTGTTTTATG 57.485 29.630 18.70 10.23 36.71 1.90
1947 1960 8.968242 GTGCTTAAAGAAGTTCTTGTTTTATGG 58.032 33.333 18.70 5.42 36.71 2.74
1948 1961 8.141268 TGCTTAAAGAAGTTCTTGTTTTATGGG 58.859 33.333 18.70 4.04 36.71 4.00
1949 1962 7.598869 GCTTAAAGAAGTTCTTGTTTTATGGGG 59.401 37.037 18.70 2.80 36.71 4.96
1950 1963 8.541899 TTAAAGAAGTTCTTGTTTTATGGGGT 57.458 30.769 18.70 1.49 36.71 4.95
1951 1964 6.405278 AAGAAGTTCTTGTTTTATGGGGTG 57.595 37.500 17.35 0.00 34.98 4.61
1952 1965 5.454966 AGAAGTTCTTGTTTTATGGGGTGT 58.545 37.500 0.00 0.00 0.00 4.16
1953 1966 6.607019 AGAAGTTCTTGTTTTATGGGGTGTA 58.393 36.000 0.00 0.00 0.00 2.90
1954 1967 6.489022 AGAAGTTCTTGTTTTATGGGGTGTAC 59.511 38.462 0.00 0.00 0.00 2.90
1955 1968 4.758165 AGTTCTTGTTTTATGGGGTGTACG 59.242 41.667 0.00 0.00 0.00 3.67
1956 1969 3.075884 TCTTGTTTTATGGGGTGTACGC 58.924 45.455 0.00 0.00 0.00 4.42
1957 1970 2.863132 TGTTTTATGGGGTGTACGCT 57.137 45.000 6.35 0.00 0.00 5.07
1958 1971 3.143211 TGTTTTATGGGGTGTACGCTT 57.857 42.857 6.35 0.00 0.00 4.68
1959 1972 3.488363 TGTTTTATGGGGTGTACGCTTT 58.512 40.909 6.35 0.00 0.00 3.51
1960 1973 4.649692 TGTTTTATGGGGTGTACGCTTTA 58.350 39.130 6.35 0.00 0.00 1.85
1961 1974 4.455190 TGTTTTATGGGGTGTACGCTTTAC 59.545 41.667 6.35 0.00 0.00 2.01
1973 1986 2.594529 CGCTTTACGTGAGCAAACAT 57.405 45.000 20.85 0.00 40.13 2.71
1974 1987 2.916111 CGCTTTACGTGAGCAAACATT 58.084 42.857 20.85 0.00 40.13 2.71
1975 1988 4.060288 CGCTTTACGTGAGCAAACATTA 57.940 40.909 20.85 0.00 40.13 1.90
1976 1989 4.647964 CGCTTTACGTGAGCAAACATTAT 58.352 39.130 20.85 0.00 40.13 1.28
1977 1990 5.086058 CGCTTTACGTGAGCAAACATTATT 58.914 37.500 20.85 0.00 40.13 1.40
1978 1991 5.567534 CGCTTTACGTGAGCAAACATTATTT 59.432 36.000 20.85 0.00 40.13 1.40
1979 1992 6.087555 CGCTTTACGTGAGCAAACATTATTTT 59.912 34.615 20.85 0.00 40.13 1.82
1980 1993 7.358023 CGCTTTACGTGAGCAAACATTATTTTT 60.358 33.333 20.85 0.00 40.13 1.94
2000 2013 6.732896 TTTTTCTAAGTGCACCCCATAAAA 57.267 33.333 14.63 12.15 0.00 1.52
2001 2014 5.715434 TTTCTAAGTGCACCCCATAAAAC 57.285 39.130 14.63 0.00 0.00 2.43
2002 2015 4.374689 TCTAAGTGCACCCCATAAAACA 57.625 40.909 14.63 0.00 0.00 2.83
2003 2016 4.929479 TCTAAGTGCACCCCATAAAACAT 58.071 39.130 14.63 0.00 0.00 2.71
2004 2017 6.068461 TCTAAGTGCACCCCATAAAACATA 57.932 37.500 14.63 0.00 0.00 2.29
2005 2018 5.883673 TCTAAGTGCACCCCATAAAACATAC 59.116 40.000 14.63 0.00 0.00 2.39
2006 2019 4.040936 AGTGCACCCCATAAAACATACA 57.959 40.909 14.63 0.00 0.00 2.29
2007 2020 3.761752 AGTGCACCCCATAAAACATACAC 59.238 43.478 14.63 0.00 0.00 2.90
2008 2021 2.750166 TGCACCCCATAAAACATACACG 59.250 45.455 0.00 0.00 0.00 4.49
2009 2022 3.011119 GCACCCCATAAAACATACACGA 58.989 45.455 0.00 0.00 0.00 4.35
2010 2023 3.440872 GCACCCCATAAAACATACACGAA 59.559 43.478 0.00 0.00 0.00 3.85
2011 2024 4.097286 GCACCCCATAAAACATACACGAAT 59.903 41.667 0.00 0.00 0.00 3.34
2012 2025 5.297278 GCACCCCATAAAACATACACGAATA 59.703 40.000 0.00 0.00 0.00 1.75
2013 2026 6.721321 CACCCCATAAAACATACACGAATAC 58.279 40.000 0.00 0.00 0.00 1.89
2014 2027 6.316640 CACCCCATAAAACATACACGAATACA 59.683 38.462 0.00 0.00 0.00 2.29
2015 2028 7.012894 CACCCCATAAAACATACACGAATACAT 59.987 37.037 0.00 0.00 0.00 2.29
2016 2029 7.227910 ACCCCATAAAACATACACGAATACATC 59.772 37.037 0.00 0.00 0.00 3.06
2017 2030 7.227711 CCCCATAAAACATACACGAATACATCA 59.772 37.037 0.00 0.00 0.00 3.07
2018 2031 8.783093 CCCATAAAACATACACGAATACATCAT 58.217 33.333 0.00 0.00 0.00 2.45
2019 2032 9.811655 CCATAAAACATACACGAATACATCATC 57.188 33.333 0.00 0.00 0.00 2.92
2022 2035 8.492673 AAAACATACACGAATACATCATCACT 57.507 30.769 0.00 0.00 0.00 3.41
2023 2036 7.468922 AACATACACGAATACATCATCACTG 57.531 36.000 0.00 0.00 0.00 3.66
2024 2037 5.463392 ACATACACGAATACATCATCACTGC 59.537 40.000 0.00 0.00 0.00 4.40
2025 2038 3.860641 ACACGAATACATCATCACTGCA 58.139 40.909 0.00 0.00 0.00 4.41
2026 2039 4.445453 ACACGAATACATCATCACTGCAT 58.555 39.130 0.00 0.00 0.00 3.96
2027 2040 4.271776 ACACGAATACATCATCACTGCATG 59.728 41.667 0.00 0.00 0.00 4.06
2028 2041 4.508861 CACGAATACATCATCACTGCATGA 59.491 41.667 0.00 0.00 43.13 3.07
2030 2043 5.761726 ACGAATACATCATCACTGCATGATT 59.238 36.000 0.00 0.61 46.54 2.57
