Multiple sequence alignment - TraesCS6A01G354900

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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 TraesCS6A01G354900 chr6A 100.000 5022 0 0 1 5022 586096181 586101202 0.000000e+00 9274.0
1 TraesCS6A01G354900 chr6A 81.179 526 70 17 1337 1845 586097367 586097880 3.640000e-106 396.0
2 TraesCS6A01G354900 chr6A 81.107 524 74 13 1187 1700 586097517 586098025 3.640000e-106 396.0
3 TraesCS6A01G354900 chr6A 94.000 50 1 2 546 595 586096665 586096712 1.940000e-09 75.0
4 TraesCS6A01G354900 chr6A 94.000 50 1 2 485 532 586096726 586096775 1.940000e-09 75.0
5 TraesCS6A01G354900 chr6B 91.723 2235 105 32 2044 4232 662511446 662513646 0.000000e+00 3029.0
6 TraesCS6A01G354900 chr6B 84.289 1203 106 51 546 1700 662510212 662511379 0.000000e+00 1098.0
7 TraesCS6A01G354900 chr6B 95.142 494 19 3 4533 5022 662513696 662514188 0.000000e+00 774.0
8 TraesCS6A01G354900 chr6B 88.037 535 53 5 1 532 662509736 662510262 1.540000e-174 623.0
9 TraesCS6A01G354900 chr6B 85.841 565 60 14 1359 1910 662510889 662511446 2.610000e-162 582.0
10 TraesCS6A01G354900 chr6D 92.996 2113 85 27 2347 4422 437804434 437806520 0.000000e+00 3024.0
11 TraesCS6A01G354900 chr6D 86.912 1933 148 43 1 1910 437802251 437804101 0.000000e+00 2071.0
12 TraesCS6A01G354900 chr6D 92.857 504 19 9 4520 5022 437806603 437807090 0.000000e+00 715.0
13 TraesCS6A01G354900 chr6D 95.115 348 17 0 2044 2391 437804101 437804448 2.640000e-152 549.0
14 TraesCS6A01G354900 chr6D 80.822 584 79 18 1140 1700 437803464 437804037 1.290000e-115 427.0
15 TraesCS6A01G354900 chr6D 79.464 448 55 16 1137 1560 437803605 437804039 2.960000e-72 283.0
16 TraesCS6A01G354900 chr6D 100.000 31 0 0 4452 4482 437806569 437806599 1.950000e-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 TraesCS6A01G354900 chr6A 586096181 586101202 5021 False 9274.0 9274 100.0000 1 5022 1 chr6A.!!$F1 5021
1 TraesCS6A01G354900 chr6A 586096665 586098025 1360 False 235.5 396 87.5715 485 1845 4 chr6A.!!$F2 1360
2 TraesCS6A01G354900 chr6B 662509736 662514188 4452 False 1221.2 3029 89.0064 1 5022 5 chr6B.!!$F1 5021
3 TraesCS6A01G354900 chr6D 437802251 437807090 4839 False 1018.2 3024 89.7380 1 5022 7 chr6D.!!$F1 5021

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
441 442 0.040058 TTGGCTGCTGTCCATTGGAT 59.960 50.000 9.01 0.0 32.73 3.41 F
1947 2002 3.123453 TGTCGATTTCAGATTTGACTGCG 59.877 43.478 0.00 0.0 37.75 5.18 F
3302 3392 0.312102 GAGCTGAGCCAACAACCAAC 59.688 55.000 0.00 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2054 0.540133 TGGAGCAAAAGGAGCATGCA 60.540 50.0 21.98 0.0 42.45 3.96 R
3368 3458 0.394352 GAACATGGATGAAGGGCCGT 60.394 55.0 0.00 0.0 0.00 5.68 R
4494 4636 0.107017 AATGCCAAGATGACCCGGAG 60.107 55.0 0.73 0.0 0.00 4.63 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
25 26 1.070105 ACTACGTTGAAGCCGGCAA 59.930 52.632 31.54 12.07 0.00 4.52
74 75 1.220236 CATCCCCTCCTCTCCTCTTCT 59.780 57.143 0.00 0.00 0.00 2.85
125 126 0.379669 GAGGCTCGCCAACAATGATG 59.620 55.000 11.02 0.00 38.92 3.07
150 151 0.246635 CCAAGGGACACTCGTGGTAG 59.753 60.000 1.77 0.00 34.19 3.18
204 205 4.142838 CGTGCAAGTGTCAACATCATGTAT 60.143 41.667 0.00 0.00 0.00 2.29
205 206 5.327091 GTGCAAGTGTCAACATCATGTATC 58.673 41.667 0.00 0.00 0.00 2.24
206 207 5.002516 TGCAAGTGTCAACATCATGTATCA 58.997 37.500 0.00 0.00 0.00 2.15
207 208 5.648960 TGCAAGTGTCAACATCATGTATCAT 59.351 36.000 0.00 0.00 0.00 2.45
208 209 5.969435 GCAAGTGTCAACATCATGTATCATG 59.031 40.000 0.00 3.65 0.00 3.07
209 210 6.403964 GCAAGTGTCAACATCATGTATCATGT 60.404 38.462 9.13 0.00 34.58 3.21
210 211 7.201635 GCAAGTGTCAACATCATGTATCATGTA 60.202 37.037 9.13 0.00 32.74 2.29
216 217 5.894298 ACATCATGTATCATGTAGGTGGT 57.106 39.130 9.13 0.00 31.20 4.16
239 240 1.270412 CCTTGTTGTGCACAATGGCAT 60.270 47.619 33.16 0.00 46.92 4.40
242 243 0.733566 GTTGTGCACAATGGCATCGG 60.734 55.000 33.16 0.00 46.92 4.18
316 317 4.831307 CTCCGCGTCGTCCTTCGG 62.831 72.222 4.92 2.27 42.96 4.30
327 328 4.203076 CCTTCGGGACCGCGGTAG 62.203 72.222 34.36 24.14 39.59 3.18
365 366 0.248539 GCATGGTCTCGACTCCGTAC 60.249 60.000 0.00 0.00 37.05 3.67
377 378 1.471684 ACTCCGTACGTCCTTCATCAC 59.528 52.381 15.21 0.00 0.00 3.06
428 429 2.263741 GGTGGCTGTCACTTGGCTG 61.264 63.158 12.66 0.00 45.38 4.85
432 433 1.895707 GCTGTCACTTGGCTGCTGT 60.896 57.895 5.53 0.00 40.70 4.40
441 442 0.040058 TTGGCTGCTGTCCATTGGAT 59.960 50.000 9.01 0.00 32.73 3.41
1922 1977 8.706492 AATGTTATGCCTTTTACATGATGTTG 57.294 30.769 2.29 0.00 31.98 3.33
1923 1978 7.225784 TGTTATGCCTTTTACATGATGTTGT 57.774 32.000 2.29 0.00 0.00 3.32
1924 1979 7.665690 TGTTATGCCTTTTACATGATGTTGTT 58.334 30.769 2.29 0.00 0.00 2.83
1925 1980 8.147058 TGTTATGCCTTTTACATGATGTTGTTT 58.853 29.630 2.29 0.00 0.00 2.83
1926 1981 8.434661 GTTATGCCTTTTACATGATGTTGTTTG 58.565 33.333 2.29 0.00 0.00 2.93
1927 1982 5.911752 TGCCTTTTACATGATGTTGTTTGT 58.088 33.333 2.29 0.00 0.00 2.83
1928 1983 5.982516 TGCCTTTTACATGATGTTGTTTGTC 59.017 36.000 2.29 0.00 0.00 3.18
