Multiple sequence alignment - TraesCS4A01G152800

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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 TraesCS4A01G152800 chr4A 100.000 2252 0 0 1 2252 309479441 309477190 0.000000e+00 4159
1 TraesCS4A01G152800 chr4A 93.567 342 11 2 1920 2252 350847338 350846999 1.200000e-137 499
2 TraesCS4A01G152800 chr4A 96.078 153 6 0 1 153 124218332 124218180 1.340000e-62 250
3 TraesCS4A01G152800 chr4A 93.333 165 9 2 2089 2252 466148701 466148538 2.230000e-60 243
4 TraesCS4A01G152800 chr4A 94.366 142 5 1 1919 2057 466148842 466148701 4.870000e-52 215
5 TraesCS4A01G152800 chr3B 97.550 1755 41 2 152 1905 101909116 101907363 0.000000e+00 3001
6 TraesCS4A01G152800 chr3B 97.500 200 5 0 152 351 795014168 795013969 2.140000e-90 342
7 TraesCS4A01G152800 chr3B 96.732 153 5 0 1 153 101909584 101909432 2.870000e-64 255
8 TraesCS4A01G152800 chr5D 97.064 1771 47 4 152 1921 503302901 503304667 0.000000e+00 2977
9 TraesCS4A01G152800 chr5D 96.956 1774 51 3 152 1924 6165884 6164113 0.000000e+00 2974
10 TraesCS4A01G152800 chr5D 96.505 1774 59 3 152 1924 329152821 329151050 0.000000e+00 2929
11 TraesCS4A01G152800 chr5D 97.351 1397 36 1 152 1547 6264911 6263515 0.000000e+00 2374
12 TraesCS4A01G152800 chr5D 96.432 1065 37 1 860 1924 6263167 6262104 0.000000e+00 1755
13 TraesCS4A01G152800 chr5D 97.386 153 4 0 1 153 6166350 6166198 6.170000e-66 261
14 TraesCS4A01G152800 chr5D 97.386 153 4 0 1 153 6265379 6265227 6.170000e-66 261
15 TraesCS4A01G152800 chr1D 96.838 1771 51 4 152 1921 254446068 254447834 0.000000e+00 2955
16 TraesCS4A01G152800 chr1D 96.561 1774 58 2 152 1924 51861004 51859233 0.000000e+00 2935
17 TraesCS4A01G152800 chr1D 96.078 153 6 0 1 153 246423076 246423228 1.340000e-62 250
18 TraesCS4A01G152800 chr4D 95.888 1605 61 3 152 1755 19879521 19881121 0.000000e+00 2593
19 TraesCS4A01G152800 chr4D 95.122 820 36 4 398 1216 206989846 206989030 0.000000e+00 1290
20 TraesCS4A01G152800 chr4D 96.732 153 5 0 1 153 19879053 19879205 2.870000e-64 255
21 TraesCS4A01G152800 chr3D 95.152 330 16 0 1923 2252 141475211 141474882 2.560000e-144 521
22 TraesCS4A01G152800 chr3D 93.865 326 13 3 1927 2252 405523859 405523541 3.360000e-133 484
23 TraesCS4A01G152800 chr6D 94.675 338 12 3 1921 2252 38563835 38564172 9.220000e-144 520
24 TraesCS4A01G152800 chr7A 89.685 349 13 10 1922 2252 455695867 455696210 7.440000e-115 424
25 TraesCS4A01G152800 chr3A 94.416 197 10 1 1921 2116 6673391 6673195 3.630000e-78 302
26 TraesCS4A01G152800 chr6B 93.970 199 10 2 1918 2115 266830804 266830607 1.310000e-77 300
27 TraesCS4A01G152800 chr6B 97.386 153 4 0 1 153 249861026 249861178 6.170000e-66 261
28 TraesCS4A01G152800 chr6B 94.545 165 7 2 2089 2252 280037766 280037603 1.030000e-63 254
29 TraesCS4A01G152800 chr2B 96.732 153 5 0 1 153 280890798 280890950 2.870000e-64 255
30 TraesCS4A01G152800 chrUn 96.078 153 6 0 1 153 439345869 439346021 1.340000e-62 250
31 TraesCS4A01G152800 chr7B 92.727 165 10 2 2089 2252 78125508 78125345 1.040000e-58 237
32 TraesCS4A01G152800 chr7B 94.964 139 5 1 1921 2057 78125646 78125508 1.350000e-52 217
33 TraesCS4A01G152800 chr5B 87.222 180 10 2 2085 2252 61558978 61559156 2.280000e-45 193


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 TraesCS4A01G152800 chr4A 309477190 309479441 2251 True 4159.000000 4159 100.000000 1 2252 1 chr4A.!!$R2 2251
1 TraesCS4A01G152800 chr3B 101907363 101909584 2221 True 1628.000000 3001 97.141000 1 1905 2 chr3B.!!$R2 1904
2 TraesCS4A01G152800 chr5D 503302901 503304667 1766 False 2977.000000 2977 97.064000 152 1921 1 chr5D.!!$F1 1769
3 TraesCS4A01G152800 chr5D 329151050 329152821 1771 True 2929.000000 2929 96.505000 152 1924 1 chr5D.!!$R1 1772
4 TraesCS4A01G152800 chr5D 6164113 6166350 2237 True 1617.500000 2974 97.171000 1 1924 2 chr5D.!!$R2 1923
5 TraesCS4A01G152800 chr5D 6262104 6265379 3275 True 1463.333333 2374 97.056333 1 1924 3 chr5D.!!$R3 1923
6 TraesCS4A01G152800 chr1D 254446068 254447834 1766 False 2955.000000 2955 96.838000 152 1921 1 chr1D.!!$F2 1769
7 TraesCS4A01G152800 chr1D 51859233 51861004 1771 True 2935.000000 2935 96.561000 152 1924 1 chr1D.!!$R1 1772
8 TraesCS4A01G152800 chr4D 19879053 19881121 2068 False 1424.000000 2593 96.310000 1 1755 2 chr4D.!!$F1 1754
9 TraesCS4A01G152800 chr4D 206989030 206989846 816 True 1290.000000 1290 95.122000 398 1216 1 chr4D.!!$R1 818

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
680 999 1.933853 CGGGGATCTGCTAAAGAAACG 59.066 52.381 0.0 0.0 38.79 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 3344 0.03213 ATGTCTATGCCGTCGCGAAT 59.968 50.0 12.06 2.67 38.08 3.34 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
67 68 2.288948 TGCATTGTTGGAACTGGATTGC 60.289 45.455 0.00 0.00 0.00 3.56
240 558 4.675063 ATGGAGTTGTTAGGTTGGGATT 57.325 40.909 0.00 0.00 0.00 3.01
