Multiple sequence alignment - TraesCS6A01G222600

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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 TraesCS6A01G222600 chr6A 100.000 4565 0 0 1 4565 416542004 416537440 0.000000e+00 8431
1 TraesCS6A01G222600 chr6A 87.633 849 100 5 2715 3559 384921533 384922380 0.000000e+00 981
2 TraesCS6A01G222600 chr6A 80.230 435 72 5 1396 1817 384915837 384916270 9.530000e-82 315
3 TraesCS6A01G222600 chr6D 96.803 1345 34 5 2464 3799 301053902 301055246 0.000000e+00 2237
4 TraesCS6A01G222600 chr6D 95.272 1269 51 7 1185 2449 301052590 301053853 0.000000e+00 2002
5 TraesCS6A01G222600 chr6D 93.750 960 40 8 212 1161 301051648 301052597 0.000000e+00 1423
6 TraesCS6A01G222600 chr6D 87.618 848 102 3 2715 3559 271086295 271085448 0.000000e+00 981
7 TraesCS6A01G222600 chr6B 96.086 1303 48 2 2460 3760 465846904 465848205 0.000000e+00 2121
8 TraesCS6A01G222600 chr6B 93.848 1333 68 10 1185 2513 465845592 465846914 0.000000e+00 1995
9 TraesCS6A01G222600 chr6B 87.913 968 69 19 212 1161 465844662 465845599 0.000000e+00 1096
10 TraesCS6A01G222600 chr6B 91.699 771 61 2 3797 4565 445849316 445850085 0.000000e+00 1066
11 TraesCS6A01G222600 chr6B 88.208 848 97 3 2715 3559 431799390 431798543 0.000000e+00 1009
12 TraesCS6A01G222600 chr6B 79.767 430 73 5 1401 1817 431805798 431805370 2.670000e-77 300
13 TraesCS6A01G222600 chr5D 93.023 774 51 2 3792 4565 410492108 410492878 0.000000e+00 1127
14 TraesCS6A01G222600 chr5D 92.308 767 59 0 3799 4565 403558321 403559087 0.000000e+00 1090
15 TraesCS6A01G222600 chr5D 75.949 711 149 21 2716 3415 453421860 453422559 3.380000e-91 346
16 TraesCS6A01G222600 chr2D 92.438 767 57 1 3799 4565 481453547 481452782 0.000000e+00 1094
17 TraesCS6A01G222600 chr2B 91.667 768 62 2 3800 4565 801146847 801147614 0.000000e+00 1062
18 TraesCS6A01G222600 chr2B 90.769 195 14 2 1 191 152605256 152605062 1.630000e-64 257
19 TraesCS6A01G222600 chr2B 88.205 195 19 2 1 191 95750454 95750260 3.550000e-56 230
20 TraesCS6A01G222600 chr2B 87.692 195 20 2 1 191 669948516 669948710 1.650000e-54 224
21 TraesCS6A01G222600 chr1B 91.569 771 64 1 3796 4565 380641525 380642295 0.000000e+00 1062
22 TraesCS6A01G222600 chr3D 91.656 767 62 1 3799 4565 252337870 252338634 0.000000e+00 1061
23 TraesCS6A01G222600 chr4D 91.525 767 65 0 3799 4565 409314531 409313765 0.000000e+00 1057
24 TraesCS6A01G222600 chr1D 91.547 769 59 4 3799 4565 400034071 400033307 0.000000e+00 1055
25 TraesCS6A01G222600 chr1D 89.691 194 16 4 2 191 410736741 410736548 1.270000e-60 244
26 TraesCS6A01G222600 chr5A 76.264 712 149 20 2714 3415 572697756 572697055 1.210000e-95 361
27 TraesCS6A01G222600 chr5B 75.809 711 156 15 2713 3415 553945678 553946380 3.380000e-91 346
28 TraesCS6A01G222600 chr5B 89.231 195 17 2 1 191 576918776 576918970 1.640000e-59 241
29 TraesCS6A01G222600 chr7D 90.769 195 14 2 1 191 419812884 419812690 1.630000e-64 257
30 TraesCS6A01G222600 chr7D 87.179 195 21 2 1 191 379318230 379318424 7.690000e-53 219
31 TraesCS6A01G222600 chr3B 87.692 195 18 4 2 191 821818829 821818636 5.940000e-54 222
32 TraesCS6A01G222600 chr3A 87.179 195 21 2 1 191 101661976 101661782 7.690000e-53 219


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 TraesCS6A01G222600 chr6A 416537440 416542004 4564 True 8431.000000 8431 100.000000 1 4565 1 chr6A.!!$R1 4564
1 TraesCS6A01G222600 chr6A 384921533 384922380 847 False 981.000000 981 87.633000 2715 3559 1 chr6A.!!$F2 844
2 TraesCS6A01G222600 chr6D 301051648 301055246 3598 False 1887.333333 2237 95.275000 212 3799 3 chr6D.!!$F1 3587
3 TraesCS6A01G222600 chr6D 271085448 271086295 847 True 981.000000 981 87.618000 2715 3559 1 chr6D.!!$R1 844
4 TraesCS6A01G222600 chr6B 465844662 465848205 3543 False 1737.333333 2121 92.615667 212 3760 3 chr6B.!!$F2 3548
5 TraesCS6A01G222600 chr6B 445849316 445850085 769 False 1066.000000 1066 91.699000 3797 4565 1 chr6B.!!$F1 768
6 TraesCS6A01G222600 chr6B 431798543 431799390 847 True 1009.000000 1009 88.208000 2715 3559 1 chr6B.!!$R1 844
7 TraesCS6A01G222600 chr5D 410492108 410492878 770 False 1127.000000 1127 93.023000 3792 4565 1 chr5D.!!$F2 773
8 TraesCS6A01G222600 chr5D 403558321 403559087 766 False 1090.000000 1090 92.308000 3799 4565 1 chr5D.!!$F1 766
9 TraesCS6A01G222600 chr5D 453421860 453422559 699 False 346.000000 346 75.949000 2716 3415 1 chr5D.!!$F3 699
10 TraesCS6A01G222600 chr2D 481452782 481453547 765 True 1094.000000 1094 92.438000 3799 4565 1 chr2D.!!$R1 766
11 TraesCS6A01G222600 chr2B 801146847 801147614 767 False 1062.000000 1062 91.667000 3800 4565 1 chr2B.!!$F2 765
12 TraesCS6A01G222600 chr1B 380641525 380642295 770 False 1062.000000 1062 91.569000 3796 4565 1 chr1B.!!$F1 769
13 TraesCS6A01G222600 chr3D 252337870 252338634 764 False 1061.000000 1061 91.656000 3799 4565 1 chr3D.!!$F1 766
14 TraesCS6A01G222600 chr4D 409313765 409314531 766 True 1057.000000 1057 91.525000 3799 4565 1 chr4D.!!$R1 766
15 TraesCS6A01G222600 chr1D 400033307 400034071 764 True 1055.000000 1055 91.547000 3799 4565 1 chr1D.!!$R1 766
16 TraesCS6A01G222600 chr5A 572697055 572697756 701 True 361.000000 361 76.264000 2714 3415 1 chr5A.!!$R1 701
