Multiple sequence alignment - TraesCS3A01G379400

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 TraesCS3A01G379400 chr3A 100.000 3890 0 0 1 3890 629055492 629059381 0.000000e+00 7184.0
1 TraesCS3A01G379400 chr3A 85.341 1262 146 24 1039 2283 696637258 696638497 0.000000e+00 1269.0
2 TraesCS3A01G379400 chr3A 84.651 1075 147 14 987 2049 629086993 629088061 0.000000e+00 1055.0
3 TraesCS3A01G379400 chr3A 84.651 1075 147 14 987 2049 696332972 696331904 0.000000e+00 1055.0
4 TraesCS3A01G379400 chr3A 82.570 1222 141 34 1121 2311 696477904 696476724 0.000000e+00 1011.0
5 TraesCS3A01G379400 chr3A 87.708 480 51 7 2440 2917 696343363 696342890 1.580000e-153 553.0
6 TraesCS3A01G379400 chr3A 83.554 529 70 15 2440 2963 629088707 629089223 2.720000e-131 479.0
7 TraesCS3A01G379400 chr3A 83.554 529 70 15 2440 2963 696331257 696330741 2.720000e-131 479.0
8 TraesCS3A01G379400 chr3A 91.228 171 13 1 55 225 121482288 121482456 8.410000e-57 231.0
9 TraesCS3A01G379400 chr3A 80.899 178 27 6 52 228 685129609 685129438 2.440000e-27 134.0
10 TraesCS3A01G379400 chr3B 89.808 2139 131 56 938 3002 747093652 747095777 0.000000e+00 2662.0
11 TraesCS3A01G379400 chr3B 91.875 1403 95 8 938 2330 744546786 744545393 0.000000e+00 1941.0
12 TraesCS3A01G379400 chr3B 85.263 1330 158 20 989 2282 744847138 744848465 0.000000e+00 1336.0
13 TraesCS3A01G379400 chr3B 85.188 1330 159 20 989 2282 744728565 744729892 0.000000e+00 1330.0
14 TraesCS3A01G379400 chr3B 82.859 1371 191 27 987 2323 745203411 745202051 0.000000e+00 1190.0
15 TraesCS3A01G379400 chr3B 86.569 1087 123 9 987 2051 747384366 747385451 0.000000e+00 1177.0
16 TraesCS3A01G379400 chr3B 86.544 1085 125 7 987 2050 744512927 744511843 0.000000e+00 1175.0
17 TraesCS3A01G379400 chr3B 86.829 987 116 10 1039 2024 745540165 745541138 0.000000e+00 1090.0
18 TraesCS3A01G379400 chr3B 94.633 559 23 4 2400 2958 744545263 744544712 0.000000e+00 859.0
19 TraesCS3A01G379400 chr3B 88.406 483 48 7 2440 2920 744511351 744510875 3.370000e-160 575.0
20 TraesCS3A01G379400 chr3B 87.708 480 50 8 2440 2917 747385859 747386331 5.680000e-153 551.0
21 TraesCS3A01G379400 chr3B 84.404 327 35 7 1972 2282 746286040 746286366 1.360000e-79 307.0
22 TraesCS3A01G379400 chr3B 87.745 204 21 1 2075 2278 745548012 745548211 6.500000e-58 235.0
23 TraesCS3A01G379400 chr3B 97.727 44 1 0 2960 3003 744544691 744544648 4.170000e-10 76.8
24 TraesCS3A01G379400 chr3D 92.527 1365 63 10 225 1559 560287502 560286147 0.000000e+00 1919.0