2031 2044 6.930722 ACGAATACATCATCACTGCATGATTA 59.069 34.615 0.00 3.24 46.54 1.75
2032 2045 7.442062 ACGAATACATCATCACTGCATGATTAA 59.558 33.333 0.00 2.73 46.54 1.40
2033 2046 8.448615 CGAATACATCATCACTGCATGATTAAT 58.551 33.333 0.00 0.00 46.54 1.40
2034 2047 9.770503 GAATACATCATCACTGCATGATTAATC 57.229 33.333 8.60 8.60 46.54 1.75
2035 2048 6.570672 ACATCATCACTGCATGATTAATCC 57.429 37.500 12.90 0.00 46.54 3.01
2036 2049 5.475909 ACATCATCACTGCATGATTAATCCC 59.524 40.000 12.90 2.47 46.54 3.85
2037 2050 5.051409 TCATCACTGCATGATTAATCCCA 57.949 39.130 12.90 6.68 46.54 4.37
2038 2051 5.637127 TCATCACTGCATGATTAATCCCAT 58.363 37.500 12.90 0.00 46.54 4.00
2039 2052 6.072649 TCATCACTGCATGATTAATCCCATT 58.927 36.000 12.90 0.02 46.54 3.16
2040 2053 7.232910 TCATCACTGCATGATTAATCCCATTA 58.767 34.615 12.90 0.00 46.54 1.90
2041 2054 7.724951 TCATCACTGCATGATTAATCCCATTAA 59.275 33.333 12.90 0.00 46.54 1.40
2042 2055 7.894753 TCACTGCATGATTAATCCCATTAAA 57.105 32.000 12.90 0.00 38.15 1.52
2043 2056 7.715657 TCACTGCATGATTAATCCCATTAAAC 58.284 34.615 12.90 0.00 38.15 2.01
2044 2057 7.560991 TCACTGCATGATTAATCCCATTAAACT 59.439 33.333 12.90 0.00 38.15 2.66
2045 2058 7.864379 CACTGCATGATTAATCCCATTAAACTC 59.136 37.037 12.90 0.00 38.15 3.01
2046 2059 7.560991 ACTGCATGATTAATCCCATTAAACTCA 59.439 33.333 12.90 0.00 38.15 3.41
2047 2060 8.303780 TGCATGATTAATCCCATTAAACTCAA 57.696 30.769 12.90 0.00 38.15 3.02
2048 2061 8.926374 TGCATGATTAATCCCATTAAACTCAAT 58.074 29.630 12.90 0.00 38.15 2.57
2049 2062 9.415544 GCATGATTAATCCCATTAAACTCAATC 57.584 33.333 12.90 0.00 38.15 2.67
2055 2068 7.568199 AATCCCATTAAACTCAATCTAACGG 57.432 36.000 0.00 0.00 0.00 4.44
2056 2069 4.879545 TCCCATTAAACTCAATCTAACGGC 59.120 41.667 0.00 0.00 0.00 5.68
2057 2070 4.881850 CCCATTAAACTCAATCTAACGGCT 59.118 41.667 0.00 0.00 0.00 5.52
2058 2071 6.053005 CCCATTAAACTCAATCTAACGGCTA 58.947 40.000 0.00 0.00 0.00 3.93
2059 2072 6.202954 CCCATTAAACTCAATCTAACGGCTAG 59.797 42.308 0.00 0.00 0.00 3.42
2060 2073 6.292919 CCATTAAACTCAATCTAACGGCTAGC 60.293 42.308 6.04 6.04 0.00 3.42
2061 2074 2.892784 ACTCAATCTAACGGCTAGCC 57.107 50.000 24.75 24.75 0.00 3.93
2062 2075 2.389715 ACTCAATCTAACGGCTAGCCT 58.610 47.619 30.55 16.25 0.00 4.58
2063 2076 2.766828 ACTCAATCTAACGGCTAGCCTT 59.233 45.455 30.55 23.63 0.00 4.35
2064 2077 3.958798 ACTCAATCTAACGGCTAGCCTTA 59.041 43.478 30.55 23.50 0.00 2.69
2065 2078 4.404715 ACTCAATCTAACGGCTAGCCTTAA 59.595 41.667 30.55 14.50 0.00 1.85
2066 2079 5.070580 ACTCAATCTAACGGCTAGCCTTAAT 59.929 40.000 30.55 15.96 0.00 1.40
2067 2080 5.539048 TCAATCTAACGGCTAGCCTTAATC 58.461 41.667 30.55 4.19 0.00 1.75
2068 2081 5.304614 TCAATCTAACGGCTAGCCTTAATCT 59.695 40.000 30.55 9.72 0.00 2.40
2069 2082 6.492429 TCAATCTAACGGCTAGCCTTAATCTA 59.508 38.462 30.55 10.37 0.00 1.98
2070 2083 6.912951 ATCTAACGGCTAGCCTTAATCTAA 57.087 37.500 30.55 9.44 0.00 2.10
2071 2084 6.912951 TCTAACGGCTAGCCTTAATCTAAT 57.087 37.500 30.55 7.85 0.00 1.73
2072 2085 6.921914 TCTAACGGCTAGCCTTAATCTAATC 58.078 40.000 30.55 0.55 0.00 1.75
2073 2086 5.810080 AACGGCTAGCCTTAATCTAATCT 57.190 39.130 30.55 0.55 0.00 2.40
2074 2087 6.912951 AACGGCTAGCCTTAATCTAATCTA 57.087 37.500 30.55 0.00 0.00 1.98
2075 2088 7.483580 AACGGCTAGCCTTAATCTAATCTAT 57.516 36.000 30.55 0.00 0.00 1.98
2076 2089 7.483580 ACGGCTAGCCTTAATCTAATCTATT 57.516 36.000 30.55 0.00 0.00 1.73
2077 2090 7.548967 ACGGCTAGCCTTAATCTAATCTATTC 58.451 38.462 30.55 0.00 0.00 1.75
2078 2091 7.397761 ACGGCTAGCCTTAATCTAATCTATTCT 59.602 37.037 30.55 0.00 0.00 2.40
2079 2092 7.918562 CGGCTAGCCTTAATCTAATCTATTCTC 59.081 40.741 30.55 0.00 0.00 2.87
2080 2093 8.977412 GGCTAGCCTTAATCTAATCTATTCTCT 58.023 37.037 27.17 0.00 0.00 3.10
2081 2094 9.801873 GCTAGCCTTAATCTAATCTATTCTCTG 57.198 37.037 2.29 0.00 0.00 3.35
2084 2097 9.153479 AGCCTTAATCTAATCTATTCTCTGTGT 57.847 33.333 0.00 0.00 0.00 3.72
2085 2098 9.202273 GCCTTAATCTAATCTATTCTCTGTGTG 57.798 37.037 0.00 0.00 0.00 3.82
2086 2099 9.202273 CCTTAATCTAATCTATTCTCTGTGTGC 57.798 37.037 0.00 0.00 0.00 4.57
2087 2100 9.755804 CTTAATCTAATCTATTCTCTGTGTGCA 57.244 33.333 0.00 0.00 0.00 4.57