1929 1984 5.116983 GCCTTTTACATGATGTTGTTTGTCG 59.883 40.000 2.29 0.00 0.00 4.35
1930 1985 6.434596 CCTTTTACATGATGTTGTTTGTCGA 58.565 36.000 2.29 0.00 0.00 4.20
1931 1986 7.083858 CCTTTTACATGATGTTGTTTGTCGAT 58.916 34.615 2.29 0.00 0.00 3.59
1932 1987 7.594758 CCTTTTACATGATGTTGTTTGTCGATT 59.405 33.333 2.29 0.00 0.00 3.34
1933 1988 8.864069 TTTTACATGATGTTGTTTGTCGATTT 57.136 26.923 2.29 0.00 0.00 2.17
1934 1989 8.500837 TTTACATGATGTTGTTTGTCGATTTC 57.499 30.769 2.29 0.00 0.00 2.17
1935 1990 6.070897 ACATGATGTTGTTTGTCGATTTCA 57.929 33.333 0.00 0.00 0.00 2.69
1936 1991 6.144854 ACATGATGTTGTTTGTCGATTTCAG 58.855 36.000 0.00 0.00 0.00 3.02
1937 1992 6.017192 ACATGATGTTGTTTGTCGATTTCAGA 60.017 34.615 0.00 0.00 0.00 3.27
1938 1993 6.558771 TGATGTTGTTTGTCGATTTCAGAT 57.441 33.333 0.00 0.00 0.00 2.90
1939 1994 6.969366 TGATGTTGTTTGTCGATTTCAGATT 58.031 32.000 0.00 0.00 0.00 2.40
1940 1995 7.424803 TGATGTTGTTTGTCGATTTCAGATTT 58.575 30.769 0.00 0.00 0.00 2.17
1941 1996 7.379262 TGATGTTGTTTGTCGATTTCAGATTTG 59.621 33.333 0.00 0.00 0.00 2.32
1942 1997 6.790282 TGTTGTTTGTCGATTTCAGATTTGA 58.210 32.000 0.00 0.00 0.00 2.69
1943 1998 6.690957 TGTTGTTTGTCGATTTCAGATTTGAC 59.309 34.615 0.00 0.00 31.71 3.18
1944 1999 6.618287 TGTTTGTCGATTTCAGATTTGACT 57.382 33.333 0.00 0.00 31.71 3.41
1945 2000 6.429624 TGTTTGTCGATTTCAGATTTGACTG 58.570 36.000 0.00 0.00 39.02 3.51
1946 2001 4.668576 TGTCGATTTCAGATTTGACTGC 57.331 40.909 0.00 0.00 37.75 4.40
1947 2002 3.123453 TGTCGATTTCAGATTTGACTGCG 59.877 43.478 0.00 0.00 37.75 5.18
1948 2003 3.123621 GTCGATTTCAGATTTGACTGCGT 59.876 43.478 0.00 0.00 37.75 5.24
1949 2004 4.326278 GTCGATTTCAGATTTGACTGCGTA 59.674 41.667 0.00 0.00 37.75 4.42
1950 2005 4.562789 TCGATTTCAGATTTGACTGCGTAG 59.437 41.667 0.00 0.00 37.75 3.51
1951 2006 4.259970 CGATTTCAGATTTGACTGCGTAGG 60.260 45.833 5.26 0.00 37.75 3.18
1952 2007 3.953712 TTCAGATTTGACTGCGTAGGA 57.046 42.857 5.26 0.00 37.75 2.94
1953 2008 4.471904 TTCAGATTTGACTGCGTAGGAT 57.528 40.909 5.26 0.00 37.75 3.24
1954 2009 4.046938 TCAGATTTGACTGCGTAGGATC 57.953 45.455 5.26 3.27 37.75 3.36
1955 2010 3.447229 TCAGATTTGACTGCGTAGGATCA 59.553 43.478 5.26 0.00 37.75 2.92
1956 2011 4.100035 TCAGATTTGACTGCGTAGGATCAT 59.900 41.667 5.26 0.00 37.75 2.45
1957 2012 5.301805 TCAGATTTGACTGCGTAGGATCATA 59.698 40.000 5.26 0.00 37.75 2.15
1958 2013 5.985530 CAGATTTGACTGCGTAGGATCATAA 59.014 40.000 5.26 0.00 0.00 1.90
1959 2014 6.648310 CAGATTTGACTGCGTAGGATCATAAT 59.352 38.462 5.26 4.00 0.00 1.28
1960 2015 7.172190 CAGATTTGACTGCGTAGGATCATAATT 59.828 37.037 5.26 0.00 0.00 1.40
1961 2016 8.367911 AGATTTGACTGCGTAGGATCATAATTA 58.632 33.333 5.26 0.00 0.00 1.40
1962 2017 7.946655 TTTGACTGCGTAGGATCATAATTAG 57.053 36.000 5.26 0.00 0.00 1.73
1963 2018 6.894339 TGACTGCGTAGGATCATAATTAGA 57.106 37.500 5.26 0.00 0.00 2.10
1964 2019 7.468141 TGACTGCGTAGGATCATAATTAGAT 57.532 36.000 5.26 0.00 0.00 1.98
1965 2020 8.575649 TGACTGCGTAGGATCATAATTAGATA 57.424 34.615 5.26 0.00 0.00 1.98
1966 2021 9.190317 TGACTGCGTAGGATCATAATTAGATAT 57.810 33.333 5.26 0.00 0.00 1.63
1967 2022 9.672086 GACTGCGTAGGATCATAATTAGATATC 57.328 37.037 5.26 0.00 0.00 1.63
1968 2023 9.415008 ACTGCGTAGGATCATAATTAGATATCT 57.585 33.333 10.73 10.73 0.00 1.98
2001 2056 9.691362 TGGAGTAAAAATCTTAAAATCACTTGC 57.309 29.630 0.00 0.00 0.00 4.01
2002 2057 9.691362 GGAGTAAAAATCTTAAAATCACTTGCA 57.309 29.630 0.00 0.00 0.00 4.08
2005 2060 9.745323 GTAAAAATCTTAAAATCACTTGCATGC 57.255 29.630 11.82 11.82 0.00 4.06
2006 2061 8.611654 AAAAATCTTAAAATCACTTGCATGCT 57.388 26.923 20.33 0.00 0.00 3.79
2007 2062 7.823149 AAATCTTAAAATCACTTGCATGCTC 57.177 32.000 20.33 0.00 0.00 4.26
2008 2063 5.314923 TCTTAAAATCACTTGCATGCTCC 57.685 39.130 20.33 0.00 0.00 4.70
2009 2064 5.012239 TCTTAAAATCACTTGCATGCTCCT 58.988 37.500 20.33 0.00 0.00 3.69
2010 2065 5.477984 TCTTAAAATCACTTGCATGCTCCTT 59.522 36.000 20.33 1.22 0.00 3.36
2011 2066 4.612264 AAAATCACTTGCATGCTCCTTT 57.388 36.364 20.33 7.24 0.00 3.11
2012 2067 4.612264 AAATCACTTGCATGCTCCTTTT 57.388 36.364 20.33 8.41 0.00 2.27
2013 2068 3.587797 ATCACTTGCATGCTCCTTTTG 57.412 42.857 20.33 7.51 0.00 2.44
2014 2069 1.000060 TCACTTGCATGCTCCTTTTGC 60.000 47.619 20.33 0.00 36.91 3.68
2015 2070 1.000506 CACTTGCATGCTCCTTTTGCT 59.999 47.619 20.33 0.00 37.28 3.91
2016 2071 1.271656 ACTTGCATGCTCCTTTTGCTC 59.728 47.619 20.33 0.00 37.28 4.26
2017 2072 0.604578 TTGCATGCTCCTTTTGCTCC 59.395 50.000 20.33 0.00 37.28 4.70
2018 2073 0.540133 TGCATGCTCCTTTTGCTCCA 60.540 50.000 20.33 0.00 37.28 3.86
2019 2074 0.604578 GCATGCTCCTTTTGCTCCAA 59.395 50.000 11.37 0.00 33.61 3.53
2020 2075 1.206371 GCATGCTCCTTTTGCTCCAAT 59.794 47.619 11.37 0.00 33.61 3.16
2021 2076 2.737679 GCATGCTCCTTTTGCTCCAATC 60.738 50.000 11.37 0.00 33.61 2.67
2022 2077 1.549203 TGCTCCTTTTGCTCCAATCC 58.451 50.000 0.00 0.00 0.00 3.01
2023 2078 1.203038 TGCTCCTTTTGCTCCAATCCA 60.203 47.619 0.00 0.00 0.00 3.41
2024 2079 1.895131 GCTCCTTTTGCTCCAATCCAA 59.105 47.619 0.00 0.00 0.00 3.53
2025 2080 2.498885 GCTCCTTTTGCTCCAATCCAAT 59.501 45.455 0.00 0.00 0.00 3.16