25 TraesCS3A01G379400 chr3D 85.575 1331 152 23 989 2282 560551562 560552889 0.000000e+00 1358.0
26 TraesCS3A01G379400 chr3D 86.248 1258 150 15 1039 2283 560826916 560828163 0.000000e+00 1343.0
27 TraesCS3A01G379400 chr3D 83.558 1338 172 33 987 2283 560235127 560233797 0.000000e+00 1208.0
28 TraesCS3A01G379400 chr3D 89.119 919 100 0 987 1905 560269608 560268690 0.000000e+00 1144.0
29 TraesCS3A01G379400 chr3D 90.909 737 12 6 1622 2330 560286133 560285424 0.000000e+00 939.0
30 TraesCS3A01G379400 chr3D 94.662 562 24 3 2400 2958 560285269 560284711 0.000000e+00 867.0
31 TraesCS3A01G379400 chr3D 87.686 471 50 7 2449 2917 560268069 560267605 3.420000e-150 542.0
32 TraesCS3A01G379400 chr3D 83.071 254 24 10 2084 2323 560784655 560784407 3.040000e-51 213.0
33 TraesCS3A01G379400 chr3D 100.000 44 0 0 2960 3003 560284690 560284647 8.960000e-12 82.4
34 TraesCS3A01G379400 chr5B 95.147 886 43 0 3003 3888 122413732 122414617 0.000000e+00 1399.0
35 TraesCS3A01G379400 chr5B 81.034 174 28 5 55 227 527015478 527015309 2.440000e-27 134.0
36 TraesCS3A01G379400 chr7A 88.649 881 88 7 3010 3888 693201673 693200803 0.000000e+00 1062.0
37 TraesCS3A01G379400 chr7A 83.429 175 22 6 52 224 102041146 102041315 5.200000e-34 156.0
38 TraesCS3A01G379400 chr6B 75.469 746 168 12 3146 3883 29876258 29875520 2.220000e-92 350.0
39 TraesCS3A01G379400 chr2A 74.186 860 209 10 3003 3854 717111233 717112087 2.880000e-91 346.0
40 TraesCS3A01G379400 chr7D 91.716 169 12 1 56 224 109524578 109524744 2.340000e-57 233.0
41 TraesCS3A01G379400 chr5A 90.588 170 14 1 55 224 535779664 535779497 1.410000e-54 224.0
42 TraesCS3A01G379400 chr1B 83.429 175 23 5 51 224 202973669 202973500 1.450000e-34 158.0
43 TraesCS3A01G379400 chr7B 82.584 178 28 3 48 224 749286367 749286542 1.870000e-33 154.0
44 TraesCS3A01G379400 chr2D 83.041 171 25 4 54 224 477274972 477274806 6.730000e-33 152.0


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 TraesCS3A01G379400 chr3A 629055492 629059381 3889 False 7184.000000 7184 100.0000 1 3890 1 chr3A.!!$F2 3889
1 TraesCS3A01G379400 chr3A 696637258 696638497 1239 False 1269.000000 1269 85.3410 1039 2283 1 chr3A.!!$F3 1244
2 TraesCS3A01G379400 chr3A 696476724 696477904 1180 True 1011.000000 1011 82.5700 1121 2311 1 chr3A.!!$R3 1190
3 TraesCS3A01G379400 chr3A 629086993 629089223 2230 False 767.000000 1055 84.1025 987 2963 2 chr3A.!!$F4 1976