17 TraesCS6A01G222600 chr5B 553945678 553946380 702 False 346.000000 346 75.809000 2713 3415 1 chr5B.!!$F1 702

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
27 28 0.035630 ACAAGAGCACCAGCATCTCC 60.036 55.0 0.00 0.0 45.49 3.71 F
32 33 0.035630 AGCACCAGCATCTCCAGAAC 60.036 55.0 0.00 0.0 45.49 3.01 F
194 195 0.036306 GCCTCCAAGAAGAAACCGGA 59.964 55.0 9.46 0.0 0.00 5.14 F
434 441 0.037975 GGCCAGTTGCAATTCACCAG 60.038 55.0 0.59 0.0 43.89 4.00 F
1846 1878 0.111061 ACATCCAGTGCTCTTTGCCA 59.889 50.0 0.00 0.0 42.00 4.92 F
2456 2488 0.037790 TGCATGCACGCTACACTGTA 60.038 50.0 18.46 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1848 0.249398 AGCACTGGATGTAACCGTCC 59.751 55.000 0.00 0.00 45.61 4.79 R
1820 1849 1.204941 AGAGCACTGGATGTAACCGTC 59.795 52.381 0.00 0.00 0.00 4.79 R
1821 1850 1.267121 AGAGCACTGGATGTAACCGT 58.733 50.000 0.00 0.00 0.00 4.83 R
2289 2321 0.037326 TGTCCGGAGTGCACAATCTC 60.037 55.000 21.04 7.49 0.00 2.75 R
2961 3038 0.168348 CGTCCATCTCGTCGAACAGT 59.832 55.000 0.00 0.00 0.00 3.55 R
3891 3973 0.102481 GTACGACCACCGCATCTCAT 59.898 55.000 0.00 0.00 43.32 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
18 19 1.949257 CCGAACCAACAAGAGCACC 59.051 57.895 0.00 0.00 0.00 5.01
19 20 0.817634 CCGAACCAACAAGAGCACCA 60.818 55.000 0.00 0.00 0.00 4.17
20 21 0.588252 CGAACCAACAAGAGCACCAG 59.412 55.000 0.00 0.00 0.00 4.00
21 22 0.312102 GAACCAACAAGAGCACCAGC 59.688 55.000 0.00 0.00 42.56 4.85
22 23 0.395586 AACCAACAAGAGCACCAGCA 60.396 50.000 0.00 0.00 45.49 4.41
23 24 0.178981 ACCAACAAGAGCACCAGCAT 60.179 50.000 0.00 0.00 45.49 3.79
24 25 0.524862 CCAACAAGAGCACCAGCATC 59.475 55.000 0.00 0.00 45.49 3.91
25 26 1.531423 CAACAAGAGCACCAGCATCT 58.469 50.000 0.00 0.00 45.49 2.90
26 27 1.467734 CAACAAGAGCACCAGCATCTC 59.532 52.381 0.00 0.00 45.49 2.75
27 28 0.035630 ACAAGAGCACCAGCATCTCC 60.036 55.000 0.00 0.00 45.49 3.71
28 29 0.035725 CAAGAGCACCAGCATCTCCA 60.036 55.000 0.00 0.00 45.49 3.86
29 30 0.252479 AAGAGCACCAGCATCTCCAG 59.748 55.000 0.00 0.00 45.49 3.86
30 31 0.616964 AGAGCACCAGCATCTCCAGA 60.617 55.000 0.00 0.00 45.49 3.86
31 32 0.251354 GAGCACCAGCATCTCCAGAA 59.749 55.000 0.00 0.00 45.49 3.02
32 33 0.035630 AGCACCAGCATCTCCAGAAC 60.036 55.000 0.00 0.00 45.49 3.01
33 34 1.028868 GCACCAGCATCTCCAGAACC 61.029 60.000 0.00 0.00 41.58 3.62
34 35 0.325933 CACCAGCATCTCCAGAACCA 59.674 55.000 0.00 0.00 0.00 3.67
35 36 1.067295 ACCAGCATCTCCAGAACCAA 58.933 50.000 0.00 0.00 0.00 3.67
36 37 1.425066 ACCAGCATCTCCAGAACCAAA 59.575 47.619 0.00 0.00 0.00 3.28
37 38 2.158475 ACCAGCATCTCCAGAACCAAAA 60.158 45.455 0.00 0.00 0.00 2.44
38 39 3.094572 CCAGCATCTCCAGAACCAAAAT 58.905 45.455 0.00 0.00 0.00 1.82
39 40 4.263905 ACCAGCATCTCCAGAACCAAAATA 60.264 41.667 0.00 0.00 0.00 1.40
40 41 4.337555 CCAGCATCTCCAGAACCAAAATAG 59.662 45.833 0.00 0.00 0.00 1.73
41 42 4.337555 CAGCATCTCCAGAACCAAAATAGG 59.662 45.833 0.00 0.00 0.00 2.57
42 43 3.633986 GCATCTCCAGAACCAAAATAGGG 59.366 47.826 0.00 0.00 0.00 3.53
43 44 4.210331 CATCTCCAGAACCAAAATAGGGG 58.790 47.826 0.00 0.00 0.00 4.79
44 45 3.537337 TCTCCAGAACCAAAATAGGGGA 58.463 45.455 0.00 0.00 0.00 4.81
45 46 3.265995 TCTCCAGAACCAAAATAGGGGAC 59.734 47.826 0.00 0.00 0.00 4.46
46 47 2.990284 TCCAGAACCAAAATAGGGGACA 59.010 45.455 0.00 0.00 0.00 4.02
47 48 3.089284 CCAGAACCAAAATAGGGGACAC 58.911 50.000 0.00 0.00 0.00 3.67
48 49 3.089284 CAGAACCAAAATAGGGGACACC 58.911 50.000 0.00 0.00 40.67 4.16
49 50 2.089201 GAACCAAAATAGGGGACACCG 58.911 52.381 0.00 0.00 46.96 4.94
50 51 0.323087 ACCAAAATAGGGGACACCGC 60.323 55.000 0.00 0.00 46.96 5.68
51 52 1.373590 CCAAAATAGGGGACACCGCG 61.374 60.000 0.00 0.00 46.96 6.46
52 53 0.391927 CAAAATAGGGGACACCGCGA 60.392 55.000 8.23 0.00 46.96 5.87
53 54 0.107848 AAAATAGGGGACACCGCGAG 60.108 55.000 8.23 1.37 46.96 5.03
66 67 2.594541 CGCGAGGGAGCAAGATAAC 58.405 57.895 0.00 0.00 36.85 1.89
67 68 1.209275 CGCGAGGGAGCAAGATAACG 61.209 60.000 0.00 0.00 36.85 3.18
68 69 1.491505 GCGAGGGAGCAAGATAACGC 61.492 60.000 0.00 0.00 38.23 4.84
69 70 0.876342 CGAGGGAGCAAGATAACGCC 60.876 60.000 0.00 0.00 0.00 5.68
70 71 0.466124 GAGGGAGCAAGATAACGCCT 59.534 55.000 0.00 0.00 0.00 5.52
71 72 0.466124 AGGGAGCAAGATAACGCCTC 59.534 55.000 0.00 0.00 0.00 4.70
72 73 0.533085 GGGAGCAAGATAACGCCTCC 60.533 60.000 0.00 0.00 0.00 4.30
73 74 0.178068 GGAGCAAGATAACGCCTCCA 59.822 55.000 0.00 0.00 0.00 3.86
74 75 1.406887 GGAGCAAGATAACGCCTCCAA 60.407 52.381 0.00 0.00 0.00 3.53
75 76 1.936547 GAGCAAGATAACGCCTCCAAG 59.063 52.381 0.00 0.00 0.00 3.61
76 77 1.555075 AGCAAGATAACGCCTCCAAGA 59.445 47.619 0.00 0.00 0.00 3.02
77 78 2.027192 AGCAAGATAACGCCTCCAAGAA 60.027 45.455 0.00 0.00 0.00 2.52
78 79 2.352960 GCAAGATAACGCCTCCAAGAAG 59.647 50.000 0.00 0.00 0.00 2.85
79 80 2.939103 CAAGATAACGCCTCCAAGAAGG 59.061 50.000 0.00 0.00 39.62 3.46
80 81 2.467880 AGATAACGCCTCCAAGAAGGA 58.532 47.619 0.00 0.00 46.75 3.36
87 88 3.388841 TCCAAGAAGGAGGACGCC 58.611 61.111 0.00 0.00 43.07 5.68
88 89 2.125512 CCAAGAAGGAGGACGCCG 60.126 66.667 0.00 0.00 41.22 6.46
89 90 2.646175 CCAAGAAGGAGGACGCCGA 61.646 63.158 0.00 0.00 41.22 5.54
90 91 1.153745 CAAGAAGGAGGACGCCGAG 60.154 63.158 0.00 0.00 0.00 4.63
91 92 1.304217 AAGAAGGAGGACGCCGAGA 60.304 57.895 0.00 0.00 0.00 4.04