2026 2081 3.055602 GCTCCTTTTGCTCCAATCCAATT 60.056 43.478 0.00 0.00 0.00 2.32
2027 2082 4.501071 CTCCTTTTGCTCCAATCCAATTG 58.499 43.478 0.00 0.00 39.94 2.32
2028 2083 4.158786 TCCTTTTGCTCCAATCCAATTGA 58.841 39.130 7.12 0.00 42.83 2.57
2029 2084 4.592351 TCCTTTTGCTCCAATCCAATTGAA 59.408 37.500 7.12 0.00 42.83 2.69
2030 2085 4.692155 CCTTTTGCTCCAATCCAATTGAAC 59.308 41.667 7.12 0.00 42.83 3.18
2031 2086 4.952071 TTTGCTCCAATCCAATTGAACA 57.048 36.364 7.12 0.00 42.83 3.18
2032 2087 4.952071 TTGCTCCAATCCAATTGAACAA 57.048 36.364 7.12 0.00 42.83 2.83
2033 2088 4.952071 TGCTCCAATCCAATTGAACAAA 57.048 36.364 7.12 0.00 42.83 2.83
2034 2089 4.630111 TGCTCCAATCCAATTGAACAAAC 58.370 39.130 7.12 0.00 42.83 2.93
2035 2090 4.344679 TGCTCCAATCCAATTGAACAAACT 59.655 37.500 7.12 0.00 42.83 2.66
2036 2091 4.925646 GCTCCAATCCAATTGAACAAACTC 59.074 41.667 7.12 0.00 42.83 3.01
2037 2092 5.279156 GCTCCAATCCAATTGAACAAACTCT 60.279 40.000 7.12 0.00 42.83 3.24
2038 2093 6.331369 TCCAATCCAATTGAACAAACTCTC 57.669 37.500 7.12 0.00 42.83 3.20
2039 2094 6.070656 TCCAATCCAATTGAACAAACTCTCT 58.929 36.000 7.12 0.00 42.83 3.10
2040 2095 6.207417 TCCAATCCAATTGAACAAACTCTCTC 59.793 38.462 7.12 0.00 42.83 3.20
2041 2096 5.869753 ATCCAATTGAACAAACTCTCTCG 57.130 39.130 7.12 0.00 0.00 4.04
2042 2097 4.065088 TCCAATTGAACAAACTCTCTCGG 58.935 43.478 7.12 0.00 0.00 4.63
2043 2098 3.815401 CCAATTGAACAAACTCTCTCGGT 59.185 43.478 7.12 0.00 0.00 4.69
2052 2107 5.308825 ACAAACTCTCTCGGTGATTGATTT 58.691 37.500 0.00 0.00 0.00 2.17
2061 2116 5.985530 TCTCGGTGATTGATTTACTGCATAG 59.014 40.000 0.00 0.00 0.00 2.23
2146 2201 8.988060 TGATTAATAATATCTCTATCGCCCCAA 58.012 33.333 0.00 0.00 0.00 4.12
2238 2293 8.175925 TGATCCTAATTCTGAGTAGAGACATG 57.824 38.462 0.00 0.00 33.70 3.21
2352 2407 6.687081 TTTGTACGTGTCTTTCAAAGGAAT 57.313 33.333 0.00 0.00 31.93 3.01
2373 2428 6.819146 GGAATACTCTACCAAGGAAAACTCTG 59.181 42.308 0.00 0.00 0.00 3.35
2391 2476 2.076863 CTGCCAAGGAAAACTCTACCG 58.923 52.381 0.00 0.00 0.00 4.02
2392 2477 1.418637 TGCCAAGGAAAACTCTACCGT 59.581 47.619 0.00 0.00 0.00 4.83
2483 2568 9.442047 TCAAATTTTCCTGCAAACTTTCTTAAA 57.558 25.926 0.00 0.00 27.25 1.52
2513 2598 3.366052 TGGGAGGTAAGCAATTTCCTC 57.634 47.619 5.38 5.38 43.84 3.71
2520 2605 5.497474 AGGTAAGCAATTTCCTCGTGTTAT 58.503 37.500 0.00 0.00 0.00 1.89
2569 2657 9.438228 AGTAAGAAGTATTTAGAAGCTTTCCAC 57.562 33.333 0.00 0.00 0.00 4.02
2572 2660 8.329203 AGAAGTATTTAGAAGCTTTCCACAAG 57.671 34.615 0.00 0.00 0.00 3.16
2592 2680 6.205853 CACAAGTACTGCCTAACCAAAACATA 59.794 38.462 0.00 0.00 0.00 2.29
2627 2716 5.490139 TTATACAGTACACCTCGCAGTAC 57.510 43.478 0.00 0.00 40.60 2.73
2715 2804 7.040961 ACGATGGTCTTAAGAGTAAGATAGAGC 60.041 40.741 5.12 0.00 45.79 4.09
2960 3050 2.229792 GGCACCAGATTTCACTTGTGA 58.770 47.619 0.00 0.00 36.19 3.58
2986 3076 1.816835 CAATCATGTGCAGGTGAAGCT 59.183 47.619 5.18 0.00 0.00 3.74
3003 3093 7.995488 AGGTGAAGCTCTAGTGCATTATTTAAT 59.005 33.333 18.36 0.00 34.99 1.40
3084 3174 5.983118 CGCTGTGATTTATGGTGTAGATGTA 59.017 40.000 0.00 0.00 0.00 2.29
3103 3193 5.703978 TGTATTGTGCACTTTGTATTGCT 57.296 34.783 19.41 0.00 39.62 3.91
3104 3194 6.083098 TGTATTGTGCACTTTGTATTGCTT 57.917 33.333 19.41 0.00 39.62 3.91
3133 3223 2.464157 AGACCTTGCTGCTAGTTGTC 57.536 50.000 10.07 10.42 0.00 3.18
3293 3383 1.740380 GCGACTAAATGAGCTGAGCCA 60.740 52.381 0.00 0.00 0.00 4.75
3302 3392 0.312102 GAGCTGAGCCAACAACCAAC 59.688 55.000 0.00 0.00 0.00 3.77
3388 3478 0.394216 CGGCCCTTCATCCATGTTCA 60.394 55.000 0.00 0.00 0.00 3.18
3394 3484 3.765511 CCCTTCATCCATGTTCACACATT 59.234 43.478 0.00 0.00 41.16 2.71
3413 3503 6.376177 CACATTATGTGTCACCATATGATGC 58.624 40.000 16.45 0.00 43.08 3.91
3414 3504 6.206048 CACATTATGTGTCACCATATGATGCT 59.794 38.462 16.45 0.00 43.08 3.79
3415 3505 6.774170 ACATTATGTGTCACCATATGATGCTT 59.226 34.615 3.65 0.00 38.75 3.91
3436 3526 3.045634 TCTTCTTCAGTGGTCCAAAGGA 58.954 45.455 0.00 0.00 0.00 3.36
3441 3531 0.890683 CAGTGGTCCAAAGGAATGGC 59.109 55.000 0.00 0.00 40.46 4.40
3475 3565 4.261801 TCAGCCATTGAACTTAGGTAAGC 58.738 43.478 0.00 0.00 36.79 3.09
3488 3578 2.852130 AGGTAAGCATCCCCTTCTTCT 58.148 47.619 0.00 0.00 0.00 2.85
3489 3579 3.193782 AGGTAAGCATCCCCTTCTTCTT 58.806 45.455 0.00 0.00 0.00 2.52
3490 3580 3.201045 AGGTAAGCATCCCCTTCTTCTTC 59.799 47.826 0.00 0.00 0.00 2.87
3500 3590 4.166144 TCCCCTTCTTCTTCAGACAAAGTT 59.834 41.667 0.00 0.00 0.00 2.66
3502 3592 4.517075 CCCTTCTTCTTCAGACAAAGTTCC 59.483 45.833 0.00 0.00 0.00 3.62
3505 3595 5.018539 TCTTCTTCAGACAAAGTTCCGAA 57.981 39.130 0.00 0.00 0.00 4.30
3566 3673 3.934457 ATTTTCCTTTAACAGGTGCCG 57.066 42.857 4.33 0.00 44.37 5.69
3568 3675 0.179015 TTCCTTTAACAGGTGCCGCA 60.179 50.000 0.00 0.00 44.37 5.69
3578 3685 1.153369 GGTGCCGCAGCTTCAGATA 60.153 57.895 15.33 0.00 40.80 1.98
3625 3732 5.422012 AGAACAAAGGAACCTCAATTTGTGT 59.578 36.000 8.71 0.00 43.17 3.72
3630 3737 5.880054 AGGAACCTCAATTTGTGTAATCG 57.120 39.130 0.00 0.00 0.00 3.34
3640 3747 2.112815 GTGTAATCGTGCCAGCCCC 61.113 63.158 0.00 0.00 0.00 5.80
3641 3748 2.270850 GTAATCGTGCCAGCCCCA 59.729 61.111 0.00 0.00 0.00 4.96
