Multiple sequence alignment - TraesCS7D01G240800

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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 TraesCS7D01G240800 chr7D 100.000 6040 0 0 1 6040 205152195 205146156 0.000000e+00 11154
1 TraesCS7D01G240800 chr7B 95.177 3691 130 22 2009 5683 169472127 169468469 0.000000e+00 5786
2 TraesCS7D01G240800 chr7B 91.227 1915 115 25 41 1924 169474024 169472132 0.000000e+00 2556
3 TraesCS7D01G240800 chr7B 92.246 374 24 2 5667 6040 169468056 169467688 5.360000e-145 525
4 TraesCS7D01G240800 chr7A 93.786 3283 113 30 2448 5685 217376681 217373445 0.000000e+00 4848
5 TraesCS7D01G240800 chr7A 90.640 1923 130 33 30 1924 217379083 217377183 0.000000e+00 2508
6 TraesCS7D01G240800 chr7A 95.957 371 15 0 5670 6040 217373132 217372762 2.410000e-168 603
7 TraesCS7D01G240800 chr7A 88.998 509 14 19 2006 2477 217377184 217376681 5.210000e-165 592
8 TraesCS7D01G240800 chr7A 88.596 114 8 5 1923 2033 143849692 143849581 3.800000e-27 134
9 TraesCS7D01G240800 chr2B 98.810 84 1 0 1922 2005 397449832 397449915 3.770000e-32 150
10 TraesCS7D01G240800 chr2B 93.814 97 5 1 1923 2018 15752836 15752740 1.750000e-30 145
11 TraesCS7D01G240800 chr6D 97.701 87 1 1 1923 2008 2103641 2103727 1.360000e-31 148
12 TraesCS7D01G240800 chr5B 95.699 93 2 2 1922 2012 550925091 550925183 1.360000e-31 148
13 TraesCS7D01G240800 chr1B 95.699 93 3 1 1921 2012 598684965 598684873 1.360000e-31 148
14 TraesCS7D01G240800 chr4A 96.629 89 2 1 1923 2010 464953605 464953517 4.880000e-31 147
15 TraesCS7D01G240800 chr6B 94.737 95 2 3 1923 2016 357123703 357123611 1.750000e-30 145
16 TraesCS7D01G240800 chr5D 92.233 103 7 1 1923 2024 226705858 226705960 1.750000e-30 145


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 TraesCS7D01G240800 chr7D 205146156 205152195 6039 True 11154.000000 11154 100.000000 1 6040 1 chr7D.!!$R1 6039
1 TraesCS7D01G240800 chr7B 169467688 169474024 6336 True 2955.666667 5786 92.883333 41 6040 3 chr7B.!!$R1 5999
2 TraesCS7D01G240800 chr7A 217372762 217379083 6321 True 2137.750000 4848 92.345250 30 6040 4 chr7A.!!$R2 6010

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
37 38 0.250727 TGCAAAGGCTGGGTGTACTC 60.251 55.000 0.00 0.0 41.91 2.59 F
154 155 0.320697 GGTGGCGTCTGGTTCTAGTT 59.679 55.000 0.00 0.0 0.00 2.24 F
384 387 0.811616 GGCGCTTGATCGTTGATCCT 60.812 55.000 7.64 0.0 38.20 3.24 F
444 473 1.604755 GTGCGGATGTGGTTGTTGTTA 59.395 47.619 0.00 0.0 0.00 2.41 F
446 475 2.227626 TGCGGATGTGGTTGTTGTTATG 59.772 45.455 0.00 0.0 0.00 1.90 F
1654 1700 0.392461 TTGCGCCTGGATTACTGGTC 60.392 55.000 4.18 0.0 40.14 4.02 F
1933 1980 0.702902 TTCTCTGGTACTCCCTCCGT 59.297 55.000 0.00 0.0 0.00 4.69 F
1935 1982 1.076677 TCTCTGGTACTCCCTCCGTTT 59.923 52.381 0.00 0.0 0.00 3.60 F
3858 3991 0.101399 CGAGAGCAGTAATGGCGACT 59.899 55.000 0.00 0.0 36.08 4.18 F
4919 5070 0.888285 GCCTGGCTGACTGCATATCC 60.888 60.000 12.43 0.0 45.15 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1523 0.030638 CGGAACAAACCACCAAGCTG 59.969 55.000 0.00 0.00 0.00 4.24 R
1610 1656 0.179240 GTGATTGACACGAAGCGCTG 60.179 55.000 12.58 0.57 39.78 5.18 R
1623 1669 0.314935 AGGCGCAAACCAAGTGATTG 59.685 50.000 10.83 0.00 0.00 2.67 R
1638 1684 0.389391 ATCGACCAGTAATCCAGGCG 59.611 55.000 0.00 0.00 0.00 5.52 R
1996 2043 0.561184 TGTCCCATCTATCCCTCCGT 59.439 55.000 0.00 0.00 0.00 4.69 R
3282 3415 1.133823 TCTGCAGTGAAAGCAAGGGAA 60.134 47.619 14.67 0.00 42.17 3.97 R
3792 3925 2.057922 TCCCATCCCTGGAGAATAAGC 58.942 52.381 0.00 0.00 46.37 3.09 R
3965 4098 8.363390 TGCAACCACATGAAAATACTGAAAATA 58.637 29.630 0.00 0.00 0.00 1.40 R
4934 5085 0.459237 CTTCGAGCGCAGACCATTCT 60.459 55.000 11.47 0.00 0.00 2.40 R
5967 6635 3.524541 TCGATGTCATGACACCAATCAG 58.475 45.455 30.09 17.84 45.05 2.90 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
26 27 4.559153 ACATACATTGTTCTTGCAAAGGC 58.441 39.130 0.00 0.00 46.24 4.35
27 28 4.281688 ACATACATTGTTCTTGCAAAGGCT 59.718 37.500 0.00 0.00 46.24 4.58
28 29 3.102052 ACATTGTTCTTGCAAAGGCTG 57.898 42.857 0.00 0.00 46.24 4.85
37 38 0.250727 TGCAAAGGCTGGGTGTACTC 60.251 55.000 0.00 0.00 41.91 2.59
39 40 1.003718 AAAGGCTGGGTGTACTCGC 60.004 57.895 5.14 5.14 0.00 5.03
44 45 1.878522 CTGGGTGTACTCGCATCGC 60.879 63.158 14.10 0.00 0.00 4.58