4 TraesCS3A01G379400 chr3A 696330741 696332972 2231 True 767.000000 1055 84.1025 987 2963 2 chr3A.!!$R4 1976
5 TraesCS3A01G379400 chr3B 747093652 747095777 2125 False 2662.000000 2662 89.8080 938 3002 1 chr3B.!!$F6 2064
6 TraesCS3A01G379400 chr3B 744847138 744848465 1327 False 1336.000000 1336 85.2630 989 2282 1 chr3B.!!$F2 1293
7 TraesCS3A01G379400 chr3B 744728565 744729892 1327 False 1330.000000 1330 85.1880 989 2282 1 chr3B.!!$F1 1293
8 TraesCS3A01G379400 chr3B 745202051 745203411 1360 True 1190.000000 1190 82.8590 987 2323 1 chr3B.!!$R1 1336
9 TraesCS3A01G379400 chr3B 745540165 745541138 973 False 1090.000000 1090 86.8290 1039 2024 1 chr3B.!!$F3 985
10 TraesCS3A01G379400 chr3B 744544648 744546786 2138 True 958.933333 1941 94.7450 938 3003 3 chr3B.!!$R3 2065
11 TraesCS3A01G379400 chr3B 744510875 744512927 2052 True 875.000000 1175 87.4750 987 2920 2 chr3B.!!$R2 1933
12 TraesCS3A01G379400 chr3B 747384366 747386331 1965 False 864.000000 1177 87.1385 987 2917 2 chr3B.!!$F7 1930
13 TraesCS3A01G379400 chr3D 560551562 560552889 1327 False 1358.000000 1358 85.5750 989 2282 1 chr3D.!!$F1 1293
14 TraesCS3A01G379400 chr3D 560826916 560828163 1247 False 1343.000000 1343 86.2480 1039 2283 1 chr3D.!!$F2 1244
15 TraesCS3A01G379400 chr3D 560233797 560235127 1330 True 1208.000000 1208 83.5580 987 2283 1 chr3D.!!$R1 1296
16 TraesCS3A01G379400 chr3D 560284647 560287502 2855 True 951.850000 1919 94.5245 225 3003 4 chr3D.!!$R4 2778
17 TraesCS3A01G379400 chr3D 560267605 560269608 2003 True 843.000000 1144 88.4025 987 2917 2 chr3D.!!$R3 1930
18 TraesCS3A01G379400 chr5B 122413732 122414617 885 False 1399.000000 1399 95.1470 3003 3888 1 chr5B.!!$F1 885
19 TraesCS3A01G379400 chr7A 693200803 693201673 870 True 1062.000000 1062 88.6490 3010 3888 1 chr7A.!!$R1 878
20 TraesCS3A01G379400 chr6B 29875520 29876258 738 True 350.000000 350 75.4690 3146 3883 1 chr6B.!!$R1 737
21 TraesCS3A01G379400 chr2A 717111233 717112087 854 False 346.000000 346 74.1860 3003 3854 1 chr2A.!!$F1 851

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
272 273 0.031585 TTCCACTCGTGTTGACGGAG 59.968 55.000 0.0 1.84 46.11 4.63 F
1063 1094 1.227380 CTCACCGGCATGGAGCTAC 60.227 63.158 0.0 0.00 44.79 3.58 F
1527 1570 1.513158 CTGGCTCGACATCCTCGTT 59.487 57.895 0.0 0.00 43.45 3.85 F
2571 3366 1.721487 CGGTCCCATGAAATGCGTC 59.279 57.895 0.0 0.00 44.97 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1147 0.523072 GCGGAAGGTAGTCGTACACA 59.477 55.000 0.0 0.0 0.00 3.72 R