2088 2101 9.534565 TTAATCTAATCTATTCTCTGTGTGCAC 57.465 33.333 10.75 10.75 0.00 4.57
2089 2102 6.782082 TCTAATCTATTCTCTGTGTGCACT 57.218 37.500 19.41 0.00 0.00 4.40
2090 2103 7.175347 TCTAATCTATTCTCTGTGTGCACTT 57.825 36.000 19.41 1.31 0.00 3.16
2091 2104 8.293699 TCTAATCTATTCTCTGTGTGCACTTA 57.706 34.615 19.41 5.91 0.00 2.24
2092 2105 8.409371 TCTAATCTATTCTCTGTGTGCACTTAG 58.591 37.037 19.41 15.55 0.00 2.18
2093 2106 4.748892 TCTATTCTCTGTGTGCACTTAGC 58.251 43.478 19.41 6.38 45.96 3.09
2110 2123 8.382003 GCACTTAGCAATTTACATTAACTGAC 57.618 34.615 0.00 0.00 44.79 3.51
2111 2124 7.484959 GCACTTAGCAATTTACATTAACTGACC 59.515 37.037 0.00 0.00 44.79 4.02
2112 2125 7.692291 CACTTAGCAATTTACATTAACTGACCG 59.308 37.037 0.00 0.00 0.00 4.79
2113 2126 7.389607 ACTTAGCAATTTACATTAACTGACCGT 59.610 33.333 0.00 0.00 0.00 4.83
2114 2127 8.774890 TTAGCAATTTACATTAACTGACCGTA 57.225 30.769 0.00 0.00 0.00 4.02
2115 2128 7.068692 AGCAATTTACATTAACTGACCGTAC 57.931 36.000 0.00 0.00 0.00 3.67
2116 2129 6.877322 AGCAATTTACATTAACTGACCGTACT 59.123 34.615 0.00 0.00 0.00 2.73
2117 2130 7.064253 AGCAATTTACATTAACTGACCGTACTC 59.936 37.037 0.00 0.00 0.00 2.59
2118 2131 7.675637 GCAATTTACATTAACTGACCGTACTCC 60.676 40.741 0.00 0.00 0.00 3.85
2119 2132 5.981088 TTACATTAACTGACCGTACTCCA 57.019 39.130 0.00 0.00 0.00 3.86
2120 2133 4.184079 ACATTAACTGACCGTACTCCAC 57.816 45.455 0.00 0.00 0.00 4.02
2121 2134 3.056322 ACATTAACTGACCGTACTCCACC 60.056 47.826 0.00 0.00 0.00 4.61
2122 2135 1.167851 TAACTGACCGTACTCCACCG 58.832 55.000 0.00 0.00 0.00 4.94
2123 2136 0.825010 AACTGACCGTACTCCACCGT 60.825 55.000 0.00 0.00 0.00 4.83
2124 2137 1.211969 CTGACCGTACTCCACCGTG 59.788 63.158 0.00 0.00 0.00 4.94
2125 2138 1.228215 TGACCGTACTCCACCGTGA 60.228 57.895 0.00 0.00 0.00 4.35
2126 2139 0.822944 TGACCGTACTCCACCGTGAA 60.823 55.000 0.00 0.00 0.00 3.18
2127 2140 0.109412 GACCGTACTCCACCGTGAAG 60.109 60.000 0.00 0.00 0.00 3.02
2129 2142 1.246056 CCGTACTCCACCGTGAAGGA 61.246 60.000 0.00 0.00 45.00 3.36
2130 2143 0.599558 CGTACTCCACCGTGAAGGAA 59.400 55.000 0.00 0.00 45.00 3.36
2131 2144 1.000060 CGTACTCCACCGTGAAGGAAA 60.000 52.381 0.00 0.00 45.00 3.13
2132 2145 2.546373 CGTACTCCACCGTGAAGGAAAA 60.546 50.000 0.00 0.00 45.00 2.29
2133 2146 2.951229 ACTCCACCGTGAAGGAAAAT 57.049 45.000 0.00 0.00 45.00 1.82
2134 2147 4.618927 CGTACTCCACCGTGAAGGAAAATA 60.619 45.833 0.00 0.00 45.00 1.40
2135 2148 4.569719 ACTCCACCGTGAAGGAAAATAT 57.430 40.909 0.00 0.00 45.00 1.28
2136 2149 4.261801 ACTCCACCGTGAAGGAAAATATG 58.738 43.478 0.00 0.00 45.00 1.78
2137 2150 4.019681 ACTCCACCGTGAAGGAAAATATGA 60.020 41.667 0.00 0.00 45.00 2.15
2138 2151 4.912586 TCCACCGTGAAGGAAAATATGAA 58.087 39.130 0.00 0.00 45.00 2.57
2139 2152 5.317808 TCCACCGTGAAGGAAAATATGAAA 58.682 37.500 0.00 0.00 45.00 2.69
2140 2153 5.414454 TCCACCGTGAAGGAAAATATGAAAG 59.586 40.000 0.00 0.00 45.00 2.62
2141 2154 5.183140 CCACCGTGAAGGAAAATATGAAAGT 59.817 40.000 0.00 0.00 45.00 2.66
2142 2155 6.314784 CACCGTGAAGGAAAATATGAAAGTC 58.685 40.000 0.00 0.00 45.00 3.01
2143 2156 5.414765 ACCGTGAAGGAAAATATGAAAGTCC 59.585 40.000 0.00 0.00 45.00 3.85
2144 2157 5.414454 CCGTGAAGGAAAATATGAAAGTCCA 59.586 40.000 0.00 0.00 45.00 4.02
2145 2158 6.314784 CGTGAAGGAAAATATGAAAGTCCAC 58.685 40.000 0.00 0.00 0.00 4.02
2146 2159 6.314784 GTGAAGGAAAATATGAAAGTCCACG 58.685 40.000 0.00 0.00 0.00 4.94
2147 2160 4.965119 AGGAAAATATGAAAGTCCACGC 57.035 40.909 0.00 0.00 0.00 5.34
2148 2161 3.694566 AGGAAAATATGAAAGTCCACGCC 59.305 43.478 0.00 0.00 0.00 5.68
2149 2162 3.694566 GGAAAATATGAAAGTCCACGCCT 59.305 43.478 0.00 0.00 0.00 5.52
2150 2163 4.438744 GGAAAATATGAAAGTCCACGCCTG 60.439 45.833 0.00 0.00 0.00 4.85
2151 2164 2.332063 ATATGAAAGTCCACGCCTGG 57.668 50.000 0.00 0.00 39.23 4.45
2152 2165 0.981183 TATGAAAGTCCACGCCTGGT 59.019 50.000 1.44 0.00 38.90 4.00
2153 2166 0.321653 ATGAAAGTCCACGCCTGGTC 60.322 55.000 1.44 0.00 38.90 4.02
2154 2167 1.070786 GAAAGTCCACGCCTGGTCA 59.929 57.895 1.44 0.00 38.90 4.02
2155 2168 0.534203 GAAAGTCCACGCCTGGTCAA 60.534 55.000 1.44 0.00 38.90 3.18
2156 2169 0.110486 AAAGTCCACGCCTGGTCAAT 59.890 50.000 1.44 0.00 38.90 2.57