3679 3786 1.209990 CAGGAGATTGCTGAGAGCCTT 59.790 52.381 0.00 0.00 41.51 4.35
3694 3801 4.575885 AGAGCCTTTTAAGCGATACACAA 58.424 39.130 0.00 0.00 34.64 3.33
3703 3810 2.895372 GATACACAAGCCCCGCCG 60.895 66.667 0.00 0.00 0.00 6.46
3725 3832 1.815613 CCGCGGATGAGAGATATCTGT 59.184 52.381 24.07 5.90 34.21 3.41
3755 3862 1.468520 TGGACTCGCTTAGCAATTTGC 59.531 47.619 13.55 13.55 45.46 3.68
3767 3874 2.758009 GCAATTTGCTTGAGAAAGGCA 58.242 42.857 14.11 0.00 40.96 4.75
3947 4054 3.034635 GCCATCTCTAGAAAGGAGTCCA 58.965 50.000 12.86 0.00 33.06 4.02
3950 4057 4.040217 CCATCTCTAGAAAGGAGTCCATGG 59.960 50.000 12.86 4.97 31.29 3.66
3951 4058 3.034635 TCTCTAGAAAGGAGTCCATGGC 58.965 50.000 12.86 2.00 33.06 4.40
3952 4059 1.757118 TCTAGAAAGGAGTCCATGGCG 59.243 52.381 12.86 0.00 0.00 5.69
3975 4082 2.186532 GGTCTGTTTGAGAACCTCCC 57.813 55.000 0.00 0.00 31.29 4.30
3985 4095 2.285818 AACCTCCCCCGCATACCA 60.286 61.111 0.00 0.00 0.00 3.25
4048 4170 4.148838 ACTCCGGATTTGGAAATGTTTCA 58.851 39.130 3.57 0.00 37.64 2.69
4065 4187 5.132502 TGTTTCAATCATGAGGAACTGTGT 58.867 37.500 11.06 0.00 41.55 3.72
4066 4188 5.008911 TGTTTCAATCATGAGGAACTGTGTG 59.991 40.000 11.06 0.00 41.55 3.82
4067 4189 3.678289 TCAATCATGAGGAACTGTGTGG 58.322 45.455 0.09 0.00 41.55 4.17
4068 4190 2.119801 ATCATGAGGAACTGTGTGGC 57.880 50.000 0.09 0.00 41.55 5.01
4069 4191 1.059098 TCATGAGGAACTGTGTGGCT 58.941 50.000 0.00 0.00 41.55 4.75
4070 4192 1.162698 CATGAGGAACTGTGTGGCTG 58.837 55.000 0.00 0.00 41.55 4.85
4071 4193 0.767375 ATGAGGAACTGTGTGGCTGT 59.233 50.000 0.00 0.00 41.55 4.40
4072 4194 0.179048 TGAGGAACTGTGTGGCTGTG 60.179 55.000 0.00 0.00 41.55 3.66
4147 4270 2.221517 GCAACAACTGAAATTTGCGCAT 59.778 40.909 12.75 0.00 35.41 4.73
4293 4416 6.422776 AGTATCCACAAATTAACAGCTTCG 57.577 37.500 0.00 0.00 0.00 3.79
4309 4432 2.033801 GCTTCGCCGGTAGAGTGTTATA 59.966 50.000 1.90 0.00 0.00 0.98
4347 4470 5.961272 TCATTCAACTACTGCATCTCGTTA 58.039 37.500 0.00 0.00 0.00 3.18
4352 4475 5.862323 TCAACTACTGCATCTCGTTACTTTC 59.138 40.000 0.00 0.00 0.00 2.62
4401 4524 4.340950 CCTTGGTAAGTGTGTTTGGATTGT 59.659 41.667 0.00 0.00 0.00 2.71
4411 4534 2.627699 TGTTTGGATTGTTTCTCCTGCC 59.372 45.455 0.00 0.00 33.69 4.85
4422 4545 1.538047 TCTCCTGCCAGCAAATGTTC 58.462 50.000 0.00 0.00 0.00 3.18
4423 4546 1.074405 TCTCCTGCCAGCAAATGTTCT 59.926 47.619 0.00 0.00 0.00 3.01
4424 4547 1.471684 CTCCTGCCAGCAAATGTTCTC 59.528 52.381 0.00 0.00 0.00 2.87
4426 4549 1.542492 CTGCCAGCAAATGTTCTCCT 58.458 50.000 0.00 0.00 0.00 3.69
4428 4551 2.421424 CTGCCAGCAAATGTTCTCCTAC 59.579 50.000 0.00 0.00 0.00 3.18
4429 4552 2.040278 TGCCAGCAAATGTTCTCCTACT 59.960 45.455 0.00 0.00 0.00 2.57
4430 4553 3.263170 TGCCAGCAAATGTTCTCCTACTA 59.737 43.478 0.00 0.00 0.00 1.82
4431 4554 3.873952 GCCAGCAAATGTTCTCCTACTAG 59.126 47.826 0.00 0.00 0.00 2.57
4433 4556 5.491982 CCAGCAAATGTTCTCCTACTAGTT 58.508 41.667 0.00 0.00 0.00 2.24
4434 4557 5.940470 CCAGCAAATGTTCTCCTACTAGTTT 59.060 40.000 0.00 0.00 0.00 2.66
4435 4558 6.092807 CCAGCAAATGTTCTCCTACTAGTTTC 59.907 42.308 0.00 0.00 0.00 2.78
4436 4559 6.650807 CAGCAAATGTTCTCCTACTAGTTTCA 59.349 38.462 0.00 0.00 0.00 2.69
4438 4561 7.335422 AGCAAATGTTCTCCTACTAGTTTCATG 59.665 37.037 0.00 0.00 0.00 3.07
4443 4566 9.823647 ATGTTCTCCTACTAGTTTCATGTTATG 57.176 33.333 0.00 0.00 0.00 1.90
4444 4567 8.258007 TGTTCTCCTACTAGTTTCATGTTATGG 58.742 37.037 0.00 0.00 0.00 2.74
4445 4568 7.973048 TCTCCTACTAGTTTCATGTTATGGT 57.027 36.000 0.00 0.00 0.00 3.55
4446 4569 9.483489 TTCTCCTACTAGTTTCATGTTATGGTA 57.517 33.333 0.00 0.00 0.00 3.25
4447 4570 9.483489 TCTCCTACTAGTTTCATGTTATGGTAA 57.517 33.333 0.00 0.00 0.00 2.85
4450 4573 9.326413 CCTACTAGTTTCATGTTATGGTAAAGG 57.674 37.037 0.00 0.00 0.00 3.11
4482 4624 1.482593 CGTTGGAGAAGCCCTGATACT 59.517 52.381 0.00 0.00 34.97 2.12
4483 4625 2.482142 CGTTGGAGAAGCCCTGATACTC 60.482 54.545 0.00 0.00 34.97 2.59
4484 4626 1.403814 TGGAGAAGCCCTGATACTCG 58.596 55.000 0.00 0.00 34.97 4.18
4485 4627 1.342076 TGGAGAAGCCCTGATACTCGT 60.342 52.381 0.00 0.00 34.97 4.18
4486 4628 1.338655 GGAGAAGCCCTGATACTCGTC 59.661 57.143 0.00 0.00 0.00 4.20
4487 4629 2.025155 GAGAAGCCCTGATACTCGTCA 58.975 52.381 0.00 0.00 0.00 4.35
4488 4630 2.427453 GAGAAGCCCTGATACTCGTCAA 59.573 50.000 0.00 0.00 0.00 3.18
4489 4631 3.034635 AGAAGCCCTGATACTCGTCAAT 58.965 45.455 0.00 0.00 0.00 2.57
4490 4632 2.898729 AGCCCTGATACTCGTCAATG 57.101 50.000 0.00 0.00 0.00 2.82
4491 4633 1.202580 AGCCCTGATACTCGTCAATGC 60.203 52.381 0.00 0.00 0.00 3.56
4492 4634 1.473257 GCCCTGATACTCGTCAATGCA 60.473 52.381 0.00 0.00 0.00 3.96
4493 4635 2.808202 GCCCTGATACTCGTCAATGCAT 60.808 50.000 0.00 0.00 0.00 3.96
4494 4636 3.062763 CCCTGATACTCGTCAATGCATC 58.937 50.000 0.00 0.00 0.00 3.91
4495 4637 3.244009 CCCTGATACTCGTCAATGCATCT 60.244 47.826 0.00 0.00 0.00 2.90
4496 4638 3.986572 CCTGATACTCGTCAATGCATCTC 59.013 47.826 0.00 0.00 0.00 2.75
4497 4639 3.982475 TGATACTCGTCAATGCATCTCC 58.018 45.455 0.00 0.00 0.00 3.71
4498 4640 2.492019 TACTCGTCAATGCATCTCCG 57.508 50.000 0.00 2.37 0.00 4.63
