Multiple sequence alignment - TraesCS2A01G210300

Loading Multiple Alignment...

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 TraesCS2A01G210300 chr2A 100.000 4906 0 0 1 4906 194425542 194420637 0.000000e+00 9060
1 TraesCS2A01G210300 chr2A 87.241 1638 209 0 2265 3902 765040534 765042171 0.000000e+00 1868
2 TraesCS2A01G210300 chr2A 84.898 735 106 5 1354 2087 765039668 765040398 0.000000e+00 737
3 TraesCS2A01G210300 chr2D 93.917 3995 125 44 195 4117 180089445 180085497 0.000000e+00 5923
4 TraesCS2A01G210300 chr2D 88.608 1580 176 4 2265 3842 639396713 639398290 0.000000e+00 1917
5 TraesCS2A01G210300 chr2D 85.976 1640 226 4 2265 3902 639667251 639668888 0.000000e+00 1751
6 TraesCS2A01G210300 chr2D 95.159 785 36 1 4124 4906 54884781 54885565 0.000000e+00 1238
7 TraesCS2A01G210300 chr2D 95.147 783 37 1 4124 4906 638387285 638388066 0.000000e+00 1234
8 TraesCS2A01G210300 chr2D 84.469 734 105 5 1354 2087 639393877 639394601 0.000000e+00 715
9 TraesCS2A01G210300 chr2D 82.749 742 112 12 1354 2093 639666404 639667131 0.000000e+00 647
10 TraesCS2A01G210300 chr2D 95.652 115 5 0 1 115 73831263 73831377 8.390000e-43 185
11 TraesCS2A01G210300 chr2D 95.652 115 5 0 1 115 179669862 179669748 8.390000e-43 185
12 TraesCS2A01G210300 chr2D 95.652 115 5 0 1 115 535229251 535229365 8.390000e-43 185
13 TraesCS2A01G210300 chr2D 77.866 253 26 13 996 1248 639393581 639393803 3.990000e-26 130
14 TraesCS2A01G210300 chr2B 95.917 1984 57 8 2164 4124 236776714 236774732 0.000000e+00 3193
15 TraesCS2A01G210300 chr2B 93.448 1862 70 23 281 2116 236778560 236776725 0.000000e+00 2715
16 TraesCS2A01G210300 chr2B 87.728 1646 185 10 2265 3905 798318257 798316624 0.000000e+00 1905
17 TraesCS2A01G210300 chr2B 86.098 1640 224 4 2265 3902 798614319 798612682 0.000000e+00 1762
18 TraesCS2A01G210300 chr2B 84.626 735 106 7 1355 2087 798615175 798614446 0.000000e+00 725
19 TraesCS2A01G210300 chr2B 84.282 738 111 4 1351 2087 798723291 798724024 0.000000e+00 715
20 TraesCS2A01G210300 chr7D 89.315 1563 164 2 2265 3824 638473426 638474988 0.000000e+00 1958
21 TraesCS2A01G210300 chr7D 95.019 783 39 0 4124 4906 418922496 418921714 0.000000e+00 1230
22 TraesCS2A01G210300 chr7D 84.211 741 107 8 1354 2092 638470777 638471509 0.000000e+00 712
23 TraesCS2A01G210300 chr7D 78.445 1016 166 32 1116 2092 638558637 638559638 9.030000e-172 614
24 TraesCS2A01G210300 chr7D 85.938 128 9 5 1121 1248 638470229 638470347 1.430000e-25 128
25 TraesCS2A01G210300 chr7A 88.846 1569 172 2 2265 3830 727431545 727429977 0.000000e+00 1925
26 TraesCS2A01G210300 chr7A 96.296 783 29 0 4124 4906 150333159 150332377 0.000000e+00 1286
27 TraesCS2A01G210300 chr7A 85.326 736 98 6 1354 2087 727433897 727433170 0.000000e+00 752
28 TraesCS2A01G210300 chr7A 82.812 128 10 6 1124 1251 727434223 727434108 2.420000e-18 104
29 TraesCS2A01G210300 chr3A 96.301 784 28 1 4124 4906 682742107 682742890 0.000000e+00 1286
30 TraesCS2A01G210300 chr3A 94.783 115 6 0 1 115 306921053 306921167 3.900000e-41 180
31 TraesCS2A01G210300 chr1D 95.536 784 31 4 4124 4906 437514990 437514210 0.000000e+00 1251
32 TraesCS2A01G210300 chr1D 95.147 783 38 0 4124 4906 490399700 490400482 0.000000e+00 1236
33 TraesCS2A01G210300 chr5D 95.402 783 36 0 4124 4906 397767252 397768034 0.000000e+00 1247
34 TraesCS2A01G210300 chr3D 95.019 783 39 0 4124 4906 602108866 602109648 0.000000e+00 1230
35 TraesCS2A01G210300 chr3D 96.522 115 4 0 1 115 360563344 360563230 1.800000e-44 191
36 TraesCS2A01G210300 chr3D 94.783 115 6 0 1 115 25698357 25698243 3.900000e-41 180
37 TraesCS2A01G210300 chr3D 94.783 115 6 0 1 115 461597993 461597879 3.900000e-41 180
38 TraesCS2A01G210300 chr6A 95.614 114 5 0 1 114 572209897 572210010 3.020000e-42 183
39 TraesCS2A01G210300 chr6D 94.783 115 6 0 1 115 412439930 412439816 3.900000e-41 180
40 TraesCS2A01G210300 chrUn 86.861 137 18 0 1119 1255 88119324 88119188 2.360000e-33 154
41 TraesCS2A01G210300 chrUn 86.861 137 18 0 1119 1255 88974600 88974464 2.360000e-33 154
42 TraesCS2A01G210300 chr7B 80.814 172 19 9 1099 1270 734252901 734252744 6.670000e-24 122


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 TraesCS2A01G210300 chr2A 194420637 194425542 4905 True 9060.000000 9060 100.000000 1 4906 1 chr2A.!!$R1 4905
1 TraesCS2A01G210300 chr2A 765039668 765042171 2503 False 1302.500000 1868 86.069500 1354 3902 2 chr2A.!!$F1 2548