2157 2170 0.110486 AAGTCCACGCCTGGTCAATT 59.890 50.000 1.44 0.00 38.90 2.32
2158 2171 0.981183 AGTCCACGCCTGGTCAATTA 59.019 50.000 1.44 0.00 38.90 1.40
2159 2172 1.066143 AGTCCACGCCTGGTCAATTAG 60.066 52.381 1.44 0.00 38.90 1.73
2160 2173 0.392461 TCCACGCCTGGTCAATTAGC 60.392 55.000 1.44 0.00 38.90 3.09
2161 2174 0.676466 CCACGCCTGGTCAATTAGCA 60.676 55.000 0.00 0.00 32.03 3.49
2162 2175 1.164411 CACGCCTGGTCAATTAGCAA 58.836 50.000 0.00 0.00 34.56 3.91
2163 2176 1.131126 CACGCCTGGTCAATTAGCAAG 59.869 52.381 0.00 0.00 34.56 4.01
2164 2177 0.099436 CGCCTGGTCAATTAGCAAGC 59.901 55.000 0.00 0.00 39.23 4.01
2165 2178 1.467920 GCCTGGTCAATTAGCAAGCT 58.532 50.000 0.00 0.00 39.46 3.74
2166 2179 2.643551 GCCTGGTCAATTAGCAAGCTA 58.356 47.619 0.00 0.00 39.46 3.32
2167 2180 3.217626 GCCTGGTCAATTAGCAAGCTAT 58.782 45.455 2.16 0.00 39.46 2.97
2168 2181 4.389374 GCCTGGTCAATTAGCAAGCTATA 58.611 43.478 2.16 0.00 39.46 1.31
2169 2182 4.821805 GCCTGGTCAATTAGCAAGCTATAA 59.178 41.667 2.16 0.00 39.46 0.98
2170 2183 5.474876 GCCTGGTCAATTAGCAAGCTATAAT 59.525 40.000 2.16 0.00 39.46 1.28
2171 2184 6.348868 GCCTGGTCAATTAGCAAGCTATAATC 60.349 42.308 2.16 0.00 39.46 1.75
2172 2185 6.712095 CCTGGTCAATTAGCAAGCTATAATCA 59.288 38.462 2.16 0.00 34.56 2.57
2173 2186 7.308229 CCTGGTCAATTAGCAAGCTATAATCAC 60.308 40.741 2.16 0.00 34.56 3.06
2174 2187 6.202762 TGGTCAATTAGCAAGCTATAATCACG 59.797 38.462 2.16 0.00 31.13 4.35
2175 2188 6.347725 GGTCAATTAGCAAGCTATAATCACGG 60.348 42.308 2.16 0.00 0.00 4.94
2176 2189 6.423905 GTCAATTAGCAAGCTATAATCACGGA 59.576 38.462 2.16 0.00 0.00 4.69
2177 2190 6.423905 TCAATTAGCAAGCTATAATCACGGAC 59.576 38.462 2.16 0.00 0.00 4.79
2178 2191 3.819564 AGCAAGCTATAATCACGGACA 57.180 42.857 0.00 0.00 0.00 4.02
2179 2192 3.458189 AGCAAGCTATAATCACGGACAC 58.542 45.455 0.00 0.00 0.00 3.67
2180 2193 3.118775 AGCAAGCTATAATCACGGACACA 60.119 43.478 0.00 0.00 0.00 3.72
2181 2194 3.809832 GCAAGCTATAATCACGGACACAT 59.190 43.478 0.00 0.00 0.00 3.21
2182 2195 4.084328 GCAAGCTATAATCACGGACACATC 60.084 45.833 0.00 0.00 0.00 3.06
2183 2196 4.258702 AGCTATAATCACGGACACATCC 57.741 45.455 0.00 0.00 42.28 3.51
2184 2197 3.898123 AGCTATAATCACGGACACATCCT 59.102 43.478 0.00 0.00 43.73 3.24
2185 2198 5.077564 AGCTATAATCACGGACACATCCTA 58.922 41.667 0.00 0.00 43.73 2.94
2186 2199 5.717178 AGCTATAATCACGGACACATCCTAT 59.283 40.000 0.00 0.00 43.73 2.57
2187 2200 6.211584 AGCTATAATCACGGACACATCCTATT 59.788 38.462 0.00 0.00 43.73 1.73
2188 2201 7.396339 AGCTATAATCACGGACACATCCTATTA 59.604 37.037 0.00 0.00 43.73 0.98
2189 2202 8.033038 GCTATAATCACGGACACATCCTATTAA 58.967 37.037 0.00 0.00 43.73 1.40
2190 2203 9.574458 CTATAATCACGGACACATCCTATTAAG 57.426 37.037 0.00 0.00 43.73 1.85
2191 2204 6.479972 AATCACGGACACATCCTATTAAGA 57.520 37.500 0.00 0.00 43.73 2.10
2192 2205 5.925506 TCACGGACACATCCTATTAAGAA 57.074 39.130 0.00 0.00 43.73 2.52
2193 2206 6.288941 TCACGGACACATCCTATTAAGAAA 57.711 37.500 0.00 0.00 43.73 2.52
2194 2207 6.103997 TCACGGACACATCCTATTAAGAAAC 58.896 40.000 0.00 0.00 43.73 2.78
2195 2208 6.070995 TCACGGACACATCCTATTAAGAAACT 60.071 38.462 0.00 0.00 43.73 2.66
2196 2209 7.123098 TCACGGACACATCCTATTAAGAAACTA 59.877 37.037 0.00 0.00 43.73 2.24
2197 2210 7.762615 CACGGACACATCCTATTAAGAAACTAA 59.237 37.037 0.00 0.00 43.73 2.24
2198 2211 8.483758 ACGGACACATCCTATTAAGAAACTAAT 58.516 33.333 0.00 0.00 43.73 1.73
2199 2212 8.979574 CGGACACATCCTATTAAGAAACTAATC 58.020 37.037 0.00 0.00 43.73 1.75
2200 2213 9.832445 GGACACATCCTATTAAGAAACTAATCA 57.168 33.333 0.00 0.00 42.45 2.57
2202 2215 9.314321 ACACATCCTATTAAGAAACTAATCACG 57.686 33.333 0.00 0.00 0.00 4.35
2203 2216 8.765219 CACATCCTATTAAGAAACTAATCACGG 58.235 37.037 0.00 0.00 0.00 4.94
2204 2217 8.701895 ACATCCTATTAAGAAACTAATCACGGA 58.298 33.333 0.00 0.00 0.00 4.69
2205 2218 8.979574 CATCCTATTAAGAAACTAATCACGGAC 58.020 37.037 0.00 0.00 0.00 4.79
2206 2219 8.070034 TCCTATTAAGAAACTAATCACGGACA 57.930 34.615 0.00 0.00 0.00 4.02
2207 2220 7.977853 TCCTATTAAGAAACTAATCACGGACAC 59.022 37.037 0.00 0.00 0.00 3.67
2208 2221 7.762615 CCTATTAAGAAACTAATCACGGACACA 59.237 37.037 0.00 0.00 0.00 3.72
2209 2222 9.314321 CTATTAAGAAACTAATCACGGACACAT 57.686 33.333 0.00 0.00 0.00 3.21