2673 3468 0.480690 TGGCCACCACAACTACCATT 59.519 50.000 0.0 0.0 0.00 3.16 R
2679 3474 0.760189 ATTTGCTGGCCACCACAACT 60.760 50.000 0.0 0.0 29.43 3.16 R
3741 4570 1.911357 AGTGAGGATGGCAGAATGTGA 59.089 47.619 0.0 0.0 39.31 3.58 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
27 28 2.711542 GGTTTCCATGAACCACGATCT 58.288 47.619 10.65 0.00 46.66 2.75
28 29 2.420022 GGTTTCCATGAACCACGATCTG 59.580 50.000 10.65 0.00 46.66 2.90
29 30 1.737838 TTCCATGAACCACGATCTGC 58.262 50.000 0.00 0.00 0.00 4.26
30 31 0.612744 TCCATGAACCACGATCTGCA 59.387 50.000 0.00 0.00 0.00 4.41
31 32 1.012086 CCATGAACCACGATCTGCAG 58.988 55.000 7.63 7.63 0.00 4.41
32 33 1.676916 CCATGAACCACGATCTGCAGT 60.677 52.381 14.67 0.42 0.00 4.40
33 34 1.662629 CATGAACCACGATCTGCAGTC 59.337 52.381 14.67 9.71 0.00 3.51
34 35 0.388520 TGAACCACGATCTGCAGTCG 60.389 55.000 26.39 26.39 44.26 4.18
35 36 0.109272 GAACCACGATCTGCAGTCGA 60.109 55.000 31.39 10.57 41.40 4.20
36 37 0.109086 AACCACGATCTGCAGTCGAG 60.109 55.000 31.39 25.82 41.40 4.04
37 38 1.875813 CCACGATCTGCAGTCGAGC 60.876 63.158 31.39 11.61 41.40 5.03
38 39 2.101185 ACGATCTGCAGTCGAGCG 59.899 61.111 31.39 22.55 44.89 5.03
39 40 2.653448 CGATCTGCAGTCGAGCGG 60.653 66.667 24.93 0.00 41.40 5.52
42 43 3.443925 TCTGCAGTCGAGCGGAGG 61.444 66.667 14.67 0.00 44.55 4.30
54 55 4.527583 CGGAGGCTCTCAGCAGGC 62.528 72.222 15.23 0.00 44.75 4.85
55 56 3.397439 GGAGGCTCTCAGCAGGCA 61.397 66.667 15.23 0.00 44.75 4.75
56 57 2.187424 GAGGCTCTCAGCAGGCAG 59.813 66.667 7.40 0.00 44.75 4.85
57 58 2.607134 AGGCTCTCAGCAGGCAGT 60.607 61.111 0.00 0.00 44.75 4.40
58 59 2.436292 GGCTCTCAGCAGGCAGTG 60.436 66.667 0.00 0.00 44.75 3.66
59 60 2.436292 GCTCTCAGCAGGCAGTGG 60.436 66.667 0.00 0.00 41.89 4.00
60 61 2.436292 CTCTCAGCAGGCAGTGGC 60.436 66.667 9.02 9.02 40.13 5.01
61 62 4.383861 TCTCAGCAGGCAGTGGCG 62.384 66.667 11.51 7.56 42.47 5.69
67 68 3.390521 CAGGCAGTGGCGGACCTA 61.391 66.667 11.46 0.00 42.47 3.08
68 69 3.077556 AGGCAGTGGCGGACCTAG 61.078 66.667 11.51 0.00 42.47 3.02
69 70 4.840005 GGCAGTGGCGGACCTAGC 62.840 72.222 0.00 0.00 42.47 3.42
76 77 4.162690 GCGGACCTAGCCCACTGG 62.163 72.222 0.00 0.00 0.00 4.00
87 88 4.684134 CCACTGGGCCAAGGTGGG 62.684 72.222 28.75 15.23 44.63 4.61
96 97 2.886382 CCAAGGTGGGCCAATAGTG 58.114 57.895 8.40 4.13 37.19 2.74
97 98 1.322538 CCAAGGTGGGCCAATAGTGC 61.323 60.000 8.40 0.00 37.19 4.40
98 99 0.611618 CAAGGTGGGCCAATAGTGCA 60.612 55.000 8.40 0.00 37.19 4.57
