Multiple sequence alignment - TraesCS2B01G271100

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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 TraesCS2B01G271100 chr2B 100.000 4212 0 0 1 4212 371162266 371158055 0.000000e+00 7779.0
1 TraesCS2B01G271100 chr2B 96.078 51 1 1 2332 2381 374247663 374247713 9.710000e-12 82.4
2 TraesCS2B01G271100 chr2B 94.872 39 1 1 2344 2381 108682582 108682620 4.550000e-05 60.2
3 TraesCS2B01G271100 chr2B 100.000 29 0 0 2193 2221 129268274 129268302 2.000000e-03 54.7
4 TraesCS2B01G271100 chr2D 94.973 1691 40 11 2561 4212 299895485 299897169 0.000000e+00 2610.0
5 TraesCS2B01G271100 chr2D 96.395 860 14 7 916 1764 299893995 299894848 0.000000e+00 1400.0
6 TraesCS2B01G271100 chr2D 93.973 896 23 5 1 888 299893135 299894007 0.000000e+00 1327.0
7 TraesCS2B01G271100 chr2D 88.235 221 19 7 1752 1968 299894868 299895085 1.500000e-64 257.0
8 TraesCS2B01G271100 chr2D 92.453 53 2 2 2332 2383 21617034 21617085 1.620000e-09 75.0
9 TraesCS2B01G271100 chr2D 95.349 43 2 0 3768 3810 360992170 360992128 7.560000e-08 69.4
10 TraesCS2B01G271100 chr2A 95.088 1079 34 2 2561 3638 376107692 376108752 0.000000e+00 1681.0
11 TraesCS2B01G271100 chr2A 95.760 849 29 6 916 1764 376100336 376101177 0.000000e+00 1362.0
12 TraesCS2B01G271100 chr2A 95.038 786 28 6 1 779 376085938 376086719 0.000000e+00 1225.0
13 TraesCS2B01G271100 chr2A 95.462 595 14 3 3624 4212 376108765 376109352 0.000000e+00 937.0
14 TraesCS2B01G271100 chr2A 86.275 204 21 6 3440 3638 279056371 279056170 9.170000e-52 215.0
15 TraesCS2B01G271100 chr2A 85.714 203 25 4 3440 3638 591275393 591275595 1.190000e-50 211.0
16 TraesCS2B01G271100 chr2A 95.238 42 2 0 3769 3810 315809755 315809796 2.720000e-07 67.6
17 TraesCS2B01G271100 chr2A 95.122 41 0 2 2341 2380 350734437 350734476 3.520000e-06 63.9
18 TraesCS2B01G271100 chr2A 100.000 31 0 0 788 818 376086714 376086744 1.640000e-04 58.4
19 TraesCS2B01G271100 chr1B 88.148 270 23 3 1495 1764 27303090 27302830 3.160000e-81 313.0
20 TraesCS2B01G271100 chr1B 85.714 196 22 5 3440 3631 641608012 641608205 7.140000e-48 202.0
21 TraesCS2B01G271100 chr1B 97.674 43 1 0 3768 3810 547029458 547029500 1.620000e-09 75.0
22 TraesCS2B01G271100 chr1B 87.755 49 2 3 2345 2392 66122282 66122237 2.000000e-03 54.7
23 TraesCS2B01G271100 chr7A 87.179 195 21 4 3440 3630 204737001 204736807 7.090000e-53 219.0
24 TraesCS2B01G271100 chr6A 86.294 197 22 5 3440 3631 504475793 504475989 4.270000e-50 209.0
25 TraesCS2B01G271100 chr3A 86.154 195 21 6 3440 3631 585472693 585472884 5.520000e-49 206.0
26 TraesCS2B01G271100 chr4A 85.294 204 23 6 3440 3638 176860069 176859868 1.990000e-48 204.0
27 TraesCS2B01G271100 chr1A 92.553 94 5 2 1671 1764 20700500 20700591 2.640000e-27 134.0
28 TraesCS2B01G271100 chr7B 92.157 51 3 1 2332 2381 485428338 485428388 2.100000e-08 71.3
29 TraesCS2B01G271100 chr7B 86.538 52 4 2 2332 2382 725608336 725608287 2.000000e-03 54.7
30 TraesCS2B01G271100 chr5B 95.349 43 2 0 3768 3810 81370553 81370511 7.560000e-08 69.4
31 TraesCS2B01G271100 chr4B 95.349 43 2 0 3768 3810 483511809 483511767 7.560000e-08 69.4
32 TraesCS2B01G271100 chr5A 93.333 45 3 0 3766 3810 78965458 78965502 2.720000e-07 67.6
33 TraesCS2B01G271100 chr7D 90.385 52 2 3 2332 2381 320265388 320265438 9.770000e-07 65.8
34 TraesCS2B01G271100 chr1D 93.023 43 3 0 3768 3810 274943927 274943969 3.520000e-06 63.9
35 TraesCS2B01G271100 chrUn 90.476 42 3 1 2332 2372 409216799 409216840 2.000000e-03 54.7


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 TraesCS2B01G271100 chr2B 371158055 371162266 4211 True 7779.0 7779 100.000 1 4212 1 chr2B.!!$R1 4211
1 TraesCS2B01G271100 chr2D 299893135 299897169 4034 False 1398.5 2610 93.394 1 4212 4 chr2D.!!$F2 4211
2 TraesCS2B01G271100 chr2A 376100336 376101177 841 False 1362.0 1362 95.760 916 1764 1 chr2A.!!$F3 848
3 TraesCS2B01G271100 chr2A 376107692 376109352 1660 False 1309.0 1681 95.275 2561 4212 2 chr2A.!!$F6 1651
4 TraesCS2B01G271100 chr2A 376085938 376086744 806 False 641.7 1225 97.519 1 818 2 chr2A.!!$F5 817

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
952 968 0.036164 CGATGGTCTGACCCAAACCA 59.964 55.0 23.42 5.23 46.51 3.67 F
1259 1275 0.185175 GAGGAGGAGGAGGAGGAGTC 59.815 65.0 0.00 0.00 0.00 3.36 F
1799 1855 0.310854 GGTCAGAAAGCGGGTTGTTG 59.689 55.0 0.00 0.00 0.00 3.33 F
2541 2735 0.323957 GAACGAAGGGGGTACTGCTT 59.676 55.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2555 2749 0.038892 CAAGGCACAACACTGGATGC 60.039 55.000 0.00 0.0 37.35 3.91 R
2559 2753 0.528249 GCAACAAGGCACAACACTGG 60.528 55.000 0.00 0.0 0.00 4.00 R
2866 3061 1.000385 TGGTTGCAAAATTCAGGAGCG 60.000 47.619 0.00 0.0 0.00 5.03 R
4188 4428 1.077501 CCTCCCGTGCACCAATGAT 60.078 57.895 12.15 0.0 0.00 2.45 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