4499 4641 0.179100 ACTCGTCAATGCATCTCCGG 60.179 55.000 0.00 0.00 0.00 5.14
4500 4642 0.877649 CTCGTCAATGCATCTCCGGG 60.878 60.000 0.00 0.00 0.00 5.73
4501 4643 1.153369 CGTCAATGCATCTCCGGGT 60.153 57.895 0.00 0.00 0.00 5.28
4502 4644 1.154205 CGTCAATGCATCTCCGGGTC 61.154 60.000 0.00 0.00 0.00 4.46
4503 4645 0.107703 GTCAATGCATCTCCGGGTCA 60.108 55.000 0.00 0.00 0.00 4.02
4504 4646 0.839277 TCAATGCATCTCCGGGTCAT 59.161 50.000 0.00 0.00 0.00 3.06
4505 4647 1.202687 TCAATGCATCTCCGGGTCATC 60.203 52.381 0.00 0.00 0.00 2.92
4506 4648 1.135094 AATGCATCTCCGGGTCATCT 58.865 50.000 0.00 0.00 0.00 2.90
4507 4649 1.135094 ATGCATCTCCGGGTCATCTT 58.865 50.000 0.00 0.00 0.00 2.40
4532 4674 5.335583 GGCATTTGTTTATGACACTAGTGCA 60.336 40.000 22.90 20.14 38.18 4.57
4576 4718 4.507756 TCATGGCGACTTCGAAATATGAAG 59.492 41.667 2.02 1.42 46.49 3.02
4580 4722 5.410132 TGGCGACTTCGAAATATGAAGAAAA 59.590 36.000 9.50 0.00 44.42 2.29
4824 4970 2.108157 AAAGACGGACGTGCTGCA 59.892 55.556 5.27 0.00 0.00 4.41
4827 4973 3.106407 GACGGACGTGCTGCAGAC 61.106 66.667 20.43 11.85 0.00 3.51
4878 5024 5.354234 AGTTGTCGGAAATGCTTAATCGATT 59.646 36.000 16.15 16.15 0.00 3.34
4939 5085 3.568538 GCTTCGTTTTCATCAAGCATGT 58.431 40.909 0.00 0.00 40.86 3.21
4952 5098 2.139323 AGCATGTTCATCAGCATGGT 57.861 45.000 0.00 0.00 45.38 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.179018 CCATTGCCGGCTTCAACG 59.821 61.111 29.70 5.97 0.00 4.10
25 26 2.894919 GGCTGCCAAATTCGCCAT 59.105 55.556 15.17 0.00 42.06 4.40
74 75 2.364317 CCGGGCTCAGAGGAGGAA 60.364 66.667 0.00 0.00 41.67 3.36
125 126 2.036256 AGTGTCCCTTGGCATGCC 59.964 61.111 30.54 30.54 0.00 4.40
133 134 0.178941 ACCTACCACGAGTGTCCCTT 60.179 55.000 2.36 0.00 0.00 3.95
140 141 2.989824 AGCGCACCTACCACGAGT 60.990 61.111 11.47 0.00 0.00 4.18
186 187 7.496920 CCTACATGATACATGATGTTGACACTT 59.503 37.037 16.86 0.00 36.12 3.16
225 226 2.992273 GCCGATGCCATTGTGCACA 61.992 57.895 17.42 17.42 45.48 4.57
227 228 2.675772 TGCCGATGCCATTGTGCA 60.676 55.556 4.54 4.54 46.94 4.57
239 240 3.348055 CTTCTGCGAGCTCTGCCGA 62.348 63.158 21.97 19.06 0.00 5.54
242 243 0.459934 ACATCTTCTGCGAGCTCTGC 60.460 55.000 19.33 19.33 0.00 4.26
252 253 1.303309 GCAATCCGGGACATCTTCTG 58.697 55.000 0.00 0.00 0.00 3.02
253 254 0.179073 CGCAATCCGGGACATCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
327 328 2.279186 GCAAAACACCGGTGTGCC 60.279 61.111 39.38 23.02 46.86 5.01
365 366 0.797249 GACGACGGTGATGAAGGACG 60.797 60.000 0.00 0.00 0.00 4.79
418 419 0.111061 AATGGACAGCAGCCAAGTGA 59.889 50.000 0.00 0.00 39.21 3.41
428 429 1.221414 GCGAGTATCCAATGGACAGC 58.779 55.000 3.09 2.26 32.98 4.40
432 433 3.631686 CCATTTTGCGAGTATCCAATGGA 59.368 43.478 3.67 3.67 32.19 3.41
483 484 9.621629 TTTAGAAAGTTTGTCCACATTTCTCTA 57.378 29.630 9.15 0.32 39.97 2.43
1853 1906 1.066858 TCCTTCGGATGAGTTGCACTC 60.067 52.381 8.75 8.75 45.26 3.51
1857 1910 3.915437 TTTTTCCTTCGGATGAGTTGC 57.085 42.857 0.00 0.00 0.00 4.17
1903 1958 6.523840 ACAAACAACATCATGTAAAAGGCAT 58.476 32.000 0.00 0.00 32.02 4.40
1910 1965 7.643579 TGAAATCGACAAACAACATCATGTAA 58.356 30.769 0.00 0.00 32.02 2.41
1911 1966 7.172361 TCTGAAATCGACAAACAACATCATGTA 59.828 33.333 0.00 0.00 32.02 2.29
1912 1967 6.017192 TCTGAAATCGACAAACAACATCATGT 60.017 34.615 0.00 0.00 34.24 3.21
1913 1968 6.372981 TCTGAAATCGACAAACAACATCATG 58.627 36.000 0.00 0.00 0.00 3.07
1914 1969 6.558771 TCTGAAATCGACAAACAACATCAT 57.441 33.333 0.00 0.00 0.00 2.45
1915 1970 6.558771 ATCTGAAATCGACAAACAACATCA 57.441 33.333 0.00 0.00 0.00 3.07
1916 1971 7.591057 TCAAATCTGAAATCGACAAACAACATC 59.409 33.333 0.00 0.00 0.00 3.06
1917 1972 7.379529 GTCAAATCTGAAATCGACAAACAACAT 59.620 33.333 0.00 0.00 31.88 2.71
1918 1973 6.690957 GTCAAATCTGAAATCGACAAACAACA 59.309 34.615 0.00 0.00 31.88 3.33
1919 1974 6.912591 AGTCAAATCTGAAATCGACAAACAAC 59.087 34.615 0.00 0.00 31.88 3.32
1920 1975 6.912051 CAGTCAAATCTGAAATCGACAAACAA 59.088 34.615 0.00 0.00 37.61 2.83
1921 1976 6.429624 CAGTCAAATCTGAAATCGACAAACA 58.570 36.000 0.00 0.00 37.61 2.83
1922 1977 5.340667 GCAGTCAAATCTGAAATCGACAAAC 59.659 40.000 0.00 0.00 37.61 2.93
1923 1978 5.451908 GCAGTCAAATCTGAAATCGACAAA 58.548 37.500 0.00 0.00 37.61 2.83
1924 1979 4.377328 CGCAGTCAAATCTGAAATCGACAA 60.377 41.667 0.00 0.00 37.61 3.18
1925 1980 3.123453 CGCAGTCAAATCTGAAATCGACA 59.877 43.478 0.00 0.00 37.61 4.35
1926 1981 3.123621 ACGCAGTCAAATCTGAAATCGAC 59.876 43.478 0.00 0.00 29.74 4.20
1927 1982 3.325870 ACGCAGTCAAATCTGAAATCGA 58.674 40.909 0.00 0.00 29.74 3.59
1928 1983 3.729526 ACGCAGTCAAATCTGAAATCG 57.270 42.857 0.00 0.00 29.74 3.34
1929 1984 4.870426 TCCTACGCAGTCAAATCTGAAATC 59.130 41.667 0.00 0.00 43.93 2.17
1930 1985 4.832248 TCCTACGCAGTCAAATCTGAAAT 58.168 39.130 0.00 0.00 43.93 2.17
1931 1986 4.265904 TCCTACGCAGTCAAATCTGAAA 57.734 40.909 0.00 0.00 43.93 2.69
1932 1987 3.953712 TCCTACGCAGTCAAATCTGAA 57.046 42.857 0.00 0.00 43.93 3.02
1933 1988 3.447229 TGATCCTACGCAGTCAAATCTGA 59.553 43.478 0.00 0.00 43.93 3.27
1934 1989 3.785486 TGATCCTACGCAGTCAAATCTG 58.215 45.455 0.00 0.00 43.93 2.90