311 629 5.316327 AGCGAGCGAATCATCTTATATCA 57.684 39.130 0.00 0.00 0.00 2.15
313 631 4.859245 GCGAGCGAATCATCTTATATCACA 59.141 41.667 0.00 0.00 0.00 3.58
576 894 3.439154 TGCCCTATTTGCAAGATGGAAA 58.561 40.909 13.10 0.00 41.75 3.13
680 999 1.933853 CGGGGATCTGCTAAAGAAACG 59.066 52.381 0.00 0.00 38.79 3.60
930 1250 4.657814 AATTCATGGGTGTTCTACTGGT 57.342 40.909 0.00 0.00 0.00 4.00
931 1251 4.657814 ATTCATGGGTGTTCTACTGGTT 57.342 40.909 0.00 0.00 0.00 3.67
950 1270 4.202284 TGGTTCCTACTCACTTGTTACACC 60.202 45.833 0.00 0.00 0.00 4.16
1018 1338 5.011635 GGAGAAATGGAAGTTTGGGCTTTAA 59.988 40.000 0.00 0.00 0.00 1.52
1033 1353 5.602978 TGGGCTTTAAAAGGATTTGGTGTTA 59.397 36.000 0.00 0.00 39.02 2.41
1111 1431 7.571428 GCCAAGAAATACTTAATGCTACGATCC 60.571 40.741 0.00 0.00 37.03 3.36
1197 1517 6.120905 ACTACGATCTTTGGCTCTAGAACTA 58.879 40.000 0.00 0.00 0.00 2.24
1355 1678 3.697166 TCCCCTCAACAAATAAAGGCTC 58.303 45.455 0.00 0.00 0.00 4.70
1394 1717 2.354704 CCTAATGGAGAAGTCGTTGGCA 60.355 50.000 0.00 0.00 34.57 4.92
1449 1772 6.894339 AACCGATAAACCAGAAAAAGATGT 57.106 33.333 0.00 0.00 0.00 3.06
1495 1818 4.222810 GGACCCATAAAAAGCAGGATTTGT 59.777 41.667 0.00 0.00 0.00 2.83
1532 2890 0.037326 AGCGAGCGGAGATGAAAACA 60.037 50.000 0.00 0.00 0.00 2.83
1580 2938 4.270008 CGGGGTAGAATTTGTGGATTCTT 58.730 43.478 5.55 0.00 42.24 2.52
1822 3184 5.205056 TGTAACCACAACATTTCTCCCTTT 58.795 37.500 0.00 0.00 0.00 3.11
1868 3230 3.924918 TTTCGAAATCGGGAAATTGCA 57.075 38.095 6.47 0.00 40.29 4.08
1874 3236 1.185315 ATCGGGAAATTGCAACAGGG 58.815 50.000 0.00 0.00 0.00 4.45
1914 3276 7.899973 AGAACAATTAGCAGATTTGGATTTGT 58.100 30.769 0.00 0.00 0.00 2.83
1921 3283 9.807649 ATTAGCAGATTTGGATTTGTGAATTAC 57.192 29.630 0.00 0.00 0.00 1.89
1924 3286 8.680903 AGCAGATTTGGATTTGTGAATTACTAG 58.319 33.333 0.00 0.00 0.00 2.57
1925 3287 8.462016 GCAGATTTGGATTTGTGAATTACTAGT 58.538 33.333 0.00 0.00 0.00 2.57
1933 3295 9.503427 GGATTTGTGAATTACTAGTACAAATGC 57.497 33.333 26.83 25.61 46.18 3.56
1934 3296 9.503427 GATTTGTGAATTACTAGTACAAATGCC 57.497 33.333 26.83 15.81 46.18 4.40
1935 3297 6.995511 TGTGAATTACTAGTACAAATGCCC 57.004 37.500 0.91 0.00 0.00 5.36
1936 3298 5.583061 TGTGAATTACTAGTACAAATGCCCG 59.417 40.000 0.91 0.00 0.00 6.13
1937 3299 5.583457 GTGAATTACTAGTACAAATGCCCGT 59.417 40.000 0.91 0.00 0.00 5.28
1938 3300 5.583061 TGAATTACTAGTACAAATGCCCGTG 59.417 40.000 0.91 0.00 0.00 4.94
1939 3301 1.734163 ACTAGTACAAATGCCCGTGC 58.266 50.000 0.00 0.00 38.26 5.34
1940 3302 0.650512 CTAGTACAAATGCCCGTGCG 59.349 55.000 0.00 0.00 41.78 5.34
1941 3303 0.037139 TAGTACAAATGCCCGTGCGT 60.037 50.000 0.00 0.00 41.78 5.24
1943 3305 0.727793 GTACAAATGCCCGTGCGTTG 60.728 55.000 0.00 1.29 45.88 4.10
1944 3306 2.465097 TACAAATGCCCGTGCGTTGC 62.465 55.000 0.00 0.00 45.88 4.17
1945 3307 3.600694 AAATGCCCGTGCGTTGCA 61.601 55.556 0.00 8.11 45.88 4.08
1946 3308 3.144120 AAATGCCCGTGCGTTGCAA 62.144 52.632 0.00 0.00 45.88 4.08
1947 3309 3.839642 AATGCCCGTGCGTTGCAAC 62.840 57.895 19.89 19.89 44.90 4.17
1976 3338 6.627690 AAAATAGAACACTACGACATGACG 57.372 37.500 15.87 15.87 39.31 4.35
1977 3339 2.631418 AGAACACTACGACATGACGG 57.369 50.000 20.92 7.33 37.61 4.79
1978 3340 1.201647 AGAACACTACGACATGACGGG 59.798 52.381 20.92 14.89 37.61 5.28
1979 3341 0.389426 AACACTACGACATGACGGGC 60.389 55.000 20.92 0.00 37.61 6.13
1980 3342 1.214325 CACTACGACATGACGGGCA 59.786 57.895 20.92 5.71 37.61 5.36
1981 3343 0.179111 CACTACGACATGACGGGCAT 60.179 55.000 20.92 0.00 37.85 4.40
1982 3344 1.066454 CACTACGACATGACGGGCATA 59.934 52.381 20.92 4.29 34.82 3.14
1983 3345 1.961394 ACTACGACATGACGGGCATAT 59.039 47.619 20.92 2.24 34.82 1.78
1984 3346 2.364324 ACTACGACATGACGGGCATATT 59.636 45.455 20.92 1.55 34.82 1.28
1985 3347 1.865865 ACGACATGACGGGCATATTC 58.134 50.000 20.92 0.00 34.82 1.75
1986 3348 0.784178 CGACATGACGGGCATATTCG 59.216 55.000 9.78 11.35 36.17 3.34
1987 3349 0.512952 GACATGACGGGCATATTCGC 59.487 55.000 0.00 0.00 34.82 4.70
1988 3350 1.221466 ACATGACGGGCATATTCGCG 61.221 55.000 10.09 10.09 46.01 5.87
1989 3351 0.943835 CATGACGGGCATATTCGCGA 60.944 55.000 17.85 3.71 43.79 5.87
1990 3352 0.944311 ATGACGGGCATATTCGCGAC 60.944 55.000 17.85 12.28 43.79 5.19
1991 3353 2.645510 GACGGGCATATTCGCGACG 61.646 63.158 17.85 10.24 43.79 5.12
1992 3354 3.403057 CGGGCATATTCGCGACGG 61.403 66.667 9.15 0.00 43.79 4.79
1993 3355 3.712881 GGGCATATTCGCGACGGC 61.713 66.667 9.15 10.26 0.00 5.68
1994 3356 2.964925 GGCATATTCGCGACGGCA 60.965 61.111 9.15 0.00 39.92 5.69
1995 3357 2.317609 GGCATATTCGCGACGGCAT 61.318 57.895 9.15 1.36 39.92 4.40
1996 3358 1.011968 GGCATATTCGCGACGGCATA 61.012 55.000 9.15 4.17 39.92 3.14
1997 3359 0.366871 GCATATTCGCGACGGCATAG 59.633 55.000 9.15 0.00 39.92 2.23
1998 3360 1.977188 CATATTCGCGACGGCATAGA 58.023 50.000 9.15 0.00 39.92 1.98
1999 3361 1.649171 CATATTCGCGACGGCATAGAC 59.351 52.381 9.15 0.00 39.92 2.59