92 93 1.596895 AAGAAGGAGGACGCCGAGAC 61.597 60.000 0.00 0.00 0.00 3.36
93 94 2.282958 AAGGAGGACGCCGAGACA 60.283 61.111 0.00 0.00 0.00 3.41
94 95 2.545165 GAAGGAGGACGCCGAGACAC 62.545 65.000 0.00 0.00 0.00 3.67
95 96 4.131088 GGAGGACGCCGAGACACC 62.131 72.222 0.00 0.00 0.00 4.16
96 97 4.477975 GAGGACGCCGAGACACCG 62.478 72.222 0.00 0.00 0.00 4.94
103 104 4.129737 CCGAGACACCGTCGCCAT 62.130 66.667 0.00 0.00 37.67 4.40
104 105 2.579787 CGAGACACCGTCGCCATC 60.580 66.667 0.00 0.00 37.67 3.51
105 106 2.202756 GAGACACCGTCGCCATCC 60.203 66.667 0.00 0.00 37.67 3.51
106 107 2.994995 AGACACCGTCGCCATCCA 60.995 61.111 0.00 0.00 37.67 3.41
107 108 2.509336 GACACCGTCGCCATCCAG 60.509 66.667 0.00 0.00 0.00 3.86
108 109 3.296709 GACACCGTCGCCATCCAGT 62.297 63.158 0.00 0.00 0.00 4.00
109 110 2.509336 CACCGTCGCCATCCAGTC 60.509 66.667 0.00 0.00 0.00 3.51
110 111 3.771160 ACCGTCGCCATCCAGTCC 61.771 66.667 0.00 0.00 0.00 3.85
111 112 4.873129 CCGTCGCCATCCAGTCCG 62.873 72.222 0.00 0.00 0.00 4.79
112 113 3.822192 CGTCGCCATCCAGTCCGA 61.822 66.667 0.00 0.00 0.00 4.55
113 114 2.577059 GTCGCCATCCAGTCCGAA 59.423 61.111 0.00 0.00 0.00 4.30
114 115 1.519455 GTCGCCATCCAGTCCGAAG 60.519 63.158 0.00 0.00 0.00 3.79
129 130 2.674796 CGAAGGAACCAGACTTAGGG 57.325 55.000 0.00 0.00 0.00 3.53
130 131 1.900486 CGAAGGAACCAGACTTAGGGT 59.100 52.381 0.00 0.00 39.65 4.34
132 133 3.244457 CGAAGGAACCAGACTTAGGGTTT 60.244 47.826 0.00 0.00 46.97 3.27
133 134 4.325119 GAAGGAACCAGACTTAGGGTTTC 58.675 47.826 0.00 0.00 46.97 2.78
134 135 2.643304 AGGAACCAGACTTAGGGTTTCC 59.357 50.000 0.00 0.00 46.97 3.13
135 136 2.290768 GGAACCAGACTTAGGGTTTCCC 60.291 54.545 0.00 0.00 46.97 3.97
145 146 3.388841 GGTTTCCCCTGAGCTCGA 58.611 61.111 9.64 0.00 0.00 4.04
146 147 1.677552 GGTTTCCCCTGAGCTCGAA 59.322 57.895 9.64 3.37 0.00 3.71
147 148 0.391793 GGTTTCCCCTGAGCTCGAAG 60.392 60.000 9.64 1.24 0.00 3.79
148 149 0.608640 GTTTCCCCTGAGCTCGAAGA 59.391 55.000 9.64 0.11 0.00 2.87
175 176 3.578456 CCGCAGGCCTTTACAGTG 58.422 61.111 0.00 0.00 46.14 3.66
176 177 2.690778 CCGCAGGCCTTTACAGTGC 61.691 63.158 0.00 0.47 46.14 4.40
177 178 2.690778 CGCAGGCCTTTACAGTGCC 61.691 63.158 0.00 0.00 45.70 5.01
180 181 4.320910 GGCCTTTACAGTGCCTCC 57.679 61.111 0.00 0.00 42.01 4.30
181 182 1.378762 GGCCTTTACAGTGCCTCCA 59.621 57.895 0.00 0.00 42.01 3.86
182 183 0.251165 GGCCTTTACAGTGCCTCCAA 60.251 55.000 0.00 0.00 42.01 3.53
183 184 1.168714 GCCTTTACAGTGCCTCCAAG 58.831 55.000 0.00 0.00 0.00 3.61
184 185 1.271379 GCCTTTACAGTGCCTCCAAGA 60.271 52.381 0.00 0.00 0.00 3.02
185 186 2.814097 GCCTTTACAGTGCCTCCAAGAA 60.814 50.000 0.00 0.00 0.00 2.52
186 187 3.077359 CCTTTACAGTGCCTCCAAGAAG 58.923 50.000 0.00 0.00 0.00 2.85
187 188 3.244561 CCTTTACAGTGCCTCCAAGAAGA 60.245 47.826 0.00 0.00 0.00 2.87
188 189 4.389374 CTTTACAGTGCCTCCAAGAAGAA 58.611 43.478 0.00 0.00 0.00 2.52
189 190 4.431416 TTACAGTGCCTCCAAGAAGAAA 57.569 40.909 0.00 0.00 0.00 2.52
190 191 2.576615 ACAGTGCCTCCAAGAAGAAAC 58.423 47.619 0.00 0.00 0.00 2.78
191 192 1.882623 CAGTGCCTCCAAGAAGAAACC 59.117 52.381 0.00 0.00 0.00 3.27
192 193 0.875059 GTGCCTCCAAGAAGAAACCG 59.125 55.000 0.00 0.00 0.00 4.44
193 194 0.250727 TGCCTCCAAGAAGAAACCGG 60.251 55.000 0.00 0.00 0.00 5.28
194 195 0.036306 GCCTCCAAGAAGAAACCGGA 59.964 55.000 9.46 0.00 0.00 5.14
195 196 1.809684 CCTCCAAGAAGAAACCGGAC 58.190 55.000 9.46 0.00 0.00 4.79
196 197 1.610886 CCTCCAAGAAGAAACCGGACC 60.611 57.143 9.46 0.00 0.00 4.46
197 198 1.348036 CTCCAAGAAGAAACCGGACCT 59.652 52.381 9.46 0.00 0.00 3.85
198 199 2.565834 CTCCAAGAAGAAACCGGACCTA 59.434 50.000 9.46 0.00 0.00 3.08
199 200 2.565834 TCCAAGAAGAAACCGGACCTAG 59.434 50.000 9.46 0.00 0.00 3.02
200 201 2.354805 CCAAGAAGAAACCGGACCTAGG 60.355 54.545 9.46 7.41 0.00 3.02
201 202 1.569653 AGAAGAAACCGGACCTAGGG 58.430 55.000 14.81 0.00 0.00 3.53
202 203 1.203275 AGAAGAAACCGGACCTAGGGT 60.203 52.381 14.81 0.00 39.44 4.34
206 207 2.380365 AACCGGACCTAGGGTTTCC 58.620 57.895 14.81 10.29 43.84 3.13
207 208 1.203441 AACCGGACCTAGGGTTTCCC 61.203 60.000 14.81 5.14 43.84 3.97
241 242 2.291741 CCAGTTCTTGAGTTGTTCTGCC 59.708 50.000 0.00 0.00 0.00 4.85
244 245 4.096984 CAGTTCTTGAGTTGTTCTGCCTTT 59.903 41.667 0.00 0.00 0.00 3.11
257 258 5.105146 TGTTCTGCCTTTTGTGGTTTAATGT 60.105 36.000 0.00 0.00 0.00 2.71
313 314 1.821216 AACTCCGGTTATTGGTGCTG 58.179 50.000 0.00 0.00 33.39 4.41
352 353 7.032580 TGAAAATCTTGTCATTTCGTTGTGTT 58.967 30.769 0.00 0.00 36.17 3.32
431 438 1.544724 TAGGGCCAGTTGCAATTCAC 58.455 50.000 6.18 0.00 43.89 3.18
434 441 0.037975 GGCCAGTTGCAATTCACCAG 60.038 55.000 0.59 0.00 43.89 4.00
436 443 1.547372 GCCAGTTGCAATTCACCAGAT 59.453 47.619 0.59 0.00 40.77 2.90
489 504 5.785940 AGTAGAGGTAAAATGTCCACCTTCT 59.214 40.000 0.00 0.00 42.78 2.85
619 635 5.187381 TCATTAAAGCTGAATGAATGGCCAA 59.813 36.000 10.96 0.00 39.71 4.52
629 653 1.758280 TGAATGGCCAAGGATTCATGC 59.242 47.619 10.96 0.00 34.40 4.06
658 682 6.319141 AGGTTTTGAGCTTAAACATCAGAC 57.681 37.500 20.31 9.24 37.25 3.51
659 683 5.241728 AGGTTTTGAGCTTAAACATCAGACC 59.758 40.000 20.31 15.80 37.25 3.85
717 741 4.406649 TGATAGCCTGATCACATGTTCTCA 59.593 41.667 0.00 0.94 30.75 3.27
781 805 2.766263 TCTGGTCGATCTGCCTTTATGT 59.234 45.455 0.00 0.00 0.00 2.29