1935 1990 4.679373 ATGATCCTACGCAGTCAAATCT 57.321 40.909 0.00 0.00 43.93 2.40
1936 1991 7.426929 AATTATGATCCTACGCAGTCAAATC 57.573 36.000 0.00 0.00 43.93 2.17
1937 1992 8.367911 TCTAATTATGATCCTACGCAGTCAAAT 58.632 33.333 0.00 0.00 43.93 2.32
1938 1993 7.722363 TCTAATTATGATCCTACGCAGTCAAA 58.278 34.615 0.00 0.00 43.93 2.69
1939 1994 7.284919 TCTAATTATGATCCTACGCAGTCAA 57.715 36.000 0.00 0.00 43.93 3.18
1940 1995 6.894339 TCTAATTATGATCCTACGCAGTCA 57.106 37.500 0.00 0.00 43.93 3.41
1941 1996 9.672086 GATATCTAATTATGATCCTACGCAGTC 57.328 37.037 0.00 0.00 43.93 3.51
1975 2030 9.691362 GCAAGTGATTTTAAGATTTTTACTCCA 57.309 29.630 0.00 0.00 0.00 3.86
1976 2031 9.691362 TGCAAGTGATTTTAAGATTTTTACTCC 57.309 29.630 0.00 0.00 0.00 3.85
1979 2034 9.745323 GCATGCAAGTGATTTTAAGATTTTTAC 57.255 29.630 14.21 0.00 0.00 2.01
1980 2035 9.709495 AGCATGCAAGTGATTTTAAGATTTTTA 57.291 25.926 21.98 0.00 0.00 1.52
1981 2036 8.611654 AGCATGCAAGTGATTTTAAGATTTTT 57.388 26.923 21.98 0.00 0.00 1.94
1982 2037 7.332678 GGAGCATGCAAGTGATTTTAAGATTTT 59.667 33.333 21.98 0.00 0.00 1.82
1983 2038 6.815142 GGAGCATGCAAGTGATTTTAAGATTT 59.185 34.615 21.98 0.00 0.00 2.17
1984 2039 6.154021 AGGAGCATGCAAGTGATTTTAAGATT 59.846 34.615 21.98 0.00 0.00 2.40
1985 2040 5.655532 AGGAGCATGCAAGTGATTTTAAGAT 59.344 36.000 21.98 0.00 0.00 2.40
1986 2041 5.012239 AGGAGCATGCAAGTGATTTTAAGA 58.988 37.500 21.98 0.00 0.00 2.10
1987 2042 5.320549 AGGAGCATGCAAGTGATTTTAAG 57.679 39.130 21.98 0.00 0.00 1.85
1988 2043 5.726980 AAGGAGCATGCAAGTGATTTTAA 57.273 34.783 21.98 0.00 0.00 1.52
1989 2044 5.726980 AAAGGAGCATGCAAGTGATTTTA 57.273 34.783 21.98 0.00 0.00 1.52
1990 2045 4.612264 AAAGGAGCATGCAAGTGATTTT 57.388 36.364 21.98 7.39 0.00 1.82
1991 2046 4.312443 CAAAAGGAGCATGCAAGTGATTT 58.688 39.130 21.98 10.04 0.00 2.17
1992 2047 3.863400 GCAAAAGGAGCATGCAAGTGATT 60.863 43.478 21.98 4.66 39.81 2.57
1993 2048 2.353406 GCAAAAGGAGCATGCAAGTGAT 60.353 45.455 21.98 0.00 39.81 3.06
1994 2049 1.000060 GCAAAAGGAGCATGCAAGTGA 60.000 47.619 21.98 0.00 39.81 3.41
1995 2050 1.000506 AGCAAAAGGAGCATGCAAGTG 59.999 47.619 21.98 9.67 42.45 3.16
1996 2051 1.271656 GAGCAAAAGGAGCATGCAAGT 59.728 47.619 21.98 0.00 42.45 3.16
1997 2052 1.403780 GGAGCAAAAGGAGCATGCAAG 60.404 52.381 21.98 2.18 42.45 4.01
1998 2053 0.604578 GGAGCAAAAGGAGCATGCAA 59.395 50.000 21.98 0.00 42.45 4.08
1999 2054 0.540133 TGGAGCAAAAGGAGCATGCA 60.540 50.000 21.98 0.00 42.45 3.96
2000 2055 0.604578 TTGGAGCAAAAGGAGCATGC 59.395 50.000 10.51 10.51 40.34 4.06
2001 2056 2.159142 GGATTGGAGCAAAAGGAGCATG 60.159 50.000 0.00 0.00 0.00 4.06
2002 2057 2.105766 GGATTGGAGCAAAAGGAGCAT 58.894 47.619 0.00 0.00 0.00 3.79
2003 2058 1.203038 TGGATTGGAGCAAAAGGAGCA 60.203 47.619 0.00 0.00 0.00 4.26
2004 2059 1.549203 TGGATTGGAGCAAAAGGAGC 58.451 50.000 0.00 0.00 0.00 4.70
2005 2060 4.221262 TCAATTGGATTGGAGCAAAAGGAG 59.779 41.667 5.42 0.00 40.61 3.69
2006 2061 4.158786 TCAATTGGATTGGAGCAAAAGGA 58.841 39.130 5.42 0.00 40.61 3.36
2007 2062 4.540359 TCAATTGGATTGGAGCAAAAGG 57.460 40.909 5.42 0.00 40.61 3.11
2008 2063 5.299148 TGTTCAATTGGATTGGAGCAAAAG 58.701 37.500 5.42 0.00 40.61 2.27
2009 2064 5.287674 TGTTCAATTGGATTGGAGCAAAA 57.712 34.783 5.42 0.00 40.61 2.44
2010 2065 4.952071 TGTTCAATTGGATTGGAGCAAA 57.048 36.364 5.42 0.00 40.61 3.68
2011 2066 4.952071 TTGTTCAATTGGATTGGAGCAA 57.048 36.364 5.42 0.00 40.61 3.91
2012 2067 4.344679 AGTTTGTTCAATTGGATTGGAGCA 59.655 37.500 5.42 0.00 40.61 4.26
2013 2068 4.886579 AGTTTGTTCAATTGGATTGGAGC 58.113 39.130 5.42 0.00 40.61 4.70
2014 2069 6.208204 AGAGAGTTTGTTCAATTGGATTGGAG 59.792 38.462 5.42 0.00 40.61 3.86
2015 2070 6.070656 AGAGAGTTTGTTCAATTGGATTGGA 58.929 36.000 5.42 0.00 40.61 3.53
2016 2071 6.336842 AGAGAGTTTGTTCAATTGGATTGG 57.663 37.500 5.42 0.00 40.61 3.16
2017 2072 6.082338 CGAGAGAGTTTGTTCAATTGGATTG 58.918 40.000 5.42 0.00 41.57 2.67
2018 2073 5.182001 CCGAGAGAGTTTGTTCAATTGGATT 59.818 40.000 5.42 0.00 0.00 3.01
2019 2074 4.697352 CCGAGAGAGTTTGTTCAATTGGAT 59.303 41.667 5.42 0.00 0.00 3.41
2020 2075 4.065088 CCGAGAGAGTTTGTTCAATTGGA 58.935 43.478 5.42 0.00 0.00 3.53
2021 2076 3.815401 ACCGAGAGAGTTTGTTCAATTGG 59.185 43.478 5.42 0.00 0.00 3.16
2022 2077 4.511454 TCACCGAGAGAGTTTGTTCAATTG 59.489 41.667 0.00 0.00 0.00 2.32
2023 2078 4.703897 TCACCGAGAGAGTTTGTTCAATT 58.296 39.130 0.00 0.00 0.00 2.32
2024 2079 4.336889 TCACCGAGAGAGTTTGTTCAAT 57.663 40.909 0.00 0.00 0.00 2.57
2025 2080 3.812156 TCACCGAGAGAGTTTGTTCAA 57.188 42.857 0.00 0.00 0.00 2.69
2026 2081 4.058124 CAATCACCGAGAGAGTTTGTTCA 58.942 43.478 0.00 0.00 0.00 3.18
2027 2082 4.307432 TCAATCACCGAGAGAGTTTGTTC 58.693 43.478 0.00 0.00 0.00 3.18
2028 2083 4.336889 TCAATCACCGAGAGAGTTTGTT 57.663 40.909 0.00 0.00 0.00 2.83
2029 2084 4.543590 ATCAATCACCGAGAGAGTTTGT 57.456 40.909 0.00 0.00 0.00 2.83
2030 2085 5.869753 AAATCAATCACCGAGAGAGTTTG 57.130 39.130 0.00 0.00 0.00 2.93
2031 2086 6.591834 CAGTAAATCAATCACCGAGAGAGTTT 59.408 38.462 0.00 0.00 0.00 2.66
2032 2087 6.102663 CAGTAAATCAATCACCGAGAGAGTT 58.897 40.000 0.00 0.00 0.00 3.01