99 100 0.114168 AAGGTGGGCCAATAGTGCAA 59.886 50.000 8.40 0.00 37.19 4.08
100 101 0.336048 AGGTGGGCCAATAGTGCAAT 59.664 50.000 8.40 0.00 37.19 3.56
101 102 1.194218 GGTGGGCCAATAGTGCAATT 58.806 50.000 8.40 0.00 34.09 2.32
102 103 1.554617 GGTGGGCCAATAGTGCAATTT 59.445 47.619 8.40 0.00 34.09 1.82
103 104 2.763448 GGTGGGCCAATAGTGCAATTTA 59.237 45.455 8.40 0.00 34.09 1.40
104 105 3.430236 GGTGGGCCAATAGTGCAATTTAC 60.430 47.826 8.40 0.00 34.09 2.01
105 106 3.194542 GTGGGCCAATAGTGCAATTTACA 59.805 43.478 8.40 0.00 0.00 2.41
106 107 4.029520 TGGGCCAATAGTGCAATTTACAT 58.970 39.130 2.13 0.00 0.00 2.29
107 108 5.068460 GTGGGCCAATAGTGCAATTTACATA 59.932 40.000 8.40 0.00 0.00 2.29
108 109 5.837979 TGGGCCAATAGTGCAATTTACATAT 59.162 36.000 2.13 0.00 0.00 1.78
109 110 7.007116 TGGGCCAATAGTGCAATTTACATATA 58.993 34.615 2.13 0.00 0.00 0.86
110 111 7.040062 TGGGCCAATAGTGCAATTTACATATAC 60.040 37.037 2.13 0.00 0.00 1.47
111 112 7.040062 GGGCCAATAGTGCAATTTACATATACA 60.040 37.037 4.39 0.00 0.00 2.29
112 113 8.522830 GGCCAATAGTGCAATTTACATATACAT 58.477 33.333 0.00 0.00 0.00 2.29
113 114 9.912634 GCCAATAGTGCAATTTACATATACATT 57.087 29.630 0.00 0.00 0.00 2.71
155 156 9.854668 TTTTATTGGCCTTTATGCTATAGTACA 57.145 29.630 3.32 0.00 0.00 2.90
156 157 9.854668 TTTATTGGCCTTTATGCTATAGTACAA 57.145 29.630 3.32 0.00 0.00 2.41
159 160 9.672673 ATTGGCCTTTATGCTATAGTACAATAG 57.327 33.333 3.32 0.00 33.37 1.73
160 161 8.202461 TGGCCTTTATGCTATAGTACAATAGT 57.798 34.615 3.32 0.00 32.89 2.12
161 162 8.094548 TGGCCTTTATGCTATAGTACAATAGTG 58.905 37.037 3.32 0.00 32.89 2.74
162 163 7.549488 GGCCTTTATGCTATAGTACAATAGTGG 59.451 40.741 0.00 3.49 32.89 4.00
163 164 7.064728 GCCTTTATGCTATAGTACAATAGTGGC 59.935 40.741 0.84 8.28 32.89 5.01
164 165 8.314751 CCTTTATGCTATAGTACAATAGTGGCT 58.685 37.037 0.84 0.00 32.89 4.75
169 170 9.877178 ATGCTATAGTACAATAGTGGCTATTTC 57.123 33.333 12.42 7.51 34.83 2.17
170 171 8.311836 TGCTATAGTACAATAGTGGCTATTTCC 58.688 37.037 12.42 5.35 34.83 3.13
171 172 8.311836 GCTATAGTACAATAGTGGCTATTTCCA 58.688 37.037 12.42 0.00 34.83 3.53
172 173 9.862371 CTATAGTACAATAGTGGCTATTTCCAG 57.138 37.037 12.42 3.84 34.83 3.86
173 174 6.808321 AGTACAATAGTGGCTATTTCCAGA 57.192 37.500 0.00 0.00 34.83 3.86
174 175 7.380423 AGTACAATAGTGGCTATTTCCAGAT 57.620 36.000 0.00 0.00 34.83 2.90
175 176 7.445945 AGTACAATAGTGGCTATTTCCAGATC 58.554 38.462 0.00 0.00 34.83 2.75
176 177 6.506538 ACAATAGTGGCTATTTCCAGATCT 57.493 37.500 0.00 0.00 34.83 2.75