2 TraesCS2A01G210300 chr2D 180085497 180089445 3948 True 5923.000000 5923 93.917000 195 4117 1 chr2D.!!$R2 3922
3 TraesCS2A01G210300 chr2D 54884781 54885565 784 False 1238.000000 1238 95.159000 4124 4906 1 chr2D.!!$F1 782
4 TraesCS2A01G210300 chr2D 638387285 638388066 781 False 1234.000000 1234 95.147000 4124 4906 1 chr2D.!!$F4 782
5 TraesCS2A01G210300 chr2D 639666404 639668888 2484 False 1199.000000 1751 84.362500 1354 3902 2 chr2D.!!$F6 2548
6 TraesCS2A01G210300 chr2D 639393581 639398290 4709 False 920.666667 1917 83.647667 996 3842 3 chr2D.!!$F5 2846
7 TraesCS2A01G210300 chr2B 236774732 236778560 3828 True 2954.000000 3193 94.682500 281 4124 2 chr2B.!!$R2 3843
8 TraesCS2A01G210300 chr2B 798316624 798318257 1633 True 1905.000000 1905 87.728000 2265 3905 1 chr2B.!!$R1 1640
9 TraesCS2A01G210300 chr2B 798612682 798615175 2493 True 1243.500000 1762 85.362000 1355 3902 2 chr2B.!!$R3 2547
10 TraesCS2A01G210300 chr2B 798723291 798724024 733 False 715.000000 715 84.282000 1351 2087 1 chr2B.!!$F1 736
11 TraesCS2A01G210300 chr7D 418921714 418922496 782 True 1230.000000 1230 95.019000 4124 4906 1 chr7D.!!$R1 782
12 TraesCS2A01G210300 chr7D 638470229 638474988 4759 False 932.666667 1958 86.488000 1121 3824 3 chr7D.!!$F2 2703
13 TraesCS2A01G210300 chr7D 638558637 638559638 1001 False 614.000000 614 78.445000 1116 2092 1 chr7D.!!$F1 976
14 TraesCS2A01G210300 chr7A 150332377 150333159 782 True 1286.000000 1286 96.296000 4124 4906 1 chr7A.!!$R1 782
15 TraesCS2A01G210300 chr7A 727429977 727434223 4246 True 927.000000 1925 85.661333 1124 3830 3 chr7A.!!$R2 2706
16 TraesCS2A01G210300 chr3A 682742107 682742890 783 False 1286.000000 1286 96.301000 4124 4906 1 chr3A.!!$F2 782
17 TraesCS2A01G210300 chr1D 437514210 437514990 780 True 1251.000000 1251 95.536000 4124 4906 1 chr1D.!!$R1 782
18 TraesCS2A01G210300 chr1D 490399700 490400482 782 False 1236.000000 1236 95.147000 4124 4906 1 chr1D.!!$F1 782
19 TraesCS2A01G210300 chr5D 397767252 397768034 782 False 1247.000000 1247 95.402000 4124 4906 1 chr5D.!!$F1 782
20 TraesCS2A01G210300 chr3D 602108866 602109648 782 False 1230.000000 1230 95.019000 4124 4906 1 chr3D.!!$F1 782

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
87 88 0.172578 TGTACTCGATGAGTTGGCGG 59.827 55.0 4.6 0.0 40.28 6.13 F
1326 1382 0.179181 CGTACCGCTACGCTTCTGAA 60.179 55.0 0.0 0.0 39.43 3.02 F
1635 2097 0.683412 AACCCCTCTTGTACACCGTC 59.317 55.0 0.0 0.0 0.00 4.79 F
2585 6231 0.395173 ACACGGCCTTTGTCCAGTTT 60.395 50.0 0.0 0.0 0.00 2.66 F
3335 6984 0.240145 TCGTCGCCGTCATATCCATC 59.760 55.0 0.0 0.0 35.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2442 0.036765 TTGCACGTACACCATCTCCC 60.037 55.0 0.00 0.00 0.00 4.30 R
2333 5979 0.927537 TGTCAACGTTGCTGAAGTCG 59.072 50.0 23.47 0.00 0.00 4.18 R
3335 6984 1.009078 ACATGCCGATCACGTGAATG 58.991 50.0 24.13 21.84 37.88 2.67 R
3708 7357 0.683504 AACGGGTAGAGGAGCACGAT 60.684 55.0 0.00 0.00 0.00 3.73 R
4834 8496 0.868406 CCAAGTTCTCAACACCGAGC 59.132 55.0 0.00 0.00 32.75 5.03 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
20 21 3.630289 CGGGAGGGAGAAATCCGT 58.370 61.111 0.00 0.00 36.38 4.69
21 22 2.816746 CGGGAGGGAGAAATCCGTA 58.183 57.895 0.00 0.00 36.38 4.02
22 23 0.388294 CGGGAGGGAGAAATCCGTAC 59.612 60.000 0.00 0.00 36.38 3.67
23 24 1.492764 GGGAGGGAGAAATCCGTACA 58.507 55.000 1.93 0.00 36.38 2.90
24 25 1.138464 GGGAGGGAGAAATCCGTACAC 59.862 57.143 1.93 0.00 36.38 2.90
25 26 1.829222 GGAGGGAGAAATCCGTACACA 59.171 52.381 0.00 0.00 0.00 3.72
26 27 2.434702 GGAGGGAGAAATCCGTACACAT 59.565 50.000 0.00 0.00 0.00 3.21
27 28 3.458189 GAGGGAGAAATCCGTACACATG 58.542 50.000 0.00 0.00 0.00 3.21
28 29 2.170607 AGGGAGAAATCCGTACACATGG 59.829 50.000 0.00 0.00 0.00 3.66
29 30 2.093128 GGGAGAAATCCGTACACATGGT 60.093 50.000 0.00 0.00 32.08 3.55
30 31 3.195661 GGAGAAATCCGTACACATGGTC 58.804 50.000 0.00 0.00 32.08 4.02
31 32 3.118738 GGAGAAATCCGTACACATGGTCT 60.119 47.826 0.00 0.00 32.08 3.85
32 33 4.113354 GAGAAATCCGTACACATGGTCTC 58.887 47.826 0.00 0.00 32.08 3.36
33 34 2.981859 AATCCGTACACATGGTCTCC 57.018 50.000 0.00 0.00 32.08 3.71
34 35 2.160721 ATCCGTACACATGGTCTCCT 57.839 50.000 0.00 0.00 32.08 3.69
35 36 1.182667 TCCGTACACATGGTCTCCTG 58.817 55.000 0.00 0.00 32.08 3.86
36 37 0.175760 CCGTACACATGGTCTCCTGG 59.824 60.000 0.00 0.00 0.00 4.45
37 38 1.182667 CGTACACATGGTCTCCTGGA 58.817 55.000 0.00 0.00 0.00 3.86