17 18 2.426023 ACTCCCACGGTGCAGAAC 59.574 61.111 1.68 0.00 0.00 3.01
45 46 0.168568 TGCATTGCATACACACGCAG 59.831 50.000 7.38 0.00 39.75 5.18
49 50 3.563508 CATTGCATACACACGCAGAAAA 58.436 40.909 0.00 0.00 39.75 2.29
125 126 1.119684 TACACCATCATAGCAGCCGT 58.880 50.000 0.00 0.00 0.00 5.68
263 264 1.593196 TCAACCGGAGCAGAACAAAG 58.407 50.000 9.46 0.00 0.00 2.77
264 265 1.134220 TCAACCGGAGCAGAACAAAGT 60.134 47.619 9.46 0.00 0.00 2.66
273 274 2.079925 GCAGAACAAAGTAGGAGGCAG 58.920 52.381 0.00 0.00 0.00 4.85
304 305 3.494626 GGTAGTCATACAATGATGCGGTG 59.505 47.826 0.00 0.00 42.04 4.94
359 360 3.005539 AGGTCGGCAGAGTGGCAT 61.006 61.111 0.00 0.00 43.94 4.40
473 474 1.467342 CAGCTTTAAGGTGTTACGGGC 59.533 52.381 15.15 0.00 38.80 6.13
496 497 2.244252 GAGGGAGAAGGTCCTACCAGTA 59.756 54.545 10.53 0.00 46.06 2.74
553 554 2.604139 GGGGTAGAAGATCAGAGGAGG 58.396 57.143 0.00 0.00 0.00 4.30
562 563 3.465403 CAGAGGAGGGGGTGAGCG 61.465 72.222 0.00 0.00 0.00 5.03
638 639 2.693074 AGCAAAGGGTGGTTTTAGTGTG 59.307 45.455 0.00 0.00 32.77 3.82
772 780 6.305272 TGGAGCAATGAAGTCTCTCTTTAT 57.695 37.500 0.00 0.00 36.40 1.40
773 781 6.111382 TGGAGCAATGAAGTCTCTCTTTATG 58.889 40.000 0.00 0.00 36.40 1.90
774 782 6.112058 GGAGCAATGAAGTCTCTCTTTATGT 58.888 40.000 0.00 0.00 36.40 2.29
775 783 6.036953 GGAGCAATGAAGTCTCTCTTTATGTG 59.963 42.308 0.00 0.00 36.40 3.21
776 784 6.705302 AGCAATGAAGTCTCTCTTTATGTGA 58.295 36.000 0.00 0.00 36.40 3.58
777 785 7.337167 AGCAATGAAGTCTCTCTTTATGTGAT 58.663 34.615 0.00 0.00 36.40 3.06
778 786 7.280428 AGCAATGAAGTCTCTCTTTATGTGATG 59.720 37.037 0.00 0.00 36.40 3.07
779 787 7.065563 GCAATGAAGTCTCTCTTTATGTGATGT 59.934 37.037 0.00 0.00 36.40 3.06
780 788 8.388853 CAATGAAGTCTCTCTTTATGTGATGTG 58.611 37.037 0.00 0.00 36.40 3.21
781 789 5.871524 TGAAGTCTCTCTTTATGTGATGTGC 59.128 40.000 0.00 0.00 36.40 4.57
782 790 5.411831 AGTCTCTCTTTATGTGATGTGCA 57.588 39.130 0.00 0.00 0.00 4.57
783 791 5.798132 AGTCTCTCTTTATGTGATGTGCAA 58.202 37.500 0.00 0.00 0.00 4.08
784 792 6.413052 AGTCTCTCTTTATGTGATGTGCAAT 58.587 36.000 0.00 0.00 0.00 3.56
785 793 6.883217 AGTCTCTCTTTATGTGATGTGCAATT 59.117 34.615 0.00 0.00 0.00 2.32
786 794 6.965500 GTCTCTCTTTATGTGATGTGCAATTG 59.035 38.462 0.00 0.00 0.00 2.32
860 876 4.148838 ACAGTTGCAAAGCCCAATAAGTA 58.851 39.130 0.00 0.00 0.00 2.24
861 877 4.586841 ACAGTTGCAAAGCCCAATAAGTAA 59.413 37.500 0.00 0.00 0.00 2.24
862 878 5.163513 CAGTTGCAAAGCCCAATAAGTAAG 58.836 41.667 0.00 0.00 0.00 2.34
863 879 4.832823 AGTTGCAAAGCCCAATAAGTAAGT 59.167 37.500 0.00 0.00 0.00 2.24
873 889 4.698304 CCCAATAAGTAAGTGAAGCCGAAA 59.302 41.667 0.00 0.00 0.00 3.46
888 904 0.179192 CGAAACGACGACGACCCATA 60.179 55.000 15.32 0.00 42.66 2.74
889 905 1.728825 CGAAACGACGACGACCCATAA 60.729 52.381 15.32 0.00 42.66 1.90
890 906 1.916000 GAAACGACGACGACCCATAAG 59.084 52.381 15.32 0.00 42.66 1.73
891 907 0.883833 AACGACGACGACCCATAAGT 59.116 50.000 15.32 0.00 42.66 2.24
892 908 0.883833 ACGACGACGACCCATAAGTT 59.116 50.000 15.32 0.00 42.66 2.66
893 909 1.135575 ACGACGACGACCCATAAGTTC 60.136 52.381 15.32 0.00 42.66 3.01
894 910 1.796617 CGACGACGACCCATAAGTTCC 60.797 57.143 0.00 0.00 42.66 3.62
895 911 0.533951 ACGACGACCCATAAGTTCCC 59.466 55.000 0.00 0.00 0.00 3.97
896 912 0.179092 CGACGACCCATAAGTTCCCC 60.179 60.000 0.00 0.00 0.00 4.81
897 913 1.201424 GACGACCCATAAGTTCCCCT 58.799 55.000 0.00 0.00 0.00 4.79
898 914 1.138464 GACGACCCATAAGTTCCCCTC 59.862 57.143 0.00 0.00 0.00 4.30
899 915 0.468648 CGACCCATAAGTTCCCCTCC 59.531 60.000 0.00 0.00 0.00 4.30
900 916 0.844660 GACCCATAAGTTCCCCTCCC 59.155 60.000 0.00 0.00 0.00 4.30
901 917 0.626574 ACCCATAAGTTCCCCTCCCC 60.627 60.000 0.00 0.00 0.00 4.81
902 918 0.328548 CCCATAAGTTCCCCTCCCCT 60.329 60.000 0.00 0.00 0.00 4.79
903 919 1.141185 CCATAAGTTCCCCTCCCCTC 58.859 60.000 0.00 0.00 0.00 4.30
904 920 1.628043 CCATAAGTTCCCCTCCCCTCA 60.628 57.143 0.00 0.00 0.00 3.86
905 921 1.771255 CATAAGTTCCCCTCCCCTCAG 59.229 57.143 0.00 0.00 0.00 3.35
906 922 1.098589 TAAGTTCCCCTCCCCTCAGA 58.901 55.000 0.00 0.00 0.00 3.27
907 923 0.196118 AAGTTCCCCTCCCCTCAGAA 59.804 55.000 0.00 0.00 0.00 3.02
908 924 0.196118 AGTTCCCCTCCCCTCAGAAA 59.804 55.000 0.00 0.00 0.00 2.52
909 925 1.073098 GTTCCCCTCCCCTCAGAAAA 58.927 55.000 0.00 0.00 0.00 2.29
910 926 1.427753 GTTCCCCTCCCCTCAGAAAAA 59.572 52.381 0.00 0.00 0.00 1.94
952 968 0.036164 CGATGGTCTGACCCAAACCA 59.964 55.000 23.42 5.23 46.51 3.67
956 972 0.765510 GGTCTGACCCAAACCAGAGT 59.234 55.000 16.14 0.00 39.77 3.24
1259 1275 0.185175 GAGGAGGAGGAGGAGGAGTC 59.815 65.000 0.00 0.00 0.00 3.36
1290 1306 2.432510 GTGGGAAGAGGATGAAGACGAT 59.567 50.000 0.00 0.00 0.00 3.73
1639 1663 3.483808 TTCTCACTGTAATGGTGCACA 57.516 42.857 20.43 5.24 34.97 4.57
1770 1826 2.825532 TCCAGTCACATCTCATGTTCGA 59.174 45.455 0.00 0.00 42.70 3.71