177 178 6.529220 ACAATAGTGGCTATTTCCAGATCTC 58.471 40.000 0.00 0.00 34.83 2.75
178 179 6.100279 ACAATAGTGGCTATTTCCAGATCTCA 59.900 38.462 0.00 0.00 34.83 3.27
179 180 4.686191 AGTGGCTATTTCCAGATCTCAG 57.314 45.455 0.00 0.00 36.67 3.35
180 181 3.390639 AGTGGCTATTTCCAGATCTCAGG 59.609 47.826 0.00 0.00 36.67 3.86
181 182 2.707791 TGGCTATTTCCAGATCTCAGGG 59.292 50.000 0.00 0.00 0.00 4.45
182 183 2.708325 GGCTATTTCCAGATCTCAGGGT 59.292 50.000 0.00 0.00 0.00 4.34
183 184 3.495806 GGCTATTTCCAGATCTCAGGGTG 60.496 52.174 0.00 0.00 0.00 4.61
184 185 3.495806 GCTATTTCCAGATCTCAGGGTGG 60.496 52.174 0.00 0.00 0.00 4.61
185 186 1.289160 TTTCCAGATCTCAGGGTGGG 58.711 55.000 0.00 0.00 0.00 4.61
186 187 1.274703 TTCCAGATCTCAGGGTGGGC 61.275 60.000 0.00 0.00 0.00 5.36
187 188 1.692042 CCAGATCTCAGGGTGGGCT 60.692 63.158 0.00 0.00 0.00 5.19
188 189 1.525923 CAGATCTCAGGGTGGGCTG 59.474 63.158 0.00 0.00 0.00 4.85
189 190 1.081833 AGATCTCAGGGTGGGCTGT 59.918 57.895 0.00 0.00 0.00 4.40
190 191 1.222936 GATCTCAGGGTGGGCTGTG 59.777 63.158 0.00 0.00 0.00 3.66
191 192 2.262774 GATCTCAGGGTGGGCTGTGG 62.263 65.000 0.00 0.00 0.00 4.17
192 193 4.729918 CTCAGGGTGGGCTGTGGC 62.730 72.222 0.00 0.00 37.82 5.01
203 204 4.351054 CTGTGGCCCACCCTGTCC 62.351 72.222 12.25 0.00 32.73 4.02
205 206 4.660938 GTGGCCCACCCTGTCCAC 62.661 72.222 1.17 0.00 41.66 4.02
211 212 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
212 213 2.124312 ACCCTGTCCACCCCCTAC 59.876 66.667 0.00 0.00 0.00 3.18
213 214 2.691252 CCCTGTCCACCCCCTACC 60.691 72.222 0.00 0.00 0.00 3.18
214 215 2.454941 CCTGTCCACCCCCTACCT 59.545 66.667 0.00 0.00 0.00 3.08
215 216 1.689582 CCTGTCCACCCCCTACCTC 60.690 68.421 0.00 0.00 0.00 3.85
216 217 1.689582 CTGTCCACCCCCTACCTCC 60.690 68.421 0.00 0.00 0.00 4.30
217 218 2.762875 GTCCACCCCCTACCTCCG 60.763 72.222 0.00 0.00 0.00 4.63
218 219 4.791069 TCCACCCCCTACCTCCGC 62.791 72.222 0.00 0.00 0.00 5.54
222 223 4.798682 CCCCCTACCTCCGCCACT 62.799 72.222 0.00 0.00 0.00 4.00
223 224 3.470888 CCCCTACCTCCGCCACTG 61.471 72.222 0.00 0.00 0.00 3.66
266 267 1.948104 TCCAGTTTCCACTCGTGTTG 58.052 50.000 0.00 0.00 0.00 3.33
267 268 1.483004 TCCAGTTTCCACTCGTGTTGA 59.517 47.619 0.00 0.00 0.00 3.18
268 269 1.597663 CCAGTTTCCACTCGTGTTGAC 59.402 52.381 0.00 0.00 0.00 3.18
270 271 0.580104 GTTTCCACTCGTGTTGACGG 59.420 55.000 0.00 0.00 46.11 4.79
271 272 0.460722 TTTCCACTCGTGTTGACGGA 59.539 50.000 0.00 0.00 46.11 4.69