2033 2088 5.655488 CAGTAAATCAATCACCGAGAGAGT 58.345 41.667 0.00 0.00 0.00 3.24
2034 2089 4.505922 GCAGTAAATCAATCACCGAGAGAG 59.494 45.833 0.00 0.00 0.00 3.20
2035 2090 4.081697 TGCAGTAAATCAATCACCGAGAGA 60.082 41.667 0.00 0.00 0.00 3.10
2036 2091 4.183865 TGCAGTAAATCAATCACCGAGAG 58.816 43.478 0.00 0.00 0.00 3.20
2037 2092 4.200838 TGCAGTAAATCAATCACCGAGA 57.799 40.909 0.00 0.00 0.00 4.04
2038 2093 5.985530 TCTATGCAGTAAATCAATCACCGAG 59.014 40.000 0.00 0.00 0.00 4.63
2039 2094 5.912892 TCTATGCAGTAAATCAATCACCGA 58.087 37.500 0.00 0.00 0.00 4.69
2040 2095 6.479990 TCTTCTATGCAGTAAATCAATCACCG 59.520 38.462 0.00 0.00 0.00 4.94
2041 2096 7.712639 TCTCTTCTATGCAGTAAATCAATCACC 59.287 37.037 0.00 0.00 0.00 4.02
2042 2097 8.654230 TCTCTTCTATGCAGTAAATCAATCAC 57.346 34.615 0.00 0.00 0.00 3.06
2043 2098 9.671279 TTTCTCTTCTATGCAGTAAATCAATCA 57.329 29.630 0.00 0.00 0.00 2.57
2052 2107 9.719355 TTAAACACATTTCTCTTCTATGCAGTA 57.281 29.630 0.00 0.00 0.00 2.74
2129 2184 6.875972 AATTAGTTGGGGCGATAGAGATAT 57.124 37.500 0.00 0.00 39.76 1.63
2138 2193 4.162698 ACACTGTATAATTAGTTGGGGCGA 59.837 41.667 0.00 0.00 0.00 5.54
2228 2283 4.937620 TCCTGCAAAACATCATGTCTCTAC 59.062 41.667 0.00 0.00 0.00 2.59
2235 2290 4.182693 ACATGTCCTGCAAAACATCATG 57.817 40.909 9.96 10.15 37.56 3.07
2238 2293 5.314923 ACATACATGTCCTGCAAAACATC 57.685 39.130 0.00 0.00 35.87 3.06
2270 2325 1.026718 CCAGTGGGAGCGGTTCATTC 61.027 60.000 0.00 0.00 35.59 2.67
2352 2407 4.020485 GGCAGAGTTTTCCTTGGTAGAGTA 60.020 45.833 0.00 0.00 0.00 2.59
2373 2428 1.804748 CACGGTAGAGTTTTCCTTGGC 59.195 52.381 0.00 0.00 0.00 4.52
2391 2476 3.357079 CACAGCAGAACGGCCCAC 61.357 66.667 0.00 0.00 0.00 4.61
2392 2477 2.616797 TTTCACAGCAGAACGGCCCA 62.617 55.000 0.00 0.00 0.00 5.36
2483 2568 4.941713 TGCTTACCTCCCAATTACCAATT 58.058 39.130 0.00 0.00 0.00 2.32
2545 2633 9.787435 TTGTGGAAAGCTTCTAAATACTTCTTA 57.213 29.630 0.00 0.00 0.00 2.10
2569 2657 5.705609 ATGTTTTGGTTAGGCAGTACTTG 57.294 39.130 0.00 0.00 0.00 3.16
2601 2689 4.751060 TGCGAGGTGTACTGTATAAAAGG 58.249 43.478 0.00 0.00 0.00 3.11
2606 2695 3.557185 CGTACTGCGAGGTGTACTGTATA 59.443 47.826 0.00 0.00 44.77 1.47
2627 2716 2.791383 TTGCAACCAAATCACCTTCG 57.209 45.000 0.00 0.00 0.00 3.79
2715 2804 6.412362 AGCAGTAATATCTAACCACTGGAG 57.588 41.667 0.71 0.00 37.63 3.86
2807 2897 9.953697 TTGATAGGTACACAAACAAACAATAAC 57.046 29.630 0.00 0.00 0.00 1.89
2843 2933 6.693315 AAAAGATTGGAAACTCGTTTGAGA 57.307 33.333 0.00 0.00 45.57 3.27
2960 3050 1.965643 ACCTGCACATGATTGCTTGTT 59.034 42.857 9.44 0.00 43.41 2.83
3003 3093 9.146984 CCGATCTTTAAGTGTTAATGTAGAACA 57.853 33.333 0.00 0.00 34.46 3.18
3028 3118 8.538409 AATTGCAACTTTCATATTTCAAGACC 57.462 30.769 0.00 0.00 0.00 3.85
3293 3383 7.170965 AGAATCTGACATGATAGTTGGTTGTT 58.829 34.615 0.00 0.00 0.00 2.83
3356 3446 1.995376 AGGGCCGTCACTTTCATTTT 58.005 45.000 0.00 0.00 0.00 1.82
3368 3458 0.394352 GAACATGGATGAAGGGCCGT 60.394 55.000 0.00 0.00 0.00 5.68
3413 3503 3.817647 CCTTTGGACCACTGAAGAAGAAG 59.182 47.826 6.04 0.00 0.00 2.85
3414 3504 3.458118 TCCTTTGGACCACTGAAGAAGAA 59.542 43.478 6.04 0.00 0.00 2.52
3415 3505 3.045634 TCCTTTGGACCACTGAAGAAGA 58.954 45.455 6.04 0.00 0.00 2.87
3436 3526 1.674441 CTGATGATGCTTCACGCCATT 59.326 47.619 4.14 0.00 38.05 3.16
3441 3531 1.306148 ATGGCTGATGATGCTTCACG 58.694 50.000 4.14 0.00 33.85 4.35
3475 3565 3.988976 TGTCTGAAGAAGAAGGGGATG 57.011 47.619 0.00 0.00 36.40 3.51
3488 3578 2.872245 CAGCTTCGGAACTTTGTCTGAA 59.128 45.455 0.00 0.00 39.96 3.02
3489 3579 2.483876 CAGCTTCGGAACTTTGTCTGA 58.516 47.619 0.00 0.00 0.00 3.27
3490 3580 1.532868 CCAGCTTCGGAACTTTGTCTG 59.467 52.381 0.00 0.00 0.00 3.51
3566 3673 2.569059 TGCTTGGATATCTGAAGCTGC 58.431 47.619 26.49 13.72 42.19 5.25
3568 3675 6.786967 ATTTTTGCTTGGATATCTGAAGCT 57.213 33.333 26.49 13.14 42.19 3.74
3625 3732 1.077787 CTTGGGGCTGGCACGATTA 60.078 57.895 2.88 0.00 0.00 1.75
3640 3747 3.568538 CTGAAATTCTTTCGGCACCTTG 58.431 45.455 0.00 0.00 42.55 3.61
3641 3748 2.558359 CCTGAAATTCTTTCGGCACCTT 59.442 45.455 3.41 0.00 43.20 3.50
3679 3786 2.361789 GGGGCTTGTGTATCGCTTAAA 58.638 47.619 0.00 0.00 0.00 1.52
3703 3810 2.088423 AGATATCTCTCATCCGCGGAC 58.912 52.381 33.75 13.84 0.00 4.79
3717 3824 3.873952 GTCCACTCTTGCCAACAGATATC 59.126 47.826 0.00 0.00 0.00 1.63
3725 3832 1.301716 GCGAGTCCACTCTTGCCAA 60.302 57.895 5.21 0.00 40.75 4.52
3755 3862 1.208614 GCGCAGTGCCTTTCTCAAG 59.791 57.895 10.11 0.00 37.76 3.02
3767 3874 2.644555 GATACGGTGGATGGCGCAGT 62.645 60.000 10.83 0.00 0.00 4.40
3947 4054 4.344865 AAACAGACCCGCCGCCAT 62.345 61.111 0.00 0.00 0.00 4.40
3950 4057 3.423154 CTCAAACAGACCCGCCGC 61.423 66.667 0.00 0.00 0.00 6.53
3951 4058 1.301401 TTCTCAAACAGACCCGCCG 60.301 57.895 0.00 0.00 0.00 6.46
3952 4059 1.235281 GGTTCTCAAACAGACCCGCC 61.235 60.000 0.00 0.00 37.10 6.13
3975 4082 2.562738 TCTGACATAGATGGTATGCGGG 59.437 50.000 0.00 0.00 0.00 6.13
3985 4095 5.644977 TGTCGAACAACTCTGACATAGAT 57.355 39.130 0.00 0.00 34.69 1.98
4048 4170 2.040813 AGCCACACAGTTCCTCATGATT 59.959 45.455 0.00 0.00 0.00 2.57