867 891 2.180204 GCACAGTGTTGCCGTCACT 61.180 57.895 1.61 0.00 45.43 3.41
912 936 1.494960 AATGGTGGTGTGCCTGTTTT 58.505 45.000 0.00 0.00 35.27 2.43
920 944 2.479560 GGTGTGCCTGTTTTCACAAGAC 60.480 50.000 0.00 0.00 43.78 3.01
1039 1067 1.407656 AAACGTCAGGTGAGCCTCCA 61.408 55.000 0.00 0.00 44.97 3.86
1107 1135 8.690203 TTGACATTTCAGTTCTCAAGGATTTA 57.310 30.769 0.00 0.00 31.71 1.40
1110 1138 6.710744 ACATTTCAGTTCTCAAGGATTTACGT 59.289 34.615 0.00 0.00 0.00 3.57
1118 1146 6.105397 TCTCAAGGATTTACGTGTTAGGTT 57.895 37.500 0.00 0.00 0.00 3.50
1123 1151 4.999311 AGGATTTACGTGTTAGGTTTCACC 59.001 41.667 0.00 0.00 38.99 4.02
1135 1163 6.951198 TGTTAGGTTTCACCAATATCACCATT 59.049 34.615 0.00 0.00 41.95 3.16
1142 1170 3.444742 CACCAATATCACCATTGCAGTGT 59.555 43.478 8.53 0.00 35.06 3.55
1153 1181 6.378848 TCACCATTGCAGTGTACTGTACTATA 59.621 38.462 17.98 0.00 45.45 1.31
1154 1182 7.069455 TCACCATTGCAGTGTACTGTACTATAT 59.931 37.037 17.98 0.21 45.45 0.86
1155 1183 7.169813 CACCATTGCAGTGTACTGTACTATATG 59.830 40.741 17.98 11.92 45.45 1.78
1156 1184 7.147724 ACCATTGCAGTGTACTGTACTATATGT 60.148 37.037 17.98 2.89 45.45 2.29
1157 1185 7.710907 CCATTGCAGTGTACTGTACTATATGTT 59.289 37.037 17.98 0.00 45.45 2.71
1158 1186 8.755941 CATTGCAGTGTACTGTACTATATGTTC 58.244 37.037 17.98 1.95 45.45 3.18
1159 1187 6.802608 TGCAGTGTACTGTACTATATGTTCC 58.197 40.000 17.98 2.17 45.45 3.62
1160 1188 6.378848 TGCAGTGTACTGTACTATATGTTCCA 59.621 38.462 17.98 4.20 45.45 3.53
1161 1189 7.093684 TGCAGTGTACTGTACTATATGTTCCAA 60.094 37.037 17.98 0.00 45.45 3.53
1162 1190 7.762615 GCAGTGTACTGTACTATATGTTCCAAA 59.237 37.037 17.98 0.00 45.45 3.28
1163 1191 9.647797 CAGTGTACTGTACTATATGTTCCAAAA 57.352 33.333 17.98 0.00 39.09 2.44
1164 1192 9.871238 AGTGTACTGTACTATATGTTCCAAAAG 57.129 33.333 17.98 0.00 0.00 2.27
1165 1193 9.095065 GTGTACTGTACTATATGTTCCAAAAGG 57.905 37.037 17.98 0.00 0.00 3.11
1166 1194 9.038072 TGTACTGTACTATATGTTCCAAAAGGA 57.962 33.333 17.98 0.00 0.00 3.36
1167 1195 9.880157 GTACTGTACTATATGTTCCAAAAGGAA 57.120 33.333 10.64 0.00 0.00 3.36
1169 1197 9.802039 ACTGTACTATATGTTCCAAAAGGAAAA 57.198 29.630 0.00 0.00 0.00 2.29
1178 1206 7.986085 TGTTCCAAAAGGAAAAATTGTTTGA 57.014 28.000 0.00 0.00 32.18 2.69
1179 1207 7.811653 TGTTCCAAAAGGAAAAATTGTTTGAC 58.188 30.769 0.00 0.00 32.18 3.18
1180 1208 7.663493 TGTTCCAAAAGGAAAAATTGTTTGACT 59.337 29.630 0.00 0.00 32.18 3.41
1181 1209 7.608308 TCCAAAAGGAAAAATTGTTTGACTG 57.392 32.000 0.00 0.00 32.18 3.51
1182 1210 7.390027 TCCAAAAGGAAAAATTGTTTGACTGA 58.610 30.769 0.00 0.00 32.18 3.41
1183 1211 8.046107 TCCAAAAGGAAAAATTGTTTGACTGAT 58.954 29.630 0.00 0.00 32.18 2.90
1184 1212 8.676401 CCAAAAGGAAAAATTGTTTGACTGATT 58.324 29.630 0.00 0.00 32.18 2.57
1196 1224 6.738114 TGTTTGACTGATTGTTTCCAGATTC 58.262 36.000 0.00 0.00 34.65 2.52
1197 1225 6.320926 TGTTTGACTGATTGTTTCCAGATTCA 59.679 34.615 0.00 0.00 34.65 2.57
1249 1278 4.640201 TGCTGCATTACCAATTCTAGGTTC 59.360 41.667 0.00 0.00 40.54 3.62
1309 1338 1.211212 CTGGAGATCCCATCAACAGCA 59.789 52.381 3.70 0.00 45.57 4.41
1317 1346 1.201647 CCCATCAACAGCAAGCAAGAG 59.798 52.381 0.00 0.00 0.00 2.85
1453 1482 1.253593 TGGAGTCGCTGATGCACTCT 61.254 55.000 14.82 0.76 41.98 3.24
1564 1593 1.258445 ACCCGCTGTTCCTCTACCTG 61.258 60.000 0.00 0.00 0.00 4.00
1729 1758 1.066502 GTGTTTGGGAGAGGAGAGCTC 60.067 57.143 5.27 5.27 0.00 4.09
1741 1770 1.670949 GAGAGCTCGTGATCCAGCCA 61.671 60.000 8.37 0.00 36.17 4.75
1762 1791 4.323028 CCATACAAGATCGCCATGAGGTAT 60.323 45.833 0.00 0.00 37.19 2.73
1765 1794 4.152647 ACAAGATCGCCATGAGGTATCTA 58.847 43.478 0.00 0.00 38.21 1.98
1819 1848 0.892755 TGCCTCTACCACAGGTAACG 59.107 55.000 0.00 0.00 46.39 3.18
1820 1849 0.175073 GCCTCTACCACAGGTAACGG 59.825 60.000 0.00 2.46 46.39 4.44
1821 1850 1.843368 CCTCTACCACAGGTAACGGA 58.157 55.000 0.00 0.00 46.39 4.69
1822 1851 1.475682 CCTCTACCACAGGTAACGGAC 59.524 57.143 0.00 0.00 46.39 4.79
1823 1852 1.131883 CTCTACCACAGGTAACGGACG 59.868 57.143 0.00 0.00 46.39 4.79
1824 1853 0.171903 CTACCACAGGTAACGGACGG 59.828 60.000 0.00 0.00 46.39 4.79
1846 1878 0.111061 ACATCCAGTGCTCTTTGCCA 59.889 50.000 0.00 0.00 42.00 4.92
1853 1885 1.741706 AGTGCTCTTTGCCATGAATCG 59.258 47.619 0.00 0.00 42.00 3.34
1873 1905 2.593257 GCAAGAACTGAAATGCTCTGC 58.407 47.619 0.00 0.00 35.93 4.26
1890 1922 4.453819 GCTCTGCACAAATCTTCTGTAACT 59.546 41.667 0.00 0.00 0.00 2.24
1891 1923 5.049129 GCTCTGCACAAATCTTCTGTAACTT 60.049 40.000 0.00 0.00 0.00 2.66
2061 2093 1.227089 GCAGATCGTCATGGCGACT 60.227 57.895 26.77 20.17 43.99 4.18
2247 2279 0.596600 TCTTCGACTGCAACACCGTC 60.597 55.000 0.00 0.00 0.00 4.79
2250 2282 1.591594 CGACTGCAACACCGTCAGT 60.592 57.895 4.20 0.00 43.06 3.41
2289 2321 1.350193 ACGAGCTGAGCAACATAACG 58.650 50.000 7.39 3.28 0.00 3.18
2361 2393 3.118223 AGGCCTTCAACTATAAGCTCACC 60.118 47.826 0.00 0.00 0.00 4.02
2376 2408 4.309950 ACCACGTCGGCCTTCACC 62.310 66.667 0.00 0.00 39.03 4.02
2432 2464 7.013369 ACTCAAGAACCTCAGGTTTGAAATTAC 59.987 37.037 11.44 0.00 46.95 1.89
2445 2477 4.374843 TGAAATTACTCCATGCATGCAC 57.625 40.909 25.37 6.02 0.00 4.57
2450 2482 1.091771 ACTCCATGCATGCACGCTAC 61.092 55.000 25.37 0.00 0.00 3.58
2451 2483 1.078567 TCCATGCATGCACGCTACA 60.079 52.632 25.37 0.00 0.00 2.74