142 143 4.988598 CGGAGCTGTTGGTGGCGT 62.989 66.667 0.00 0.00 0.00 5.68
154 155 0.320697 GGTGGCGTCTGGTTCTAGTT 59.679 55.000 0.00 0.00 0.00 2.24
166 167 1.714460 GTTCTAGTTGCGACACGACTG 59.286 52.381 6.90 0.00 43.32 3.51
181 182 2.125229 CTGCCTGCTCATGCGAGT 60.125 61.111 0.00 0.00 41.71 4.18
233 235 1.366111 GACCGCGGTGTGCATGTAAT 61.366 55.000 39.65 5.66 46.97 1.89
236 238 1.133363 CGCGGTGTGCATGTAATTGC 61.133 55.000 0.00 0.00 46.97 3.56
247 249 5.008316 GTGCATGTAATTGCTGAGATCATGA 59.992 40.000 0.00 0.00 43.18 3.07
252 254 9.529325 CATGTAATTGCTGAGATCATGAAAAAT 57.471 29.630 0.00 0.00 34.90 1.82
253 255 8.920509 TGTAATTGCTGAGATCATGAAAAATG 57.079 30.769 0.00 0.00 0.00 2.32
255 257 5.988310 TTGCTGAGATCATGAAAAATGGT 57.012 34.783 0.00 0.00 0.00 3.55
256 258 5.319140 TGCTGAGATCATGAAAAATGGTG 57.681 39.130 0.00 0.00 0.00 4.17
257 259 5.011586 TGCTGAGATCATGAAAAATGGTGA 58.988 37.500 0.00 0.00 0.00 4.02
258 260 5.106038 TGCTGAGATCATGAAAAATGGTGAC 60.106 40.000 0.00 0.00 0.00 3.67
259 261 5.550232 TGAGATCATGAAAAATGGTGACG 57.450 39.130 0.00 0.00 0.00 4.35
260 262 4.395854 TGAGATCATGAAAAATGGTGACGG 59.604 41.667 0.00 0.00 0.00 4.79
261 263 4.335416 AGATCATGAAAAATGGTGACGGT 58.665 39.130 0.00 0.00 0.00 4.83
331 334 2.091885 AGCTCTGAGGTGAAAACCCAAA 60.092 45.455 8.83 0.00 0.00 3.28
335 338 3.895041 TCTGAGGTGAAAACCCAAAATCC 59.105 43.478 0.00 0.00 0.00 3.01
339 342 1.069358 GTGAAAACCCAAAATCCGGCA 59.931 47.619 0.00 0.00 0.00 5.69
343 346 1.638529 AACCCAAAATCCGGCATTCA 58.361 45.000 0.00 0.00 0.00 2.57
355 358 1.106285 GGCATTCAGTGGTTGGATCC 58.894 55.000 4.20 4.20 0.00 3.36
366 369 3.439513 TTGGATCCGACGGCGATGG 62.440 63.158 15.16 15.23 40.82 3.51
380 383 1.420641 CGATGGCGCTTGATCGTTGA 61.421 55.000 21.15 0.00 37.33 3.18
384 387 0.811616 GGCGCTTGATCGTTGATCCT 60.812 55.000 7.64 0.00 38.20 3.24
432 461 2.251409 AGAGATGATTGGTGCGGATG 57.749 50.000 0.00 0.00 0.00 3.51
444 473 1.604755 GTGCGGATGTGGTTGTTGTTA 59.395 47.619 0.00 0.00 0.00 2.41
446 475 2.227626 TGCGGATGTGGTTGTTGTTATG 59.772 45.455 0.00 0.00 0.00 1.90
450 479 3.119990 GGATGTGGTTGTTGTTATGGTCG 60.120 47.826 0.00 0.00 0.00 4.79
453 482 4.138290 TGTGGTTGTTGTTATGGTCGATT 58.862 39.130 0.00 0.00 0.00 3.34
454 483 4.214545 TGTGGTTGTTGTTATGGTCGATTC 59.785 41.667 0.00 0.00 0.00 2.52
460 489 8.241367 GGTTGTTGTTATGGTCGATTCTTTTAT 58.759 33.333 0.00 0.00 0.00 1.40
483 512 7.798596 ATCATTATTTTGATCGCTTCAGAGT 57.201 32.000 0.00 0.00 35.27 3.24
557 586 4.072131 AGTCGCTGGTGTGATTTTTATGT 58.928 39.130 0.00 0.00 34.99 2.29
569 598 7.702772 GTGTGATTTTTATGTGTGTTGGTGTTA 59.297 33.333 0.00 0.00 0.00 2.41
571 600 7.918562 GTGATTTTTATGTGTGTTGGTGTTAGT 59.081 33.333 0.00 0.00 0.00 2.24
573 602 8.641499 ATTTTTATGTGTGTTGGTGTTAGTTG 57.359 30.769 0.00 0.00 0.00 3.16
574 603 3.708563 ATGTGTGTTGGTGTTAGTTGC 57.291 42.857 0.00 0.00 0.00 4.17
607 636 4.697514 CCTATACAGAGGTTGGATGTGTG 58.302 47.826 0.00 0.00 31.05 3.82
614 643 3.264193 AGAGGTTGGATGTGTGCTCATTA 59.736 43.478 0.00 0.00 0.00 1.90
618 647 4.881273 GGTTGGATGTGTGCTCATTATGTA 59.119 41.667 0.00 0.00 0.00 2.29
898 929 5.997746 GGCTCCTACATGCTAAACATAATCA 59.002 40.000 0.00 0.00 36.64 2.57
1114 1154 4.354162 TTACTGCCGCCCCCAACC 62.354 66.667 0.00 0.00 0.00 3.77
1123 1163 3.260100 CCCCCAACCCTGTGCTCT 61.260 66.667 0.00 0.00 0.00 4.09
1481 1524 5.243426 GCAACCGCTATATTTTTCCTTCA 57.757 39.130 0.00 0.00 34.30 3.02
1623 1669 2.765250 TTCCCTCAGCGCTTCGTGTC 62.765 60.000 7.50 0.00 0.00 3.67
1638 1684 2.032799 TCGTGTCAATCACTTGGTTTGC 59.967 45.455 0.00 0.00 44.16 3.68
1654 1700 0.392461 TTGCGCCTGGATTACTGGTC 60.392 55.000 4.18 0.00 40.14 4.02
1691 1737 3.888930 TGTTGTTTGAATCAAGGGGAGAC 59.111 43.478 0.00 0.00 0.00 3.36
1814 1860 5.047377 TGTTTAATTTGGTTCCAGAGGATGC 60.047 40.000 0.00 0.00 0.00 3.91
1842 1888 5.551760 TTTTTGCTCTTCTGGATCGATTC 57.448 39.130 0.00 0.00 0.00 2.52
1908 1955 7.962918 CCTAACGGTTTTCTGATAATTTCTGTG 59.037 37.037 0.00 0.00 0.00 3.66
1924 1971 4.585955 TCTGTGAAGTGTTCTCTGGTAC 57.414 45.455 0.00 0.00 0.00 3.34
1925 1972 4.215908 TCTGTGAAGTGTTCTCTGGTACT 58.784 43.478 0.00 0.00 0.00 2.73
1926 1973 4.278669 TCTGTGAAGTGTTCTCTGGTACTC 59.721 45.833 0.00 0.00 0.00 2.59
1927 1974 3.321111 TGTGAAGTGTTCTCTGGTACTCC 59.679 47.826 0.00 0.00 0.00 3.85