2000 3362 0.664224 TATTCGCGACGGCATAGACA 59.336 50.000 9.15 0.00 39.92 3.41
2001 3363 0.032130 ATTCGCGACGGCATAGACAT 59.968 50.000 9.15 0.00 39.92 3.06
2002 3364 0.869880 TTCGCGACGGCATAGACATG 60.870 55.000 9.15 0.00 39.92 3.21
2003 3365 2.302952 CGCGACGGCATAGACATGG 61.303 63.158 0.00 0.00 39.92 3.66
2004 3366 1.956170 GCGACGGCATAGACATGGG 60.956 63.158 0.00 0.00 39.62 4.00
2005 3367 1.441729 CGACGGCATAGACATGGGT 59.558 57.895 0.00 0.00 32.36 4.51
2006 3368 0.671796 CGACGGCATAGACATGGGTA 59.328 55.000 0.00 0.00 32.36 3.69
2007 3369 1.272490 CGACGGCATAGACATGGGTAT 59.728 52.381 0.00 0.00 32.36 2.73
2008 3370 2.490509 CGACGGCATAGACATGGGTATA 59.509 50.000 0.00 0.00 32.36 1.47
2009 3371 3.130516 CGACGGCATAGACATGGGTATAT 59.869 47.826 0.00 0.00 31.79 0.86
2010 3372 4.683832 GACGGCATAGACATGGGTATATC 58.316 47.826 0.00 0.00 29.22 1.63
2011 3373 4.093743 ACGGCATAGACATGGGTATATCA 58.906 43.478 0.00 0.00 29.22 2.15
2012 3374 4.716784 ACGGCATAGACATGGGTATATCAT 59.283 41.667 0.00 0.00 29.22 2.45
2013 3375 5.163405 ACGGCATAGACATGGGTATATCATC 60.163 44.000 0.00 0.00 29.22 2.92
2014 3376 5.615289 GGCATAGACATGGGTATATCATCC 58.385 45.833 0.00 0.00 29.22 3.51
2015 3377 5.130975 GGCATAGACATGGGTATATCATCCA 59.869 44.000 0.00 0.00 29.22 3.41
2016 3378 6.183361 GGCATAGACATGGGTATATCATCCAT 60.183 42.308 0.00 0.00 41.53 3.41
2026 3388 8.391305 TGGGTATATCATCCATGACATAATCA 57.609 34.615 0.00 0.00 43.13 2.57
2028 3390 9.499479 GGGTATATCATCCATGACATAATCATC 57.501 37.037 0.00 0.00 45.52 2.92
2034 3396 9.969001 ATCATCCATGACATAATCATCACATAA 57.031 29.630 0.00 0.00 45.52 1.90
2035 3397 9.444600 TCATCCATGACATAATCATCACATAAG 57.555 33.333 0.00 0.00 45.52 1.73
2036 3398 7.677454 TCCATGACATAATCATCACATAAGC 57.323 36.000 0.00 0.00 45.52 3.09
2037 3399 7.225725 TCCATGACATAATCATCACATAAGCA 58.774 34.615 0.00 0.00 45.52 3.91
2038 3400 7.389607 TCCATGACATAATCATCACATAAGCAG 59.610 37.037 0.00 0.00 45.52 4.24
2039 3401 7.389607 CCATGACATAATCATCACATAAGCAGA 59.610 37.037 0.00 0.00 45.52 4.26
2040 3402 7.719778 TGACATAATCATCACATAAGCAGAC 57.280 36.000 0.00 0.00 29.99 3.51
2041 3403 7.274447 TGACATAATCATCACATAAGCAGACA 58.726 34.615 0.00 0.00 29.99 3.41
2042 3404 7.935210 TGACATAATCATCACATAAGCAGACAT 59.065 33.333 0.00 0.00 29.99 3.06
2043 3405 8.320396 ACATAATCATCACATAAGCAGACATC 57.680 34.615 0.00 0.00 0.00 3.06
2044 3406 7.935210 ACATAATCATCACATAAGCAGACATCA 59.065 33.333 0.00 0.00 0.00 3.07
2045 3407 6.615264 AATCATCACATAAGCAGACATCAC 57.385 37.500 0.00 0.00 0.00 3.06
2046 3408 5.349061 TCATCACATAAGCAGACATCACT 57.651 39.130 0.00 0.00 0.00 3.41
2047 3409 5.114081 TCATCACATAAGCAGACATCACTG 58.886 41.667 0.00 0.00 40.43 3.66
2048 3410 3.865446 TCACATAAGCAGACATCACTGG 58.135 45.455 0.00 0.00 38.22 4.00
2050 3412 4.466015 TCACATAAGCAGACATCACTGGTA 59.534 41.667 0.00 0.00 45.82 3.25
2051 3413 5.129320 TCACATAAGCAGACATCACTGGTAT 59.871 40.000 0.00 0.00 45.82 2.73
2052 3414 5.464722 CACATAAGCAGACATCACTGGTATC 59.535 44.000 0.00 0.00 45.82 2.24
2053 3415 5.365025 ACATAAGCAGACATCACTGGTATCT 59.635 40.000 0.00 0.00 45.82 1.98
2054 3416 4.833478 AAGCAGACATCACTGGTATCTT 57.167 40.909 0.00 0.00 45.82 2.40
2055 3417 4.833478 AGCAGACATCACTGGTATCTTT 57.167 40.909 0.00 0.00 44.94 2.52
2056 3418 5.171339 AGCAGACATCACTGGTATCTTTT 57.829 39.130 0.00 0.00 44.94 2.27
2057 3419 5.181748 AGCAGACATCACTGGTATCTTTTC 58.818 41.667 0.00 0.00 44.94 2.29
2058 3420 4.333926 GCAGACATCACTGGTATCTTTTCC 59.666 45.833 0.00 0.00 38.22 3.13
2059 3421 5.491070 CAGACATCACTGGTATCTTTTCCA 58.509 41.667 0.00 0.00 34.64 3.53
2060 3422 5.939883 CAGACATCACTGGTATCTTTTCCAA 59.060 40.000 0.00 0.00 34.64 3.53
2061 3423 6.430925 CAGACATCACTGGTATCTTTTCCAAA 59.569 38.462 0.00 0.00 34.64 3.28
2062 3424 7.004086 AGACATCACTGGTATCTTTTCCAAAA 58.996 34.615 0.00 0.00 33.06 2.44
2063 3425 7.505585 AGACATCACTGGTATCTTTTCCAAAAA 59.494 33.333 0.00 0.00 33.06 1.94
2064 3426 8.193953 ACATCACTGGTATCTTTTCCAAAAAT 57.806 30.769 0.00 0.00 33.06 1.82
2065 3427 9.308000 ACATCACTGGTATCTTTTCCAAAAATA 57.692 29.630 0.00 0.00 33.06 1.40
2071 3433 9.450807 CTGGTATCTTTTCCAAAAATAATAGCG 57.549 33.333 0.00 0.00 33.06 4.26
2072 3434 7.918562 TGGTATCTTTTCCAAAAATAATAGCGC 59.081 33.333 0.00 0.00 30.23 5.92
2073 3435 7.918562 GGTATCTTTTCCAAAAATAATAGCGCA 59.081 33.333 11.47 0.00 0.00 6.09
2074 3436 7.755582 ATCTTTTCCAAAAATAATAGCGCAC 57.244 32.000 11.47 0.00 0.00 5.34
2075 3437 6.682746 TCTTTTCCAAAAATAATAGCGCACA 58.317 32.000 11.47 0.00 0.00 4.57
2076 3438 6.584563 TCTTTTCCAAAAATAATAGCGCACAC 59.415 34.615 11.47 0.00 0.00 3.82
2077 3439 4.364415 TCCAAAAATAATAGCGCACACC 57.636 40.909 11.47 0.00 0.00 4.16
2078 3440 3.129638 TCCAAAAATAATAGCGCACACCC 59.870 43.478 11.47 0.00 0.00 4.61
2079 3441 3.130340 CCAAAAATAATAGCGCACACCCT 59.870 43.478 11.47 0.00 0.00 4.34
2080 3442 4.381505 CCAAAAATAATAGCGCACACCCTT 60.382 41.667 11.47 0.00 0.00 3.95