2452 2484 1.063006 CCATGCATGCACGCTACAC 59.937 57.895 25.37 0.00 0.00 2.90
2453 2485 1.371337 CCATGCATGCACGCTACACT 61.371 55.000 25.37 0.38 0.00 3.55
2454 2486 0.247934 CATGCATGCACGCTACACTG 60.248 55.000 25.37 11.08 0.00 3.66
2456 2488 0.037790 TGCATGCACGCTACACTGTA 60.038 50.000 18.46 0.00 0.00 2.74
2467 2536 6.669278 CACGCTACACTGTAGTATGTATCAT 58.331 40.000 16.08 0.00 31.10 2.45
2517 2592 7.481275 AATACAAAAATGTTTCAGTTGCCTG 57.519 32.000 0.00 0.00 40.25 4.85
2578 2653 1.669502 GCTTTGCAATCGTCATTGGCA 60.670 47.619 0.00 0.00 40.03 4.92
2589 2664 0.041535 TCATTGGCATCCTTGGGCTT 59.958 50.000 0.00 0.00 0.00 4.35
2592 2667 0.407528 TTGGCATCCTTGGGCTTGTA 59.592 50.000 0.00 0.00 0.00 2.41
2636 2711 5.675575 GCAACATGCAAGTAAGATCTCCTTG 60.676 44.000 22.03 22.03 44.26 3.61
2727 2804 6.371809 TTTTTGTCTTTGCAGTCGTATCTT 57.628 33.333 0.00 0.00 0.00 2.40
3443 3520 2.512286 CGCGTCCATGGAGCACAT 60.512 61.111 25.86 0.00 41.57 3.21
3573 3655 7.281100 GTGGAACAAGAGATCTAAATTGTAGGG 59.719 40.741 16.54 0.00 44.16 3.53
3654 3736 2.667473 CGTTGGATAGGAAACGGACT 57.333 50.000 0.21 0.00 44.08 3.85
3659 3741 3.104512 TGGATAGGAAACGGACTGACAT 58.895 45.455 0.00 0.00 0.00 3.06
3731 3813 1.825191 CATTGCATCCGGGGGACAG 60.825 63.158 0.00 0.00 32.98 3.51
3842 3924 0.814010 AACGAACGTCTGCTTTGCCT 60.814 50.000 0.00 0.00 0.00 4.75
3852 3934 0.539438 TGCTTTGCCTGGAATCGGTT 60.539 50.000 0.00 0.00 0.00 4.44
3854 3936 1.533625 CTTTGCCTGGAATCGGTTCA 58.466 50.000 11.19 0.00 36.01 3.18
3863 3945 4.013728 CTGGAATCGGTTCATTTGGGTAA 58.986 43.478 11.19 0.00 36.01 2.85
3891 3973 3.228017 TCGTGTTCGGGCCTGTCA 61.228 61.111 12.43 9.69 37.69 3.58
3909 3991 0.102300 CATGAGATGCGGTGGTCGTA 59.898 55.000 0.00 0.00 41.72 3.43
3948 4030 0.482446 TCTGTTTGCCCCATCCTGTT 59.518 50.000 0.00 0.00 0.00 3.16
3951 4033 0.893727 GTTTGCCCCATCCTGTTCGT 60.894 55.000 0.00 0.00 0.00 3.85
3967 4050 2.270352 TCGTCAGGGTCAAAAATGCT 57.730 45.000 0.00 0.00 0.00 3.79
4184 4272 6.810182 GTCATTTTGAAGATCCAAATGAGTGG 59.190 38.462 15.70 0.00 40.33 4.00
4254 4342 1.531602 GTTCTTGGTGCAGGGGCTT 60.532 57.895 0.00 0.00 41.91 4.35
4289 4377 5.973565 CCTTGATAATCAAATCCTTTGTCGC 59.026 40.000 0.00 0.00 41.36 5.19
4357 4445 1.417517 ACACAAGCAGTCATCACCTCA 59.582 47.619 0.00 0.00 0.00 3.86
4365 4453 2.740981 CAGTCATCACCTCACAAAGCTC 59.259 50.000 0.00 0.00 0.00 4.09
4469 4557 6.605471 TTCTAGCACTCTCTTACATTTGGA 57.395 37.500 0.00 0.00 0.00 3.53
4480 4568 8.553459 TCTCTTACATTTGGACAAATCTCTTC 57.447 34.615 7.28 0.00 38.84 2.87
4482 4570 6.659242 TCTTACATTTGGACAAATCTCTTCCC 59.341 38.462 7.28 0.00 38.84 3.97
4525 4613 6.483307 TCGAGATTGTCTTCACAAAAGTTGAT 59.517 34.615 0.00 0.00 45.78 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.817634 TGGTGCTCTTGTTGGTTCGG 60.818 55.000 0.00 0.00 0.00 4.30
2 3 0.312102 GCTGGTGCTCTTGTTGGTTC 59.688 55.000 0.00 0.00 36.03 3.62
4 5 0.178981 ATGCTGGTGCTCTTGTTGGT 60.179 50.000 0.00 0.00 40.48 3.67
5 6 0.524862 GATGCTGGTGCTCTTGTTGG 59.475 55.000 0.00 0.00 40.48 3.77
6 7 1.467734 GAGATGCTGGTGCTCTTGTTG 59.532 52.381 0.00 0.00 40.48 3.33
7 8 1.612726 GGAGATGCTGGTGCTCTTGTT 60.613 52.381 0.00 0.00 40.48 2.83
8 9 0.035630 GGAGATGCTGGTGCTCTTGT 60.036 55.000 0.00 0.00 40.48 3.16
9 10 0.035725 TGGAGATGCTGGTGCTCTTG 60.036 55.000 0.00 0.00 40.48 3.02
10 11 0.252479 CTGGAGATGCTGGTGCTCTT 59.748 55.000 0.00 0.00 40.48 2.85
11 12 0.616964 TCTGGAGATGCTGGTGCTCT 60.617 55.000 0.00 0.00 40.48 4.09
12 13 0.251354 TTCTGGAGATGCTGGTGCTC 59.749 55.000 0.00 0.00 40.48 4.26
13 14 0.035630 GTTCTGGAGATGCTGGTGCT 60.036 55.000 0.00 0.00 40.48 4.40
14 15 1.028868 GGTTCTGGAGATGCTGGTGC 61.029 60.000 0.00 0.00 40.20 5.01
15 16 0.325933 TGGTTCTGGAGATGCTGGTG 59.674 55.000 0.00 0.00 0.00 4.17
16 17 1.067295 TTGGTTCTGGAGATGCTGGT 58.933 50.000 0.00 0.00 0.00 4.00
17 18 2.205022 TTTGGTTCTGGAGATGCTGG 57.795 50.000 0.00 0.00 0.00 4.85
18 19 4.337555 CCTATTTTGGTTCTGGAGATGCTG 59.662 45.833 0.00 0.00 0.00 4.41
19 20 4.530875 CCTATTTTGGTTCTGGAGATGCT 58.469 43.478 0.00 0.00 0.00 3.79
20 21 3.633986 CCCTATTTTGGTTCTGGAGATGC 59.366 47.826 0.00 0.00 0.00 3.91
21 22 4.079787 TCCCCTATTTTGGTTCTGGAGATG 60.080 45.833 0.00 0.00 0.00 2.90
22 23 4.079730 GTCCCCTATTTTGGTTCTGGAGAT 60.080 45.833 0.00 0.00 0.00 2.75
23 24 3.265995 GTCCCCTATTTTGGTTCTGGAGA 59.734 47.826 0.00 0.00 0.00 3.71
24 25 3.010138 TGTCCCCTATTTTGGTTCTGGAG 59.990 47.826 0.00 0.00 0.00 3.86
25 26 2.990284 TGTCCCCTATTTTGGTTCTGGA 59.010 45.455 0.00 0.00 0.00 3.86
26 27 3.089284 GTGTCCCCTATTTTGGTTCTGG 58.911 50.000 0.00 0.00 0.00 3.86
27 28 3.089284 GGTGTCCCCTATTTTGGTTCTG 58.911 50.000 0.00 0.00 0.00 3.02
28 29 2.290705 CGGTGTCCCCTATTTTGGTTCT 60.291 50.000 0.00 0.00 0.00 3.01
29 30 2.089201 CGGTGTCCCCTATTTTGGTTC 58.911 52.381 0.00 0.00 0.00 3.62
30 31 1.889262 GCGGTGTCCCCTATTTTGGTT 60.889 52.381 0.00 0.00 0.00 3.67
31 32 0.323087 GCGGTGTCCCCTATTTTGGT 60.323 55.000 0.00 0.00 0.00 3.67
32 33 1.373590 CGCGGTGTCCCCTATTTTGG 61.374 60.000 0.00 0.00 0.00 3.28
33 34 0.391927 TCGCGGTGTCCCCTATTTTG 60.392 55.000 6.13 0.00 0.00 2.44
34 35 0.107848 CTCGCGGTGTCCCCTATTTT 60.108 55.000 6.13 0.00 0.00 1.82
35 36 1.520666 CTCGCGGTGTCCCCTATTT 59.479 57.895 6.13 0.00 0.00 1.40
36 37 2.432300 CCTCGCGGTGTCCCCTATT 61.432 63.158 6.13 0.00 0.00 1.73