272 273 0.031585 TTCCACTCGTGTTGACGGAG 59.968 55.000 0.00 1.84 46.11 4.63
273 274 1.372997 CCACTCGTGTTGACGGAGG 60.373 63.158 0.00 0.00 46.11 4.30
274 275 2.022129 CACTCGTGTTGACGGAGGC 61.022 63.158 0.00 0.00 46.11 4.70
275 276 2.805353 CTCGTGTTGACGGAGGCG 60.805 66.667 0.00 0.00 46.11 5.52
286 287 3.775654 GGAGGCGGTGGGAGACAG 61.776 72.222 0.00 0.00 0.00 3.51
291 292 1.690219 GGCGGTGGGAGACAGATGAT 61.690 60.000 0.00 0.00 0.00 2.45
375 376 8.496751 GTGCGTATAAGAAAGAAAAGACTCTTT 58.503 33.333 0.00 0.00 46.06 2.52
390 391 3.809905 ACTCTTTGTGTGGGAGAAGAAC 58.190 45.455 0.00 0.00 0.00 3.01
402 403 4.262617 GGGAGAAGAACGGCTTTAGAATT 58.737 43.478 0.00 0.00 36.83 2.17
415 416 5.594317 GGCTTTAGAATTGAAGATGGCCTAA 59.406 40.000 3.32 0.00 33.87 2.69
486 489 5.203528 AGCATGTGATAGGCCAAACTAAAT 58.796 37.500 5.01 0.00 36.57 1.40
692 695 7.304497 TGGGAGCTAAAAATATAGTCTCTCC 57.696 40.000 0.00 0.00 31.28 3.71
693 696 6.015350 TGGGAGCTAAAAATATAGTCTCTCCG 60.015 42.308 0.00 0.00 31.28 4.63
733 736 7.041721 AGTGCGTTTAGATCATCACTAAATCA 58.958 34.615 0.00 0.00 40.37 2.57
780 783 9.933723 AATTTATTTTTGAGAGCTGCAAATACT 57.066 25.926 11.00 3.94 35.41 2.12
784 787 1.280133 TGAGAGCTGCAAATACTGGCT 59.720 47.619 1.02 0.00 35.86 4.75
788 791 3.575687 AGAGCTGCAAATACTGGCTTTTT 59.424 39.130 1.02 0.00 33.13 1.94
1041 1072 2.721167 CGGCACCTCCATCTCCGAA 61.721 63.158 0.00 0.00 42.43 4.30
1063 1094 1.227380 CTCACCGGCATGGAGCTAC 60.227 63.158 0.00 0.00 44.79 3.58
1116 1147 5.334879 CGGCACAAACTATCTGCTTTACTTT 60.335 40.000 0.00 0.00 0.00 2.66
1131 1162 5.693555 GCTTTACTTTGTGTACGACTACCTT 59.306 40.000 0.00 0.00 0.00 3.50
1527 1570 1.513158 CTGGCTCGACATCCTCGTT 59.487 57.895 0.00 0.00 43.45 3.85
1969 2069 3.765511 CTCTTCCAGGATCAAAATTGGCA 59.234 43.478 0.00 0.00 0.00 4.92
2068 2257 6.918067 TGGTACTCCCAATCTATGTATCTG 57.082 41.667 0.00 0.00 41.50 2.90
2069 2258 6.382087 TGGTACTCCCAATCTATGTATCTGT 58.618 40.000 0.00 0.00 41.50 3.41
2070 2259 6.267699 TGGTACTCCCAATCTATGTATCTGTG 59.732 42.308 0.00 0.00 41.50 3.66
2071 2260 5.220710 ACTCCCAATCTATGTATCTGTGC 57.779 43.478 0.00 0.00 0.00 4.57
2072 2261 4.904251 ACTCCCAATCTATGTATCTGTGCT 59.096 41.667 0.00 0.00 0.00 4.40
2073 2262 5.219343 TCCCAATCTATGTATCTGTGCTG 57.781 43.478 0.00 0.00 0.00 4.41
2074 2263 4.901250 TCCCAATCTATGTATCTGTGCTGA 59.099 41.667 0.00 0.00 0.00 4.26
2075 2264 5.545335 TCCCAATCTATGTATCTGTGCTGAT 59.455 40.000 0.00 0.00 0.00 2.90