38 39 1.757118 CGTACACATGGTCTCCTGGAT 59.243 52.381 0.00 0.00 0.00 3.41
39 40 2.481969 CGTACACATGGTCTCCTGGATG 60.482 54.545 0.00 0.00 0.00 3.51
40 41 0.914644 ACACATGGTCTCCTGGATGG 59.085 55.000 0.00 0.00 37.10 3.51
41 42 0.465097 CACATGGTCTCCTGGATGGC 60.465 60.000 0.00 0.00 35.26 4.40
42 43 1.150081 CATGGTCTCCTGGATGGCC 59.850 63.158 0.00 0.00 35.26 5.36
43 44 1.308128 ATGGTCTCCTGGATGGCCA 60.308 57.895 8.56 8.56 43.47 5.36
44 45 1.639635 ATGGTCTCCTGGATGGCCAC 61.640 60.000 8.16 1.35 39.92 5.01
45 46 2.300967 GGTCTCCTGGATGGCCACA 61.301 63.158 8.16 0.36 39.92 4.17
46 47 1.685224 GTCTCCTGGATGGCCACAA 59.315 57.895 8.16 0.00 39.92 3.33
47 48 0.257039 GTCTCCTGGATGGCCACAAT 59.743 55.000 8.16 0.00 39.92 2.71
48 49 1.490490 GTCTCCTGGATGGCCACAATA 59.510 52.381 8.16 0.00 39.92 1.90
49 50 2.107204 GTCTCCTGGATGGCCACAATAT 59.893 50.000 8.16 0.00 39.92 1.28
50 51 2.373169 TCTCCTGGATGGCCACAATATC 59.627 50.000 8.16 0.00 39.92 1.63
51 52 2.107031 CTCCTGGATGGCCACAATATCA 59.893 50.000 8.16 0.00 39.92 2.15
52 53 2.513317 TCCTGGATGGCCACAATATCAA 59.487 45.455 8.16 0.00 39.92 2.57
53 54 3.140707 TCCTGGATGGCCACAATATCAAT 59.859 43.478 8.16 0.00 39.92 2.57
54 55 3.257375 CCTGGATGGCCACAATATCAATG 59.743 47.826 8.16 0.00 39.92 2.82
55 56 3.893200 CTGGATGGCCACAATATCAATGT 59.107 43.478 8.16 0.00 39.92 2.71
56 57 3.637694 TGGATGGCCACAATATCAATGTG 59.362 43.478 8.16 0.00 46.05 3.21
57 58 3.638160 GGATGGCCACAATATCAATGTGT 59.362 43.478 8.16 0.00 45.23 3.72
58 59 4.099881 GGATGGCCACAATATCAATGTGTT 59.900 41.667 8.16 0.00 45.23 3.32
59 60 4.717233 TGGCCACAATATCAATGTGTTC 57.283 40.909 0.00 0.00 45.23 3.18
60 61 3.128415 TGGCCACAATATCAATGTGTTCG 59.872 43.478 0.00 0.00 45.23 3.95
61 62 3.128589 GGCCACAATATCAATGTGTTCGT 59.871 43.478 0.00 0.00 45.23 3.85
62 63 4.342772 GCCACAATATCAATGTGTTCGTC 58.657 43.478 5.99 0.00 45.23 4.20
63 64 4.730613 GCCACAATATCAATGTGTTCGTCC 60.731 45.833 5.99 0.00 45.23 4.79
64 65 4.201910 CCACAATATCAATGTGTTCGTCCC 60.202 45.833 5.99 0.00 45.23 4.46
65 66 3.621268 ACAATATCAATGTGTTCGTCCCG 59.379 43.478 0.00 0.00 0.00 5.14
66 67 3.812156 ATATCAATGTGTTCGTCCCGA 57.188 42.857 0.00 0.00 0.00 5.14
67 68 2.465860 ATCAATGTGTTCGTCCCGAA 57.534 45.000 0.00 0.00 43.75 4.30
76 77 1.452110 TTCGTCCCGAATGTACTCGA 58.548 50.000 6.12 0.00 41.05 4.04
77 78 1.671979 TCGTCCCGAATGTACTCGAT 58.328 50.000 6.12 0.00 41.44 3.59
78 79 1.332686 TCGTCCCGAATGTACTCGATG 59.667 52.381 6.12 0.00 41.44 3.84
79 80 1.332686 CGTCCCGAATGTACTCGATGA 59.667 52.381 6.12 0.57 41.44 2.92
80 81 2.602456 CGTCCCGAATGTACTCGATGAG 60.602 54.545 6.12 0.00 41.44 2.90
81 82 2.358267 GTCCCGAATGTACTCGATGAGT 59.642 50.000 6.12 4.70 45.54 3.41
82 83 3.021695 TCCCGAATGTACTCGATGAGTT 58.978 45.455 4.60 0.00 40.28 3.01
83 84 3.116300 CCCGAATGTACTCGATGAGTTG 58.884 50.000 4.60 0.00 40.28 3.16
84 85 3.116300 CCGAATGTACTCGATGAGTTGG 58.884 50.000 4.60 0.00 40.28 3.77
85 86 2.535984 CGAATGTACTCGATGAGTTGGC 59.464 50.000 4.60 0.00 40.28 4.52
86 87 2.209838 ATGTACTCGATGAGTTGGCG 57.790 50.000 4.60 0.00 40.28 5.69
87 88 0.172578 TGTACTCGATGAGTTGGCGG 59.827 55.000 4.60 0.00 40.28 6.13
88 89 1.141019 TACTCGATGAGTTGGCGGC 59.859 57.895 0.00 0.00 40.28 6.53
89 90 2.607668 TACTCGATGAGTTGGCGGCG 62.608 60.000 0.51 0.51 40.28 6.46
90 91 4.812476 TCGATGAGTTGGCGGCGG 62.812 66.667 9.78 0.00 0.00 6.13
111 112 3.496131 CCGTCATGGCCGAAACCG 61.496 66.667 0.00 0.00 0.00 4.44
112 113 4.160635 CGTCATGGCCGAAACCGC 62.161 66.667 0.00 0.00 0.00 5.68
113 114 4.160635 GTCATGGCCGAAACCGCG 62.161 66.667 0.00 0.00 0.00 6.46
126 127 4.937193 CCGCGGGGTGTATGTTAA 57.063 55.556 20.10 0.00 0.00 2.01
127 128 3.156157 CCGCGGGGTGTATGTTAAA 57.844 52.632 20.10 0.00 0.00 1.52
128 129 0.728542 CCGCGGGGTGTATGTTAAAC 59.271 55.000 20.10 0.00 0.00 2.01
129 130 1.440708 CGCGGGGTGTATGTTAAACA 58.559 50.000 0.00 0.00 0.00 2.83
130 131 1.129064 CGCGGGGTGTATGTTAAACAC 59.871 52.381 0.00 1.03 45.21 3.32
131 132 2.429478 GCGGGGTGTATGTTAAACACT 58.571 47.619 8.42 0.00 45.26 3.55
132 133 3.598299 GCGGGGTGTATGTTAAACACTA 58.402 45.455 8.42 0.00 45.26 2.74
133 134 3.619929 GCGGGGTGTATGTTAAACACTAG 59.380 47.826 8.42 0.00 45.26 2.57
134 135 4.186159 CGGGGTGTATGTTAAACACTAGG 58.814 47.826 8.42 0.00 45.26 3.02
135 136 4.520179 GGGGTGTATGTTAAACACTAGGG 58.480 47.826 8.42 0.00 45.26 3.53
136 137 4.019051 GGGGTGTATGTTAAACACTAGGGT 60.019 45.833 8.42 0.00 45.26 4.34
137 138 4.939439 GGGTGTATGTTAAACACTAGGGTG 59.061 45.833 0.00 0.00 45.26 4.61