37 38 2.838225 CCTCGCGGTGTCCCCTAT 60.838 66.667 6.13 0.00 0.00 2.57
43 44 4.373116 TTGCTCCCTCGCGGTGTC 62.373 66.667 6.13 0.00 0.00 3.67
44 45 4.379243 CTTGCTCCCTCGCGGTGT 62.379 66.667 6.13 0.00 0.00 4.16
45 46 2.016393 TATCTTGCTCCCTCGCGGTG 62.016 60.000 6.13 0.00 0.00 4.94
46 47 1.327690 TTATCTTGCTCCCTCGCGGT 61.328 55.000 6.13 0.00 0.00 5.68
47 48 0.876342 GTTATCTTGCTCCCTCGCGG 60.876 60.000 6.13 0.00 0.00 6.46
48 49 1.209275 CGTTATCTTGCTCCCTCGCG 61.209 60.000 0.00 0.00 0.00 5.87
49 50 1.491505 GCGTTATCTTGCTCCCTCGC 61.492 60.000 0.00 0.00 36.06 5.03
50 51 0.876342 GGCGTTATCTTGCTCCCTCG 60.876 60.000 0.00 0.00 0.00 4.63
51 52 0.466124 AGGCGTTATCTTGCTCCCTC 59.534 55.000 0.00 0.00 0.00 4.30
52 53 0.466124 GAGGCGTTATCTTGCTCCCT 59.534 55.000 0.00 0.00 0.00 4.20
53 54 0.533085 GGAGGCGTTATCTTGCTCCC 60.533 60.000 0.00 0.00 0.00 4.30
54 55 0.178068 TGGAGGCGTTATCTTGCTCC 59.822 55.000 0.00 0.00 0.00 4.70
55 56 1.936547 CTTGGAGGCGTTATCTTGCTC 59.063 52.381 0.00 0.00 0.00 4.26
56 57 1.555075 TCTTGGAGGCGTTATCTTGCT 59.445 47.619 0.00 0.00 0.00 3.91
57 58 2.024176 TCTTGGAGGCGTTATCTTGC 57.976 50.000 0.00 0.00 0.00 4.01
58 59 2.939103 CCTTCTTGGAGGCGTTATCTTG 59.061 50.000 0.00 0.00 38.35 3.02
59 60 2.838202 TCCTTCTTGGAGGCGTTATCTT 59.162 45.455 0.00 0.00 40.56 2.40
60 61 2.467880 TCCTTCTTGGAGGCGTTATCT 58.532 47.619 0.00 0.00 40.56 1.98
61 62 2.981859 TCCTTCTTGGAGGCGTTATC 57.018 50.000 0.00 0.00 40.56 1.75
70 71 2.646175 CGGCGTCCTCCTTCTTGGA 61.646 63.158 0.00 0.00 43.86 3.53
71 72 2.125512 CGGCGTCCTCCTTCTTGG 60.126 66.667 0.00 0.00 37.10 3.61
72 73 1.153745 CTCGGCGTCCTCCTTCTTG 60.154 63.158 6.85 0.00 0.00 3.02
73 74 1.304217 TCTCGGCGTCCTCCTTCTT 60.304 57.895 6.85 0.00 0.00 2.52
74 75 2.047443 GTCTCGGCGTCCTCCTTCT 61.047 63.158 6.85 0.00 0.00 2.85
75 76 2.341101 TGTCTCGGCGTCCTCCTTC 61.341 63.158 6.85 0.00 0.00 3.46
76 77 2.282958 TGTCTCGGCGTCCTCCTT 60.283 61.111 6.85 0.00 0.00 3.36
77 78 3.063084 GTGTCTCGGCGTCCTCCT 61.063 66.667 6.85 0.00 0.00 3.69
78 79 4.131088 GGTGTCTCGGCGTCCTCC 62.131 72.222 6.85 2.78 0.00 4.30
79 80 4.477975 CGGTGTCTCGGCGTCCTC 62.478 72.222 6.85 0.00 0.00 3.71
81 82 4.773117 GACGGTGTCTCGGCGTCC 62.773 72.222 6.85 2.47 0.00 4.79
86 87 4.129737 ATGGCGACGGTGTCTCGG 62.130 66.667 0.00 0.00 0.00 4.63
87 88 2.579787 GATGGCGACGGTGTCTCG 60.580 66.667 0.00 0.00 0.00 4.04
88 89 2.202756 GGATGGCGACGGTGTCTC 60.203 66.667 0.00 0.00 0.00 3.36
89 90 2.994995 TGGATGGCGACGGTGTCT 60.995 61.111 0.00 0.00 0.00 3.41
90 91 2.509336 CTGGATGGCGACGGTGTC 60.509 66.667 0.00 0.00 0.00 3.67
91 92 3.296709 GACTGGATGGCGACGGTGT 62.297 63.158 0.00 0.00 0.00 4.16
92 93 2.509336 GACTGGATGGCGACGGTG 60.509 66.667 0.00 0.00 0.00 4.94
93 94 3.771160 GGACTGGATGGCGACGGT 61.771 66.667 0.00 0.00 0.00 4.83
94 95 4.873129 CGGACTGGATGGCGACGG 62.873 72.222 0.00 0.00 0.00 4.79
95 96 3.350909 TTCGGACTGGATGGCGACG 62.351 63.158 0.00 0.00 0.00 5.12
96 97 1.519455 CTTCGGACTGGATGGCGAC 60.519 63.158 0.00 0.00 0.00 5.19
97 98 2.721167 CCTTCGGACTGGATGGCGA 61.721 63.158 0.00 0.00 0.00 5.54
98 99 2.202932 CCTTCGGACTGGATGGCG 60.203 66.667 0.00 0.00 0.00 5.69
99 100 0.744771 GTTCCTTCGGACTGGATGGC 60.745 60.000 0.53 0.00 32.70 4.40
100 101 0.107654 GGTTCCTTCGGACTGGATGG 60.108 60.000 0.53 0.00 33.66 3.51
101 102 0.613260 TGGTTCCTTCGGACTGGATG 59.387 55.000 0.53 0.00 31.76 3.51
102 103 0.905357 CTGGTTCCTTCGGACTGGAT 59.095 55.000 0.53 0.00 31.76 3.41
103 104 0.178944 TCTGGTTCCTTCGGACTGGA 60.179 55.000 0.00 0.00 0.00 3.86
104 105 0.037232 GTCTGGTTCCTTCGGACTGG 60.037 60.000 0.00 0.00 37.50 4.00
105 106 0.969894 AGTCTGGTTCCTTCGGACTG 59.030 55.000 4.94 0.00 45.86 3.51
106 107 3.459386 AGTCTGGTTCCTTCGGACT 57.541 52.632 0.00 0.00 43.68 3.85
107 108 2.094130 CCTAAGTCTGGTTCCTTCGGAC 60.094 54.545 0.00 0.00 39.97 4.79
108 109 2.176889 CCTAAGTCTGGTTCCTTCGGA 58.823 52.381 0.00 0.00 0.00 4.55
109 110 1.207329 CCCTAAGTCTGGTTCCTTCGG 59.793 57.143 0.00 0.00 0.00 4.30
110 111 1.900486 ACCCTAAGTCTGGTTCCTTCG 59.100 52.381 0.00 0.00 0.00 3.79
111 112 4.325119 GAAACCCTAAGTCTGGTTCCTTC 58.675 47.826 0.00 0.00 43.94 3.46
112 113 3.074094 GGAAACCCTAAGTCTGGTTCCTT 59.926 47.826 0.00 0.00 43.94 3.36
113 114 2.643304 GGAAACCCTAAGTCTGGTTCCT 59.357 50.000 0.00 0.00 43.94 3.36
114 115 3.069079 GGAAACCCTAAGTCTGGTTCC 57.931 52.381 0.00 0.00 43.94 3.62
129 130 0.608640 TCTTCGAGCTCAGGGGAAAC 59.391 55.000 15.40 0.00 0.00 2.78
130 131 0.898320 CTCTTCGAGCTCAGGGGAAA 59.102 55.000 15.40 0.00 0.00 3.13
131 132 0.972983 CCTCTTCGAGCTCAGGGGAA 60.973 60.000 13.68 7.73 31.27 3.97
132 133 1.380515 CCTCTTCGAGCTCAGGGGA 60.381 63.158 13.68 0.00 31.27 4.81
133 134 2.430610 CCCTCTTCGAGCTCAGGGG 61.431 68.421 23.52 18.30 41.96 4.79
134 135 2.430610 CCCCTCTTCGAGCTCAGGG 61.431 68.421 24.05 24.05 44.92 4.45
135 136 3.087666 GCCCCTCTTCGAGCTCAGG 62.088 68.421 15.40 12.51 0.00 3.86
136 137 2.498726 GCCCCTCTTCGAGCTCAG 59.501 66.667 15.40 4.49 0.00 3.35
137 138 3.452786 CGCCCCTCTTCGAGCTCA 61.453 66.667 15.40 0.00 0.00 4.26
138 139 4.882396 GCGCCCCTCTTCGAGCTC 62.882 72.222 2.73 2.73 0.00 4.09
158 159 2.690778 GCACTGTAAAGGCCTGCGG 61.691 63.158 5.69 7.83 0.00 5.69
159 160 2.690778 GGCACTGTAAAGGCCTGCG 61.691 63.158 5.69 0.00 44.32 5.18