2081 3443 5.163602 CCAAAAATAATAGCGCACACCCTTA 60.164 40.000 11.47 0.00 0.00 2.69
2082 3444 5.494632 AAAATAATAGCGCACACCCTTAC 57.505 39.130 11.47 0.00 0.00 2.34
2083 3445 2.607631 TAATAGCGCACACCCTTACC 57.392 50.000 11.47 0.00 0.00 2.85
2084 3446 0.107361 AATAGCGCACACCCTTACCC 60.107 55.000 11.47 0.00 0.00 3.69
2085 3447 0.981277 ATAGCGCACACCCTTACCCT 60.981 55.000 11.47 0.00 0.00 4.34
2086 3448 0.324552 TAGCGCACACCCTTACCCTA 60.325 55.000 11.47 0.00 0.00 3.53
2087 3449 1.196104 AGCGCACACCCTTACCCTAA 61.196 55.000 11.47 0.00 0.00 2.69
2088 3450 0.107361 GCGCACACCCTTACCCTAAT 60.107 55.000 0.30 0.00 0.00 1.73
2089 3451 1.139455 GCGCACACCCTTACCCTAATA 59.861 52.381 0.30 0.00 0.00 0.98
2090 3452 2.420408 GCGCACACCCTTACCCTAATAA 60.420 50.000 0.30 0.00 0.00 1.40
2091 3453 3.463944 CGCACACCCTTACCCTAATAAG 58.536 50.000 0.00 0.00 32.78 1.73
2092 3454 3.211865 GCACACCCTTACCCTAATAAGC 58.788 50.000 0.00 0.00 31.80 3.09
2093 3455 3.371166 GCACACCCTTACCCTAATAAGCA 60.371 47.826 0.00 0.00 31.80 3.91
2094 3456 4.688874 GCACACCCTTACCCTAATAAGCAT 60.689 45.833 0.00 0.00 31.80 3.79
2095 3457 4.821805 CACACCCTTACCCTAATAAGCATG 59.178 45.833 0.00 0.00 31.80 4.06
2096 3458 4.141251 ACACCCTTACCCTAATAAGCATGG 60.141 45.833 0.00 0.00 31.80 3.66
2097 3459 3.181433 ACCCTTACCCTAATAAGCATGGC 60.181 47.826 0.00 0.00 31.80 4.40
2098 3460 3.074538 CCCTTACCCTAATAAGCATGGCT 59.925 47.826 0.00 0.00 42.56 4.75
2099 3461 4.327680 CCTTACCCTAATAAGCATGGCTC 58.672 47.826 0.00 0.00 38.25 4.70
2100 3462 4.202461 CCTTACCCTAATAAGCATGGCTCA 60.202 45.833 0.00 0.00 38.25 4.26
2101 3463 3.951563 ACCCTAATAAGCATGGCTCAA 57.048 42.857 0.00 0.00 38.25 3.02
2102 3464 3.825328 ACCCTAATAAGCATGGCTCAAG 58.175 45.455 0.00 0.00 38.25 3.02
2103 3465 3.152341 CCCTAATAAGCATGGCTCAAGG 58.848 50.000 0.00 0.00 38.25 3.61
2104 3466 3.181440 CCCTAATAAGCATGGCTCAAGGA 60.181 47.826 0.00 0.00 38.25 3.36
2105 3467 3.817647 CCTAATAAGCATGGCTCAAGGAC 59.182 47.826 0.00 0.00 38.25 3.85
2106 3468 2.355010 ATAAGCATGGCTCAAGGACC 57.645 50.000 0.00 0.00 38.25 4.46
2107 3469 0.255890 TAAGCATGGCTCAAGGACCC 59.744 55.000 0.00 0.00 38.25 4.46
2108 3470 1.504275 AAGCATGGCTCAAGGACCCT 61.504 55.000 0.00 0.00 38.25 4.34
2109 3471 1.452833 GCATGGCTCAAGGACCCTC 60.453 63.158 0.00 0.00 0.00 4.30
2110 3472 1.919600 GCATGGCTCAAGGACCCTCT 61.920 60.000 0.00 0.00 0.00 3.69
2111 3473 0.179936 CATGGCTCAAGGACCCTCTC 59.820 60.000 0.00 0.00 0.00 3.20
2112 3474 0.985490 ATGGCTCAAGGACCCTCTCC 60.985 60.000 0.00 0.00 39.81 3.71
2113 3475 1.613630 GGCTCAAGGACCCTCTCCA 60.614 63.158 0.00 0.00 42.46 3.86
2114 3476 1.599576 GCTCAAGGACCCTCTCCAC 59.400 63.158 0.00 0.00 42.46 4.02
2115 3477 0.907230 GCTCAAGGACCCTCTCCACT 60.907 60.000 0.00 0.00 42.46 4.00
2116 3478 1.190643 CTCAAGGACCCTCTCCACTC 58.809 60.000 0.00 0.00 42.46 3.51
2117 3479 0.487325 TCAAGGACCCTCTCCACTCA 59.513 55.000 0.00 0.00 42.46 3.41
2118 3480 1.132849 TCAAGGACCCTCTCCACTCAA 60.133 52.381 0.00 0.00 42.46 3.02
2119 3481 1.912043 CAAGGACCCTCTCCACTCAAT 59.088 52.381 0.00 0.00 42.46 2.57
2120 3482 2.307098 CAAGGACCCTCTCCACTCAATT 59.693 50.000 0.00 0.00 42.46 2.32
2121 3483 2.637165 AGGACCCTCTCCACTCAATTT 58.363 47.619 0.00 0.00 42.46 1.82
2122 3484 2.573915 AGGACCCTCTCCACTCAATTTC 59.426 50.000 0.00 0.00 42.46 2.17
2123 3485 2.305927 GGACCCTCTCCACTCAATTTCA 59.694 50.000 0.00 0.00 39.21 2.69
2124 3486 3.244911 GGACCCTCTCCACTCAATTTCAA 60.245 47.826 0.00 0.00 39.21 2.69
2125 3487 3.753797 GACCCTCTCCACTCAATTTCAAC 59.246 47.826 0.00 0.00 0.00 3.18
2126 3488 3.138283 ACCCTCTCCACTCAATTTCAACA 59.862 43.478 0.00 0.00 0.00 3.33
2127 3489 4.202609 ACCCTCTCCACTCAATTTCAACAT 60.203 41.667 0.00 0.00 0.00 2.71
2128 3490 4.157289 CCCTCTCCACTCAATTTCAACATG 59.843 45.833 0.00 0.00 0.00 3.21
2129 3491 4.380233 CCTCTCCACTCAATTTCAACATGC 60.380 45.833 0.00 0.00 0.00 4.06
2130 3492 4.401022 TCTCCACTCAATTTCAACATGCT 58.599 39.130 0.00 0.00 0.00 3.79
2131 3493 4.216902 TCTCCACTCAATTTCAACATGCTG 59.783 41.667 0.00 0.00 0.00 4.41
2132 3494 2.991190 CCACTCAATTTCAACATGCTGC 59.009 45.455 0.00 0.00 0.00 5.25
2133 3495 3.305813 CCACTCAATTTCAACATGCTGCT 60.306 43.478 0.00 0.00 0.00 4.24
2134 3496 4.304110 CACTCAATTTCAACATGCTGCTT 58.696 39.130 0.00 0.00 0.00 3.91
2135 3497 5.463286 CACTCAATTTCAACATGCTGCTTA 58.537 37.500 0.00 0.00 0.00 3.09
2136 3498 6.097356 CACTCAATTTCAACATGCTGCTTAT 58.903 36.000 0.00 0.00 0.00 1.73
2137 3499 6.252869 CACTCAATTTCAACATGCTGCTTATC 59.747 38.462 0.00 0.00 0.00 1.75
2138 3500 5.653507 TCAATTTCAACATGCTGCTTATCC 58.346 37.500 0.00 0.00 0.00 2.59
2139 3501 4.660789 ATTTCAACATGCTGCTTATCCC 57.339 40.909 0.00 0.00 0.00 3.85
2140 3502 2.057137 TCAACATGCTGCTTATCCCC 57.943 50.000 0.00 0.00 0.00 4.81
2141 3503 1.284491 TCAACATGCTGCTTATCCCCA 59.716 47.619 0.00 0.00 0.00 4.96
2142 3504 2.101783 CAACATGCTGCTTATCCCCAA 58.898 47.619 0.00 0.00 0.00 4.12