153 154 6.863645 CACTAGGGTGTATGATGTCTTTATCG 59.136 42.308 0.00 0.00 38.54 2.92
154 155 5.215252 AGGGTGTATGATGTCTTTATCGG 57.785 43.478 0.00 0.00 0.00 4.18
155 156 3.746492 GGGTGTATGATGTCTTTATCGGC 59.254 47.826 0.00 0.00 0.00 5.54
156 157 3.428870 GGTGTATGATGTCTTTATCGGCG 59.571 47.826 0.00 0.00 0.00 6.46
157 158 3.428870 GTGTATGATGTCTTTATCGGCGG 59.571 47.826 7.21 0.00 0.00 6.13
158 159 1.512926 ATGATGTCTTTATCGGCGGC 58.487 50.000 7.21 0.00 0.00 6.53
159 160 0.531974 TGATGTCTTTATCGGCGGCC 60.532 55.000 9.54 9.54 0.00 6.13
160 161 0.249911 GATGTCTTTATCGGCGGCCT 60.250 55.000 18.34 1.06 0.00 5.19
161 162 0.180406 ATGTCTTTATCGGCGGCCTT 59.820 50.000 18.34 7.02 0.00 4.35
162 163 0.825410 TGTCTTTATCGGCGGCCTTA 59.175 50.000 18.34 5.34 0.00 2.69
163 164 1.202486 TGTCTTTATCGGCGGCCTTAG 60.202 52.381 18.34 1.23 0.00 2.18
164 165 0.391597 TCTTTATCGGCGGCCTTAGG 59.608 55.000 18.34 0.81 0.00 2.69
165 166 0.602905 CTTTATCGGCGGCCTTAGGG 60.603 60.000 18.34 0.39 0.00 3.53
166 167 2.047213 TTTATCGGCGGCCTTAGGGG 62.047 60.000 18.34 0.00 38.36 4.79
167 168 3.761690 TATCGGCGGCCTTAGGGGT 62.762 63.158 18.34 0.00 37.43 4.95
170 171 3.723922 GGCGGCCTTAGGGGTGAA 61.724 66.667 12.87 0.00 37.43 3.18
171 172 2.124695 GCGGCCTTAGGGGTGAAG 60.125 66.667 0.00 0.00 37.43 3.02
172 173 2.967946 GCGGCCTTAGGGGTGAAGT 61.968 63.158 0.00 0.00 37.43 3.01
173 174 1.078426 CGGCCTTAGGGGTGAAGTG 60.078 63.158 0.00 0.00 37.43 3.16
174 175 1.378646 GGCCTTAGGGGTGAAGTGC 60.379 63.158 0.00 0.00 37.43 4.40
175 176 1.685820 GCCTTAGGGGTGAAGTGCT 59.314 57.895 0.00 0.00 37.43 4.40
176 177 0.909623 GCCTTAGGGGTGAAGTGCTA 59.090 55.000 0.00 0.00 37.43 3.49
177 178 1.280998 GCCTTAGGGGTGAAGTGCTAA 59.719 52.381 0.00 0.00 37.43 3.09
178 179 2.290705 GCCTTAGGGGTGAAGTGCTAAA 60.291 50.000 0.00 0.00 37.43 1.85
179 180 3.610911 CCTTAGGGGTGAAGTGCTAAAG 58.389 50.000 0.00 0.00 0.00 1.85
180 181 2.781681 TAGGGGTGAAGTGCTAAAGC 57.218 50.000 0.00 0.00 42.50 3.51
181 182 1.068121 AGGGGTGAAGTGCTAAAGCT 58.932 50.000 3.26 0.00 42.66 3.74
182 183 1.425448 AGGGGTGAAGTGCTAAAGCTT 59.575 47.619 3.26 0.00 42.66 3.74
183 184 2.158460 AGGGGTGAAGTGCTAAAGCTTT 60.158 45.455 17.30 17.30 42.66 3.51
184 185 3.073946 AGGGGTGAAGTGCTAAAGCTTTA 59.926 43.478 17.71 17.71 42.66 1.85
185 186 3.190744 GGGGTGAAGTGCTAAAGCTTTAC 59.809 47.826 14.96 8.56 42.66 2.01
186 187 4.072839 GGGTGAAGTGCTAAAGCTTTACT 58.927 43.478 14.96 10.78 42.66 2.24
187 188 4.519350 GGGTGAAGTGCTAAAGCTTTACTT 59.481 41.667 20.58 20.58 41.70 2.24
189 190 6.461092 GGGTGAAGTGCTAAAGCTTTACTTTT 60.461 38.462 21.12 11.65 46.73 2.27
190 191 6.978659 GGTGAAGTGCTAAAGCTTTACTTTTT 59.021 34.615 21.12 11.93 46.73 1.94
191 192 8.132995 GGTGAAGTGCTAAAGCTTTACTTTTTA 58.867 33.333 21.12 11.79 46.73 1.52
192 193 9.170584 GTGAAGTGCTAAAGCTTTACTTTTTAG 57.829 33.333 21.12 11.50 46.73 1.85
193 194 7.860872 TGAAGTGCTAAAGCTTTACTTTTTAGC 59.139 33.333 21.12 19.18 46.73 3.09
204 205 6.863126 GCTTTACTTTTTAGCATGTGTGATGT 59.137 34.615 0.00 0.00 35.05 3.06
205 206 7.061094 GCTTTACTTTTTAGCATGTGTGATGTC 59.939 37.037 0.00 0.00 35.05 3.06
223 224 2.729360 TGTCTTTATCGCACACAGTTCG 59.271 45.455 0.00 0.00 0.00 3.95
250 251 6.113411 GCTAGGGTGTATGTTAGATGTGTTT 58.887 40.000 0.00 0.00 0.00 2.83
309 310 7.863375 ACGTCTCCTTCTTTTCGATGAATATAG 59.137 37.037 0.00 0.00 0.00 1.31
345 346 4.789012 TCATGCATTGAGGAACCTTTTC 57.211 40.909 0.00 0.00 0.00 2.29
347 348 4.460382 TCATGCATTGAGGAACCTTTTCTC 59.540 41.667 0.00 0.00 31.71 2.87
349 350 4.473444 TGCATTGAGGAACCTTTTCTCTT 58.527 39.130 0.00 0.00 31.71 2.85
485 488 9.785982 AGCTGAAAAGAATTTAGAGAGTTTAGT 57.214 29.630 0.00 0.00 37.28 2.24
554 557 0.928451 CATGCTGATTCATGCGCACG 60.928 55.000 14.90 3.71 37.60 5.34
592 596 1.270550 GTCGTTCTCCGGTACCTTTCA 59.729 52.381 10.90 0.00 37.11 2.69
593 597 1.962807 TCGTTCTCCGGTACCTTTCAA 59.037 47.619 10.90 0.00 37.11 2.69
697 705 8.950007 TGTCACTCCATACCAATACAGATATA 57.050 34.615 0.00 0.00 0.00 0.86
755 794 2.552599 TGTCGGTTGTATTTGCTCCA 57.447 45.000 0.00 0.00 0.00 3.86
772 811 3.691609 GCTCCATCAGAACTCGGAAAATT 59.308 43.478 0.00 0.00 0.00 1.82
888 927 0.676466 CAACTGGCAGCCGATGGTTA 60.676 55.000 15.89 0.00 0.00 2.85
954 993 2.751436 GCCGGGCAAGCATCTGAA 60.751 61.111 15.62 0.00 0.00 3.02
970 1009 2.284150 TCTGAACGACACGAAAAAGCTG 59.716 45.455 0.00 0.00 0.00 4.24
971 1010 2.004017 TGAACGACACGAAAAAGCTGT 58.996 42.857 0.00 0.00 0.00 4.40