160 161 3.278157 GGCACTGTAAAGGCCTGC 58.722 61.111 5.69 3.65 44.32 4.85
164 165 1.168714 CTTGGAGGCACTGTAAAGGC 58.831 55.000 0.00 0.00 41.55 4.35
165 166 2.859165 TCTTGGAGGCACTGTAAAGG 57.141 50.000 0.00 0.00 41.55 3.11
166 167 4.008074 TCTTCTTGGAGGCACTGTAAAG 57.992 45.455 0.00 0.00 41.55 1.85
167 168 4.431416 TTCTTCTTGGAGGCACTGTAAA 57.569 40.909 0.00 0.00 41.55 2.01
168 169 4.134563 GTTTCTTCTTGGAGGCACTGTAA 58.865 43.478 0.00 0.00 41.55 2.41
169 170 3.496160 GGTTTCTTCTTGGAGGCACTGTA 60.496 47.826 0.00 0.00 41.55 2.74
170 171 2.576615 GTTTCTTCTTGGAGGCACTGT 58.423 47.619 0.00 0.00 41.55 3.55
171 172 1.882623 GGTTTCTTCTTGGAGGCACTG 59.117 52.381 0.00 0.00 41.55 3.66
173 174 0.875059 CGGTTTCTTCTTGGAGGCAC 59.125 55.000 0.00 0.00 0.00 5.01
174 175 0.250727 CCGGTTTCTTCTTGGAGGCA 60.251 55.000 0.00 0.00 0.00 4.75
175 176 0.036306 TCCGGTTTCTTCTTGGAGGC 59.964 55.000 0.00 0.00 0.00 4.70
176 177 1.610886 GGTCCGGTTTCTTCTTGGAGG 60.611 57.143 0.00 0.00 0.00 4.30
177 178 1.348036 AGGTCCGGTTTCTTCTTGGAG 59.652 52.381 0.00 0.00 0.00 3.86
178 179 1.430992 AGGTCCGGTTTCTTCTTGGA 58.569 50.000 0.00 0.00 0.00 3.53
179 180 2.354805 CCTAGGTCCGGTTTCTTCTTGG 60.355 54.545 0.00 0.00 0.00 3.61
180 181 2.354805 CCCTAGGTCCGGTTTCTTCTTG 60.355 54.545 8.29 0.00 0.00 3.02
181 182 1.907255 CCCTAGGTCCGGTTTCTTCTT 59.093 52.381 8.29 0.00 0.00 2.52
182 183 1.203275 ACCCTAGGTCCGGTTTCTTCT 60.203 52.381 8.29 0.00 0.00 2.85
183 184 1.273759 ACCCTAGGTCCGGTTTCTTC 58.726 55.000 8.29 0.00 0.00 2.87
184 185 1.738474 AACCCTAGGTCCGGTTTCTT 58.262 50.000 8.29 0.00 39.36 2.52
185 186 1.738474 AAACCCTAGGTCCGGTTTCT 58.262 50.000 8.29 0.00 47.00 2.52
188 189 2.380365 GGAAACCCTAGGTCCGGTT 58.620 57.895 8.29 1.41 44.35 4.44
189 190 4.142045 GGAAACCCTAGGTCCGGT 57.858 61.111 8.29 0.00 33.12 5.28
201 202 0.668535 GTGCACTGTTGAGGGGAAAC 59.331 55.000 10.32 0.00 0.00 2.78
202 203 0.467290 GGTGCACTGTTGAGGGGAAA 60.467 55.000 17.98 0.00 0.00 3.13
203 204 1.150536 GGTGCACTGTTGAGGGGAA 59.849 57.895 17.98 0.00 0.00 3.97
204 205 2.055689 CTGGTGCACTGTTGAGGGGA 62.056 60.000 17.98 0.00 0.00 4.81
205 206 1.601759 CTGGTGCACTGTTGAGGGG 60.602 63.158 17.98 0.00 0.00 4.79
206 207 0.466189 AACTGGTGCACTGTTGAGGG 60.466 55.000 17.98 1.19 39.42 4.30
207 208 0.947244 GAACTGGTGCACTGTTGAGG 59.053 55.000 25.10 9.11 40.74 3.86
208 209 1.959042 AGAACTGGTGCACTGTTGAG 58.041 50.000 25.10 13.43 40.74 3.02
209 210 2.016318 CAAGAACTGGTGCACTGTTGA 58.984 47.619 25.10 3.90 40.74 3.18
210 211 2.016318 TCAAGAACTGGTGCACTGTTG 58.984 47.619 25.10 16.83 40.74 3.33
241 242 7.814107 ACTATGATGCACATTAAACCACAAAAG 59.186 33.333 7.02 0.00 40.07 2.27
244 245 6.432472 TCACTATGATGCACATTAAACCACAA 59.568 34.615 7.02 0.00 40.07 3.33
257 258 6.721704 ACTACTCAAGATCACTATGATGCA 57.278 37.500 0.00 0.00 37.20 3.96
300 301 1.812571 CTGTCCACAGCACCAATAACC 59.187 52.381 0.00 0.00 37.15 2.85
313 314 3.760684 AGATTTTCAGGAATGCTGTCCAC 59.239 43.478 0.85 0.00 40.48 4.02
327 328 6.559810 ACACAACGAAATGACAAGATTTTCA 58.440 32.000 0.00 0.00 31.29 2.69
352 353 5.449297 TCATGGGATGTTGGAGTTTATGA 57.551 39.130 0.00 0.00 0.00 2.15
619 635 6.189859 TCAAAACCTAGAATGCATGAATCCT 58.810 36.000 0.00 0.00 0.00 3.24
629 653 8.514594 TGATGTTTAAGCTCAAAACCTAGAATG 58.485 33.333 17.40 0.00 36.26 2.67
658 682 5.048294 ACGCTCCTTTATTGTTTACTTTGGG 60.048 40.000 0.00 0.00 0.00 4.12
659 683 6.009115 ACGCTCCTTTATTGTTTACTTTGG 57.991 37.500 0.00 0.00 0.00 3.28
717 741 2.665165 TCATTTGGACAGGCAAACACT 58.335 42.857 0.00 0.00 0.00 3.55
781 805 4.339530 CAGGGATCTCGTGATTCTTCTGTA 59.660 45.833 5.77 0.00 33.39 2.74
867 891 3.636764 GTCTTCTTCAGCCAAAGGGAAAA 59.363 43.478 0.00 0.00 35.59 2.29
912 936 3.325870 CAAGAGTATTGGCGTCTTGTGA 58.674 45.455 3.62 0.00 41.47 3.58
920 944 6.604735 AACTTATAAGCAAGAGTATTGGCG 57.395 37.500 12.54 0.00 0.00 5.69
950 977 8.147704 TCAAAATTATCACGTATAGAGGCATGA 58.852 33.333 0.00 0.00 0.00 3.07
1039 1067 2.501723 AGCAAGGTGATATTGGTCGAGT 59.498 45.455 0.00 0.00 33.28 4.18
1118 1146 4.158209 CACTGCAATGGTGATATTGGTGAA 59.842 41.667 0.00 0.00 38.25 3.18
1123 1151 5.813717 CAGTACACTGCAATGGTGATATTG 58.186 41.667 11.19 4.30 40.25 1.90
1135 1163 7.093684 TTGGAACATATAGTACAGTACACTGCA 60.094 37.037 13.37 0.00 43.22 4.41
1158 1186 7.608308 TCAGTCAAACAATTTTTCCTTTTGG 57.392 32.000 0.00 0.00 42.21 3.28
1159 1187 9.493206 CAATCAGTCAAACAATTTTTCCTTTTG 57.507 29.630 0.00 0.00 0.00 2.44
1160 1188 9.230122 ACAATCAGTCAAACAATTTTTCCTTTT 57.770 25.926 0.00 0.00 0.00 2.27
1161 1189 8.791327 ACAATCAGTCAAACAATTTTTCCTTT 57.209 26.923 0.00 0.00 0.00 3.11
1162 1190 8.791327 AACAATCAGTCAAACAATTTTTCCTT 57.209 26.923 0.00 0.00 0.00 3.36
1163 1191 8.791327 AAACAATCAGTCAAACAATTTTTCCT 57.209 26.923 0.00 0.00 0.00 3.36
1164 1192 8.122330 GGAAACAATCAGTCAAACAATTTTTCC 58.878 33.333 0.00 0.00 32.68 3.13
1165 1193 8.663911 TGGAAACAATCAGTCAAACAATTTTTC 58.336 29.630 0.00 0.00 37.44 2.29
1166 1194 8.558973 TGGAAACAATCAGTCAAACAATTTTT 57.441 26.923 0.00 0.00 37.44 1.94
1167 1195 8.040132 TCTGGAAACAATCAGTCAAACAATTTT 58.960 29.630 0.00 0.00 42.06 1.82
1168 1196 7.555087 TCTGGAAACAATCAGTCAAACAATTT 58.445 30.769 0.00 0.00 42.06 1.82
1169 1197 7.111247 TCTGGAAACAATCAGTCAAACAATT 57.889 32.000 0.00 0.00 42.06 2.32
1170 1198 6.713762 TCTGGAAACAATCAGTCAAACAAT 57.286 33.333 0.00 0.00 42.06 2.71