2210 2223 7.591006 TTAAGAAACTAATCACGGACACATC 57.409 36.000 0.00 0.00 0.00 3.06
2211 2224 5.407407 AGAAACTAATCACGGACACATCT 57.593 39.130 0.00 0.00 0.00 2.90
2212 2225 6.525578 AGAAACTAATCACGGACACATCTA 57.474 37.500 0.00 0.00 0.00 1.98
2213 2226 6.931838 AGAAACTAATCACGGACACATCTAA 58.068 36.000 0.00 0.00 0.00 2.10
2214 2227 7.556844 AGAAACTAATCACGGACACATCTAAT 58.443 34.615 0.00 0.00 0.00 1.73
2215 2228 8.041323 AGAAACTAATCACGGACACATCTAATT 58.959 33.333 0.00 0.00 0.00 1.40
2216 2229 9.309516 GAAACTAATCACGGACACATCTAATTA 57.690 33.333 0.00 0.00 0.00 1.40
2217 2230 9.832445 AAACTAATCACGGACACATCTAATTAT 57.168 29.630 0.00 0.00 0.00 1.28
2218 2231 9.832445 AACTAATCACGGACACATCTAATTATT 57.168 29.630 0.00 0.00 0.00 1.40
2221 2234 8.833231 AATCACGGACACATCTAATTATTAGG 57.167 34.615 11.54 0.32 34.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.687780 TGATCCAACATATCTGCAGTCATT 58.312 37.500 14.67 0.00 0.00 2.57
114 115 7.505585 TCATGACAGAGAAACCAAATACCTTTT 59.494 33.333 0.00 0.00 0.00 2.27
235 240 4.652822 AGAAACTAATCCGGCTGAGTTTT 58.347 39.130 19.52 8.94 41.10 2.43
236 241 4.287766 AGAAACTAATCCGGCTGAGTTT 57.712 40.909 18.78 18.78 43.11 2.66
349 354 4.499357 GGGTCACATGACTCCGTAACTATC 60.499 50.000 11.63 0.00 44.20 2.08
592 597 6.871492 TGATCAGTGTGTGTTTTACGTATGAT 59.129 34.615 0.00 0.00 0.00 2.45
638 643 4.079958 GGTAACACCATCCCCTTGATTAGT 60.080 45.833 0.00 0.00 38.42 2.24
666 671 6.348458 CCATATGCATTAAACTGGACCGTATG 60.348 42.308 3.54 0.00 0.00 2.39
712 717 2.234661 TCTGATGTTCATGTCGGCTTCT 59.765 45.455 0.00 0.00 0.00 2.85
730 735 4.815308 CAGAGTCTATTTCCCATGCTTCTG 59.185 45.833 0.00 0.00 0.00 3.02
1033 1043 3.430929 GCTACTTCAACGACTCCATCCAT 60.431 47.826 0.00 0.00 0.00 3.41
1047 1057 0.108615 GCTCTTCTGCCGCTACTTCA 60.109 55.000 0.00 0.00 0.00 3.02
1049 1059 1.153745 CGCTCTTCTGCCGCTACTT 60.154 57.895 0.00 0.00 0.00 2.24
1077 1087 0.721718 CCGCCATCGTCTTCTGTTTC 59.278 55.000 0.00 0.00 0.00 2.78
1105 1115 0.395312 TCTTTCTCCGGGAACACACC 59.605 55.000 0.00 0.00 33.13 4.16
1371 1382 6.714810 ACTTAGCAATTTACATTGACTGACCA 59.285 34.615 5.78 0.00 42.35 4.02
1544 1555 1.546476 GAGGAGCTTCGTCTTTCTCCA 59.454 52.381 9.47 0.00 45.69 3.86
1546 1557 1.902840 CGAGGAGCTTCGTCTTTCTC 58.097 55.000 0.00 0.00 35.91 2.87
1605 1617 0.253044 AGGAAGCTAATCGCAAGCCA 59.747 50.000 0.00 0.00 41.02 4.75
1914 1927 3.525800 ACTTCTTTAAGCACACCCCAT 57.474 42.857 0.00 0.00 36.05 4.00
1943 1956 2.582728 CGTAAAGCGTACACCCCATA 57.417 50.000 0.00 0.00 35.54 2.74
1954 1967 2.594529 ATGTTTGCTCACGTAAAGCG 57.405 45.000 15.07 0.00 42.83 4.68
1955 1968 6.927933 AAATAATGTTTGCTCACGTAAAGC 57.072 33.333 13.65 13.65 40.26 3.51
1977 1990 6.098409 TGTTTTATGGGGTGCACTTAGAAAAA 59.902 34.615 17.98 14.55 0.00 1.94
1978 1991 5.598830 TGTTTTATGGGGTGCACTTAGAAAA 59.401 36.000 17.98 14.88 0.00 2.29
1979 1992 5.141182 TGTTTTATGGGGTGCACTTAGAAA 58.859 37.500 17.98 10.02 0.00 2.52
1980 1993 4.730966 TGTTTTATGGGGTGCACTTAGAA 58.269 39.130 17.98 4.26 0.00 2.10
1981 1994 4.374689 TGTTTTATGGGGTGCACTTAGA 57.625 40.909 17.98 0.00 0.00 2.10
1982 1995 5.650266 TGTATGTTTTATGGGGTGCACTTAG 59.350 40.000 17.98 0.00 0.00 2.18
1983 1996 5.416326 GTGTATGTTTTATGGGGTGCACTTA 59.584 40.000 17.98 3.67 0.00 2.24
1984 1997 4.219725 GTGTATGTTTTATGGGGTGCACTT 59.780 41.667 17.98 2.17 0.00 3.16
1985 1998 3.761752 GTGTATGTTTTATGGGGTGCACT 59.238 43.478 17.98 0.00 0.00 4.40
1986 1999 3.426963 CGTGTATGTTTTATGGGGTGCAC 60.427 47.826 8.80 8.80 0.00 4.57
1987 2000 2.750166 CGTGTATGTTTTATGGGGTGCA 59.250 45.455 0.00 0.00 0.00 4.57
1988 2001 3.011119 TCGTGTATGTTTTATGGGGTGC 58.989 45.455 0.00 0.00 0.00 5.01
1989 2002 5.828299 ATTCGTGTATGTTTTATGGGGTG 57.172 39.130 0.00 0.00 0.00 4.61
1990 2003 6.416415 TGTATTCGTGTATGTTTTATGGGGT 58.584 36.000 0.00 0.00 0.00 4.95
1991 2004 6.928979 TGTATTCGTGTATGTTTTATGGGG 57.071 37.500 0.00 0.00 0.00 4.96
1992 2005 8.148807 TGATGTATTCGTGTATGTTTTATGGG 57.851 34.615 0.00 0.00 0.00 4.00
1993 2006 9.811655 GATGATGTATTCGTGTATGTTTTATGG 57.188 33.333 0.00 0.00 0.00 2.74
1996 2009 9.594478 AGTGATGATGTATTCGTGTATGTTTTA 57.406 29.630 0.00 0.00 0.00 1.52