2143 3505 2.496871 CAACATGCTGCTTATCCCCAAA 59.503 45.455 0.00 0.00 0.00 3.28
2144 3506 2.102578 ACATGCTGCTTATCCCCAAAC 58.897 47.619 0.00 0.00 0.00 2.93
2145 3507 1.066002 CATGCTGCTTATCCCCAAACG 59.934 52.381 0.00 0.00 0.00 3.60
2146 3508 0.326595 TGCTGCTTATCCCCAAACGA 59.673 50.000 0.00 0.00 0.00 3.85
2147 3509 1.064758 TGCTGCTTATCCCCAAACGAT 60.065 47.619 0.00 0.00 0.00 3.73
2148 3510 1.334869 GCTGCTTATCCCCAAACGATG 59.665 52.381 0.00 0.00 0.00 3.84
2160 3522 4.637483 CCAAACGATGGCTATCAAATGT 57.363 40.909 10.94 0.00 43.80 2.71
2161 3523 4.997565 CCAAACGATGGCTATCAAATGTT 58.002 39.130 10.94 3.31 43.80 2.71
2162 3524 6.130298 CCAAACGATGGCTATCAAATGTTA 57.870 37.500 10.94 0.00 43.80 2.41
2163 3525 6.559810 CCAAACGATGGCTATCAAATGTTAA 58.440 36.000 10.94 0.00 43.80 2.01
2164 3526 7.032580 CCAAACGATGGCTATCAAATGTTAAA 58.967 34.615 10.94 0.00 43.80 1.52
2165 3527 7.543868 CCAAACGATGGCTATCAAATGTTAAAA 59.456 33.333 10.94 0.00 43.80 1.52
2166 3528 8.920665 CAAACGATGGCTATCAAATGTTAAAAA 58.079 29.630 10.94 0.00 32.67 1.94
2211 3573 9.841295 TTTATAGACCTGTATTTACAACCCATC 57.159 33.333 0.00 0.00 35.50 3.51
2212 3574 7.691993 ATAGACCTGTATTTACAACCCATCT 57.308 36.000 0.00 0.00 35.50 2.90
2213 3575 5.990668 AGACCTGTATTTACAACCCATCTC 58.009 41.667 0.00 0.00 35.50 2.75
2214 3576 5.487488 AGACCTGTATTTACAACCCATCTCA 59.513 40.000 0.00 0.00 35.50 3.27
2215 3577 5.497474 ACCTGTATTTACAACCCATCTCAC 58.503 41.667 0.00 0.00 35.50 3.51
2216 3578 5.013704 ACCTGTATTTACAACCCATCTCACA 59.986 40.000 0.00 0.00 35.50 3.58
2217 3579 6.122277 CCTGTATTTACAACCCATCTCACAT 58.878 40.000 0.00 0.00 35.50 3.21
2218 3580 6.260936 CCTGTATTTACAACCCATCTCACATC 59.739 42.308 0.00 0.00 35.50 3.06
2219 3581 6.716284 TGTATTTACAACCCATCTCACATCA 58.284 36.000 0.00 0.00 32.40 3.07
2220 3582 7.171653 TGTATTTACAACCCATCTCACATCAA 58.828 34.615 0.00 0.00 32.40 2.57
2221 3583 7.667635 TGTATTTACAACCCATCTCACATCAAA 59.332 33.333 0.00 0.00 32.40 2.69
2222 3584 6.968263 TTTACAACCCATCTCACATCAAAA 57.032 33.333 0.00 0.00 0.00 2.44
2223 3585 7.537596 TTTACAACCCATCTCACATCAAAAT 57.462 32.000 0.00 0.00 0.00 1.82
2224 3586 5.395682 ACAACCCATCTCACATCAAAATG 57.604 39.130 0.00 0.00 38.93 2.32
2225 3587 5.078949 ACAACCCATCTCACATCAAAATGA 58.921 37.500 0.00 0.00 36.67 2.57
2226 3588 5.718130 ACAACCCATCTCACATCAAAATGAT 59.282 36.000 0.00 0.00 37.65 2.45
2227 3589 6.891361 ACAACCCATCTCACATCAAAATGATA 59.109 34.615 0.00 0.00 34.28 2.15
2228 3590 7.562454 ACAACCCATCTCACATCAAAATGATAT 59.438 33.333 0.00 0.00 34.28 1.63
2229 3591 9.070179 CAACCCATCTCACATCAAAATGATATA 57.930 33.333 0.00 0.00 34.28 0.86
2230 3592 8.859236 ACCCATCTCACATCAAAATGATATAG 57.141 34.615 0.00 0.00 34.28 1.31
2231 3593 7.886970 ACCCATCTCACATCAAAATGATATAGG 59.113 37.037 0.00 0.00 34.28 2.57
2232 3594 8.105197 CCCATCTCACATCAAAATGATATAGGA 58.895 37.037 0.00 0.00 34.28 2.94
2233 3595 9.511272 CCATCTCACATCAAAATGATATAGGAA 57.489 33.333 0.00 0.00 34.28 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.895530 TCGGACCGAGAAAGCAGAAT 59.104 50.000 13.88 0.00 0.00 2.40
67 68 1.795768 TCTAGAGCTGTTTGGCGTTG 58.204 50.000 0.00 0.00 37.29 4.10
240 558 6.636454 AAATATCACCAGTTTCTACCCAGA 57.364 37.500 0.00 0.00 0.00 3.86
311 629 3.744530 GCCCGTAATAATCCAGCTTCTGT 60.745 47.826 0.00 0.00 0.00 3.41
313 631 2.224548 GGCCCGTAATAATCCAGCTTCT 60.225 50.000 0.00 0.00 0.00 2.85
401 719 3.526534 TCCATTTCACATCGATAACGCA 58.473 40.909 0.00 0.00 39.58 5.24
467 785 5.009210 CCCCAACTTTGATTTCACGTTTCTA 59.991 40.000 0.00 0.00 0.00 2.10
576 894 3.992943 TGAAGACCATATCAACGGGTT 57.007 42.857 0.00 0.00 34.39 4.11
680 999 8.150945 TCTCATCAAAGGGTGCTATTCTATAAC 58.849 37.037 0.00 0.00 0.00 1.89
784 1103 2.103601 CCGGGTACTCGGGTTCAAATAT 59.896 50.000 27.18 0.00 45.78 1.28
899 1219 5.909621 ACACCCATGAATTTTCTCATCAG 57.090 39.130 0.00 0.00 33.66 2.90
930 1250 4.406326 TGTGGTGTAACAAGTGAGTAGGAA 59.594 41.667 0.00 0.00 39.98 3.36
931 1251 3.962063 TGTGGTGTAACAAGTGAGTAGGA 59.038 43.478 0.00 0.00 39.98 2.94
950 1270 2.931320 GCTCTTCCTCTAACCGGTTGTG 60.931 54.545 30.08 20.92 0.00 3.33
1062 1382 5.119898 GCGAGCTATAAGATGGTCAGATTTG 59.880 44.000 0.00 0.00 0.00 2.32
1111 1431 6.770785 TCATGATTAGGTATTCTTTTTCCCCG 59.229 38.462 0.00 0.00 0.00 5.73
1312 1635 5.406477 GGAAATGAGTCCAATTTGAAGTTGC 59.594 40.000 0.00 0.00 37.65 4.17
1355 1678 2.786777 AGGTAGGTTTTTGTTAGCCCG 58.213 47.619 0.00 0.00 0.00 6.13
1394 1717 2.339769 AGTAGAGGGCCTTGTGACTTT 58.660 47.619 7.89 0.00 0.00 2.66
1449 1772 7.381139 GTCCAAAGATTCTTTCGCAAAACAATA 59.619 33.333 8.71 0.00 0.00 1.90
1548 2906 2.296073 TTCTACCCCGCATTTTTGGT 57.704 45.000 0.00 0.00 34.85 3.67
1580 2938 6.680148 TCCCATTTGATATCTTCGTATCCA 57.320 37.500 3.98 0.00 31.47 3.41
1781 3143 5.393461 GGTTACAGGATGCAATTTCCTCTTG 60.393 44.000 4.28 0.00 41.78 3.02
1868 3230 1.212935 CTAATAGCACCTGCCCCTGTT 59.787 52.381 0.00 0.00 43.38 3.16