1928 1975 2.897969 TGAAGTGTTCTCTGGTACTCCC 59.102 50.000 0.00 0.00 0.00 4.30
1929 1976 3.166679 GAAGTGTTCTCTGGTACTCCCT 58.833 50.000 0.00 0.00 0.00 4.20
1930 1977 2.810164 AGTGTTCTCTGGTACTCCCTC 58.190 52.381 0.00 0.00 0.00 4.30
1931 1978 1.826096 GTGTTCTCTGGTACTCCCTCC 59.174 57.143 0.00 0.00 0.00 4.30
1932 1979 1.104630 GTTCTCTGGTACTCCCTCCG 58.895 60.000 0.00 0.00 0.00 4.63
1933 1980 0.702902 TTCTCTGGTACTCCCTCCGT 59.297 55.000 0.00 0.00 0.00 4.69
1934 1981 0.702902 TCTCTGGTACTCCCTCCGTT 59.297 55.000 0.00 0.00 0.00 4.44
1935 1982 1.076677 TCTCTGGTACTCCCTCCGTTT 59.923 52.381 0.00 0.00 0.00 3.60
1936 1983 1.477295 CTCTGGTACTCCCTCCGTTTC 59.523 57.143 0.00 0.00 0.00 2.78
1937 1984 1.203087 TCTGGTACTCCCTCCGTTTCA 60.203 52.381 0.00 0.00 0.00 2.69
1938 1985 1.621814 CTGGTACTCCCTCCGTTTCAA 59.378 52.381 0.00 0.00 0.00 2.69
1939 1986 2.038033 CTGGTACTCCCTCCGTTTCAAA 59.962 50.000 0.00 0.00 0.00 2.69
1940 1987 2.438763 TGGTACTCCCTCCGTTTCAAAA 59.561 45.455 0.00 0.00 0.00 2.44
1941 1988 3.073356 TGGTACTCCCTCCGTTTCAAAAT 59.927 43.478 0.00 0.00 0.00 1.82
1942 1989 4.286549 TGGTACTCCCTCCGTTTCAAAATA 59.713 41.667 0.00 0.00 0.00 1.40
1943 1990 4.874396 GGTACTCCCTCCGTTTCAAAATAG 59.126 45.833 0.00 0.00 0.00 1.73
1944 1991 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1945 1992 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1946 1993 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1947 1994 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1948 1995 6.001449 TCCCTCCGTTTCAAAATAGATGAT 57.999 37.500 0.00 0.00 0.00 2.45
1949 1996 6.055588 TCCCTCCGTTTCAAAATAGATGATC 58.944 40.000 0.00 0.00 0.00 2.92
1950 1997 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
1951 1998 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
1952 1999 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
1953 2000 7.083875 TCCGTTTCAAAATAGATGATCCAAC 57.916 36.000 0.00 0.00 0.00 3.77
1954 2001 6.884295 TCCGTTTCAAAATAGATGATCCAACT 59.116 34.615 0.00 0.00 0.00 3.16
1955 2002 7.393234 TCCGTTTCAAAATAGATGATCCAACTT 59.607 33.333 0.00 0.00 0.00 2.66
1956 2003 8.028938 CCGTTTCAAAATAGATGATCCAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
1957 2004 8.853345 CGTTTCAAAATAGATGATCCAACTTTG 58.147 33.333 0.00 0.00 0.00 2.77
1958 2005 9.696917 GTTTCAAAATAGATGATCCAACTTTGT 57.303 29.630 0.00 0.00 0.00 2.83
1961 2008 9.739276 TCAAAATAGATGATCCAACTTTGTACT 57.261 29.630 0.00 0.00 0.00 2.73
1984 2031 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
1985 2032 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
1986 2033 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
1987 2034 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
1988 2035 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
1989 2036 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
1990 2037 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
1991 2038 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
1992 2039 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1993 2040 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1994 2041 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1995 2042 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1996 2043 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1997 2044 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1998 2045 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1999 2046 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2000 2047 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2001 2048 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2002 2049 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2003 2050 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2004 2051 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2005 2052 4.412199 TCATCTATTTTGGAACGGAGGGAT 59.588 41.667 0.00 0.00 0.00 3.85
2006 2053 5.605069 TCATCTATTTTGGAACGGAGGGATA 59.395 40.000 0.00 0.00 0.00 2.59
2036 2086 4.761739 ACATGAGTTGGTTGTGGTATTGAG 59.238 41.667 0.00 0.00 0.00 3.02
2037 2087 4.431416 TGAGTTGGTTGTGGTATTGAGT 57.569 40.909 0.00 0.00 0.00 3.41
2331 2398 4.437682 ACTGGAGTTCAACATTCCTCAA 57.562 40.909 0.00 0.00 32.12 3.02