972 1011 2.029970 TGAACGACACGAAAAAGCTGTC 59.970 45.455 0.00 0.00 0.00 3.51
973 1012 1.935933 ACGACACGAAAAAGCTGTCT 58.064 45.000 0.00 0.00 33.50 3.41
987 1039 0.456221 CTGTCTAGGTGCACGTAGGG 59.544 60.000 34.29 23.96 35.63 3.53
1317 1373 3.399350 CGTACGTACGTACCGCTAC 57.601 57.895 38.76 24.33 45.80 3.58
1324 1380 3.978373 CGTACCGCTACGCTTCTG 58.022 61.111 0.00 0.00 39.43 3.02
1325 1381 1.426621 CGTACCGCTACGCTTCTGA 59.573 57.895 0.00 0.00 39.43 3.27
1326 1382 0.179181 CGTACCGCTACGCTTCTGAA 60.179 55.000 0.00 0.00 39.43 3.02
1327 1383 1.730121 CGTACCGCTACGCTTCTGAAA 60.730 52.381 0.00 0.00 39.43 2.69
1392 1805 3.989698 CTTGGTCGCCATCGTCGCT 62.990 63.158 0.00 0.00 36.96 4.93
1635 2097 0.683412 AACCCCTCTTGTACACCGTC 59.317 55.000 0.00 0.00 0.00 4.79
1767 2229 0.823356 ATTTCGCTGTGCTGTGGGTT 60.823 50.000 0.00 0.00 0.00 4.11
1835 2297 1.035923 TTTGGGATGAAAACGCAGCA 58.964 45.000 0.00 0.00 32.23 4.41
1971 2433 3.776340 TGATGCGTATAACTCGAGCAAA 58.224 40.909 13.61 0.00 41.37 3.68
1974 2442 4.577687 TGCGTATAACTCGAGCAAAAAG 57.422 40.909 13.61 1.61 34.66 2.27
2087 2558 4.460382 ACATGCTGGAATTGTTCAGGTAAG 59.540 41.667 0.00 0.00 0.00 2.34
2270 5916 3.757745 AACGTGTTTTTCTCACAGGTG 57.242 42.857 0.00 0.00 41.27 4.00
2333 5979 2.125512 AGCGCCGACAATCCACTC 60.126 61.111 2.29 0.00 0.00 3.51
2393 6039 2.363795 ATGTCCCGGGAGAAGCGA 60.364 61.111 27.72 3.87 0.00 4.93
2576 6222 1.597027 CGGTCAGAACACGGCCTTT 60.597 57.895 0.00 0.00 0.00 3.11
2585 6231 0.395173 ACACGGCCTTTGTCCAGTTT 60.395 50.000 0.00 0.00 0.00 2.66
2588 6234 0.537371 CGGCCTTTGTCCAGTTTCCT 60.537 55.000 0.00 0.00 0.00 3.36
2630 6276 3.711541 GACGGACCGCTACGCCAAT 62.712 63.158 15.39 0.00 0.00 3.16
3158 6804 1.452651 CAATGCTCTCATGGCCGGT 60.453 57.895 1.90 0.00 32.23 5.28
3330 6979 0.590195 GTACCTCGTCGCCGTCATAT 59.410 55.000 0.00 0.00 35.01 1.78
3335 6984 0.240145 TCGTCGCCGTCATATCCATC 59.760 55.000 0.00 0.00 35.01 3.51
3708 7357 1.225855 GCTGTTCAACGTGTGGATCA 58.774 50.000 0.00 0.00 0.00 2.92
3885 7534 2.005451 CTTCTCTTGGTGAAGCATCGG 58.995 52.381 0.00 0.00 35.21 4.18
3922 7573 2.448219 GTAGACACGTACGGCTCATTC 58.552 52.381 21.06 6.12 0.00 2.67
3976 7627 7.020602 TGCAATAATTTGAGTGTGTGTATTCG 58.979 34.615 0.00 0.00 34.60 3.34
4222 7878 7.676004 TGTCACCTCTTCTGTTCAATATTGTA 58.324 34.615 14.97 2.85 0.00 2.41
4349 8005 5.351458 CCGATGACACTATTCTGTTCATGA 58.649 41.667 0.00 0.00 0.00 3.07
4420 8076 5.103290 TCGAACAATTGTCTGGCTTAAAC 57.897 39.130 12.39 0.00 0.00 2.01
4447 8103 5.803020 ATTTTCATAAGAGCGAGGTGTTC 57.197 39.130 0.00 0.00 0.00 3.18
4469 8126 1.760029 GTTTTGGGAAGGCCAAAGACA 59.240 47.619 5.01 0.00 38.21 3.41
4509 8166 6.150976 AGACAATTGTTTGGATGCGAATTAGA 59.849 34.615 13.36 0.00 37.15 2.10
4633 8293 0.034670 GGAAGGGCAAGCTGATGTCT 60.035 55.000 0.00 0.00 0.00 3.41
4668 8328 7.491372 TCGGCTAGTTTTGATTAACTCAGTATG 59.509 37.037 0.00 0.00 39.08 2.39
4711 8371 9.640963 TTTTTACTTTCGTTCTTCAAAATTCCA 57.359 25.926 0.00 0.00 0.00 3.53
4719 8379 4.972751 TCTTCAAAATTCCAAAAGGGGG 57.027 40.909 0.00 0.00 37.22 5.40
4891 8553 7.886629 ATGTCTTATGAGCAAATGGTTGTAT 57.113 32.000 0.00 0.00 37.06 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.757935 TACGGATTTCTCCCTCCCGG 60.758 60.000 0.00 0.00 43.98 5.73
6 7 3.458189 CATGTGTACGGATTTCTCCCTC 58.542 50.000 0.00 0.00 38.45 4.30
7 8 2.170607 CCATGTGTACGGATTTCTCCCT 59.829 50.000 0.00 0.00 38.45 4.20
8 9 2.093128 ACCATGTGTACGGATTTCTCCC 60.093 50.000 0.00 0.00 38.45 4.30
9 10 3.118738 AGACCATGTGTACGGATTTCTCC 60.119 47.826 0.00 0.00 38.29 3.71
10 11 4.113354 GAGACCATGTGTACGGATTTCTC 58.887 47.826 0.00 0.00 0.00 2.87
11 12 3.118738 GGAGACCATGTGTACGGATTTCT 60.119 47.826 0.00 0.00 0.00 2.52
12 13 3.118738 AGGAGACCATGTGTACGGATTTC 60.119 47.826 0.00 0.00 0.00 2.17
13 14 2.838202 AGGAGACCATGTGTACGGATTT 59.162 45.455 0.00 0.00 0.00 2.17
14 15 2.168521 CAGGAGACCATGTGTACGGATT 59.831 50.000 0.00 0.00 0.00 3.01
15 16 1.757118 CAGGAGACCATGTGTACGGAT 59.243 52.381 0.00 0.00 0.00 4.18
16 17 1.182667 CAGGAGACCATGTGTACGGA 58.817 55.000 0.00 0.00 0.00 4.69
17 18 0.175760 CCAGGAGACCATGTGTACGG 59.824 60.000 0.00 0.00 0.00 4.02
18 19 1.182667 TCCAGGAGACCATGTGTACG 58.817 55.000 0.00 0.00 0.00 3.67
19 20 2.158900 CCATCCAGGAGACCATGTGTAC 60.159 54.545 0.00 0.00 41.22 2.90
20 21 2.118679 CCATCCAGGAGACCATGTGTA 58.881 52.381 0.00 0.00 41.22 2.90
21 22 0.914644 CCATCCAGGAGACCATGTGT 59.085 55.000 0.00 0.00 41.22 3.72