1874 3236 3.543680 TGTTCTCTAATAGCACCTGCC 57.456 47.619 0.00 0.00 43.38 4.85
1914 3276 5.583061 CACGGGCATTTGTACTAGTAATTCA 59.417 40.000 3.61 0.00 0.00 2.57
1921 3283 0.650512 CGCACGGGCATTTGTACTAG 59.349 55.000 11.77 0.00 41.24 2.57
1924 3286 0.727793 CAACGCACGGGCATTTGTAC 60.728 55.000 11.77 0.00 41.24 2.90
1925 3287 1.576920 CAACGCACGGGCATTTGTA 59.423 52.632 11.77 0.00 41.24 2.41
1926 3288 2.334653 CAACGCACGGGCATTTGT 59.665 55.556 11.77 0.00 41.24 2.83
1927 3289 3.105157 GCAACGCACGGGCATTTG 61.105 61.111 11.77 13.80 41.24 2.32
1928 3290 3.144120 TTGCAACGCACGGGCATTT 62.144 52.632 11.77 0.00 38.71 2.32
1929 3291 3.600694 TTGCAACGCACGGGCATT 61.601 55.556 11.77 0.00 38.71 3.56
1930 3292 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
1952 3314 6.090358 CCGTCATGTCGTAGTGTTCTATTTTT 59.910 38.462 11.29 0.00 0.00 1.94
1953 3315 5.575606 CCGTCATGTCGTAGTGTTCTATTTT 59.424 40.000 11.29 0.00 0.00 1.82
1954 3316 5.100259 CCGTCATGTCGTAGTGTTCTATTT 58.900 41.667 11.29 0.00 0.00 1.40
1955 3317 4.439700 CCCGTCATGTCGTAGTGTTCTATT 60.440 45.833 11.29 0.00 0.00 1.73
1956 3318 3.066342 CCCGTCATGTCGTAGTGTTCTAT 59.934 47.826 11.29 0.00 0.00 1.98
1957 3319 2.421073 CCCGTCATGTCGTAGTGTTCTA 59.579 50.000 11.29 0.00 0.00 2.10
1958 3320 1.201647 CCCGTCATGTCGTAGTGTTCT 59.798 52.381 11.29 0.00 0.00 3.01
1959 3321 1.625616 CCCGTCATGTCGTAGTGTTC 58.374 55.000 11.29 0.00 0.00 3.18
1960 3322 0.389426 GCCCGTCATGTCGTAGTGTT 60.389 55.000 11.29 0.00 0.00 3.32
1961 3323 1.214589 GCCCGTCATGTCGTAGTGT 59.785 57.895 11.29 0.00 0.00 3.55
1962 3324 0.179111 ATGCCCGTCATGTCGTAGTG 60.179 55.000 11.29 0.00 33.26 2.74
1963 3325 1.395635 TATGCCCGTCATGTCGTAGT 58.604 50.000 11.29 0.00 36.63 2.73
1964 3326 2.724977 ATATGCCCGTCATGTCGTAG 57.275 50.000 11.29 3.79 36.63 3.51
1965 3327 2.606065 CGAATATGCCCGTCATGTCGTA 60.606 50.000 11.29 0.00 38.32 3.43
1966 3328 1.865865 GAATATGCCCGTCATGTCGT 58.134 50.000 11.29 0.00 36.63 4.34
1967 3329 0.784178 CGAATATGCCCGTCATGTCG 59.216 55.000 5.32 5.32 37.55 4.35
1968 3330 0.512952 GCGAATATGCCCGTCATGTC 59.487 55.000 0.00 0.00 36.63 3.06
1969 3331 1.221466 CGCGAATATGCCCGTCATGT 61.221 55.000 0.00 0.00 36.63 3.21
1970 3332 0.943835 TCGCGAATATGCCCGTCATG 60.944 55.000 6.20 0.00 36.63 3.07
1971 3333 0.944311 GTCGCGAATATGCCCGTCAT 60.944 55.000 12.06 0.00 39.17 3.06
1972 3334 1.590525 GTCGCGAATATGCCCGTCA 60.591 57.895 12.06 0.00 0.00 4.35
1973 3335 2.645510 CGTCGCGAATATGCCCGTC 61.646 63.158 12.06 0.00 0.00 4.79
1974 3336 2.657296 CGTCGCGAATATGCCCGT 60.657 61.111 12.06 0.00 0.00 5.28
1975 3337 3.403057 CCGTCGCGAATATGCCCG 61.403 66.667 12.06 8.40 0.00 6.13
1976 3338 3.712881 GCCGTCGCGAATATGCCC 61.713 66.667 12.06 0.00 0.00 5.36
1977 3339 1.011968 TATGCCGTCGCGAATATGCC 61.012 55.000 12.06 0.00 38.08 4.40
1978 3340 0.366871 CTATGCCGTCGCGAATATGC 59.633 55.000 12.06 11.97 38.08 3.14
1979 3341 1.649171 GTCTATGCCGTCGCGAATATG 59.351 52.381 12.06 0.43 38.08 1.78
1980 3342 1.268625 TGTCTATGCCGTCGCGAATAT 59.731 47.619 12.06 5.62 38.08 1.28
1981 3343 0.664224 TGTCTATGCCGTCGCGAATA 59.336 50.000 12.06 3.95 38.08 1.75
1982 3344 0.032130 ATGTCTATGCCGTCGCGAAT 59.968 50.000 12.06 2.67 38.08 3.34
1983 3345 0.869880 CATGTCTATGCCGTCGCGAA 60.870 55.000 12.06 0.00 38.08 4.70
1984 3346 1.299089 CATGTCTATGCCGTCGCGA 60.299 57.895 3.71 3.71 38.08 5.87
1985 3347 2.302952 CCATGTCTATGCCGTCGCG 61.303 63.158 0.00 0.00 38.08 5.87
1986 3348 1.956170 CCCATGTCTATGCCGTCGC 60.956 63.158 0.00 0.00 32.79 5.19
1987 3349 0.671796 TACCCATGTCTATGCCGTCG 59.328 55.000 0.00 0.00 32.79 5.12
1988 3350 4.159693 TGATATACCCATGTCTATGCCGTC 59.840 45.833 0.00 0.00 32.79 4.79
1989 3351 4.093743 TGATATACCCATGTCTATGCCGT 58.906 43.478 0.00 0.00 32.79 5.68
1990 3352 4.736126 TGATATACCCATGTCTATGCCG 57.264 45.455 0.00 0.00 32.79 5.69
1991 3353 5.130975 TGGATGATATACCCATGTCTATGCC 59.869 44.000 0.00 0.00 32.79 4.40
1992 3354 6.239217 TGGATGATATACCCATGTCTATGC 57.761 41.667 0.00 0.00 32.79 3.14
2000 3362 9.006405 TGATTATGTCATGGATGATATACCCAT 57.994 33.333 5.78 0.00 39.54 4.00
2001 3363 8.391305 TGATTATGTCATGGATGATATACCCA 57.609 34.615 5.78 4.93 39.54 4.51
2016 3378 7.274447 TGTCTGCTTATGTGATGATTATGTCA 58.726 34.615 0.00 0.00 42.06 3.58
2017 3379 7.719778 TGTCTGCTTATGTGATGATTATGTC 57.280 36.000 0.00 0.00 0.00 3.06
2018 3380 7.935210 TGATGTCTGCTTATGTGATGATTATGT 59.065 33.333 0.00 0.00 0.00 2.29
2019 3381 8.228464 GTGATGTCTGCTTATGTGATGATTATG 58.772 37.037 0.00 0.00 0.00 1.90
2020 3382 8.155510 AGTGATGTCTGCTTATGTGATGATTAT 58.844 33.333 0.00 0.00 0.00 1.28
2021 3383 7.440255 CAGTGATGTCTGCTTATGTGATGATTA 59.560 37.037 0.00 0.00 0.00 1.75
2022 3384 6.260271 CAGTGATGTCTGCTTATGTGATGATT 59.740 38.462 0.00 0.00 0.00 2.57
2023 3385 5.758784 CAGTGATGTCTGCTTATGTGATGAT 59.241 40.000 0.00 0.00 0.00 2.45
2024 3386 5.114081 CAGTGATGTCTGCTTATGTGATGA 58.886 41.667 0.00 0.00 0.00 2.92