2332 2399 4.792068 ACTGGAGTTCAACATTCCTCAAA 58.208 39.130 0.00 0.00 32.12 2.69
2383 2458 9.581289 TTATTCCTCAAAAACATCTGGAGTTTA 57.419 29.630 0.00 0.00 38.17 2.01
2408 2483 4.411540 ACTGAAGAGAGGTGCAATATGGAT 59.588 41.667 0.00 0.00 0.00 3.41
2442 2529 8.651589 TTCATTTCTTGAGAACTAGGACTAGA 57.348 34.615 13.00 0.00 35.27 2.43
2524 2640 6.793492 AAGATGACAGCAAAGAGAGTTTAC 57.207 37.500 0.00 0.00 0.00 2.01
2671 2795 5.050490 TGAATCAGCCTTTAGTTCTATCGC 58.950 41.667 0.00 0.00 0.00 4.58
2673 2797 3.031736 TCAGCCTTTAGTTCTATCGCCT 58.968 45.455 0.00 0.00 0.00 5.52
2716 2841 7.555554 CCTTGACAGTCTTTTCTCATATCCATT 59.444 37.037 1.31 0.00 0.00 3.16
2718 2843 7.623630 TGACAGTCTTTTCTCATATCCATTCA 58.376 34.615 1.31 0.00 0.00 2.57
2747 2872 9.988815 CTTTGAGATATAAGTTATACTGGCAGT 57.011 33.333 25.34 25.34 0.00 4.40
2762 2887 6.811253 ACTGGCAGTCAAATTTTTATCGTA 57.189 33.333 15.88 0.00 0.00 3.43
2854 2985 6.016276 GTCATTCCAGTGGTTATGAAACAAGT 60.016 38.462 22.66 0.00 37.34 3.16
2857 2988 6.428083 TCCAGTGGTTATGAAACAAGTCTA 57.572 37.500 9.54 0.00 37.34 2.59
2858 2989 6.833041 TCCAGTGGTTATGAAACAAGTCTAA 58.167 36.000 9.54 0.00 37.34 2.10
2916 3047 3.446516 AGTTAACCTTGACTAGCTACCGG 59.553 47.826 0.00 0.00 0.00 5.28
2921 3052 2.418334 CCTTGACTAGCTACCGGGTTTC 60.418 54.545 4.31 0.00 0.00 2.78
2950 3081 9.211485 CCTCGTTTCTTTAGGTACTATTTGAAA 57.789 33.333 0.00 0.00 42.38 2.69
3081 3213 9.625747 TTTCATGGTGAAAATATGAGCATACTA 57.374 29.630 2.84 0.00 42.72 1.82
3104 3236 8.861086 ACTAGACGTGTAAGATTCCATCAATAT 58.139 33.333 0.00 0.00 0.00 1.28
3109 3241 9.477484 ACGTGTAAGATTCCATCAATATAGTTC 57.523 33.333 0.00 0.00 0.00 3.01
3120 3252 8.650490 TCCATCAATATAGTTCATTGTAGCTCA 58.350 33.333 0.00 0.00 35.36 4.26
3138 3270 3.181456 GCTCAGCCCATCTCTTTGATACT 60.181 47.826 0.00 0.00 33.36 2.12
3144 3276 5.420104 AGCCCATCTCTTTGATACTTTTTGG 59.580 40.000 0.00 0.00 33.36 3.28
3146 3278 5.951747 CCCATCTCTTTGATACTTTTTGGGA 59.048 40.000 0.00 0.00 32.93 4.37
3148 3280 7.124750 CCCATCTCTTTGATACTTTTTGGGAAT 59.875 37.037 0.00 0.00 32.93 3.01
3149 3281 9.189156 CCATCTCTTTGATACTTTTTGGGAATA 57.811 33.333 0.00 0.00 33.36 1.75
3151 3283 9.981460 ATCTCTTTGATACTTTTTGGGAATAGT 57.019 29.630 0.00 0.00 32.79 2.12
3233 3366 3.581332 TCACTTGATACCGAGGGAAAAGT 59.419 43.478 1.25 1.25 33.34 2.66
3565 3698 5.999044 AGTGATATGCTTCCTGAGACATTT 58.001 37.500 0.00 0.00 0.00 2.32
3693 3826 6.664816 ACATTGGTCAAACAGGTGATTGATAT 59.335 34.615 6.02 0.00 38.70 1.63
3792 3925 1.004628 TGGTGGATGAACTGGACATGG 59.995 52.381 0.00 0.00 0.00 3.66
3858 3991 0.101399 CGAGAGCAGTAATGGCGACT 59.899 55.000 0.00 0.00 36.08 4.18
3991 4124 5.781210 TTCAGTATTTTCATGTGGTTGCA 57.219 34.783 0.00 0.00 0.00 4.08
4347 4497 1.212688 CCACTGATGGGGTATGCTTCA 59.787 52.381 0.00 0.00 43.04 3.02
4505 4656 2.287608 CGTTCTTTCAAACAAGGAGGCC 60.288 50.000 0.00 0.00 0.00 5.19
4835 4986 4.391830 TCATCCACGCTAAGAAATGTTGAC 59.608 41.667 0.00 0.00 0.00 3.18
4919 5070 0.888285 GCCTGGCTGACTGCATATCC 60.888 60.000 12.43 0.00 45.15 2.59
4934 5085 3.681594 GCATATCCACAAACGAGGAGGAA 60.682 47.826 0.00 0.00 37.34 3.36
5104 5255 2.603473 TAGGGTGCTCGCAGTGGT 60.603 61.111 5.59 0.00 0.00 4.16
5213 5371 3.568007 GGCAGGTGTGTACATTCAAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
5274 5432 4.678840 GCATTCCATACTTGGGCTTCTTTG 60.679 45.833 0.00 0.00 43.81 2.77
5372 5530 1.732259 GGATGTTCGGTTGTAGCTGTG 59.268 52.381 0.00 0.00 0.00 3.66
5373 5531 1.128692 GATGTTCGGTTGTAGCTGTGC 59.871 52.381 0.00 0.00 0.00 4.57
5374 5532 0.882927 TGTTCGGTTGTAGCTGTGCC 60.883 55.000 0.00 0.00 0.00 5.01
5375 5533 0.602905 GTTCGGTTGTAGCTGTGCCT 60.603 55.000 0.00 0.00 0.00 4.75
5376 5534 0.602638 TTCGGTTGTAGCTGTGCCTG 60.603 55.000 0.00 0.00 0.00 4.85
5377 5535 1.301716 CGGTTGTAGCTGTGCCTGT 60.302 57.895 0.00 0.00 0.00 4.00
5491 5650 5.882557 TCTCAAGATTATCACTTTCTTGCCC 59.117 40.000 6.95 0.00 43.78 5.36
5525 5684 6.041423 ACTTGAATTTGGCAGGAATTTAGG 57.959 37.500 0.00 0.00 0.00 2.69
5526 5685 4.470334 TGAATTTGGCAGGAATTTAGGC 57.530 40.909 0.00 0.00 0.00 3.93
5527 5686 3.837146 TGAATTTGGCAGGAATTTAGGCA 59.163 39.130 0.00 0.00 35.94 4.75
5528 5687 4.285517 TGAATTTGGCAGGAATTTAGGCAA 59.714 37.500 9.55 9.55 44.55 4.52
5530 5689 3.959535 TTGGCAGGAATTTAGGCAAAG 57.040 42.857 10.71 0.00 43.51 2.77