1997 2010 8.390354 CAGTGATGATGTATTCGTGTATGTTTT 58.610 33.333 0.00 0.00 0.00 2.43
1998 2011 7.465916 GCAGTGATGATGTATTCGTGTATGTTT 60.466 37.037 0.00 0.00 0.00 2.83
1999 2012 6.018751 GCAGTGATGATGTATTCGTGTATGTT 60.019 38.462 0.00 0.00 0.00 2.71
2000 2013 5.463392 GCAGTGATGATGTATTCGTGTATGT 59.537 40.000 0.00 0.00 0.00 2.29
2001 2014 5.463061 TGCAGTGATGATGTATTCGTGTATG 59.537 40.000 0.00 0.00 0.00 2.39
2002 2015 5.600696 TGCAGTGATGATGTATTCGTGTAT 58.399 37.500 0.00 0.00 0.00 2.29
2003 2016 5.004922 TGCAGTGATGATGTATTCGTGTA 57.995 39.130 0.00 0.00 0.00 2.90
2004 2017 3.860641 TGCAGTGATGATGTATTCGTGT 58.139 40.909 0.00 0.00 0.00 4.49
2005 2018 4.508861 TCATGCAGTGATGATGTATTCGTG 59.491 41.667 0.00 0.00 0.00 4.35
2006 2019 4.696455 TCATGCAGTGATGATGTATTCGT 58.304 39.130 0.00 0.00 0.00 3.85
2007 2020 5.857822 ATCATGCAGTGATGATGTATTCG 57.142 39.130 13.79 0.00 45.76 3.34
2008 2021 9.770503 GATTAATCATGCAGTGATGATGTATTC 57.229 33.333 10.68 11.63 46.80 1.75
2009 2022 8.737175 GGATTAATCATGCAGTGATGATGTATT 58.263 33.333 17.07 6.60 46.80 1.89
2010 2023 7.338703 GGGATTAATCATGCAGTGATGATGTAT 59.661 37.037 17.07 11.93 46.80 2.29
2011 2024 6.656270 GGGATTAATCATGCAGTGATGATGTA 59.344 38.462 17.07 9.05 46.80 2.29
2012 2025 5.475909 GGGATTAATCATGCAGTGATGATGT 59.524 40.000 17.07 9.84 46.80 3.06
2013 2026 5.475564 TGGGATTAATCATGCAGTGATGATG 59.524 40.000 17.07 5.29 46.80 3.07
2014 2027 5.637127 TGGGATTAATCATGCAGTGATGAT 58.363 37.500 17.07 10.48 46.80 2.45
2015 2028 5.051409 TGGGATTAATCATGCAGTGATGA 57.949 39.130 17.07 0.87 46.80 2.92
2016 2029 5.977489 ATGGGATTAATCATGCAGTGATG 57.023 39.130 17.07 0.00 46.80 3.07
2018 2031 7.560991 AGTTTAATGGGATTAATCATGCAGTGA 59.439 33.333 17.07 0.00 42.06 3.41
2019 2032 7.719483 AGTTTAATGGGATTAATCATGCAGTG 58.281 34.615 17.07 0.00 34.92 3.66
2020 2033 7.560991 TGAGTTTAATGGGATTAATCATGCAGT 59.439 33.333 17.07 0.24 34.92 4.40
2021 2034 7.944061 TGAGTTTAATGGGATTAATCATGCAG 58.056 34.615 17.07 0.00 34.92 4.41
2022 2035 7.894753 TGAGTTTAATGGGATTAATCATGCA 57.105 32.000 17.07 0.00 34.92 3.96
2023 2036 9.415544 GATTGAGTTTAATGGGATTAATCATGC 57.584 33.333 17.07 0.01 34.92 4.06
2029 2042 9.116067 CCGTTAGATTGAGTTTAATGGGATTAA 57.884 33.333 0.00 0.00 32.34 1.40
2030 2043 7.227910 GCCGTTAGATTGAGTTTAATGGGATTA 59.772 37.037 0.00 0.00 35.13 1.75
2031 2044 6.039382 GCCGTTAGATTGAGTTTAATGGGATT 59.961 38.462 0.00 0.00 35.13 3.01
2032 2045 5.531287 GCCGTTAGATTGAGTTTAATGGGAT 59.469 40.000 0.00 0.00 35.13 3.85
2033 2046 4.879545 GCCGTTAGATTGAGTTTAATGGGA 59.120 41.667 0.00 0.00 35.13 4.37
2034 2047 4.881850 AGCCGTTAGATTGAGTTTAATGGG 59.118 41.667 0.00 0.00 35.13 4.00
2035 2048 6.292919 GCTAGCCGTTAGATTGAGTTTAATGG 60.293 42.308 2.29 0.00 36.81 3.16
2036 2049 6.292919 GGCTAGCCGTTAGATTGAGTTTAATG 60.293 42.308 20.16 0.00 0.00 1.90
2037 2050 5.758784 GGCTAGCCGTTAGATTGAGTTTAAT 59.241 40.000 20.16 0.00 0.00 1.40
2038 2051 5.105064 AGGCTAGCCGTTAGATTGAGTTTAA 60.105 40.000 27.83 0.00 41.95 1.52
2039 2052 4.404715 AGGCTAGCCGTTAGATTGAGTTTA 59.595 41.667 27.83 0.00 41.95 2.01
2040 2053 3.197983 AGGCTAGCCGTTAGATTGAGTTT 59.802 43.478 27.83 2.04 41.95 2.66
2041 2054 2.766828 AGGCTAGCCGTTAGATTGAGTT 59.233 45.455 27.83 2.52 41.95 3.01
2042 2055 2.389715 AGGCTAGCCGTTAGATTGAGT 58.610 47.619 27.83 2.75 41.95 3.41
2043 2056 3.460857 AAGGCTAGCCGTTAGATTGAG 57.539 47.619 27.83 0.00 41.95 3.02
2044 2057 5.304614 AGATTAAGGCTAGCCGTTAGATTGA 59.695 40.000 27.50 12.38 41.95 2.57
2045 2058 5.542779 AGATTAAGGCTAGCCGTTAGATTG 58.457 41.667 27.50 0.00 41.95 2.67
2046 2059 5.810080 AGATTAAGGCTAGCCGTTAGATT 57.190 39.130 27.50 17.21 41.95 2.40
2047 2060 6.912951 TTAGATTAAGGCTAGCCGTTAGAT 57.087 37.500 27.50 17.86 41.95 1.98
2048 2061 6.720288 AGATTAGATTAAGGCTAGCCGTTAGA 59.280 38.462 27.50 14.06 41.95 2.10
2049 2062 6.926313 AGATTAGATTAAGGCTAGCCGTTAG 58.074 40.000 27.50 0.00 41.95 2.34
2050 2063 6.912951 AGATTAGATTAAGGCTAGCCGTTA 57.087 37.500 27.50 19.09 41.95 3.18
2051 2064 5.810080 AGATTAGATTAAGGCTAGCCGTT 57.190 39.130 27.50 22.19 41.95 4.44
2052 2065 7.397761 AGAATAGATTAGATTAAGGCTAGCCGT 59.602 37.037 27.83 26.74 41.95 5.68