22 23 0.465097 GCCATCCAGGAGACCATGTG 60.465 60.000 0.00 0.00 41.22 3.21
23 24 1.639635 GGCCATCCAGGAGACCATGT 61.640 60.000 0.00 0.00 41.22 3.21
24 25 1.150081 GGCCATCCAGGAGACCATG 59.850 63.158 0.00 0.00 41.22 3.66
25 26 1.308128 TGGCCATCCAGGAGACCAT 60.308 57.895 0.00 0.00 41.22 3.55
26 27 2.124768 TGGCCATCCAGGAGACCA 59.875 61.111 0.00 4.11 41.22 4.02
27 28 1.852157 TTGTGGCCATCCAGGAGACC 61.852 60.000 9.72 0.00 44.48 3.85
28 29 0.257039 ATTGTGGCCATCCAGGAGAC 59.743 55.000 9.72 0.00 44.48 3.36
29 30 1.891933 TATTGTGGCCATCCAGGAGA 58.108 50.000 9.72 0.00 44.48 3.71
30 31 2.107031 TGATATTGTGGCCATCCAGGAG 59.893 50.000 9.72 0.00 44.48 3.69
31 32 2.134354 TGATATTGTGGCCATCCAGGA 58.866 47.619 9.72 0.00 44.48 3.86
32 33 2.662535 TGATATTGTGGCCATCCAGG 57.337 50.000 9.72 0.00 44.48 4.45
33 34 3.893200 ACATTGATATTGTGGCCATCCAG 59.107 43.478 9.72 0.00 44.48 3.86
34 35 3.637694 CACATTGATATTGTGGCCATCCA 59.362 43.478 9.72 0.00 40.60 3.41
35 36 3.638160 ACACATTGATATTGTGGCCATCC 59.362 43.478 9.72 0.00 46.89 3.51
36 37 4.924305 ACACATTGATATTGTGGCCATC 57.076 40.909 9.72 1.58 46.89 3.51
37 38 4.202040 CGAACACATTGATATTGTGGCCAT 60.202 41.667 9.72 0.00 46.89 4.40
38 39 3.128415 CGAACACATTGATATTGTGGCCA 59.872 43.478 0.00 0.00 46.89 5.36
39 40 3.128589 ACGAACACATTGATATTGTGGCC 59.871 43.478 10.09 0.00 46.89 5.36
40 41 4.342772 GACGAACACATTGATATTGTGGC 58.657 43.478 10.09 2.41 46.89 5.01
41 42 4.201910 GGGACGAACACATTGATATTGTGG 60.202 45.833 10.09 0.00 46.89 4.17
60 61 2.358267 ACTCATCGAGTACATTCGGGAC 59.642 50.000 4.87 0.00 41.51 4.46
61 62 2.651455 ACTCATCGAGTACATTCGGGA 58.349 47.619 4.87 3.17 41.51 5.14
62 63 3.116300 CAACTCATCGAGTACATTCGGG 58.884 50.000 4.87 0.00 42.59 5.14
63 64 3.116300 CCAACTCATCGAGTACATTCGG 58.884 50.000 4.87 0.00 42.59 4.30
64 65 2.535984 GCCAACTCATCGAGTACATTCG 59.464 50.000 0.00 0.00 42.59 3.34
65 66 2.535984 CGCCAACTCATCGAGTACATTC 59.464 50.000 0.00 0.00 42.59 2.67
66 67 2.540515 CGCCAACTCATCGAGTACATT 58.459 47.619 0.00 0.00 42.59 2.71
67 68 1.202417 CCGCCAACTCATCGAGTACAT 60.202 52.381 0.00 0.00 42.59 2.29
68 69 0.172578 CCGCCAACTCATCGAGTACA 59.827 55.000 0.00 0.00 42.59 2.90
69 70 1.146358 GCCGCCAACTCATCGAGTAC 61.146 60.000 0.00 0.00 42.59 2.73
70 71 1.141019 GCCGCCAACTCATCGAGTA 59.859 57.895 0.00 0.00 42.59 2.59
71 72 2.125512 GCCGCCAACTCATCGAGT 60.126 61.111 0.00 0.00 45.64 4.18
72 73 3.257561 CGCCGCCAACTCATCGAG 61.258 66.667 0.00 0.00 35.52 4.04
73 74 4.812476 CCGCCGCCAACTCATCGA 62.812 66.667 0.00 0.00 0.00 3.59
94 95 3.496131 CGGTTTCGGCCATGACGG 61.496 66.667 2.24 0.00 33.33 4.79
95 96 4.160635 GCGGTTTCGGCCATGACG 62.161 66.667 2.24 0.97 36.79 4.35
96 97 4.160635 CGCGGTTTCGGCCATGAC 62.161 66.667 2.24 0.00 36.79 3.06
104 105 2.125431 ATACACCCCGCGGTTTCG 60.125 61.111 26.12 11.96 42.04 3.46
105 106 0.956902 AACATACACCCCGCGGTTTC 60.957 55.000 26.12 0.00 42.04 2.78
106 107 0.324285 TAACATACACCCCGCGGTTT 59.676 50.000 26.12 7.24 42.04 3.27
107 108 0.324285 TTAACATACACCCCGCGGTT 59.676 50.000 26.12 11.59 42.04 4.44
108 109 0.324285 TTTAACATACACCCCGCGGT 59.676 50.000 26.12 7.98 46.31 5.68
109 110 0.728542 GTTTAACATACACCCCGCGG 59.271 55.000 21.04 21.04 0.00 6.46
110 111 1.129064 GTGTTTAACATACACCCCGCG 59.871 52.381 0.00 0.00 39.93 6.46
111 112 2.429478 AGTGTTTAACATACACCCCGC 58.571 47.619 0.00 0.00 45.42 6.13
112 113 4.186159 CCTAGTGTTTAACATACACCCCG 58.814 47.826 0.00 0.00 45.42 5.73
113 114 4.019051 ACCCTAGTGTTTAACATACACCCC 60.019 45.833 0.00 0.00 45.42 4.95
114 115 4.939439 CACCCTAGTGTTTAACATACACCC 59.061 45.833 0.00 0.00 45.42 4.61
129 130 6.015350 CCGATAAAGACATCATACACCCTAGT 60.015 42.308 0.00 0.00 0.00 2.57
130 131 6.390721 CCGATAAAGACATCATACACCCTAG 58.609 44.000 0.00 0.00 0.00 3.02
131 132 5.279306 GCCGATAAAGACATCATACACCCTA 60.279 44.000 0.00 0.00 0.00 3.53
132 133 4.503296 GCCGATAAAGACATCATACACCCT 60.503 45.833 0.00 0.00 0.00 4.34
133 134 3.746492 GCCGATAAAGACATCATACACCC 59.254 47.826 0.00 0.00 0.00 4.61
134 135 3.428870 CGCCGATAAAGACATCATACACC 59.571 47.826 0.00 0.00 0.00 4.16
135 136 3.428870 CCGCCGATAAAGACATCATACAC 59.571 47.826 0.00 0.00 0.00 2.90
136 137 3.649073 CCGCCGATAAAGACATCATACA 58.351 45.455 0.00 0.00 0.00 2.29
137 138 2.412089 GCCGCCGATAAAGACATCATAC 59.588 50.000 0.00 0.00 0.00 2.39
138 139 2.611971 GGCCGCCGATAAAGACATCATA 60.612 50.000 0.00 0.00 0.00 2.15
139 140 1.512926 GCCGCCGATAAAGACATCAT 58.487 50.000 0.00 0.00 0.00 2.45