5531 5690 1.550072 TGGCAGGAATTTAGGCAAAGC 59.450 47.619 0.00 0.00 34.72 3.51
5532 5691 1.550072 GGCAGGAATTTAGGCAAAGCA 59.450 47.619 0.00 0.00 0.00 3.91
5533 5692 2.028203 GGCAGGAATTTAGGCAAAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
5534 5693 3.369787 GGCAGGAATTTAGGCAAAGCAAT 60.370 43.478 0.00 0.00 0.00 3.56
5535 5694 3.619929 GCAGGAATTTAGGCAAAGCAATG 59.380 43.478 0.00 0.00 0.00 2.82
5556 5726 8.796475 GCAATGGCTTCTTATCAAATATAGGAA 58.204 33.333 0.00 0.00 36.96 3.36
5619 5808 8.951954 ATTTCTACATAGTCGCTATAAAGTCG 57.048 34.615 0.08 0.00 0.00 4.18
5670 5859 8.919145 TGAAAATACCAAAGGTGAACATAGTTT 58.081 29.630 0.00 0.00 36.19 2.66
5685 5874 1.896220 AGTTTCACGTGCATCCACAT 58.104 45.000 11.67 0.00 42.17 3.21
5686 5875 3.052455 AGTTTCACGTGCATCCACATA 57.948 42.857 11.67 0.00 42.17 2.29
5899 6567 3.218398 CAGTGCTTTTTCGTAGCTTTCG 58.782 45.455 0.00 0.00 39.38 3.46
5910 6578 3.492011 TCGTAGCTTTCGTTTTGACCTTC 59.508 43.478 0.00 0.00 0.00 3.46
5919 6587 6.963049 TTCGTTTTGACCTTCTATAGCTTC 57.037 37.500 0.00 0.00 0.00 3.86
5945 6613 9.653287 CTTTTACTCAGGTCTTACACATGATTA 57.347 33.333 0.00 0.00 44.65 1.75
5967 6635 3.848272 TTTTTGCGGAAGACATGGATC 57.152 42.857 0.00 0.00 0.00 3.36
5990 6658 3.934579 TGATTGGTGTCATGACATCGAAG 59.065 43.478 28.63 0.00 45.12 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.467131 GCCTTTGCAAGAACAATGTATGTTTTT 60.467 33.333 0.00 0.00 44.59 1.94
1 2 6.018016 GCCTTTGCAAGAACAATGTATGTTTT 60.018 34.615 0.00 0.00 44.33 2.43
2 3 5.466393 GCCTTTGCAAGAACAATGTATGTTT 59.534 36.000 0.00 0.00 44.33 2.83
3 4 4.990426 GCCTTTGCAAGAACAATGTATGTT 59.010 37.500 0.00 0.00 45.80 2.71
4 5 4.281688 AGCCTTTGCAAGAACAATGTATGT 59.718 37.500 0.00 0.00 42.07 2.29
5 6 4.624024 CAGCCTTTGCAAGAACAATGTATG 59.376 41.667 0.00 0.00 41.13 2.39
6 7 4.322198 CCAGCCTTTGCAAGAACAATGTAT 60.322 41.667 0.00 0.00 41.13 2.29
7 8 3.005684 CCAGCCTTTGCAAGAACAATGTA 59.994 43.478 0.00 0.00 41.13 2.29
8 9 2.224113 CCAGCCTTTGCAAGAACAATGT 60.224 45.455 0.00 0.00 41.13 2.71
9 10 2.409975 CCAGCCTTTGCAAGAACAATG 58.590 47.619 0.00 0.00 41.13 2.82
10 11 1.345415 CCCAGCCTTTGCAAGAACAAT 59.655 47.619 0.00 0.00 41.13 2.71
11 12 0.752054 CCCAGCCTTTGCAAGAACAA 59.248 50.000 0.00 0.00 41.13 2.83
12 13 0.396974 ACCCAGCCTTTGCAAGAACA 60.397 50.000 0.00 0.00 41.13 3.18
13 14 0.032540 CACCCAGCCTTTGCAAGAAC 59.967 55.000 0.00 0.00 41.13 3.01
14 15 0.396974 ACACCCAGCCTTTGCAAGAA 60.397 50.000 0.00 0.00 41.13 2.52
15 16 0.476338 TACACCCAGCCTTTGCAAGA 59.524 50.000 0.00 0.00 41.13 3.02
16 17 0.598065 GTACACCCAGCCTTTGCAAG 59.402 55.000 0.00 0.00 41.13 4.01
17 18 0.184933 AGTACACCCAGCCTTTGCAA 59.815 50.000 0.00 0.00 41.13 4.08
18 19 0.250727 GAGTACACCCAGCCTTTGCA 60.251 55.000 0.00 0.00 41.13 4.08
19 20 1.298859 CGAGTACACCCAGCCTTTGC 61.299 60.000 0.00 0.00 37.95 3.68
20 21 1.298859 GCGAGTACACCCAGCCTTTG 61.299 60.000 0.00 0.00 0.00 2.77
21 22 1.003718 GCGAGTACACCCAGCCTTT 60.004 57.895 0.00 0.00 0.00 3.11
22 23 1.553690 ATGCGAGTACACCCAGCCTT 61.554 55.000 0.00 0.00 0.00 4.35
23 24 1.961180 GATGCGAGTACACCCAGCCT 61.961 60.000 0.00 0.00 0.00 4.58
24 25 1.521681 GATGCGAGTACACCCAGCC 60.522 63.158 0.00 0.00 0.00 4.85
25 26 1.878522 CGATGCGAGTACACCCAGC 60.879 63.158 0.00 0.00 0.00 4.85
26 27 1.878522 GCGATGCGAGTACACCCAG 60.879 63.158 0.00 0.00 0.00 4.45
27 28 2.183300 GCGATGCGAGTACACCCA 59.817 61.111 0.00 0.00 0.00 4.51
39 40 8.820933 AGGAAATGTATTAATATCATCGCGATG 58.179 33.333 37.19 37.19 40.09 3.84
103 104 0.951040 CAGCAAAGGACACCGACTCC 60.951 60.000 0.00 0.00 0.00 3.85
142 143 1.335597 CGTGTCGCAACTAGAACCAGA 60.336 52.381 0.00 0.00 0.00 3.86
166 167 1.226686 CCATACTCGCATGAGCAGGC 61.227 60.000 0.00 0.00 46.69 4.85
233 235 5.477637 TCACCATTTTTCATGATCTCAGCAA 59.522 36.000 0.00 0.00 0.00 3.91
236 238 5.448225 CCGTCACCATTTTTCATGATCTCAG 60.448 44.000 0.00 0.00 0.00 3.35
255 257 6.169800 TCAAAATCATCTTGTGATACCGTCA 58.830 36.000 0.00 0.00 46.80 4.35
256 258 6.662414 TCAAAATCATCTTGTGATACCGTC 57.338 37.500 0.00 0.00 46.80 4.79
257 259 7.630242 AATCAAAATCATCTTGTGATACCGT 57.370 32.000 0.00 0.00 46.80 4.83
258 260 8.183536 TCAAATCAAAATCATCTTGTGATACCG 58.816 33.333 0.00 0.00 46.80 4.02
274 277 5.787953 TGAGAAGCACCATCAAATCAAAA 57.212 34.783 0.00 0.00 0.00 2.44
331 334 1.176527 CAACCACTGAATGCCGGATT 58.823 50.000 5.05 1.53 0.00 3.01