1784 1840 3.812156 TGTTCGACTTCTCTTTGGTCA 57.188 42.857 0.00 0.00 0.00 4.02
1785 1841 3.717707 TGTTCGACTTCTCTTTGGTCAG 58.282 45.455 0.00 0.00 0.00 3.51
1788 1844 4.665833 TCGACTTCTCTTTGGTCAGAAA 57.334 40.909 0.00 0.00 0.00 2.52
1796 1852 1.001378 CTTTGGTCAGAAAGCGGGTTG 60.001 52.381 0.00 0.00 0.00 3.77
1799 1855 0.310854 GGTCAGAAAGCGGGTTGTTG 59.689 55.000 0.00 0.00 0.00 3.33
1808 1864 1.600485 AGCGGGTTGTTGTACTTTTCG 59.400 47.619 0.00 0.00 0.00 3.46
1809 1865 1.922880 GCGGGTTGTTGTACTTTTCGC 60.923 52.381 0.00 0.00 0.00 4.70
1810 1866 1.600485 CGGGTTGTTGTACTTTTCGCT 59.400 47.619 0.00 0.00 0.00 4.93
1811 1867 2.349155 CGGGTTGTTGTACTTTTCGCTC 60.349 50.000 0.00 0.00 0.00 5.03
1835 1891 6.261603 TCATTGATATGATTGAGTGTGGCTTC 59.738 38.462 0.00 0.00 35.87 3.86
1874 1930 7.753580 GCTGTACCTATAAACATTTGTGGTTTC 59.246 37.037 0.00 0.00 39.12 2.78
1875 1931 8.693120 TGTACCTATAAACATTTGTGGTTTCA 57.307 30.769 0.00 0.00 39.12 2.69
1962 2019 8.135529 GGTACCATTAAAGTTAAATCTCATGGC 58.864 37.037 7.15 0.00 0.00 4.40
1970 2027 8.579850 AAAGTTAAATCTCATGGCTGTATTGA 57.420 30.769 0.00 0.00 0.00 2.57
1974 2031 4.767578 ATCTCATGGCTGTATTGAGTGT 57.232 40.909 0.00 0.00 38.39 3.55
1975 2032 5.876651 ATCTCATGGCTGTATTGAGTGTA 57.123 39.130 0.00 0.00 38.39 2.90
2010 2155 6.576662 TTTCGCAAAATATTCAGTAACCCA 57.423 33.333 0.00 0.00 0.00 4.51
2013 2158 6.791303 TCGCAAAATATTCAGTAACCCATTC 58.209 36.000 0.00 0.00 0.00 2.67
2042 2187 3.367321 TGCATTGTCATTCCACCATGAT 58.633 40.909 0.00 0.00 35.60 2.45
2048 2193 3.523157 TGTCATTCCACCATGATGTACCT 59.477 43.478 0.00 0.00 35.60 3.08
2054 2199 3.055167 TCCACCATGATGTACCTTGACAG 60.055 47.826 0.00 0.00 31.51 3.51
2059 2204 7.272244 CACCATGATGTACCTTGACAGTATAA 58.728 38.462 0.00 0.00 31.51 0.98
2096 2242 1.613925 CCGTTCAGAGTTCAGTCTCCA 59.386 52.381 0.00 0.00 35.28 3.86
2101 2247 5.926542 CGTTCAGAGTTCAGTCTCCAATTTA 59.073 40.000 0.00 0.00 35.28 1.40
2102 2248 6.423905 CGTTCAGAGTTCAGTCTCCAATTTAA 59.576 38.462 0.00 0.00 35.28 1.52
2162 2355 7.717568 TCTGTTCACTTAGACTAGATAATGCC 58.282 38.462 0.00 0.00 0.00 4.40
2163 2356 6.817184 TGTTCACTTAGACTAGATAATGCCC 58.183 40.000 0.00 0.00 0.00 5.36
2165 2358 7.093068 TGTTCACTTAGACTAGATAATGCCCAA 60.093 37.037 0.00 0.00 0.00 4.12
2166 2359 7.432148 TCACTTAGACTAGATAATGCCCAAA 57.568 36.000 0.00 0.00 0.00 3.28
2167 2360 7.857456 TCACTTAGACTAGATAATGCCCAAAA 58.143 34.615 0.00 0.00 0.00 2.44
2168 2361 8.325787 TCACTTAGACTAGATAATGCCCAAAAA 58.674 33.333 0.00 0.00 0.00 1.94
2169 2362 8.616076 CACTTAGACTAGATAATGCCCAAAAAG 58.384 37.037 0.00 0.00 0.00 2.27
2170 2363 7.775561 ACTTAGACTAGATAATGCCCAAAAAGG 59.224 37.037 0.00 0.00 37.03 3.11
2171 2364 6.079712 AGACTAGATAATGCCCAAAAAGGT 57.920 37.500 0.00 0.00 34.66 3.50
2172 2365 6.122964 AGACTAGATAATGCCCAAAAAGGTC 58.877 40.000 0.00 0.00 34.66 3.85
2173 2366 5.201243 ACTAGATAATGCCCAAAAAGGTCC 58.799 41.667 0.00 0.00 34.66 4.46
2204 2398 1.762957 TGCCTTGGCTATCACCTACTC 59.237 52.381 13.18 0.00 0.00 2.59
2205 2399 1.070914 GCCTTGGCTATCACCTACTCC 59.929 57.143 4.11 0.00 0.00 3.85
2206 2400 1.694696 CCTTGGCTATCACCTACTCCC 59.305 57.143 0.00 0.00 0.00 4.30
2208 2402 2.383442 TGGCTATCACCTACTCCCTC 57.617 55.000 0.00 0.00 0.00 4.30
2209 2403 1.133136 TGGCTATCACCTACTCCCTCC 60.133 57.143 0.00 0.00 0.00 4.30
2210 2404 1.133136 GGCTATCACCTACTCCCTCCA 60.133 57.143 0.00 0.00 0.00 3.86
2211 2405 2.493687 GGCTATCACCTACTCCCTCCAT 60.494 54.545 0.00 0.00 0.00 3.41
2213 2407 3.259625 GCTATCACCTACTCCCTCCATTC 59.740 52.174 0.00 0.00 0.00 2.67
2214 2408 2.176247 TCACCTACTCCCTCCATTCC 57.824 55.000 0.00 0.00 0.00 3.01
2216 2410 2.196595 CACCTACTCCCTCCATTCCAA 58.803 52.381 0.00 0.00 0.00 3.53
2217 2411 2.576191 CACCTACTCCCTCCATTCCAAA 59.424 50.000 0.00 0.00 0.00 3.28
2218 2412 3.010138 CACCTACTCCCTCCATTCCAAAA 59.990 47.826 0.00 0.00 0.00 2.44
2220 2414 5.043762 ACCTACTCCCTCCATTCCAAAATA 58.956 41.667 0.00 0.00 0.00 1.40
2221 2415 5.104067 ACCTACTCCCTCCATTCCAAAATAC 60.104 44.000 0.00 0.00 0.00 1.89
2222 2416 5.132816 CCTACTCCCTCCATTCCAAAATACT 59.867 44.000 0.00 0.00 0.00 2.12
2223 2417 5.536497 ACTCCCTCCATTCCAAAATACTT 57.464 39.130 0.00 0.00 0.00 2.24
2225 2419 4.609301 TCCCTCCATTCCAAAATACTTGG 58.391 43.478 0.00 0.00 40.87 3.61
2226 2420 4.293634 TCCCTCCATTCCAAAATACTTGGA 59.706 41.667 2.04 2.04 46.08 3.53
2235 2429 5.745227 TCCAAAATACTTGGAAGCTCTAGG 58.255 41.667 3.72 0.00 44.90 3.02
2238 2432 6.434340 CCAAAATACTTGGAAGCTCTAGGTTT 59.566 38.462 0.00 0.00 42.06 3.27
2239 2433 7.308435 CAAAATACTTGGAAGCTCTAGGTTTG 58.692 38.462 0.00 0.00 35.69 2.93
2240 2434 6.374417 AATACTTGGAAGCTCTAGGTTTGA 57.626 37.500 0.00 0.00 35.69 2.69
2241 2435 4.009370 ACTTGGAAGCTCTAGGTTTGAC 57.991 45.455 0.00 0.00 35.69 3.18
2242 2436 3.244596 ACTTGGAAGCTCTAGGTTTGACC 60.245 47.826 0.00 0.00 38.99 4.02