2053 2066 7.777095 AGAATAGATTAGATTAAGGCTAGCCG 58.223 38.462 27.83 0.00 41.95 5.52
2054 2067 8.977412 AGAGAATAGATTAGATTAAGGCTAGCC 58.023 37.037 27.19 27.19 0.00 3.93
2055 2068 9.801873 CAGAGAATAGATTAGATTAAGGCTAGC 57.198 37.037 6.04 6.04 0.00 3.42
2058 2071 9.153479 ACACAGAGAATAGATTAGATTAAGGCT 57.847 33.333 0.00 0.00 0.00 4.58
2059 2072 9.202273 CACACAGAGAATAGATTAGATTAAGGC 57.798 37.037 0.00 0.00 0.00 4.35
2060 2073 9.202273 GCACACAGAGAATAGATTAGATTAAGG 57.798 37.037 0.00 0.00 0.00 2.69
2061 2074 9.755804 TGCACACAGAGAATAGATTAGATTAAG 57.244 33.333 0.00 0.00 0.00 1.85
2062 2075 9.534565 GTGCACACAGAGAATAGATTAGATTAA 57.465 33.333 13.17 0.00 0.00 1.40
2063 2076 8.918116 AGTGCACACAGAGAATAGATTAGATTA 58.082 33.333 21.04 0.00 0.00 1.75
2064 2077 7.790027 AGTGCACACAGAGAATAGATTAGATT 58.210 34.615 21.04 0.00 0.00 2.40
2065 2078 7.358770 AGTGCACACAGAGAATAGATTAGAT 57.641 36.000 21.04 0.00 0.00 1.98
2066 2079 6.782082 AGTGCACACAGAGAATAGATTAGA 57.218 37.500 21.04 0.00 0.00 2.10
2067 2080 7.168972 GCTAAGTGCACACAGAGAATAGATTAG 59.831 40.741 21.04 13.34 42.31 1.73
2068 2081 6.980978 GCTAAGTGCACACAGAGAATAGATTA 59.019 38.462 21.04 3.04 42.31 1.75
2069 2082 5.814705 GCTAAGTGCACACAGAGAATAGATT 59.185 40.000 21.04 1.88 42.31 2.40
2070 2083 5.355596 GCTAAGTGCACACAGAGAATAGAT 58.644 41.667 21.04 0.00 42.31 1.98
2071 2084 4.748892 GCTAAGTGCACACAGAGAATAGA 58.251 43.478 21.04 0.00 42.31 1.98
2085 2098 7.484959 GGTCAGTTAATGTAAATTGCTAAGTGC 59.515 37.037 0.00 0.00 43.25 4.40
2086 2099 7.692291 CGGTCAGTTAATGTAAATTGCTAAGTG 59.308 37.037 0.00 0.00 0.00 3.16
2087 2100 7.389607 ACGGTCAGTTAATGTAAATTGCTAAGT 59.610 33.333 0.00 0.00 0.00 2.24
2088 2101 7.748847 ACGGTCAGTTAATGTAAATTGCTAAG 58.251 34.615 0.00 0.00 0.00 2.18
2089 2102 7.675962 ACGGTCAGTTAATGTAAATTGCTAA 57.324 32.000 0.00 0.00 0.00 3.09
2090 2103 8.036575 AGTACGGTCAGTTAATGTAAATTGCTA 58.963 33.333 0.00 0.00 0.00 3.49
2091 2104 6.877322 AGTACGGTCAGTTAATGTAAATTGCT 59.123 34.615 0.00 0.00 0.00 3.91
2092 2105 7.068692 AGTACGGTCAGTTAATGTAAATTGC 57.931 36.000 0.00 0.00 0.00 3.56
2093 2106 7.332430 TGGAGTACGGTCAGTTAATGTAAATTG 59.668 37.037 0.00 0.00 0.00 2.32
2094 2107 7.332678 GTGGAGTACGGTCAGTTAATGTAAATT 59.667 37.037 0.00 0.00 0.00 1.82
2095 2108 6.815142 GTGGAGTACGGTCAGTTAATGTAAAT 59.185 38.462 0.00 0.00 0.00 1.40
2096 2109 6.158598 GTGGAGTACGGTCAGTTAATGTAAA 58.841 40.000 0.00 0.00 0.00 2.01
2097 2110 5.336690 GGTGGAGTACGGTCAGTTAATGTAA 60.337 44.000 0.00 0.00 0.00 2.41
2098 2111 4.158394 GGTGGAGTACGGTCAGTTAATGTA 59.842 45.833 0.00 0.00 0.00 2.29
2099 2112 3.056322 GGTGGAGTACGGTCAGTTAATGT 60.056 47.826 0.00 0.00 0.00 2.71
2100 2113 3.518590 GGTGGAGTACGGTCAGTTAATG 58.481 50.000 0.00 0.00 0.00 1.90
2101 2114 2.165030 CGGTGGAGTACGGTCAGTTAAT 59.835 50.000 0.00 0.00 0.00 1.40
2102 2115 1.541147 CGGTGGAGTACGGTCAGTTAA 59.459 52.381 0.00 0.00 0.00 2.01
2103 2116 1.167851 CGGTGGAGTACGGTCAGTTA 58.832 55.000 0.00 0.00 0.00 2.24
2104 2117 0.825010 ACGGTGGAGTACGGTCAGTT 60.825 55.000 0.00 0.00 38.30 3.16
2105 2118 1.228367 ACGGTGGAGTACGGTCAGT 60.228 57.895 0.00 0.00 38.30 3.41
2106 2119 1.211969 CACGGTGGAGTACGGTCAG 59.788 63.158 0.00 0.00 40.42 3.51
2107 2120 0.822944 TTCACGGTGGAGTACGGTCA 60.823 55.000 8.50 0.00 40.42 4.02
2108 2121 0.109412 CTTCACGGTGGAGTACGGTC 60.109 60.000 8.34 0.00 40.42 4.79
2109 2122 1.530013 CCTTCACGGTGGAGTACGGT 61.530 60.000 15.11 0.00 42.80 4.83
2110 2123 1.214589 CCTTCACGGTGGAGTACGG 59.785 63.158 15.11 0.00 35.86 4.02
2111 2124 0.599558 TTCCTTCACGGTGGAGTACG 59.400 55.000 15.11 0.56 33.46 3.67
2112 2125 2.825861 TTTCCTTCACGGTGGAGTAC 57.174 50.000 15.11 0.00 33.46 2.73
2113 2126 5.188163 TCATATTTTCCTTCACGGTGGAGTA 59.812 40.000 15.11 0.00 33.46 2.59
2114 2127 2.951229 ATTTTCCTTCACGGTGGAGT 57.049 45.000 15.11 0.00 33.46 3.85
2115 2128 4.513442 TCATATTTTCCTTCACGGTGGAG 58.487 43.478 9.58 9.58 33.46 3.86
2116 2129 4.561500 TCATATTTTCCTTCACGGTGGA 57.438 40.909 8.50 0.00 0.00 4.02
2117 2130 5.183140 ACTTTCATATTTTCCTTCACGGTGG 59.817 40.000 8.50 0.00 0.00 4.61
2118 2131 6.254281 ACTTTCATATTTTCCTTCACGGTG 57.746 37.500 0.56 0.56 0.00 4.94
2119 2132 5.414765 GGACTTTCATATTTTCCTTCACGGT 59.585 40.000 0.00 0.00 0.00 4.83