335 338 0.734889 GATCCAACCACTGAATGCCG 59.265 55.000 0.00 0.00 0.00 5.69
339 342 1.405526 CGTCGGATCCAACCACTGAAT 60.406 52.381 13.41 0.00 0.00 2.57
343 346 2.978824 CCGTCGGATCCAACCACT 59.021 61.111 13.41 0.00 0.00 4.00
366 369 1.009829 AAGGATCAACGATCAAGCGC 58.990 50.000 0.00 0.00 40.50 5.92
375 378 5.886960 AGAAATTCTCCAAAGGATCAACG 57.113 39.130 0.00 0.00 0.00 4.10
380 383 7.673082 ACAATGAGAAGAAATTCTCCAAAGGAT 59.327 33.333 13.81 0.00 45.16 3.24
409 430 2.027285 TCCGCACCAATCATCTCTTTCA 60.027 45.455 0.00 0.00 0.00 2.69
413 434 1.487976 ACATCCGCACCAATCATCTCT 59.512 47.619 0.00 0.00 0.00 3.10
416 437 0.664761 CCACATCCGCACCAATCATC 59.335 55.000 0.00 0.00 0.00 2.92
417 438 0.034186 ACCACATCCGCACCAATCAT 60.034 50.000 0.00 0.00 0.00 2.45
432 461 4.454504 AGAATCGACCATAACAACAACCAC 59.545 41.667 0.00 0.00 0.00 4.16
460 489 7.615582 AACTCTGAAGCGATCAAAATAATGA 57.384 32.000 0.00 0.00 37.67 2.57
495 524 2.804828 AAGCTACGCCTTGGTGGAGC 62.805 60.000 25.39 25.39 39.39 4.70
541 570 5.127845 ACCAACACACATAAAAATCACACCA 59.872 36.000 0.00 0.00 0.00 4.17
557 586 1.398739 CACGCAACTAACACCAACACA 59.601 47.619 0.00 0.00 0.00 3.72
569 598 3.543680 ATAGGTAAGATGCACGCAACT 57.456 42.857 0.00 0.00 0.00 3.16
571 600 4.098807 TCTGTATAGGTAAGATGCACGCAA 59.901 41.667 0.00 0.00 0.00 4.85
573 602 4.230657 CTCTGTATAGGTAAGATGCACGC 58.769 47.826 0.00 0.00 0.00 5.34
574 603 4.799678 CCTCTGTATAGGTAAGATGCACG 58.200 47.826 0.00 0.00 31.46 5.34
600 629 7.065085 GGGATACATACATAATGAGCACACATC 59.935 40.741 0.00 0.00 39.07 3.06
607 636 9.331282 GGATTAAGGGATACATACATAATGAGC 57.669 37.037 0.00 0.00 39.07 4.26
614 643 6.702449 TGCAGGATTAAGGGATACATACAT 57.298 37.500 0.00 0.00 39.74 2.29
618 647 7.177392 GCTTAAATGCAGGATTAAGGGATACAT 59.823 37.037 21.39 0.00 38.79 2.29
671 702 2.961741 TGTGCATTCTTGTGGGCTTTTA 59.038 40.909 0.00 0.00 0.00 1.52
760 791 6.641169 TGTCTAGGCTTCTATAGTGATGTG 57.359 41.667 0.00 0.00 0.00 3.21
898 929 4.529769 GGTTAGGTTGGGAGTAGTACAAGT 59.470 45.833 2.52 0.00 0.00 3.16
1114 1154 2.281070 AACACGGCAGAGCACAGG 60.281 61.111 0.00 0.00 0.00 4.00
1281 1324 4.767255 AGCTTCTTGCCGCCTCCG 62.767 66.667 0.00 0.00 44.23 4.63
1480 1523 0.030638 CGGAACAAACCACCAAGCTG 59.969 55.000 0.00 0.00 0.00 4.24
1481 1524 1.106944 CCGGAACAAACCACCAAGCT 61.107 55.000 0.00 0.00 0.00 3.74
1532 1578 3.325201 AAGAATCGGCCGTGGACCC 62.325 63.158 27.15 9.62 0.00 4.46
1608 1654 0.368227 GATTGACACGAAGCGCTGAG 59.632 55.000 12.58 11.21 0.00 3.35
1610 1656 0.179240 GTGATTGACACGAAGCGCTG 60.179 55.000 12.58 0.57 39.78 5.18
1623 1669 0.314935 AGGCGCAAACCAAGTGATTG 59.685 50.000 10.83 0.00 0.00 2.67
1638 1684 0.389391 ATCGACCAGTAATCCAGGCG 59.611 55.000 0.00 0.00 0.00 5.52
1699 1745 0.670546 ATCAAACACTCCGCTGGACG 60.671 55.000 0.00 0.00 43.15 4.79
1842 1888 3.996032 GCAGACTGCTCGTTTTCATAAG 58.004 45.455 20.41 0.00 40.96 1.73
1908 1955 3.166679 AGGGAGTACCAGAGAACACTTC 58.833 50.000 0.00 0.00 43.89 3.01
1924 1971 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
1925 1972 5.429681 TCATCTATTTTGAAACGGAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
1926 1973 5.239525 GGATCATCTATTTTGAAACGGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
1927 1974 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
1928 1975 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
1929 1976 6.884295 AGTTGGATCATCTATTTTGAAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
1930 1977 7.088589 AGTTGGATCATCTATTTTGAAACGG 57.911 36.000 0.00 0.00 0.00 4.44
1931 1978 8.853345 CAAAGTTGGATCATCTATTTTGAAACG 58.147 33.333 0.00 0.00 0.00 3.60
1932 1979 9.696917 ACAAAGTTGGATCATCTATTTTGAAAC 57.303 29.630 12.56 0.00 0.00 2.78
1935 1982 9.739276 AGTACAAAGTTGGATCATCTATTTTGA 57.261 29.630 12.56 0.00 0.00 2.69
1958 2005 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
1959 2006 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
1960 2007 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
1961 2008 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
1962 2009 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
1963 2010 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
1964 2011 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
1965 2012 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