140 141 0.531974 GGCCGCCGATAAAGACATCA 60.532 55.000 0.00 0.00 0.00 3.07
141 142 0.249911 AGGCCGCCGATAAAGACATC 60.250 55.000 3.05 0.00 0.00 3.06
142 143 0.180406 AAGGCCGCCGATAAAGACAT 59.820 50.000 3.05 0.00 0.00 3.06
143 144 0.825410 TAAGGCCGCCGATAAAGACA 59.175 50.000 3.05 0.00 0.00 3.41
144 145 1.499049 CTAAGGCCGCCGATAAAGAC 58.501 55.000 3.05 0.00 0.00 3.01
145 146 0.391597 CCTAAGGCCGCCGATAAAGA 59.608 55.000 3.05 0.00 0.00 2.52
146 147 0.602905 CCCTAAGGCCGCCGATAAAG 60.603 60.000 3.05 0.00 0.00 1.85
147 148 1.448497 CCCTAAGGCCGCCGATAAA 59.552 57.895 3.05 0.00 0.00 1.40
148 149 2.513259 CCCCTAAGGCCGCCGATAA 61.513 63.158 3.05 0.00 0.00 1.75
149 150 2.920912 CCCCTAAGGCCGCCGATA 60.921 66.667 3.05 0.68 0.00 2.92
153 154 3.699134 CTTCACCCCTAAGGCCGCC 62.699 68.421 0.00 0.00 40.58 6.13
154 155 2.124695 CTTCACCCCTAAGGCCGC 60.125 66.667 0.00 0.00 40.58 6.53
155 156 1.078426 CACTTCACCCCTAAGGCCG 60.078 63.158 0.00 0.00 40.58 6.13
156 157 1.378646 GCACTTCACCCCTAAGGCC 60.379 63.158 0.00 0.00 40.58 5.19
157 158 0.909623 TAGCACTTCACCCCTAAGGC 59.090 55.000 0.00 0.00 40.58 4.35
158 159 3.610911 CTTTAGCACTTCACCCCTAAGG 58.389 50.000 0.00 0.00 43.78 2.69
159 160 3.010420 GCTTTAGCACTTCACCCCTAAG 58.990 50.000 0.00 0.00 41.59 2.18
160 161 2.642807 AGCTTTAGCACTTCACCCCTAA 59.357 45.455 4.33 0.00 45.16 2.69
161 162 2.266279 AGCTTTAGCACTTCACCCCTA 58.734 47.619 4.33 0.00 45.16 3.53
162 163 1.068121 AGCTTTAGCACTTCACCCCT 58.932 50.000 4.33 0.00 45.16 4.79
163 164 1.911057 AAGCTTTAGCACTTCACCCC 58.089 50.000 4.33 0.00 45.16 4.95
164 165 4.072839 AGTAAAGCTTTAGCACTTCACCC 58.927 43.478 19.16 3.86 45.16 4.61
165 166 5.690997 AAGTAAAGCTTTAGCACTTCACC 57.309 39.130 19.16 4.55 45.16 4.02
166 167 7.987268 AAAAAGTAAAGCTTTAGCACTTCAC 57.013 32.000 20.66 10.34 45.91 3.18
174 175 8.905702 CACACATGCTAAAAAGTAAAGCTTTAG 58.094 33.333 19.16 8.69 45.91 1.85
175 176 8.625651 TCACACATGCTAAAAAGTAAAGCTTTA 58.374 29.630 14.96 14.96 45.91 1.85
177 178 7.038154 TCACACATGCTAAAAAGTAAAGCTT 57.962 32.000 0.00 0.00 39.52 3.74
178 179 6.633500 TCACACATGCTAAAAAGTAAAGCT 57.367 33.333 0.00 0.00 37.16 3.74
179 180 6.863126 ACATCACACATGCTAAAAAGTAAAGC 59.137 34.615 0.00 0.00 36.77 3.51
180 181 8.292448 AGACATCACACATGCTAAAAAGTAAAG 58.708 33.333 0.00 0.00 0.00 1.85
181 182 8.165239 AGACATCACACATGCTAAAAAGTAAA 57.835 30.769 0.00 0.00 0.00 2.01
182 183 7.744087 AGACATCACACATGCTAAAAAGTAA 57.256 32.000 0.00 0.00 0.00 2.24
183 184 7.744087 AAGACATCACACATGCTAAAAAGTA 57.256 32.000 0.00 0.00 0.00 2.24
184 185 6.639632 AAGACATCACACATGCTAAAAAGT 57.360 33.333 0.00 0.00 0.00 2.66
185 186 9.282247 GATAAAGACATCACACATGCTAAAAAG 57.718 33.333 0.00 0.00 0.00 2.27
186 187 7.962373 CGATAAAGACATCACACATGCTAAAAA 59.038 33.333 0.00 0.00 0.00 1.94
187 188 7.463544 CGATAAAGACATCACACATGCTAAAA 58.536 34.615 0.00 0.00 0.00 1.52
188 189 6.456853 GCGATAAAGACATCACACATGCTAAA 60.457 38.462 0.00 0.00 0.00 1.85
189 190 5.006649 GCGATAAAGACATCACACATGCTAA 59.993 40.000 0.00 0.00 0.00 3.09
190 191 4.507756 GCGATAAAGACATCACACATGCTA 59.492 41.667 0.00 0.00 0.00 3.49
191 192 3.310774 GCGATAAAGACATCACACATGCT 59.689 43.478 0.00 0.00 0.00 3.79
192 193 3.063861 TGCGATAAAGACATCACACATGC 59.936 43.478 0.00 0.00 0.00 4.06
193 194 4.093261 TGTGCGATAAAGACATCACACATG 59.907 41.667 3.51 0.00 40.97 3.21
197 198 3.658709 TGTGTGCGATAAAGACATCACA 58.341 40.909 0.00 0.00 33.24 3.58
204 205 2.984471 GTCGAACTGTGTGCGATAAAGA 59.016 45.455 4.01 0.00 45.75 2.52
205 206 2.222289 CGTCGAACTGTGTGCGATAAAG 60.222 50.000 4.01 0.00 45.75 1.85
223 224 4.037684 ACATCTAACATACACCCTAGCGTC 59.962 45.833 0.00 0.00 0.00 5.19
354 355 9.589111 AAAAAGTTCCTCAATAGCGTTTTTAAA 57.411 25.926 0.00 0.00 0.00 1.52
398 399 1.454201 GAGCACTTCACCCCTAAAGC 58.546 55.000 0.00 0.00 0.00 3.51
485 488 2.948979 CAGGAGTTGTTGGCTTTGTGTA 59.051 45.455 0.00 0.00 0.00 2.90
486 489 1.750778 CAGGAGTTGTTGGCTTTGTGT 59.249 47.619 0.00 0.00 0.00 3.72
487 490 2.023673 TCAGGAGTTGTTGGCTTTGTG 58.976 47.619 0.00 0.00 0.00 3.33
488 491 2.024414 GTCAGGAGTTGTTGGCTTTGT 58.976 47.619 0.00 0.00 0.00 2.83
554 557 1.164041 ACGTAGTGTTGCCAAGGTGC 61.164 55.000 0.00 0.00 42.51 5.01
592 596 2.162681 CGGAAGAAAACCAGCTGGATT 58.837 47.619 39.19 30.31 38.94 3.01
593 597 1.073923 ACGGAAGAAAACCAGCTGGAT 59.926 47.619 39.19 25.96 38.94 3.41
626 630 6.197468 GCTTACAGTTAGTAGAAGCGAAGATG 59.803 42.308 0.00 0.00 33.51 2.90