2025 3387 4.272748 CCAGTGATGTCTGCTTATGTGATG 59.727 45.833 0.00 0.00 34.47 3.07
2026 3388 4.080695 ACCAGTGATGTCTGCTTATGTGAT 60.081 41.667 0.00 0.00 34.47 3.06
2027 3389 3.261643 ACCAGTGATGTCTGCTTATGTGA 59.738 43.478 0.00 0.00 34.47 3.58
2028 3390 3.603532 ACCAGTGATGTCTGCTTATGTG 58.396 45.455 0.00 0.00 34.47 3.21
2029 3391 3.988976 ACCAGTGATGTCTGCTTATGT 57.011 42.857 0.00 0.00 34.47 2.29
2030 3392 5.851720 AGATACCAGTGATGTCTGCTTATG 58.148 41.667 0.00 0.00 34.47 1.90
2031 3393 6.491714 AAGATACCAGTGATGTCTGCTTAT 57.508 37.500 0.00 0.00 34.47 1.73
2032 3394 5.939764 AAGATACCAGTGATGTCTGCTTA 57.060 39.130 0.00 0.00 34.47 3.09
2033 3395 4.833478 AAGATACCAGTGATGTCTGCTT 57.167 40.909 0.00 0.00 34.47 3.91
2034 3396 4.833478 AAAGATACCAGTGATGTCTGCT 57.167 40.909 0.00 0.00 34.47 4.24
2035 3397 4.333926 GGAAAAGATACCAGTGATGTCTGC 59.666 45.833 0.00 0.00 34.47 4.26
2036 3398 5.491070 TGGAAAAGATACCAGTGATGTCTG 58.509 41.667 0.00 0.00 35.45 3.51
2037 3399 5.762179 TGGAAAAGATACCAGTGATGTCT 57.238 39.130 0.00 0.00 0.00 3.41
2038 3400 6.817765 TTTGGAAAAGATACCAGTGATGTC 57.182 37.500 0.00 0.00 37.48 3.06
2039 3401 7.595819 TTTTTGGAAAAGATACCAGTGATGT 57.404 32.000 0.00 0.00 37.48 3.06
2045 3407 9.450807 CGCTATTATTTTTGGAAAAGATACCAG 57.549 33.333 0.00 0.00 37.48 4.00
2046 3408 7.918562 GCGCTATTATTTTTGGAAAAGATACCA 59.081 33.333 0.00 0.00 0.00 3.25
2047 3409 7.918562 TGCGCTATTATTTTTGGAAAAGATACC 59.081 33.333 9.73 0.00 0.00 2.73
2048 3410 8.743099 GTGCGCTATTATTTTTGGAAAAGATAC 58.257 33.333 9.73 0.00 0.00 2.24
2049 3411 8.462811 TGTGCGCTATTATTTTTGGAAAAGATA 58.537 29.630 9.73 0.00 0.00 1.98
2050 3412 7.275560 GTGTGCGCTATTATTTTTGGAAAAGAT 59.724 33.333 9.73 0.00 0.00 2.40
2051 3413 6.584563 GTGTGCGCTATTATTTTTGGAAAAGA 59.415 34.615 9.73 0.00 0.00 2.52
2052 3414 6.183360 GGTGTGCGCTATTATTTTTGGAAAAG 60.183 38.462 9.73 0.00 0.00 2.27
2053 3415 5.635700 GGTGTGCGCTATTATTTTTGGAAAA 59.364 36.000 9.73 0.00 0.00 2.29
2054 3416 5.164954 GGTGTGCGCTATTATTTTTGGAAA 58.835 37.500 9.73 0.00 0.00 3.13
2055 3417 4.381079 GGGTGTGCGCTATTATTTTTGGAA 60.381 41.667 9.73 0.00 0.00 3.53
2056 3418 3.129638 GGGTGTGCGCTATTATTTTTGGA 59.870 43.478 9.73 0.00 0.00 3.53
2057 3419 3.130340 AGGGTGTGCGCTATTATTTTTGG 59.870 43.478 9.73 0.00 36.04 3.28
2058 3420 4.370364 AGGGTGTGCGCTATTATTTTTG 57.630 40.909 9.73 0.00 36.04 2.44
2059 3421 5.163591 GGTAAGGGTGTGCGCTATTATTTTT 60.164 40.000 9.73 0.00 36.86 1.94
2060 3422 4.337274 GGTAAGGGTGTGCGCTATTATTTT 59.663 41.667 9.73 0.00 36.86 1.82
2061 3423 3.881089 GGTAAGGGTGTGCGCTATTATTT 59.119 43.478 9.73 0.00 36.86 1.40
2062 3424 3.473625 GGTAAGGGTGTGCGCTATTATT 58.526 45.455 9.73 0.00 36.86 1.40
2063 3425 2.224450 GGGTAAGGGTGTGCGCTATTAT 60.224 50.000 9.73 0.00 36.86 1.28
2064 3426 1.139455 GGGTAAGGGTGTGCGCTATTA 59.861 52.381 9.73 0.00 36.86 0.98
2065 3427 0.107361 GGGTAAGGGTGTGCGCTATT 60.107 55.000 9.73 0.00 36.86 1.73
2066 3428 0.981277 AGGGTAAGGGTGTGCGCTAT 60.981 55.000 9.73 0.00 36.86 2.97
2067 3429 0.324552 TAGGGTAAGGGTGTGCGCTA 60.325 55.000 9.73 0.00 36.86 4.26
2068 3430 1.196104 TTAGGGTAAGGGTGTGCGCT 61.196 55.000 9.73 0.00 39.77 5.92
2069 3431 0.107361 ATTAGGGTAAGGGTGTGCGC 60.107 55.000 0.00 0.00 0.00 6.09
2070 3432 3.463944 CTTATTAGGGTAAGGGTGTGCG 58.536 50.000 0.00 0.00 0.00 5.34
2071 3433 3.211865 GCTTATTAGGGTAAGGGTGTGC 58.788 50.000 0.00 0.00 33.31 4.57
2072 3434 4.497291 TGCTTATTAGGGTAAGGGTGTG 57.503 45.455 0.00 0.00 33.31 3.82
2073 3435 4.141251 CCATGCTTATTAGGGTAAGGGTGT 60.141 45.833 0.00 0.00 33.31 4.16
2074 3436 4.398319 CCATGCTTATTAGGGTAAGGGTG 58.602 47.826 0.00 0.00 33.31 4.61
2075 3437 3.181433 GCCATGCTTATTAGGGTAAGGGT 60.181 47.826 0.00 0.00 33.31 4.34
2076 3438 3.074538 AGCCATGCTTATTAGGGTAAGGG 59.925 47.826 0.00 0.00 33.89 3.95
2077 3439 4.202461 TGAGCCATGCTTATTAGGGTAAGG 60.202 45.833 0.00 0.00 39.88 2.69
2078 3440 4.973168 TGAGCCATGCTTATTAGGGTAAG 58.027 43.478 0.00 0.00 39.88 2.34
2079 3441 5.376625 CTTGAGCCATGCTTATTAGGGTAA 58.623 41.667 0.00 0.00 39.88 2.85
2080 3442 4.202461 CCTTGAGCCATGCTTATTAGGGTA 60.202 45.833 0.00 0.00 39.88 3.69
2081 3443 3.435601 CCTTGAGCCATGCTTATTAGGGT 60.436 47.826 0.00 0.00 39.88 4.34
2082 3444 3.152341 CCTTGAGCCATGCTTATTAGGG 58.848 50.000 0.00 0.00 39.88 3.53
2083 3445 3.817647 GTCCTTGAGCCATGCTTATTAGG 59.182 47.826 0.00 0.00 39.88 2.69
2084 3446 3.817647 GGTCCTTGAGCCATGCTTATTAG 59.182 47.826 0.00 0.00 39.88 1.73
2085 3447 3.820557 GGTCCTTGAGCCATGCTTATTA 58.179 45.455 0.00 0.00 39.88 0.98
2086 3448 2.659428 GGTCCTTGAGCCATGCTTATT 58.341 47.619 0.00 0.00 39.88 1.40
2087 3449 2.355010 GGTCCTTGAGCCATGCTTAT 57.645 50.000 0.00 0.00 39.88 1.73
2088 3450 3.882131 GGTCCTTGAGCCATGCTTA 57.118 52.632 0.00 0.00 39.88 3.09
2089 3451 4.751431 GGTCCTTGAGCCATGCTT 57.249 55.556 0.00 0.00 39.88 3.91
2103 3465 3.703001 TGAAATTGAGTGGAGAGGGTC 57.297 47.619 0.00 0.00 0.00 4.46