1966 2013 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1967 2014 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1968 2015 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1969 2016 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1970 2017 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1971 2018 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1972 2019 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1973 2020 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1974 2021 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1975 2022 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1976 2023 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1977 2024 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1978 2025 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1979 2026 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1980 2027 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1981 2028 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1982 2029 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1983 2030 4.150897 TCCCTCCGTTCCAAAATAGATG 57.849 45.455 0.00 0.00 0.00 2.90
1984 2031 5.844516 TCTATCCCTCCGTTCCAAAATAGAT 59.155 40.000 0.00 0.00 0.00 1.98
1985 2032 5.213519 TCTATCCCTCCGTTCCAAAATAGA 58.786 41.667 0.00 0.00 0.00 1.98
1986 2033 5.546621 TCTATCCCTCCGTTCCAAAATAG 57.453 43.478 0.00 0.00 0.00 1.73
1987 2034 5.221843 CCATCTATCCCTCCGTTCCAAAATA 60.222 44.000 0.00 0.00 0.00 1.40
1988 2035 4.446311 CCATCTATCCCTCCGTTCCAAAAT 60.446 45.833 0.00 0.00 0.00 1.82
1989 2036 3.118038 CCATCTATCCCTCCGTTCCAAAA 60.118 47.826 0.00 0.00 0.00 2.44
1990 2037 2.438021 CCATCTATCCCTCCGTTCCAAA 59.562 50.000 0.00 0.00 0.00 3.28
1991 2038 2.047061 CCATCTATCCCTCCGTTCCAA 58.953 52.381 0.00 0.00 0.00 3.53
1992 2039 1.717032 CCATCTATCCCTCCGTTCCA 58.283 55.000 0.00 0.00 0.00 3.53
1993 2040 0.977395 CCCATCTATCCCTCCGTTCC 59.023 60.000 0.00 0.00 0.00 3.62
1994 2041 1.619332 GTCCCATCTATCCCTCCGTTC 59.381 57.143 0.00 0.00 0.00 3.95
1995 2042 1.062428 TGTCCCATCTATCCCTCCGTT 60.062 52.381 0.00 0.00 0.00 4.44
1996 2043 0.561184 TGTCCCATCTATCCCTCCGT 59.439 55.000 0.00 0.00 0.00 4.69
1997 2044 1.552337 CATGTCCCATCTATCCCTCCG 59.448 57.143 0.00 0.00 0.00 4.63
1998 2045 2.836981 CTCATGTCCCATCTATCCCTCC 59.163 54.545 0.00 0.00 0.00 4.30
1999 2046 3.515562 ACTCATGTCCCATCTATCCCTC 58.484 50.000 0.00 0.00 0.00 4.30
2000 2047 3.645053 ACTCATGTCCCATCTATCCCT 57.355 47.619 0.00 0.00 0.00 4.20
2001 2048 3.244700 CCAACTCATGTCCCATCTATCCC 60.245 52.174 0.00 0.00 0.00 3.85
2002 2049 3.392616 ACCAACTCATGTCCCATCTATCC 59.607 47.826 0.00 0.00 0.00 2.59
2003 2050 4.696479 ACCAACTCATGTCCCATCTATC 57.304 45.455 0.00 0.00 0.00 2.08
2004 2051 4.228210 ACAACCAACTCATGTCCCATCTAT 59.772 41.667 0.00 0.00 0.00 1.98
2005 2052 3.587061 ACAACCAACTCATGTCCCATCTA 59.413 43.478 0.00 0.00 0.00 1.98
2006 2053 2.376518 ACAACCAACTCATGTCCCATCT 59.623 45.455 0.00 0.00 0.00 2.90
2036 2086 0.954452 CCAAGGGCAAGAACAGTGAC 59.046 55.000 0.00 0.00 0.00 3.67
2037 2087 3.419793 CCAAGGGCAAGAACAGTGA 57.580 52.632 0.00 0.00 0.00 3.41
2251 2301 6.889198 AGCAGTTAAGCTGGACTGATTAATA 58.111 36.000 25.68 0.00 44.65 0.98
2383 2458 4.946157 CCATATTGCACCTCTCTTCAGTTT 59.054 41.667 0.00 0.00 0.00 2.66
2524 2640 5.218885 CACTATTCTGAGAATCTACAGGCG 58.781 45.833 11.53 0.00 34.92 5.52
2577 2701 6.837568 CCCACTCCAATAAAGTAGGTAGTAGA 59.162 42.308 0.00 0.00 0.00 2.59
2578 2702 6.837568 TCCCACTCCAATAAAGTAGGTAGTAG 59.162 42.308 0.00 0.00 28.94 2.57
2671 2795 4.242336 AGGAGAAGGAATAAAAGCCAGG 57.758 45.455 0.00 0.00 0.00 4.45
2673 2797 5.010282 GTCAAGGAGAAGGAATAAAAGCCA 58.990 41.667 0.00 0.00 0.00 4.75
2823 2948 7.194112 TCATAACCACTGGAATGACATTCTA 57.806 36.000 23.87 18.61 39.24 2.10
2827 2952 6.009589 TGTTTCATAACCACTGGAATGACAT 58.990 36.000 13.97 0.00 32.01 3.06
2831 2962 6.207417 AGACTTGTTTCATAACCACTGGAATG 59.793 38.462 0.71 5.55 33.15 2.67
2832 2963 6.306987 AGACTTGTTTCATAACCACTGGAAT 58.693 36.000 0.71 0.00 33.15 3.01
2833 2964 5.690865 AGACTTGTTTCATAACCACTGGAA 58.309 37.500 0.71 0.00 33.15 3.53
2834 2965 5.304686 AGACTTGTTTCATAACCACTGGA 57.695 39.130 0.71 0.00 33.15 3.86
2835 2966 7.390440 TCATTAGACTTGTTTCATAACCACTGG 59.610 37.037 0.00 0.00 33.15 4.00