2347 2541 9.856488 AAATATATTTCATGATCAAGCTGATGC 57.144 29.630 4.81 0.00 37.20 3.91
2348 2542 6.894339 ATATTTCATGATCAAGCTGATGCA 57.106 33.333 0.00 0.00 37.20 3.96
2349 2543 4.632538 TTTCATGATCAAGCTGATGCAG 57.367 40.909 0.00 0.00 37.20 4.41
2350 2544 3.553828 TCATGATCAAGCTGATGCAGA 57.446 42.857 0.00 0.00 37.20 4.26
2351 2545 3.467803 TCATGATCAAGCTGATGCAGAG 58.532 45.455 0.00 0.00 37.20 3.35
2352 2546 2.327200 TGATCAAGCTGATGCAGAGG 57.673 50.000 0.00 0.00 37.20 3.69
2353 2547 0.945813 GATCAAGCTGATGCAGAGGC 59.054 55.000 0.00 0.00 37.20 4.70
2354 2548 0.547075 ATCAAGCTGATGCAGAGGCT 59.453 50.000 4.57 4.57 42.74 4.58
2355 2549 0.392595 TCAAGCTGATGCAGAGGCTG 60.393 55.000 10.14 0.00 42.74 4.85
2356 2550 1.077644 AAGCTGATGCAGAGGCTGG 60.078 57.895 10.14 0.00 42.74 4.85
2357 2551 2.516460 GCTGATGCAGAGGCTGGG 60.516 66.667 0.00 0.00 41.91 4.45
2358 2552 2.192443 CTGATGCAGAGGCTGGGG 59.808 66.667 0.00 0.00 41.91 4.96
2359 2553 3.414193 TGATGCAGAGGCTGGGGG 61.414 66.667 0.00 0.00 41.91 5.40
2360 2554 3.415087 GATGCAGAGGCTGGGGGT 61.415 66.667 0.00 0.00 41.91 4.95
2361 2555 2.943265 ATGCAGAGGCTGGGGGTT 60.943 61.111 0.00 0.00 41.91 4.11
2362 2556 1.619363 ATGCAGAGGCTGGGGGTTA 60.619 57.895 0.00 0.00 41.91 2.85
2363 2557 0.995675 ATGCAGAGGCTGGGGGTTAT 60.996 55.000 0.00 0.00 41.91 1.89
2364 2558 1.149401 GCAGAGGCTGGGGGTTATC 59.851 63.158 0.00 0.00 36.96 1.75
2365 2559 1.839894 CAGAGGCTGGGGGTTATCC 59.160 63.158 0.00 0.00 0.00 2.59
2366 2560 0.695803 CAGAGGCTGGGGGTTATCCT 60.696 60.000 0.00 0.00 35.33 3.24
2367 2561 0.400670 AGAGGCTGGGGGTTATCCTC 60.401 60.000 0.00 0.00 42.68 3.71
2376 2570 3.750501 GGGGTTATCCTCCTTTTCCAA 57.249 47.619 0.00 0.00 35.33 3.53
2377 2571 4.055710 GGGGTTATCCTCCTTTTCCAAA 57.944 45.455 0.00 0.00 35.33 3.28
2378 2572 4.422057 GGGGTTATCCTCCTTTTCCAAAA 58.578 43.478 0.00 0.00 35.33 2.44
2379 2573 4.841813 GGGGTTATCCTCCTTTTCCAAAAA 59.158 41.667 0.00 0.00 35.33 1.94
2417 2611 8.752766 ACTTCATGATCAAACAACATCAAATC 57.247 30.769 0.00 0.00 32.76 2.17
2418 2612 8.582437 ACTTCATGATCAAACAACATCAAATCT 58.418 29.630 0.00 0.00 32.76 2.40
2446 2640 7.524717 AAACCTAATTTTGTGCTGTAGATGT 57.475 32.000 0.00 0.00 0.00 3.06
2447 2641 7.524717 AACCTAATTTTGTGCTGTAGATGTT 57.475 32.000 0.00 0.00 0.00 2.71
2448 2642 6.913170 ACCTAATTTTGTGCTGTAGATGTTG 58.087 36.000 0.00 0.00 0.00 3.33
2449 2643 6.071952 ACCTAATTTTGTGCTGTAGATGTTGG 60.072 38.462 0.00 0.00 0.00 3.77
2450 2644 5.789643 AATTTTGTGCTGTAGATGTTGGT 57.210 34.783 0.00 0.00 0.00 3.67
2451 2645 6.892658 AATTTTGTGCTGTAGATGTTGGTA 57.107 33.333 0.00 0.00 0.00 3.25
2452 2646 7.466746 AATTTTGTGCTGTAGATGTTGGTAT 57.533 32.000 0.00 0.00 0.00 2.73
2453 2647 8.574251 AATTTTGTGCTGTAGATGTTGGTATA 57.426 30.769 0.00 0.00 0.00 1.47
2454 2648 8.752005 ATTTTGTGCTGTAGATGTTGGTATAT 57.248 30.769 0.00 0.00 0.00 0.86
2455 2649 8.574251 TTTTGTGCTGTAGATGTTGGTATATT 57.426 30.769 0.00 0.00 0.00 1.28
2456 2650 8.574251 TTTGTGCTGTAGATGTTGGTATATTT 57.426 30.769 0.00 0.00 0.00 1.40
2457 2651 8.574251 TTGTGCTGTAGATGTTGGTATATTTT 57.426 30.769 0.00 0.00 0.00 1.82
2458 2652 8.574251 TGTGCTGTAGATGTTGGTATATTTTT 57.426 30.769 0.00 0.00 0.00 1.94
2459 2653 8.673711 TGTGCTGTAGATGTTGGTATATTTTTC 58.326 33.333 0.00 0.00 0.00 2.29
2460 2654 8.673711 GTGCTGTAGATGTTGGTATATTTTTCA 58.326 33.333 0.00 0.00 0.00 2.69
2461 2655 9.237187 TGCTGTAGATGTTGGTATATTTTTCAA 57.763 29.630 0.00 0.00 0.00 2.69
2470 2664 9.703892 TGTTGGTATATTTTTCAATTGACTTGG 57.296 29.630 7.89 0.00 35.43 3.61
2471 2665 9.705290 GTTGGTATATTTTTCAATTGACTTGGT 57.295 29.630 7.89 0.00 35.43 3.67
2472 2666 9.921637 TTGGTATATTTTTCAATTGACTTGGTC 57.078 29.630 7.89 0.00 35.43 4.02
2473 2667 9.083422 TGGTATATTTTTCAATTGACTTGGTCA 57.917 29.630 7.89 0.00 41.09 4.02
2499 2693 9.495572 AAACTTAAAATGTTTGAGTTGGAACAA 57.504 25.926 10.51 0.00 38.79 2.83
2531 2725 8.999220 AACTTTAAGTATTCTAGAACGAAGGG 57.001 34.615 7.48 0.00 0.00 3.95
2532 2726 7.554211 ACTTTAAGTATTCTAGAACGAAGGGG 58.446 38.462 7.48 0.00 0.00 4.79
2533 2727 6.475596 TTAAGTATTCTAGAACGAAGGGGG 57.524 41.667 7.48 0.00 0.00 5.40
2534 2728 3.991683 AGTATTCTAGAACGAAGGGGGT 58.008 45.455 7.48 0.00 0.00 4.95
2535 2729 5.134725 AGTATTCTAGAACGAAGGGGGTA 57.865 43.478 7.48 0.00 0.00 3.69
2536 2730 4.892345 AGTATTCTAGAACGAAGGGGGTAC 59.108 45.833 7.48 3.35 0.00 3.34
2537 2731 3.463048 TTCTAGAACGAAGGGGGTACT 57.537 47.619 0.00 0.00 0.00 2.73
2538 2732 2.731572 TCTAGAACGAAGGGGGTACTG 58.268 52.381 0.00 0.00 0.00 2.74
2539 2733 1.136500 CTAGAACGAAGGGGGTACTGC 59.864 57.143 0.00 0.00 0.00 4.40
2540 2734 0.544595 AGAACGAAGGGGGTACTGCT 60.545 55.000 0.00 0.00 0.00 4.24
2541 2735 0.323957 GAACGAAGGGGGTACTGCTT 59.676 55.000 0.00 0.00 0.00 3.91
2542 2736 1.551883 GAACGAAGGGGGTACTGCTTA 59.448 52.381 0.00 0.00 0.00 3.09
2543 2737 1.875488 ACGAAGGGGGTACTGCTTAT 58.125 50.000 0.00 0.00 0.00 1.73