2104 3466 3.138283 TGTTGAAATTGAGTGGAGAGGGT 59.862 43.478 0.00 0.00 0.00 4.34
2105 3467 3.754965 TGTTGAAATTGAGTGGAGAGGG 58.245 45.455 0.00 0.00 0.00 4.30
2106 3468 4.380233 GCATGTTGAAATTGAGTGGAGAGG 60.380 45.833 0.00 0.00 0.00 3.69
2107 3469 4.458295 AGCATGTTGAAATTGAGTGGAGAG 59.542 41.667 0.00 0.00 0.00 3.20
2108 3470 4.216902 CAGCATGTTGAAATTGAGTGGAGA 59.783 41.667 2.97 0.00 0.00 3.71
2109 3471 4.482386 CAGCATGTTGAAATTGAGTGGAG 58.518 43.478 2.97 0.00 0.00 3.86
2110 3472 3.305539 GCAGCATGTTGAAATTGAGTGGA 60.306 43.478 14.38 0.00 39.31 4.02
2111 3473 2.991190 GCAGCATGTTGAAATTGAGTGG 59.009 45.455 14.38 0.00 39.31 4.00
2112 3474 3.909430 AGCAGCATGTTGAAATTGAGTG 58.091 40.909 14.38 0.00 39.31 3.51
2113 3475 4.595762 AAGCAGCATGTTGAAATTGAGT 57.404 36.364 14.38 0.00 39.31 3.41
2114 3476 5.747197 GGATAAGCAGCATGTTGAAATTGAG 59.253 40.000 14.38 0.00 39.31 3.02
2115 3477 5.394443 GGGATAAGCAGCATGTTGAAATTGA 60.394 40.000 14.38 0.00 39.31 2.57
2116 3478 4.807304 GGGATAAGCAGCATGTTGAAATTG 59.193 41.667 14.38 0.00 39.31 2.32
2117 3479 4.141869 GGGGATAAGCAGCATGTTGAAATT 60.142 41.667 14.38 6.98 39.31 1.82
2118 3480 3.385755 GGGGATAAGCAGCATGTTGAAAT 59.614 43.478 14.38 2.74 39.31 2.17
2119 3481 2.760092 GGGGATAAGCAGCATGTTGAAA 59.240 45.455 14.38 0.00 39.31 2.69
2120 3482 2.291475 TGGGGATAAGCAGCATGTTGAA 60.291 45.455 14.38 0.00 39.31 2.69
2121 3483 1.284491 TGGGGATAAGCAGCATGTTGA 59.716 47.619 14.38 0.00 39.31 3.18
2122 3484 1.766494 TGGGGATAAGCAGCATGTTG 58.234 50.000 5.00 5.00 39.31 3.33
2123 3485 2.497273 GTTTGGGGATAAGCAGCATGTT 59.503 45.455 0.00 0.00 39.31 2.71
2124 3486 2.102578 GTTTGGGGATAAGCAGCATGT 58.897 47.619 0.00 0.00 39.31 3.21
2125 3487 1.066002 CGTTTGGGGATAAGCAGCATG 59.934 52.381 0.00 0.00 40.87 4.06
2126 3488 1.064758 TCGTTTGGGGATAAGCAGCAT 60.065 47.619 0.00 0.00 0.00 3.79
2127 3489 0.326595 TCGTTTGGGGATAAGCAGCA 59.673 50.000 0.00 0.00 0.00 4.41
2128 3490 1.334869 CATCGTTTGGGGATAAGCAGC 59.665 52.381 0.00 0.00 0.00 5.25
2129 3491 1.949525 CCATCGTTTGGGGATAAGCAG 59.050 52.381 0.00 0.00 42.33 4.24
2130 3492 2.021723 GCCATCGTTTGGGGATAAGCA 61.022 52.381 8.81 0.00 46.55 3.91
2131 3493 0.668535 GCCATCGTTTGGGGATAAGC 59.331 55.000 8.81 0.00 46.55 3.09
2132 3494 2.348411 AGCCATCGTTTGGGGATAAG 57.652 50.000 8.81 0.00 46.55 1.73
2133 3495 3.392947 TGATAGCCATCGTTTGGGGATAA 59.607 43.478 8.81 0.00 46.55 1.75
2134 3496 2.976185 TGATAGCCATCGTTTGGGGATA 59.024 45.455 8.81 0.00 46.55 2.59
2135 3497 1.774254 TGATAGCCATCGTTTGGGGAT 59.226 47.619 8.81 0.00 46.55 3.85
2136 3498 1.208706 TGATAGCCATCGTTTGGGGA 58.791 50.000 8.81 0.00 46.55 4.81
2137 3499 2.051334 TTGATAGCCATCGTTTGGGG 57.949 50.000 8.81 0.00 46.55 4.96
2138 3500 3.381272 ACATTTGATAGCCATCGTTTGGG 59.619 43.478 8.81 0.00 46.55 4.12
2140 3502 8.459521 TTTTAACATTTGATAGCCATCGTTTG 57.540 30.769 0.00 0.00 33.51 2.93
2185 3547 9.841295 GATGGGTTGTAAATACAGGTCTATAAA 57.159 33.333 0.00 0.00 37.52 1.40
2186 3548 9.220906 AGATGGGTTGTAAATACAGGTCTATAA 57.779 33.333 0.00 0.00 37.52 0.98
2187 3549 8.792830 AGATGGGTTGTAAATACAGGTCTATA 57.207 34.615 0.00 0.00 37.52 1.31
2188 3550 7.347222 TGAGATGGGTTGTAAATACAGGTCTAT 59.653 37.037 0.00 0.00 37.52 1.98
2189 3551 6.670464 TGAGATGGGTTGTAAATACAGGTCTA 59.330 38.462 0.00 0.00 37.52 2.59
2190 3552 5.487488 TGAGATGGGTTGTAAATACAGGTCT 59.513 40.000 0.00 0.00 37.52 3.85
2191 3553 5.585047 GTGAGATGGGTTGTAAATACAGGTC 59.415 44.000 0.00 0.00 37.52 3.85
2192 3554 5.013704 TGTGAGATGGGTTGTAAATACAGGT 59.986 40.000 0.00 0.00 37.52 4.00
2193 3555 5.496556 TGTGAGATGGGTTGTAAATACAGG 58.503 41.667 0.00 0.00 37.52 4.00
2194 3556 6.823182 TGATGTGAGATGGGTTGTAAATACAG 59.177 38.462 0.00 0.00 37.52 2.74
2195 3557 6.716284 TGATGTGAGATGGGTTGTAAATACA 58.284 36.000 0.00 0.00 0.00 2.29
2196 3558 7.624360 TTGATGTGAGATGGGTTGTAAATAC 57.376 36.000 0.00 0.00 0.00 1.89
2197 3559 8.642935 TTTTGATGTGAGATGGGTTGTAAATA 57.357 30.769 0.00 0.00 0.00 1.40
2198 3560 7.537596 TTTTGATGTGAGATGGGTTGTAAAT 57.462 32.000 0.00 0.00 0.00 1.40
2199 3561 6.968263 TTTTGATGTGAGATGGGTTGTAAA 57.032 33.333 0.00 0.00 0.00 2.01
2200 3562 6.718912 TCATTTTGATGTGAGATGGGTTGTAA 59.281 34.615 0.00 0.00 0.00 2.41
2201 3563 6.244654 TCATTTTGATGTGAGATGGGTTGTA 58.755 36.000 0.00 0.00 0.00 2.41
2202 3564 5.078949 TCATTTTGATGTGAGATGGGTTGT 58.921 37.500 0.00 0.00 0.00 3.32
2203 3565 5.648178 TCATTTTGATGTGAGATGGGTTG 57.352 39.130 0.00 0.00 0.00 3.77
2204 3566 9.293404 CTATATCATTTTGATGTGAGATGGGTT 57.707 33.333 0.30 0.00 37.70 4.11
2205 3567 7.886970 CCTATATCATTTTGATGTGAGATGGGT 59.113 37.037 4.77 0.00 38.86 4.51
2206 3568 8.105197 TCCTATATCATTTTGATGTGAGATGGG 58.895 37.037 6.17 6.17 42.55 4.00
2207 3569 9.511272 TTCCTATATCATTTTGATGTGAGATGG 57.489 33.333 0.30 0.00 37.70 3.51


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

AutoCloner maintained by Alex Coulton.