702 716 8.524487 ACCTGCTAGATACAGTATAATACAAGC 58.476 37.037 0.00 0.00 33.09 4.01
792 831 2.275547 ATTCCGTCTGGTCGTACCGC 62.276 60.000 0.00 0.00 42.58 5.68
795 834 4.325472 CACTTTTATTCCGTCTGGTCGTAC 59.675 45.833 0.00 0.00 36.30 3.67
796 835 4.487948 CACTTTTATTCCGTCTGGTCGTA 58.512 43.478 0.00 0.00 36.30 3.43
797 836 3.323243 CACTTTTATTCCGTCTGGTCGT 58.677 45.455 0.00 0.00 36.30 4.34
798 837 2.093783 GCACTTTTATTCCGTCTGGTCG 59.906 50.000 0.00 0.00 36.30 4.79
799 838 3.071479 TGCACTTTTATTCCGTCTGGTC 58.929 45.455 0.00 0.00 36.30 4.02
888 927 3.553597 GCTAGTCGCTATTGCTCGT 57.446 52.632 0.00 0.00 36.97 4.18
940 979 0.955428 TGTCGTTCAGATGCTTGCCC 60.955 55.000 0.00 0.00 0.00 5.36
953 992 2.277084 AGACAGCTTTTTCGTGTCGTT 58.723 42.857 0.00 0.00 44.41 3.85
954 993 1.935933 AGACAGCTTTTTCGTGTCGT 58.064 45.000 0.00 0.00 44.41 4.34
970 1009 0.893447 AACCCTACGTGCACCTAGAC 59.107 55.000 20.43 0.00 0.00 2.59
971 1010 0.892755 CAACCCTACGTGCACCTAGA 59.107 55.000 20.43 0.23 0.00 2.43
972 1011 0.108329 CCAACCCTACGTGCACCTAG 60.108 60.000 12.15 13.25 0.00 3.02
973 1012 1.976898 CCAACCCTACGTGCACCTA 59.023 57.895 12.15 3.08 0.00 3.08
987 1039 1.800681 GGCCATCGTGTAAGCCAAC 59.199 57.895 0.00 0.00 45.07 3.77
1314 1370 5.174035 CCGTATTCAGATTTCAGAAGCGTAG 59.826 44.000 9.64 0.00 0.00 3.51
1315 1371 5.041287 CCGTATTCAGATTTCAGAAGCGTA 58.959 41.667 9.64 0.00 0.00 4.42
1316 1372 3.865745 CCGTATTCAGATTTCAGAAGCGT 59.134 43.478 9.64 0.00 0.00 5.07
1317 1373 3.302740 GCCGTATTCAGATTTCAGAAGCG 60.303 47.826 0.00 0.00 0.00 4.68
1318 1374 3.873952 AGCCGTATTCAGATTTCAGAAGC 59.126 43.478 0.00 0.00 0.00 3.86
1321 1377 4.433615 GACAGCCGTATTCAGATTTCAGA 58.566 43.478 0.00 0.00 0.00 3.27
1323 1379 3.186909 CGACAGCCGTATTCAGATTTCA 58.813 45.455 0.00 0.00 0.00 2.69
1324 1380 3.843426 CGACAGCCGTATTCAGATTTC 57.157 47.619 0.00 0.00 0.00 2.17
1611 2029 0.599558 TGTACAAGAGGGGTTCGTCG 59.400 55.000 0.00 0.00 33.41 5.12
1635 2097 1.842562 AGGATGGAGAGGATGGTGTTG 59.157 52.381 0.00 0.00 0.00 3.33
1767 2229 4.124238 CACAGTACTTCCGACAAAAAGGA 58.876 43.478 0.00 0.00 34.19 3.36
1835 2297 2.496291 GCCATACTCCCGGCGTACT 61.496 63.158 6.01 0.00 38.82 2.73
1854 2316 2.034878 TGATCCCTCATGAACTCTCCG 58.965 52.381 0.00 0.00 0.00 4.63
1971 2433 1.338769 GCACGTACACCATCTCCCTTT 60.339 52.381 0.00 0.00 0.00 3.11
1974 2442 0.036765 TTGCACGTACACCATCTCCC 60.037 55.000 0.00 0.00 0.00 4.30
2333 5979 0.927537 TGTCAACGTTGCTGAAGTCG 59.072 50.000 23.47 0.00 0.00 4.18
2576 6222 1.301716 GCGCTGAGGAAACTGGACA 60.302 57.895 0.00 0.00 44.43 4.02
2585 6231 3.053896 TCGTCGAAGCGCTGAGGA 61.054 61.111 12.58 13.56 0.00 3.71
2588 6234 3.923356 GACGTCGTCGAAGCGCTGA 62.923 63.158 12.58 0.62 40.62 4.26
2630 6276 2.797087 GTCGAAGAAGACACGGTTGTGA 60.797 50.000 1.91 0.00 44.56 3.58
3068 6714 2.678934 AGGCGCTCGGTGAGGTTA 60.679 61.111 7.64 0.00 0.00 2.85
3330 6979 1.806247 GCCGATCACGTGAATGATGGA 60.806 52.381 24.13 0.00 39.48 3.41
3335 6984 1.009078 ACATGCCGATCACGTGAATG 58.991 50.000 24.13 21.84 37.88 2.67
3690 7339 2.092681 CGATGATCCACACGTTGAACAG 59.907 50.000 0.00 0.00 0.00 3.16
3708 7357 0.683504 AACGGGTAGAGGAGCACGAT 60.684 55.000 0.00 0.00 0.00 3.73
3885 7534 2.584608 CCCAGATGGTCCGGTCAC 59.415 66.667 0.00 0.00 0.00 3.67
3922 7573 7.277981 AGTGACTGTGACTGTACTTGTAAAAAG 59.722 37.037 0.00 0.00 0.00 2.27
3976 7627 6.987386 ACCAGTTCTCATGCTATATAGACAC 58.013 40.000 14.16 0.00 0.00 3.67
4222 7878 3.492102 ATTACGGCCAACATATCTGCT 57.508 42.857 2.24 0.00 0.00 4.24
4262 7918 4.884961 ACTAGACCCTCTACATGACCATT 58.115 43.478 0.00 0.00 0.00 3.16
4267 7923 4.229812 TGAGGAACTAGACCCTCTACATGA 59.770 45.833 24.75 9.89 46.94 3.07
4349 8005 2.493278 GTGCCTTAGCCATGTCATGTTT 59.507 45.455 11.84 2.29 38.69 2.83
4420 8076 6.183360 ACACCTCGCTCTTATGAAAATTGATG 60.183 38.462 0.00 0.00 0.00 3.07
4509 8166 5.010282 CCAAGTAACTGAAAGGTAAGGCAT 58.990 41.667 0.00 0.00 38.27 4.40
4602 8262 1.376942 CCCTTCCAGCAGCTGAGTG 60.377 63.158 24.90 13.72 32.44 3.51
4633 8293 3.516300 TCAAAACTAGCCGACCTCCATAA 59.484 43.478 0.00 0.00 0.00 1.90
4668 8328 3.874392 AAAACATTGGCATGCTAGTCC 57.126 42.857 18.92 0.10 33.05 3.85
4711 8371 2.989253 CGCTTTCGGCCCCCTTTT 60.989 61.111 0.00 0.00 37.74 2.27
4719 8379 1.464997 AGAAATCAAGTCGCTTTCGGC 59.535 47.619 0.00 0.00 41.36 5.54
4834 8496 0.868406 CCAAGTTCTCAACACCGAGC 59.132 55.000 0.00 0.00 32.75 5.03


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

AutoCloner maintained by Alex Coulton.