2544 2738 2.193993 ACGAAGGGGGTACTGCTTATT 58.806 47.619 0.00 0.00 0.00 1.40
2545 2739 2.093128 ACGAAGGGGGTACTGCTTATTG 60.093 50.000 0.00 0.00 0.00 1.90
2546 2740 2.093128 CGAAGGGGGTACTGCTTATTGT 60.093 50.000 0.00 0.00 0.00 2.71
2547 2741 3.279434 GAAGGGGGTACTGCTTATTGTG 58.721 50.000 0.00 0.00 0.00 3.33
2548 2742 1.064685 AGGGGGTACTGCTTATTGTGC 60.065 52.381 0.00 0.00 0.00 4.57
2549 2743 1.340600 GGGGGTACTGCTTATTGTGCA 60.341 52.381 0.00 0.00 38.81 4.57
2696 2891 5.045724 TGGGCAAAATGGCAATCTTATTTCT 60.046 36.000 6.25 0.00 45.76 2.52
2705 2900 4.159693 GGCAATCTTATTTCTTTCCCCGTT 59.840 41.667 0.00 0.00 0.00 4.44
2866 3061 5.988561 TGCCAAAATTTCTTACACAATGGTC 59.011 36.000 0.00 0.00 0.00 4.02
3105 3300 2.876645 GAAGCTCGCGGACGTCAG 60.877 66.667 18.91 15.23 41.18 3.51
3415 3610 4.273318 ACATTATGTTTCAGGGCCTCTTC 58.727 43.478 0.95 0.00 0.00 2.87
3487 3682 4.354387 TCCTACAGGATTTGGGGTTGTTTA 59.646 41.667 0.00 0.00 39.78 2.01
3493 3688 3.682377 GGATTTGGGGTTGTTTAATTGCG 59.318 43.478 0.00 0.00 0.00 4.85
3544 3749 7.063898 TCGAAGAGTTTGATTGAATGCTAGAAG 59.936 37.037 0.00 0.00 0.00 2.85
3744 3976 5.941647 TCTGCATTCAAAGATGTTCTCATGA 59.058 36.000 0.00 0.00 34.06 3.07
4059 4299 1.267732 GCGAGATCAACAATCTTGGCG 60.268 52.381 0.00 0.00 45.06 5.69
4068 4308 0.374758 CAATCTTGGCGTGTCCATCG 59.625 55.000 0.00 0.00 46.04 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.941999 GCAATGCAGGGAGGCTGTTC 61.942 60.000 0.00 0.00 34.04 3.18
17 18 0.466739 TATGCAATGCAGGGAGGCTG 60.467 55.000 14.98 0.00 43.65 4.85
49 50 1.909700 TGCGCCTGAGGAATTTCTTT 58.090 45.000 0.65 0.00 0.00 2.52
125 126 1.739667 CCGAGACCGATGGTATGCA 59.260 57.895 0.00 0.00 35.25 3.96
263 264 0.459489 CTGTCTGCTCTGCCTCCTAC 59.541 60.000 0.00 0.00 0.00 3.18
264 265 0.685785 CCTGTCTGCTCTGCCTCCTA 60.686 60.000 0.00 0.00 0.00 2.94
273 274 4.720649 TTGTATGACTACCTGTCTGCTC 57.279 45.455 0.00 0.00 45.54 4.26
359 360 1.305219 GCATCTACCACGGCAAGCAA 61.305 55.000 0.00 0.00 0.00 3.91
427 428 8.145316 ACATCATTTTTGTTCTTGGTGATTTG 57.855 30.769 0.00 0.00 0.00 2.32
430 431 7.053316 TGACATCATTTTTGTTCTTGGTGAT 57.947 32.000 0.00 0.00 0.00 3.06
473 474 0.756070 GGTAGGACCTTCTCCCTCCG 60.756 65.000 0.00 0.00 40.53 4.63
496 497 2.146342 CCAGACATCGCAGTGAACTTT 58.854 47.619 0.00 0.00 0.00 2.66
553 554 1.966451 CAAACTGACCGCTCACCCC 60.966 63.158 0.00 0.00 0.00 4.95
562 563 2.427506 CTGCTCTTACCCAAACTGACC 58.572 52.381 0.00 0.00 0.00 4.02
638 639 5.872963 TCTCACCTTTACCCCTAAAAGAAC 58.127 41.667 0.00 0.00 36.27 3.01
772 780 2.231721 CCATCCACAATTGCACATCACA 59.768 45.455 5.05 0.00 0.00 3.58
773 781 2.492881 TCCATCCACAATTGCACATCAC 59.507 45.455 5.05 0.00 0.00 3.06
774 782 2.756207 CTCCATCCACAATTGCACATCA 59.244 45.455 5.05 0.00 0.00 3.07
775 783 2.100252 CCTCCATCCACAATTGCACATC 59.900 50.000 5.05 0.00 0.00 3.06
776 784 2.104967 CCTCCATCCACAATTGCACAT 58.895 47.619 5.05 0.00 0.00 3.21
777 785 1.075212 TCCTCCATCCACAATTGCACA 59.925 47.619 5.05 0.00 0.00 4.57
778 786 1.747355 CTCCTCCATCCACAATTGCAC 59.253 52.381 5.05 0.00 0.00 4.57
779 787 1.634973 TCTCCTCCATCCACAATTGCA 59.365 47.619 5.05 0.00 0.00 4.08
780 788 2.092753 TCTCTCCTCCATCCACAATTGC 60.093 50.000 5.05 0.00 0.00 3.56
781 789 3.920231 TCTCTCCTCCATCCACAATTG 57.080 47.619 3.24 3.24 0.00 2.32
782 790 3.848975 ACTTCTCTCCTCCATCCACAATT 59.151 43.478 0.00 0.00 0.00 2.32
783 791 3.199508 CACTTCTCTCCTCCATCCACAAT 59.800 47.826 0.00 0.00 0.00 2.71
784 792 2.568956 CACTTCTCTCCTCCATCCACAA 59.431 50.000 0.00 0.00 0.00 3.33
785 793 2.182827 CACTTCTCTCCTCCATCCACA 58.817 52.381 0.00 0.00 0.00 4.17
786 794 2.461695 TCACTTCTCTCCTCCATCCAC 58.538 52.381 0.00 0.00 0.00 4.02
860 876 0.249155 TCGTCGTTTCGGCTTCACTT 60.249 50.000 0.00 0.00 0.00 3.16
861 877 0.938168 GTCGTCGTTTCGGCTTCACT 60.938 55.000 0.00 0.00 32.43 3.41
862 878 1.485943 GTCGTCGTTTCGGCTTCAC 59.514 57.895 0.00 0.00 32.43 3.18
863 879 2.012414 CGTCGTCGTTTCGGCTTCA 61.012 57.895 0.00 0.00 33.02 3.02
873 889 0.883833 AACTTATGGGTCGTCGTCGT 59.116 50.000 1.33 0.00 38.33 4.34
888 904 0.196118 TTCTGAGGGGAGGGGAACTT 59.804 55.000 0.00 0.00 0.00 2.66
889 905 0.196118 TTTCTGAGGGGAGGGGAACT 59.804 55.000 0.00 0.00 0.00 3.01
890 906 1.073098 TTTTCTGAGGGGAGGGGAAC 58.927 55.000 0.00 0.00 0.00 3.62
891 907 1.841334 TTTTTCTGAGGGGAGGGGAA 58.159 50.000 0.00 0.00 0.00 3.97
892 908 3.608912 TTTTTCTGAGGGGAGGGGA 57.391 52.632 0.00 0.00 0.00 4.81
910 926 3.992427 GACTTATGGGTCGTCGTCTTTTT 59.008 43.478 0.00 0.00 0.00 1.94
911 927 3.582780 GACTTATGGGTCGTCGTCTTTT 58.417 45.455 0.00 0.00 0.00 2.27
912 928 2.094338 GGACTTATGGGTCGTCGTCTTT 60.094 50.000 0.00 0.00 37.12 2.52
913 929 1.475682 GGACTTATGGGTCGTCGTCTT 59.524 52.381 0.00 0.00 37.12 3.01
914 930 1.101331 GGACTTATGGGTCGTCGTCT 58.899 55.000 0.00 0.00 37.12 4.18
917 933 0.666913 ATCGGACTTATGGGTCGTCG 59.333 55.000 0.00 0.00 37.12 5.12