1171 1199 6.713762 ATCTGGAAACAATCAGTCAAACAA 57.286 33.333 0.00 0.00 42.06 2.83
1172 1200 6.320926 TGAATCTGGAAACAATCAGTCAAACA 59.679 34.615 0.00 0.00 42.06 2.83
1173 1201 6.738114 TGAATCTGGAAACAATCAGTCAAAC 58.262 36.000 0.00 0.00 42.06 2.93
1174 1202 6.772233 TCTGAATCTGGAAACAATCAGTCAAA 59.228 34.615 0.00 0.00 42.10 2.69
1175 1203 6.298361 TCTGAATCTGGAAACAATCAGTCAA 58.702 36.000 0.00 0.00 42.10 3.18
1176 1204 5.868454 TCTGAATCTGGAAACAATCAGTCA 58.132 37.500 0.00 0.00 42.10 3.41
1177 1205 6.596888 TCATCTGAATCTGGAAACAATCAGTC 59.403 38.462 0.00 0.00 42.10 3.51
1178 1206 6.479006 TCATCTGAATCTGGAAACAATCAGT 58.521 36.000 0.00 0.00 42.10 3.41
1179 1207 6.997239 TCATCTGAATCTGGAAACAATCAG 57.003 37.500 0.00 0.00 42.48 2.90
1213 1242 6.183360 TGGTAATGCAGCAGAGAAAATATGTG 60.183 38.462 0.00 0.00 0.00 3.21
1296 1325 1.202915 TCTTGCTTGCTGTTGATGGGA 60.203 47.619 0.00 0.00 0.00 4.37
1309 1338 1.803366 GCTTGCTGTGGCTCTTGCTT 61.803 55.000 6.66 0.00 39.59 3.91
1317 1346 3.745803 GAGGCAGCTTGCTGTGGC 61.746 66.667 21.55 11.50 44.28 5.01
1453 1482 0.674581 CGAAGAAGATGTGGCTGCCA 60.675 55.000 19.30 19.30 0.00 4.92
1564 1593 1.671379 GTTCTGCTGGGTTCCGGTC 60.671 63.158 0.00 0.00 31.34 4.79
1696 1725 1.227734 AAACACACGGGAAGACGGG 60.228 57.895 0.00 0.00 44.31 5.28
1708 1737 0.687354 GCTCTCCTCTCCCAAACACA 59.313 55.000 0.00 0.00 0.00 3.72
1729 1758 2.602257 TCTTGTATGGCTGGATCACG 57.398 50.000 0.00 0.00 0.00 4.35
1741 1770 4.774726 AGATACCTCATGGCGATCTTGTAT 59.225 41.667 0.00 0.00 36.49 2.29
1762 1791 0.325296 ACCAGAAGGCCCGTGATAGA 60.325 55.000 0.00 0.00 39.06 1.98
1765 1794 0.609131 CAAACCAGAAGGCCCGTGAT 60.609 55.000 0.00 0.00 39.06 3.06
1819 1848 0.249398 AGCACTGGATGTAACCGTCC 59.751 55.000 0.00 0.00 45.61 4.79
1820 1849 1.204941 AGAGCACTGGATGTAACCGTC 59.795 52.381 0.00 0.00 0.00 4.79
1821 1850 1.267121 AGAGCACTGGATGTAACCGT 58.733 50.000 0.00 0.00 0.00 4.83
1822 1851 2.386661 AAGAGCACTGGATGTAACCG 57.613 50.000 0.00 0.00 0.00 4.44
1823 1852 2.162408 GCAAAGAGCACTGGATGTAACC 59.838 50.000 0.00 0.00 44.79 2.85
1824 1853 3.477899 GCAAAGAGCACTGGATGTAAC 57.522 47.619 0.00 0.00 44.79 2.50
1846 1878 4.157289 AGCATTTCAGTTCTTGCGATTCAT 59.843 37.500 0.00 0.00 40.00 2.57
1853 1885 2.030540 TGCAGAGCATTTCAGTTCTTGC 60.031 45.455 0.00 0.00 31.71 4.01
1890 1922 2.702592 ACCGAGGAGAAACACACAAA 57.297 45.000 0.00 0.00 0.00 2.83
1891 1923 3.306502 GGATACCGAGGAGAAACACACAA 60.307 47.826 0.00 0.00 0.00 3.33
1983 2015 1.303309 GGAAGATGATGCTGAACCGG 58.697 55.000 0.00 0.00 0.00 5.28
2061 2093 1.596934 GTTCTCCGTCATGGCTCCA 59.403 57.895 0.00 0.00 37.80 3.86
2235 2267 0.599991 TGCTACTGACGGTGTTGCAG 60.600 55.000 8.91 0.00 40.12 4.41
2247 2279 2.625737 CAGATGGTCCTGTTGCTACTG 58.374 52.381 0.00 0.00 0.00 2.74
2289 2321 0.037326 TGTCCGGAGTGCACAATCTC 60.037 55.000 21.04 7.49 0.00 2.75
2361 2393 4.308458 TGGGTGAAGGCCGACGTG 62.308 66.667 0.00 0.00 0.00 4.49
2432 2464 1.091197 TGTAGCGTGCATGCATGGAG 61.091 55.000 34.64 21.90 37.31 3.86
2445 2477 9.114965 GTAAATGATACATACTACAGTGTAGCG 57.885 37.037 26.79 18.45 39.40 4.26
2456 2488 9.979897 ATGGCCAATATGTAAATGATACATACT 57.020 29.630 10.96 0.00 41.48 2.12
2467 2536 8.588290 AGTTAGAAACATGGCCAATATGTAAA 57.412 30.769 10.96 0.43 37.77 2.01
2517 2592 1.519455 CGTCGCCAGATTCTGTCCC 60.519 63.158 12.54 0.43 0.00 4.46
2578 2653 3.055891 GCAAACAATACAAGCCCAAGGAT 60.056 43.478 0.00 0.00 0.00 3.24
2589 2664 4.082625 CCAATGAGCAGAGCAAACAATACA 60.083 41.667 0.00 0.00 0.00 2.29
2592 2667 2.353406 GCCAATGAGCAGAGCAAACAAT 60.353 45.455 0.00 0.00 0.00 2.71
2630 2705 1.280133 TGATGGAGTGGAAGCAAGGAG 59.720 52.381 0.00 0.00 0.00 3.69
2636 2711 2.098770 GCAAGATTGATGGAGTGGAAGC 59.901 50.000 0.00 0.00 0.00 3.86
2727 2804 0.248498 GTCGGATCATCGTCGCTTGA 60.248 55.000 0.00 1.04 0.00 3.02
2961 3038 0.168348 CGTCCATCTCGTCGAACAGT 59.832 55.000 0.00 0.00 0.00 3.55
3573 3655 2.032620 TCTCCTCAAGAATAGGCGGTC 58.967 52.381 0.00 0.00 33.84 4.79
3654 3736 6.673583 TGGAGGTAGAAGAGAAGATATGTCA 58.326 40.000 0.00 0.00 0.00 3.58
3659 3741 5.950549 ACGTTTGGAGGTAGAAGAGAAGATA 59.049 40.000 0.00 0.00 0.00 1.98
3731 3813 0.963962 TACGTCAAGGACACCAGGTC 59.036 55.000 0.00 0.00 46.20 3.85
3842 3924 2.595750 ACCCAAATGAACCGATTCCA 57.404 45.000 0.00 0.00 33.49 3.53
3852 3934 2.374184 CCCATCGCTTTACCCAAATGA 58.626 47.619 0.00 0.00 0.00 2.57
3854 3936 1.006639 ACCCCATCGCTTTACCCAAAT 59.993 47.619 0.00 0.00 0.00 2.32
3891 3973 0.102481 GTACGACCACCGCATCTCAT 59.898 55.000 0.00 0.00 43.32 2.90
3948 4030 2.151202 GAGCATTTTTGACCCTGACGA 58.849 47.619 0.00 0.00 0.00 4.20
3951 4033 6.855763 AAATATGAGCATTTTTGACCCTGA 57.144 33.333 0.00 0.00 0.00 3.86
4184 4272 2.747460 TGAGCTGCGTGATTGGCC 60.747 61.111 0.00 0.00 0.00 5.36
4289 4377 2.223363 ACGAGCGTGATGACAGTATCTG 60.223 50.000 0.00 0.00 37.52 2.90
4357 4445 0.332972 GGGATGAAGGGGAGCTTTGT 59.667 55.000 0.00 0.00 0.00 2.83
4365 4453 0.921896 ACTGTCATGGGATGAAGGGG 59.078 55.000 0.00 0.00 41.69 4.79
4469 4557 3.009584 GGTGAGAAGGGGAAGAGATTTGT 59.990 47.826 0.00 0.00 0.00 2.83
4525 4613 6.497640 AGCTGATGGTATATATCCTCAGTGA 58.502 40.000 22.06 0.00 35.15 3.41


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

AutoCloner maintained by Alex Coulton.