2120 2133 5.414454 TGGACTTTCATATTTTCCTTCACGG 59.586 40.000 0.00 0.00 0.00 4.94
2121 2134 6.314784 GTGGACTTTCATATTTTCCTTCACG 58.685 40.000 0.00 0.00 0.00 4.35
2122 2135 6.314784 CGTGGACTTTCATATTTTCCTTCAC 58.685 40.000 0.00 0.00 0.00 3.18
2123 2136 5.106317 GCGTGGACTTTCATATTTTCCTTCA 60.106 40.000 0.00 0.00 0.00 3.02
2124 2137 5.332707 GCGTGGACTTTCATATTTTCCTTC 58.667 41.667 0.00 0.00 0.00 3.46
2125 2138 4.157840 GGCGTGGACTTTCATATTTTCCTT 59.842 41.667 0.00 0.00 0.00 3.36
2126 2139 3.694566 GGCGTGGACTTTCATATTTTCCT 59.305 43.478 0.00 0.00 0.00 3.36
2127 2140 3.694566 AGGCGTGGACTTTCATATTTTCC 59.305 43.478 0.00 0.00 0.00 3.13
2128 2141 4.662145 CAGGCGTGGACTTTCATATTTTC 58.338 43.478 0.00 0.00 0.00 2.29
2129 2142 4.701956 CAGGCGTGGACTTTCATATTTT 57.298 40.909 0.00 0.00 0.00 1.82
2143 2156 1.131126 CTTGCTAATTGACCAGGCGTG 59.869 52.381 0.00 0.00 0.00 5.34
2144 2157 1.453155 CTTGCTAATTGACCAGGCGT 58.547 50.000 0.00 0.00 0.00 5.68
2145 2158 0.099436 GCTTGCTAATTGACCAGGCG 59.901 55.000 0.00 0.00 0.00 5.52
2146 2159 1.467920 AGCTTGCTAATTGACCAGGC 58.532 50.000 0.00 0.00 32.48 4.85
2147 2160 6.712095 TGATTATAGCTTGCTAATTGACCAGG 59.288 38.462 6.42 0.00 0.00 4.45
2148 2161 7.570140 CGTGATTATAGCTTGCTAATTGACCAG 60.570 40.741 6.42 0.00 0.00 4.00
2149 2162 6.202762 CGTGATTATAGCTTGCTAATTGACCA 59.797 38.462 6.42 0.00 0.00 4.02
2150 2163 6.347725 CCGTGATTATAGCTTGCTAATTGACC 60.348 42.308 6.42 0.00 0.00 4.02
2151 2164 6.423905 TCCGTGATTATAGCTTGCTAATTGAC 59.576 38.462 6.42 0.00 0.00 3.18
2152 2165 6.423905 GTCCGTGATTATAGCTTGCTAATTGA 59.576 38.462 6.42 0.00 0.00 2.57
2153 2166 6.202762 TGTCCGTGATTATAGCTTGCTAATTG 59.797 38.462 6.42 0.00 0.00 2.32
2154 2167 6.202954 GTGTCCGTGATTATAGCTTGCTAATT 59.797 38.462 6.42 0.00 0.00 1.40
2155 2168 5.696724 GTGTCCGTGATTATAGCTTGCTAAT 59.303 40.000 6.42 0.00 0.00 1.73
2156 2169 5.047847 GTGTCCGTGATTATAGCTTGCTAA 58.952 41.667 6.42 0.00 0.00 3.09
2157 2170 4.098807 TGTGTCCGTGATTATAGCTTGCTA 59.901 41.667 4.72 4.72 0.00 3.49
2158 2171 3.118775 TGTGTCCGTGATTATAGCTTGCT 60.119 43.478 0.00 0.00 0.00 3.91
2159 2172 3.194861 TGTGTCCGTGATTATAGCTTGC 58.805 45.455 0.00 0.00 0.00 4.01
2160 2173 4.449068 GGATGTGTCCGTGATTATAGCTTG 59.551 45.833 0.00 0.00 34.13 4.01
2161 2174 4.632153 GGATGTGTCCGTGATTATAGCTT 58.368 43.478 0.00 0.00 34.13 3.74
2162 2175 4.258702 GGATGTGTCCGTGATTATAGCT 57.741 45.455 0.00 0.00 34.13 3.32
2174 2187 9.832445 TGATTAGTTTCTTAATAGGATGTGTCC 57.168 33.333 0.00 0.00 45.45 4.02
2176 2189 9.314321 CGTGATTAGTTTCTTAATAGGATGTGT 57.686 33.333 0.00 0.00 0.00 3.72
2177 2190 8.765219 CCGTGATTAGTTTCTTAATAGGATGTG 58.235 37.037 0.00 0.00 0.00 3.21
2178 2191 8.701895 TCCGTGATTAGTTTCTTAATAGGATGT 58.298 33.333 0.00 0.00 0.00 3.06
2179 2192 8.979574 GTCCGTGATTAGTTTCTTAATAGGATG 58.020 37.037 0.00 0.00 30.75 3.51
2180 2193 8.701895 TGTCCGTGATTAGTTTCTTAATAGGAT 58.298 33.333 0.00 0.00 30.75 3.24
2181 2194 7.977853 GTGTCCGTGATTAGTTTCTTAATAGGA 59.022 37.037 0.00 0.00 0.00 2.94
2182 2195 7.762615 TGTGTCCGTGATTAGTTTCTTAATAGG 59.237 37.037 0.00 0.00 0.00 2.57
2183 2196 8.697846 TGTGTCCGTGATTAGTTTCTTAATAG 57.302 34.615 0.00 0.00 0.00 1.73
2184 2197 9.309516 GATGTGTCCGTGATTAGTTTCTTAATA 57.690 33.333 0.00 0.00 0.00 0.98
2185 2198 8.041323 AGATGTGTCCGTGATTAGTTTCTTAAT 58.959 33.333 0.00 0.00 0.00 1.40
2186 2199 7.383687 AGATGTGTCCGTGATTAGTTTCTTAA 58.616 34.615 0.00 0.00 0.00 1.85
2187 2200 6.931838 AGATGTGTCCGTGATTAGTTTCTTA 58.068 36.000 0.00 0.00 0.00 2.10
2188 2201 5.794894 AGATGTGTCCGTGATTAGTTTCTT 58.205 37.500 0.00 0.00 0.00 2.52
2189 2202 5.407407 AGATGTGTCCGTGATTAGTTTCT 57.593 39.130 0.00 0.00 0.00 2.52
2190 2203 7.772332 ATTAGATGTGTCCGTGATTAGTTTC 57.228 36.000 0.00 0.00 0.00 2.78
2191 2204 9.832445 ATAATTAGATGTGTCCGTGATTAGTTT 57.168 29.630 0.00 0.00 0.00 2.66
2192 2205 9.832445 AATAATTAGATGTGTCCGTGATTAGTT 57.168 29.630 0.00 0.00 0.00 2.24
2195 2208 9.923143 CCTAATAATTAGATGTGTCCGTGATTA 57.077 33.333 0.00 0.00 35.20 1.75
2196 2209 8.833231 CCTAATAATTAGATGTGTCCGTGATT 57.167 34.615 0.00 0.00 35.20 2.57


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

AutoCloner maintained by Alex Coulton.