923 939 2.039418 TCAGACCATCGGACTTATGGG 58.961 52.381 7.02 0.00 46.89 4.00
952 968 1.153745 GCTTCGTGGCGATGACTCT 60.154 57.895 8.29 0.00 35.23 3.24
1239 1255 1.293683 ACTCCTCCTCCTCCTCCTCC 61.294 65.000 0.00 0.00 0.00 4.30
1240 1256 0.185175 GACTCCTCCTCCTCCTCCTC 59.815 65.000 0.00 0.00 0.00 3.71
1241 1257 0.254107 AGACTCCTCCTCCTCCTCCT 60.254 60.000 0.00 0.00 0.00 3.69
1259 1275 0.390860 CTCTTCCCACTCCGCCATAG 59.609 60.000 0.00 0.00 0.00 2.23
1290 1306 3.993865 TACCTCAGCATCGGCCCCA 62.994 63.158 0.00 0.00 42.56 4.96
1639 1663 7.377766 ACAGTCTAATTCGTTTATTGTGCAT 57.622 32.000 0.00 0.00 0.00 3.96
1648 1672 3.986277 ACACCGACAGTCTAATTCGTTT 58.014 40.909 0.00 0.00 0.00 3.60
1652 1676 7.117236 TGTGATTTTACACCGACAGTCTAATTC 59.883 37.037 0.00 0.00 39.69 2.17
1728 1752 7.038799 ACTGGATTTGACATTAATTCAGCCTTT 60.039 33.333 7.74 0.00 40.70 3.11
1745 1769 5.446875 CGAACATGAGATGTGACTGGATTTG 60.447 44.000 0.00 0.00 44.07 2.32
1770 1826 3.134458 CGCTTTCTGACCAAAGAGAAGT 58.866 45.455 0.00 0.00 35.76 3.01
1784 1840 2.632987 AGTACAACAACCCGCTTTCT 57.367 45.000 0.00 0.00 0.00 2.52
1785 1841 3.703286 AAAGTACAACAACCCGCTTTC 57.297 42.857 0.00 0.00 0.00 2.62
1788 1844 1.600485 CGAAAAGTACAACAACCCGCT 59.400 47.619 0.00 0.00 0.00 5.52
1796 1852 7.684670 TCATATCAATGAGCGAAAAGTACAAC 58.315 34.615 0.00 0.00 37.20 3.32
1799 1855 8.551205 TCAATCATATCAATGAGCGAAAAGTAC 58.449 33.333 0.00 0.00 45.17 2.73
1808 1864 5.562307 GCCACACTCAATCATATCAATGAGC 60.562 44.000 0.00 0.00 45.17 4.26
1809 1865 5.763698 AGCCACACTCAATCATATCAATGAG 59.236 40.000 0.00 0.00 45.17 2.90
1810 1866 5.687780 AGCCACACTCAATCATATCAATGA 58.312 37.500 0.00 0.00 46.01 2.57
1811 1867 6.262496 AGAAGCCACACTCAATCATATCAATG 59.738 38.462 0.00 0.00 0.00 2.82
1892 1948 9.639563 AATATGGAGAAATGTTTTTGGGTTTTT 57.360 25.926 0.00 0.00 0.00 1.94
1946 2003 7.831193 ACTCAATACAGCCATGAGATTTAACTT 59.169 33.333 8.84 0.00 42.48 2.66
1950 2007 6.653020 ACACTCAATACAGCCATGAGATTTA 58.347 36.000 8.84 0.00 42.48 1.40
1954 2011 4.442052 GCTACACTCAATACAGCCATGAGA 60.442 45.833 8.84 0.00 42.48 3.27
1955 2012 3.806521 GCTACACTCAATACAGCCATGAG 59.193 47.826 0.00 0.00 44.77 2.90
1956 2013 3.197549 TGCTACACTCAATACAGCCATGA 59.802 43.478 0.00 0.00 0.00 3.07
1962 2019 5.327091 GCACAATTGCTACACTCAATACAG 58.673 41.667 5.05 0.00 46.17 2.74
1986 2131 7.164230 TGGGTTACTGAATATTTTGCGAAAT 57.836 32.000 16.10 16.10 38.88 2.17
1991 2136 8.947055 ATTGAATGGGTTACTGAATATTTTGC 57.053 30.769 0.00 0.00 0.00 3.68
1998 2143 8.538701 TGCATAAAATTGAATGGGTTACTGAAT 58.461 29.630 3.27 0.00 0.00 2.57
2010 2155 8.885722 GTGGAATGACAATGCATAAAATTGAAT 58.114 29.630 0.00 0.00 38.21 2.57
2013 2158 6.594547 TGGTGGAATGACAATGCATAAAATTG 59.405 34.615 0.00 0.00 40.23 2.32
2020 2165 3.367321 TCATGGTGGAATGACAATGCAT 58.633 40.909 0.00 0.00 31.58 3.96
2042 2187 7.892241 AGGAGTTACTTATACTGTCAAGGTACA 59.108 37.037 0.00 0.00 0.00 2.90
2076 2221 1.613925 TGGAGACTGAACTCTGAACGG 59.386 52.381 0.00 0.00 37.13 4.44
2136 2329 8.364142 GGCATTATCTAGTCTAAGTGAACAGAT 58.636 37.037 0.00 0.00 34.13 2.90
2137 2330 7.201920 GGGCATTATCTAGTCTAAGTGAACAGA 60.202 40.741 0.00 0.00 0.00 3.41
2160 2353 0.608130 GACATGGGACCTTTTTGGGC 59.392 55.000 0.00 0.00 45.48 5.36
2161 2354 2.008242 TGACATGGGACCTTTTTGGG 57.992 50.000 0.00 0.00 41.11 4.12
2162 2355 4.414337 TTTTGACATGGGACCTTTTTGG 57.586 40.909 0.00 0.00 42.93 3.28
2163 2356 4.213906 GCATTTTGACATGGGACCTTTTTG 59.786 41.667 0.00 0.00 0.00 2.44
2165 2358 3.244526 GGCATTTTGACATGGGACCTTTT 60.245 43.478 0.00 0.00 0.00 2.27
2166 2359 2.302733 GGCATTTTGACATGGGACCTTT 59.697 45.455 0.00 0.00 0.00 3.11
2167 2360 1.901833 GGCATTTTGACATGGGACCTT 59.098 47.619 0.00 0.00 0.00 3.50
2168 2361 1.077663 AGGCATTTTGACATGGGACCT 59.922 47.619 0.00 0.00 0.00 3.85
2169 2362 1.560505 AGGCATTTTGACATGGGACC 58.439 50.000 0.00 0.00 0.00 4.46
2170 2363 2.354003 CCAAGGCATTTTGACATGGGAC 60.354 50.000 0.00 0.00 0.00 4.46
2171 2364 1.901159 CCAAGGCATTTTGACATGGGA 59.099 47.619 0.00 0.00 0.00 4.37
2172 2365 1.676615 GCCAAGGCATTTTGACATGGG 60.677 52.381 6.14 0.00 41.49 4.00
2173 2366 1.276989 AGCCAAGGCATTTTGACATGG 59.723 47.619 14.40 0.24 44.88 3.66
2204 2398 4.609301 TCCAAGTATTTTGGAATGGAGGG 58.391 43.478 6.18 0.00 44.90 4.30
2213 2407 5.501156 ACCTAGAGCTTCCAAGTATTTTGG 58.499 41.667 0.00 0.00 40.87 3.28
2214 2408 7.174946 TCAAACCTAGAGCTTCCAAGTATTTTG 59.825 37.037 0.00 0.00 0.00 2.44
2216 2410 6.655425 GTCAAACCTAGAGCTTCCAAGTATTT 59.345 38.462 0.00 0.00 0.00 1.40
2217 2411 6.174049 GTCAAACCTAGAGCTTCCAAGTATT 58.826 40.000 0.00 0.00 0.00 1.89
2218 2412 5.338463 GGTCAAACCTAGAGCTTCCAAGTAT 60.338 44.000 0.00 0.00 34.73 2.12
2220 2414 3.244596 GGTCAAACCTAGAGCTTCCAAGT 60.245 47.826 0.00 0.00 34.73 3.16
2221 2415 3.339141 GGTCAAACCTAGAGCTTCCAAG 58.661 50.000 0.00 0.00 34.73 3.61