4067 4189 2.772287 ACAAGTCTAAGAAGGCACAGC 58.228 47.619 0.00 0.00 0.00 4.40
4068 4190 5.506317 CCAAAACAAGTCTAAGAAGGCACAG 60.506 44.000 0.00 0.00 0.00 3.66
4069 4191 4.338118 CCAAAACAAGTCTAAGAAGGCACA 59.662 41.667 0.00 0.00 0.00 4.57
4070 4192 4.338400 ACCAAAACAAGTCTAAGAAGGCAC 59.662 41.667 0.00 0.00 0.00 5.01
4071 4193 4.532834 ACCAAAACAAGTCTAAGAAGGCA 58.467 39.130 0.00 0.00 0.00 4.75
4072 4194 4.023107 GGACCAAAACAAGTCTAAGAAGGC 60.023 45.833 0.00 0.00 33.39 4.35
4147 4270 2.304761 AGTAAGAACAGCGAAATGGGGA 59.695 45.455 0.00 0.00 0.00 4.81
4210 4333 3.869065 CCTTAGTATCGGCTTGTTGGAA 58.131 45.455 0.00 0.00 0.00 3.53
4293 4416 3.451526 GTTGGTATAACACTCTACCGGC 58.548 50.000 0.00 0.00 40.28 6.13
4309 4432 2.649312 TGAATGATCTTGGAGGGTTGGT 59.351 45.455 0.00 0.00 0.00 3.67
4347 4470 3.821033 ACAAGATGCGGCTAAAAGAAAGT 59.179 39.130 0.00 0.00 0.00 2.66
4352 4475 4.946784 AGTAACAAGATGCGGCTAAAAG 57.053 40.909 0.00 0.00 0.00 2.27
4401 4524 1.999648 ACATTTGCTGGCAGGAGAAA 58.000 45.000 17.64 6.08 0.00 2.52
4411 4534 6.650807 TGAAACTAGTAGGAGAACATTTGCTG 59.349 38.462 0.00 0.00 0.00 4.41
4424 4547 9.326413 CCTTTACCATAACATGAAACTAGTAGG 57.674 37.037 0.00 0.00 0.00 3.18
4426 4549 8.828751 ACCCTTTACCATAACATGAAACTAGTA 58.171 33.333 0.00 0.00 0.00 1.82
4428 4551 7.827236 TCACCCTTTACCATAACATGAAACTAG 59.173 37.037 0.00 0.00 0.00 2.57
4429 4552 7.691213 TCACCCTTTACCATAACATGAAACTA 58.309 34.615 0.00 0.00 0.00 2.24
4430 4553 6.548321 TCACCCTTTACCATAACATGAAACT 58.452 36.000 0.00 0.00 0.00 2.66
4431 4554 6.827586 TCACCCTTTACCATAACATGAAAC 57.172 37.500 0.00 0.00 0.00 2.78
4433 4556 7.723616 CCATATCACCCTTTACCATAACATGAA 59.276 37.037 0.00 0.00 0.00 2.57
4434 4557 7.073088 TCCATATCACCCTTTACCATAACATGA 59.927 37.037 0.00 0.00 0.00 3.07
4435 4558 7.174946 GTCCATATCACCCTTTACCATAACATG 59.825 40.741 0.00 0.00 0.00 3.21
4436 4559 7.231467 GTCCATATCACCCTTTACCATAACAT 58.769 38.462 0.00 0.00 0.00 2.71
4438 4561 6.002082 GGTCCATATCACCCTTTACCATAAC 58.998 44.000 0.00 0.00 0.00 1.89
4441 4564 3.072476 CGGTCCATATCACCCTTTACCAT 59.928 47.826 0.00 0.00 0.00 3.55
4443 4566 2.436911 ACGGTCCATATCACCCTTTACC 59.563 50.000 0.00 0.00 0.00 2.85
4444 4567 3.832615 ACGGTCCATATCACCCTTTAC 57.167 47.619 0.00 0.00 0.00 2.01
4445 4568 3.118186 CCAACGGTCCATATCACCCTTTA 60.118 47.826 0.00 0.00 0.00 1.85
4446 4569 2.356741 CCAACGGTCCATATCACCCTTT 60.357 50.000 0.00 0.00 0.00 3.11
4447 4570 1.211949 CCAACGGTCCATATCACCCTT 59.788 52.381 0.00 0.00 0.00 3.95
4448 4571 0.837272 CCAACGGTCCATATCACCCT 59.163 55.000 0.00 0.00 0.00 4.34
4449 4572 0.834612 TCCAACGGTCCATATCACCC 59.165 55.000 0.00 0.00 0.00 4.61
4450 4573 1.760613 TCTCCAACGGTCCATATCACC 59.239 52.381 0.00 0.00 0.00 4.02
4482 4624 1.143838 CCCGGAGATGCATTGACGA 59.856 57.895 0.73 0.00 0.00 4.20
4483 4625 1.153369 ACCCGGAGATGCATTGACG 60.153 57.895 0.73 5.76 0.00 4.35
4484 4626 0.107703 TGACCCGGAGATGCATTGAC 60.108 55.000 0.73 0.00 0.00 3.18
4485 4627 0.839277 ATGACCCGGAGATGCATTGA 59.161 50.000 0.73 0.00 0.00 2.57
4486 4628 1.202734 AGATGACCCGGAGATGCATTG 60.203 52.381 0.73 0.00 0.00 2.82
4487 4629 1.135094 AGATGACCCGGAGATGCATT 58.865 50.000 0.73 0.00 0.00 3.56
4488 4630 1.135094 AAGATGACCCGGAGATGCAT 58.865 50.000 0.73 0.00 0.00 3.96
4489 4631 0.178767 CAAGATGACCCGGAGATGCA 59.821 55.000 0.73 0.00 0.00 3.96
4490 4632 0.533755 CCAAGATGACCCGGAGATGC 60.534 60.000 0.73 0.00 0.00 3.91
4491 4633 0.533755 GCCAAGATGACCCGGAGATG 60.534 60.000 0.73 0.00 0.00 2.90
4492 4634 0.982852 TGCCAAGATGACCCGGAGAT 60.983 55.000 0.73 0.00 0.00 2.75
4493 4635 0.982852 ATGCCAAGATGACCCGGAGA 60.983 55.000 0.73 0.00 0.00 3.71
4494 4636 0.107017 AATGCCAAGATGACCCGGAG 60.107 55.000 0.73 0.00 0.00 4.63
4495 4637 0.331278 AAATGCCAAGATGACCCGGA 59.669 50.000 0.73 0.00 0.00 5.14
4496 4638 0.457035 CAAATGCCAAGATGACCCGG 59.543 55.000 0.00 0.00 0.00 5.73
4497 4639 1.176527 ACAAATGCCAAGATGACCCG 58.823 50.000 0.00 0.00 0.00 5.28
4498 4640 3.683365 AAACAAATGCCAAGATGACCC 57.317 42.857 0.00 0.00 0.00 4.46
4499 4641 5.807011 GTCATAAACAAATGCCAAGATGACC 59.193 40.000 0.00 0.00 37.19 4.02
4500 4642 6.308766 GTGTCATAAACAAATGCCAAGATGAC 59.691 38.462 0.00 0.00 40.31 3.06
4501 4643 6.209192 AGTGTCATAAACAAATGCCAAGATGA 59.791 34.615 0.00 0.00 40.31 2.92
4502 4644 6.392354 AGTGTCATAAACAAATGCCAAGATG 58.608 36.000 0.00 0.00 40.31 2.90
4503 4645 6.594788 AGTGTCATAAACAAATGCCAAGAT 57.405 33.333 0.00 0.00 40.31 2.40
4504 4646 6.714810 ACTAGTGTCATAAACAAATGCCAAGA 59.285 34.615 0.00 0.00 40.31 3.02
4505 4647 6.803320 CACTAGTGTCATAAACAAATGCCAAG 59.197 38.462 15.06 0.00 40.31 3.61
4506 4648 6.676950 CACTAGTGTCATAAACAAATGCCAA 58.323 36.000 15.06 0.00 40.31 4.52
4507 4649 5.335583 GCACTAGTGTCATAAACAAATGCCA 60.336 40.000 23.44 0.00 40.31 4.92
4532 4674 7.444487 CCATGACATCTGATCTACAAATGTGAT 59.556 37.037 0.00 0.00 39.85 3.06
4887 5033 3.706373 GGAGAAGAGGCGCCACCA 61.706 66.667 31.54 0.00 43.14 4.17
4939 5085 1.951895 GCAGGTGACCATGCTGATGAA 60.952 52.381 15.65 0.00 39.38 2.57


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

AutoCloner maintained by Alex Coulton.