2836 2967 8.322906 TCATTAGACTTGTTTCATAACCACTG 57.677 34.615 0.00 0.00 33.15 3.66
2837 2968 8.918202 TTCATTAGACTTGTTTCATAACCACT 57.082 30.769 0.00 0.00 33.15 4.00
2869 3000 5.708736 TGGGACATTATACCATGTGACTT 57.291 39.130 0.00 0.00 37.52 3.01
2887 3018 4.081087 GCTAGTCAAGGTTAACTCATGGGA 60.081 45.833 0.00 0.00 0.00 4.37
2921 3052 4.532314 AGTACCTAAAGAAACGAGGGTG 57.468 45.455 0.00 0.00 34.41 4.61
2950 3081 5.596361 ACGGACAGAATCAGATAATCAGACT 59.404 40.000 0.00 0.00 0.00 3.24
2953 3084 6.015856 ACCTACGGACAGAATCAGATAATCAG 60.016 42.308 0.00 0.00 0.00 2.90
2992 3124 7.619302 TGGCATAAAGGATTTTTAGGAGACAAT 59.381 33.333 0.00 0.00 40.09 2.71
3002 3134 6.267471 TGACTTCACTGGCATAAAGGATTTTT 59.733 34.615 8.07 0.00 40.09 1.94
3059 3191 7.600375 CGTCTAGTATGCTCATATTTTCACCAT 59.400 37.037 0.00 0.00 0.00 3.55
3081 3213 8.861086 ACTATATTGATGGAATCTTACACGTCT 58.139 33.333 0.00 0.00 45.81 4.18
3104 3236 2.837591 TGGGCTGAGCTACAATGAACTA 59.162 45.455 3.72 0.00 0.00 2.24
3109 3241 2.104451 AGAGATGGGCTGAGCTACAATG 59.896 50.000 3.72 0.00 0.00 2.82
3120 3252 5.420104 CCAAAAAGTATCAAAGAGATGGGCT 59.580 40.000 0.00 0.00 37.57 5.19
3138 3270 4.714308 CCATGCCCTTACTATTCCCAAAAA 59.286 41.667 0.00 0.00 0.00 1.94
3144 3276 2.508526 CAGCCATGCCCTTACTATTCC 58.491 52.381 0.00 0.00 0.00 3.01
3176 3309 9.372369 GCTAGTAGTGACTATTGTTCATTTCTT 57.628 33.333 0.00 0.00 37.53 2.52
3194 3327 6.125719 TCAAGTGATCTGATCAGCTAGTAGT 58.874 40.000 20.09 2.82 40.53 2.73
3275 3408 5.125417 GCAGTGAAAGCAAGGGAATATTACA 59.875 40.000 0.00 0.00 0.00 2.41
3280 3413 3.084039 CTGCAGTGAAAGCAAGGGAATA 58.916 45.455 5.25 0.00 42.17 1.75
3282 3415 1.133823 TCTGCAGTGAAAGCAAGGGAA 60.134 47.619 14.67 0.00 42.17 3.97
3565 3698 9.621629 TTCAAATAAGACTGTTTAAGTGGAAGA 57.378 29.630 0.00 0.00 40.07 2.87
3693 3826 5.761234 ACGAACACTAAGGCATGTTTAGAAA 59.239 36.000 19.47 0.00 39.13 2.52
3792 3925 2.057922 TCCCATCCCTGGAGAATAAGC 58.942 52.381 0.00 0.00 46.37 3.09
3965 4098 8.363390 TGCAACCACATGAAAATACTGAAAATA 58.637 29.630 0.00 0.00 0.00 1.40
3981 4114 4.032960 TGGAAGAGTATTGCAACCACAT 57.967 40.909 0.00 0.00 0.00 3.21
3989 4122 4.706962 ACAGGGAAAATGGAAGAGTATTGC 59.293 41.667 0.00 0.00 0.00 3.56
3991 4124 8.971073 CATTTACAGGGAAAATGGAAGAGTATT 58.029 33.333 0.00 0.00 39.55 1.89
4347 4497 8.823220 AAGGACCATTGTTAGTAAAATGCTAT 57.177 30.769 0.00 2.47 33.34 2.97
4473 4624 3.842007 TGAAAGAACGTCCCAAACCTA 57.158 42.857 0.00 0.00 0.00 3.08
4703 4854 5.048852 GGCATCTGAGATTAAAGCATCCTTC 60.049 44.000 5.10 0.00 0.00 3.46
4835 4986 0.939577 CGTCCACCGGCATAATCTCG 60.940 60.000 0.00 0.00 0.00 4.04
4919 5070 2.744202 CCATTCTTCCTCCTCGTTTGTG 59.256 50.000 0.00 0.00 0.00 3.33
4934 5085 0.459237 CTTCGAGCGCAGACCATTCT 60.459 55.000 11.47 0.00 0.00 2.40
5104 5255 1.534336 AAAATGCCGGCTGTGATGCA 61.534 50.000 29.70 4.25 38.23 3.96
5260 5418 1.780503 ACAAGCAAAGAAGCCCAAGT 58.219 45.000 0.00 0.00 34.23 3.16
5274 5432 7.816945 AAAACTTTCATATGCACATACAAGC 57.183 32.000 0.00 0.00 0.00 4.01
5372 5530 8.494016 AATTGAGTTATTGTTCTAGTACAGGC 57.506 34.615 2.27 0.00 0.00 4.85
5373 5531 9.877178 AGAATTGAGTTATTGTTCTAGTACAGG 57.123 33.333 2.27 0.00 0.00 4.00
5408 5566 3.364964 GGCGAAAATTCATATGGCCTACG 60.365 47.826 3.32 4.19 36.21 3.51
5491 5650 5.927689 TGCCAAATTCAAGTCTTATGCAAAG 59.072 36.000 0.00 0.00 0.00 2.77
5502 5661 5.569428 GCCTAAATTCCTGCCAAATTCAAGT 60.569 40.000 0.00 0.00 0.00 3.16
5530 5689 8.340618 TCCTATATTTGATAAGAAGCCATTGC 57.659 34.615 0.00 0.00 37.95 3.56
5532 5691 9.018582 GCTTCCTATATTTGATAAGAAGCCATT 57.981 33.333 13.44 0.00 45.57 3.16
5533 5692 8.572855 GCTTCCTATATTTGATAAGAAGCCAT 57.427 34.615 13.44 0.00 45.57 4.40
5534 5693 7.986085 GCTTCCTATATTTGATAAGAAGCCA 57.014 36.000 13.44 0.00 45.57 4.75
5556 5726 1.074405 TCAGCACCAAATCTCTTGGCT 59.926 47.619 3.40 0.00 43.23 4.75
5670 5859 4.765273 ACTATTTATGTGGATGCACGTGA 58.235 39.130 22.23 11.06 0.00 4.35
5910 6578 9.738832 GTAAGACCTGAGTAAAAGAAGCTATAG 57.261 37.037 0.00 0.00 0.00 1.31
5919 6587 8.553459 AATCATGTGTAAGACCTGAGTAAAAG 57.447 34.615 0.00 0.00 33.29 2.27
5967 6635 3.524541 TCGATGTCATGACACCAATCAG 58.475 45.455 30.09 17.84 45.05 2.90


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

AutoCloner maintained by Alex Coulton.