2222 2416 3.418684 GGTCAAACCTAGAGCTTCCAA 57.581 47.619 0.00 0.00 34.73 3.53
2321 2515 9.856488 GCATCAGCTTGATCATGAAATATATTT 57.144 29.630 10.51 10.51 34.28 1.40
2322 2516 9.020731 TGCATCAGCTTGATCATGAAATATATT 57.979 29.630 12.54 0.00 42.74 1.28
2323 2517 8.575649 TGCATCAGCTTGATCATGAAATATAT 57.424 30.769 12.54 0.00 42.74 0.86
2324 2518 7.881232 TCTGCATCAGCTTGATCATGAAATATA 59.119 33.333 12.54 0.00 42.74 0.86
2325 2519 6.715264 TCTGCATCAGCTTGATCATGAAATAT 59.285 34.615 12.54 0.00 42.74 1.28
2326 2520 6.059484 TCTGCATCAGCTTGATCATGAAATA 58.941 36.000 12.54 0.00 42.74 1.40
2327 2521 4.887655 TCTGCATCAGCTTGATCATGAAAT 59.112 37.500 12.54 0.00 42.74 2.17
2328 2522 4.266714 TCTGCATCAGCTTGATCATGAAA 58.733 39.130 12.54 0.00 42.74 2.69
2329 2523 3.877508 CTCTGCATCAGCTTGATCATGAA 59.122 43.478 12.54 0.00 42.74 2.57
2330 2524 3.467803 CTCTGCATCAGCTTGATCATGA 58.532 45.455 12.54 6.38 42.74 3.07
2331 2525 2.550180 CCTCTGCATCAGCTTGATCATG 59.450 50.000 0.00 0.00 42.74 3.07
2332 2526 2.852449 CCTCTGCATCAGCTTGATCAT 58.148 47.619 0.00 0.00 42.74 2.45
2333 2527 1.746171 GCCTCTGCATCAGCTTGATCA 60.746 52.381 0.00 0.00 42.74 2.92
2334 2528 0.945813 GCCTCTGCATCAGCTTGATC 59.054 55.000 0.00 0.00 42.74 2.92
2335 2529 0.547075 AGCCTCTGCATCAGCTTGAT 59.453 50.000 0.00 0.00 42.74 2.57
2336 2530 0.392595 CAGCCTCTGCATCAGCTTGA 60.393 55.000 2.04 0.00 42.74 3.02
2337 2531 1.377366 CCAGCCTCTGCATCAGCTTG 61.377 60.000 2.04 0.00 42.74 4.01
2338 2532 1.077644 CCAGCCTCTGCATCAGCTT 60.078 57.895 2.04 0.00 42.74 3.74
2339 2533 2.590645 CCAGCCTCTGCATCAGCT 59.409 61.111 0.00 0.00 42.74 4.24
2340 2534 2.516460 CCCAGCCTCTGCATCAGC 60.516 66.667 0.00 0.00 41.13 4.26
2341 2535 2.192443 CCCCAGCCTCTGCATCAG 59.808 66.667 0.00 0.00 41.13 2.90
2342 2536 3.414193 CCCCCAGCCTCTGCATCA 61.414 66.667 0.00 0.00 41.13 3.07
2343 2537 1.635817 TAACCCCCAGCCTCTGCATC 61.636 60.000 0.00 0.00 41.13 3.91
2344 2538 0.995675 ATAACCCCCAGCCTCTGCAT 60.996 55.000 0.00 0.00 41.13 3.96
2345 2539 1.619363 ATAACCCCCAGCCTCTGCA 60.619 57.895 0.00 0.00 41.13 4.41
2346 2540 1.149401 GATAACCCCCAGCCTCTGC 59.851 63.158 0.00 0.00 37.95 4.26
2347 2541 0.695803 AGGATAACCCCCAGCCTCTG 60.696 60.000 0.00 0.00 36.73 3.35
2348 2542 0.400670 GAGGATAACCCCCAGCCTCT 60.401 60.000 0.00 0.00 43.75 3.69
2349 2543 1.419720 GGAGGATAACCCCCAGCCTC 61.420 65.000 0.00 0.00 45.88 4.70
2350 2544 1.386057 GGAGGATAACCCCCAGCCT 60.386 63.158 0.00 0.00 33.53 4.58
2351 2545 0.994050 AAGGAGGATAACCCCCAGCC 60.994 60.000 0.00 0.00 36.73 4.85
2352 2546 0.927029 AAAGGAGGATAACCCCCAGC 59.073 55.000 0.00 0.00 36.73 4.85
2353 2547 2.091830 GGAAAAGGAGGATAACCCCCAG 60.092 54.545 0.00 0.00 36.73 4.45
2354 2548 1.927371 GGAAAAGGAGGATAACCCCCA 59.073 52.381 0.00 0.00 36.73 4.96
2355 2549 1.927371 TGGAAAAGGAGGATAACCCCC 59.073 52.381 0.00 0.00 36.73 5.40
2356 2550 3.750501 TTGGAAAAGGAGGATAACCCC 57.249 47.619 0.00 0.00 36.73 4.95
2391 2585 9.844790 GATTTGATGTTGTTTGATCATGAAGTA 57.155 29.630 0.00 0.00 0.00 2.24
2392 2586 8.582437 AGATTTGATGTTGTTTGATCATGAAGT 58.418 29.630 0.00 0.00 0.00 3.01
2393 2587 8.981724 AGATTTGATGTTGTTTGATCATGAAG 57.018 30.769 0.00 0.00 0.00 3.02
2420 2614 9.243105 ACATCTACAGCACAAAATTAGGTTTAT 57.757 29.630 0.00 0.00 0.00 1.40
2421 2615 8.630054 ACATCTACAGCACAAAATTAGGTTTA 57.370 30.769 0.00 0.00 0.00 2.01
2422 2616 7.524717 ACATCTACAGCACAAAATTAGGTTT 57.475 32.000 0.00 0.00 0.00 3.27
2423 2617 7.370383 CAACATCTACAGCACAAAATTAGGTT 58.630 34.615 0.00 0.00 0.00 3.50
2424 2618 6.071952 CCAACATCTACAGCACAAAATTAGGT 60.072 38.462 0.00 0.00 0.00 3.08
2425 2619 6.071952 ACCAACATCTACAGCACAAAATTAGG 60.072 38.462 0.00 0.00 0.00 2.69
2426 2620 6.913170 ACCAACATCTACAGCACAAAATTAG 58.087 36.000 0.00 0.00 0.00 1.73
2427 2621 6.892658 ACCAACATCTACAGCACAAAATTA 57.107 33.333 0.00 0.00 0.00 1.40
2428 2622 5.789643 ACCAACATCTACAGCACAAAATT 57.210 34.783 0.00 0.00 0.00 1.82
2429 2623 8.752005 ATATACCAACATCTACAGCACAAAAT 57.248 30.769 0.00 0.00 0.00 1.82
2430 2624 8.574251 AATATACCAACATCTACAGCACAAAA 57.426 30.769 0.00 0.00 0.00 2.44
2431 2625 8.574251 AAATATACCAACATCTACAGCACAAA 57.426 30.769 0.00 0.00 0.00 2.83
2432 2626 8.574251 AAAATATACCAACATCTACAGCACAA 57.426 30.769 0.00 0.00 0.00 3.33
2433 2627 8.574251 AAAAATATACCAACATCTACAGCACA 57.426 30.769 0.00 0.00 0.00 4.57
2434 2628 8.673711 TGAAAAATATACCAACATCTACAGCAC 58.326 33.333 0.00 0.00 0.00 4.40
2435 2629 8.800370 TGAAAAATATACCAACATCTACAGCA 57.200 30.769 0.00 0.00 0.00 4.41
2444 2638 9.703892 CCAAGTCAATTGAAAAATATACCAACA 57.296 29.630 10.35 0.00 41.83 3.33
2445 2639 9.705290 ACCAAGTCAATTGAAAAATATACCAAC 57.295 29.630 10.35 0.00 41.83 3.77
2446 2640 9.921637 GACCAAGTCAATTGAAAAATATACCAA 57.078 29.630 10.35 0.00 41.83 3.67
2447 2641 9.083422 TGACCAAGTCAATTGAAAAATATACCA 57.917 29.630 10.35 0.00 39.78 3.25
2448 2642 9.921637 TTGACCAAGTCAATTGAAAAATATACC 57.078 29.630 10.35 0.00 45.88 2.73
2473 2667 9.495572 TTGTTCCAACTCAAACATTTTAAGTTT 57.504 25.926 0.00 0.00 39.61 2.66
2474 2668 9.495572 TTTGTTCCAACTCAAACATTTTAAGTT 57.504 25.926 0.00 0.00 35.46 2.66
2475 2669 8.931775 GTTTGTTCCAACTCAAACATTTTAAGT 58.068 29.630 13.45 0.00 46.91 2.24
2484 2678 7.094631 AGTTTTAGGTTTGTTCCAACTCAAAC 58.905 34.615 10.90 10.90 46.95 2.93
2485 2679 7.234661 AGTTTTAGGTTTGTTCCAACTCAAA 57.765 32.000 0.00 0.00 0.00 2.69
2486 2680 6.844097 AGTTTTAGGTTTGTTCCAACTCAA 57.156 33.333 0.00 0.00 0.00 3.02
2487 2681 6.844097 AAGTTTTAGGTTTGTTCCAACTCA 57.156 33.333 0.00 0.00 0.00 3.41
2488 2682 9.297586 CTTAAAGTTTTAGGTTTGTTCCAACTC 57.702 33.333 0.00 0.00 0.00 3.01
2489 2683 8.809066 ACTTAAAGTTTTAGGTTTGTTCCAACT 58.191 29.630 6.58 0.00 29.94 3.16
2490 2684 8.991243 ACTTAAAGTTTTAGGTTTGTTCCAAC 57.009 30.769 6.58 0.00 29.94 3.77
2505 2699 9.433153 CCCTTCGTTCTAGAATACTTAAAGTTT 57.567 33.333 8.75 0.00 0.00 2.66
2506 2700 8.039538 CCCCTTCGTTCTAGAATACTTAAAGTT 58.960 37.037 8.75 0.00 0.00 2.66
2507 2701 7.364497 CCCCCTTCGTTCTAGAATACTTAAAGT 60.364 40.741 8.75 0.00 0.00 2.66
2508 2702 6.985059 CCCCCTTCGTTCTAGAATACTTAAAG 59.015 42.308 8.75 6.50 0.00 1.85
2509 2703 6.441604 ACCCCCTTCGTTCTAGAATACTTAAA 59.558 38.462 8.75 0.00 0.00 1.52
2510 2704 5.960202 ACCCCCTTCGTTCTAGAATACTTAA 59.040 40.000 8.75 0.00 0.00 1.85
2511 2705 5.522641 ACCCCCTTCGTTCTAGAATACTTA 58.477 41.667 8.75 0.00 0.00 2.24
2512 2706 4.359996 ACCCCCTTCGTTCTAGAATACTT 58.640 43.478 8.75 0.00 0.00 2.24
2513 2707 3.991683 ACCCCCTTCGTTCTAGAATACT 58.008 45.455 8.75 0.00 0.00 2.12
2514 2708 4.892345 AGTACCCCCTTCGTTCTAGAATAC 59.108 45.833 8.75 3.95 0.00 1.89
2515 2709 4.891756 CAGTACCCCCTTCGTTCTAGAATA 59.108 45.833 8.75 0.00 0.00 1.75
2516 2710 3.705072 CAGTACCCCCTTCGTTCTAGAAT 59.295 47.826 8.75 0.00 0.00 2.40
2517 2711 3.094572 CAGTACCCCCTTCGTTCTAGAA 58.905 50.000 0.00 0.00 0.00 2.10
2518 2712 2.731572 CAGTACCCCCTTCGTTCTAGA 58.268 52.381 0.00 0.00 0.00 2.43
2519 2713 1.136500 GCAGTACCCCCTTCGTTCTAG 59.864 57.143 0.00 0.00 0.00 2.43
2520 2714 1.188863 GCAGTACCCCCTTCGTTCTA 58.811 55.000 0.00 0.00 0.00 2.10
2521 2715 0.544595 AGCAGTACCCCCTTCGTTCT 60.545 55.000 0.00 0.00 0.00 3.01
2522 2716 0.323957 AAGCAGTACCCCCTTCGTTC 59.676 55.000 0.00 0.00 0.00 3.95
2523 2717 1.648116 TAAGCAGTACCCCCTTCGTT 58.352 50.000 0.00 0.00 0.00 3.85
2524 2718 1.875488 ATAAGCAGTACCCCCTTCGT 58.125 50.000 0.00 0.00 0.00 3.85
2525 2719 2.093128 ACAATAAGCAGTACCCCCTTCG 60.093 50.000 0.00 0.00 0.00 3.79
2526 2720 3.279434 CACAATAAGCAGTACCCCCTTC 58.721 50.000 0.00 0.00 0.00 3.46
2527 2721 2.620627 GCACAATAAGCAGTACCCCCTT 60.621 50.000 0.00 0.00 0.00 3.95
2528 2722 1.064685 GCACAATAAGCAGTACCCCCT 60.065 52.381 0.00 0.00 0.00 4.79
2529 2723 1.340600 TGCACAATAAGCAGTACCCCC 60.341 52.381 0.00 0.00 37.02 5.40
2530 2724 2.122783 TGCACAATAAGCAGTACCCC 57.877 50.000 0.00 0.00 37.02 4.95
2551 2745 1.403249 GGCACAACACTGGATGCAATC 60.403 52.381 0.00 0.00 44.55 2.67
2552 2746 0.604578 GGCACAACACTGGATGCAAT 59.395 50.000 0.00 0.00 39.92 3.56
2553 2747 0.467844 AGGCACAACACTGGATGCAA 60.468 50.000 0.00 0.00 39.92 4.08
2554 2748 0.467844 AAGGCACAACACTGGATGCA 60.468 50.000 0.00 0.00 39.92 3.96
2555 2749 0.038892 CAAGGCACAACACTGGATGC 60.039 55.000 0.00 0.00 37.35 3.91
2556 2750 1.321474 ACAAGGCACAACACTGGATG 58.679 50.000 0.00 0.00 0.00 3.51
2557 2751 1.682854 CAACAAGGCACAACACTGGAT 59.317 47.619 0.00 0.00 0.00 3.41
2558 2752 1.102154 CAACAAGGCACAACACTGGA 58.898 50.000 0.00 0.00 0.00 3.86
2559 2753 0.528249 GCAACAAGGCACAACACTGG 60.528 55.000 0.00 0.00 0.00 4.00
2563 2757 1.064803 CTAACGCAACAAGGCACAACA 59.935 47.619 0.00 0.00 0.00 3.33
2696 2891 5.828859 TGTAGAAATTTCTCAAACGGGGAAA 59.171 36.000 23.70 0.00 38.70 3.13
2705 2900 6.884295 CACCCATACCTGTAGAAATTTCTCAA 59.116 38.462 23.70 12.39 38.70 3.02
2866 3061 1.000385 TGGTTGCAAAATTCAGGAGCG 60.000 47.619 0.00 0.00 0.00 5.03
3105 3300 2.781595 TTTCCCAGCTCGGTTCTCGC 62.782 60.000 0.00 0.00 39.05 5.03
3327 3522 3.055094 ACGATACAACCTGCTCCAGAATT 60.055 43.478 0.00 0.00 32.44 2.17
3395 3590 3.199946 TCGAAGAGGCCCTGAAACATAAT 59.800 43.478 0.00 0.00 0.00 1.28
3415 3610 4.201851 ACATTTTGAGAATCCTGCGAATCG 60.202 41.667 0.00 0.00 0.00 3.34
3487 3682 7.662897 TCCTTTGTTTTTCCTATAACGCAATT 58.337 30.769 0.00 0.00 0.00 2.32
3631 3836 2.979678 TCAAACACTAAGGGCTCCTTCT 59.020 45.455 9.46 0.00 43.57 2.85
3744 3976 4.799428 CCAAATGTACCAACGAACGTTTTT 59.201 37.500 9.87 4.91 36.00 1.94
3958 4198 2.601314 CGCGGTTTGTTTCGATCTGATA 59.399 45.455 0.00 0.00 0.00 2.15
4041 4281 2.744202 ACACGCCAAGATTGTTGATCTC 59.256 45.455 0.00 0.00 44.41 2.75
4068 4308 2.334653 CTCGCCGAGCTCATCCTC 59.665 66.667 15.40 0.00 0.00 3.71
4188 4428 1.077501 CCTCCCGTGCACCAATGAT 60.078 57.895 12.15 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.