2076 2265 6.725834 TCCCAATCTATGTATCTGTGCTGATA 59.274 38.462 0.00 0.00 0.00 2.15
2077 2266 6.815641 CCCAATCTATGTATCTGTGCTGATAC 59.184 42.308 16.99 16.99 45.30 2.24
2078 2267 7.310299 CCCAATCTATGTATCTGTGCTGATACT 60.310 40.741 21.38 13.59 45.31 2.12
2079 2268 7.758980 CCAATCTATGTATCTGTGCTGATACTC 59.241 40.741 21.38 5.71 45.31 2.59
2080 2269 6.825944 TCTATGTATCTGTGCTGATACTCC 57.174 41.667 21.38 5.20 45.31 3.85
2081 2270 4.881019 ATGTATCTGTGCTGATACTCCC 57.119 45.455 21.38 4.95 45.31 4.30
2082 2271 3.642141 TGTATCTGTGCTGATACTCCCA 58.358 45.455 21.38 6.80 45.31 4.37
2083 2272 4.030216 TGTATCTGTGCTGATACTCCCAA 58.970 43.478 21.38 6.50 45.31 4.12
2084 2273 4.655649 TGTATCTGTGCTGATACTCCCAAT 59.344 41.667 21.38 0.00 45.31 3.16
2085 2274 3.827008 TCTGTGCTGATACTCCCAATC 57.173 47.619 0.00 0.00 0.00 2.67
2086 2275 3.378512 TCTGTGCTGATACTCCCAATCT 58.621 45.455 0.00 0.00 0.00 2.40
2087 2276 4.546674 TCTGTGCTGATACTCCCAATCTA 58.453 43.478 0.00 0.00 0.00 1.98
2097 2286 6.562223 TGATACTCCCAATCTATGATCCCAAA 59.438 38.462 0.00 0.00 0.00 3.28
2166 2603 1.985159 AGCATTGTCCCTAGTGTCCAA 59.015 47.619 0.00 0.00 0.00 3.53
2375 3126 2.234661 TCTAGCATGGTCAGAACTGTGG 59.765 50.000 0.00 0.00 0.00 4.17
2423 3214 6.650120 TCCTGAACTTGTTTGAGACTAAAGT 58.350 36.000 0.00 0.00 0.00 2.66
2494 3289 2.871022 ACTGATCGATTTCATCTGCAGC 59.129 45.455 9.47 0.00 0.00 5.25
2571 3366 1.721487 CGGTCCCATGAAATGCGTC 59.279 57.895 0.00 0.00 44.97 5.19
2809 3604 0.957395 CAAGAGCCCGCACACTGAAT 60.957 55.000 0.00 0.00 0.00 2.57
2897 3693 3.206964 TCGAGTACCACTAGATGCAGAG 58.793 50.000 0.00 0.00 0.00 3.35
3153 3969 2.798364 GCCTTCCCGAGCCTCTACC 61.798 68.421 0.00 0.00 0.00 3.18
3197 4013 2.485302 CCCTGTGGTAATGATCATGCGA 60.485 50.000 9.46 0.04 0.00 5.10
3204 4020 4.019411 TGGTAATGATCATGCGATATGGGT 60.019 41.667 9.46 0.00 29.66 4.51
3234 4050 2.738147 CTGACGAACAGGCTAACCG 58.262 57.895 0.00 0.00 42.39 4.44
3345 4161 0.761802 CAAGGGATACTCCTCCAGGC 59.238 60.000 0.00 0.00 36.57 4.85
3629 4454 3.095912 TCGTCAAGATTCCAGGACCTA 57.904 47.619 0.00 0.00 0.00 3.08
3741 4570 0.743345 GGCTGCCTTCCGTAACGAAT 60.743 55.000 12.43 0.00 0.00 3.34
3829 4658 2.113139 CCCGGTTGACAAGGCAGT 59.887 61.111 0.00 0.00 0.00 4.40
3888 4717 1.365699 CGTGACCTTGTAATTCCCCG 58.634 55.000 0.00 0.00 0.00 5.73
3889 4718 1.092348 GTGACCTTGTAATTCCCCGC 58.908 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.159517 GCAGATCGTGGTTCATGGAAAC 60.160 50.000 0.00 0.00 0.00 2.78
9 10 2.083774 GCAGATCGTGGTTCATGGAAA 58.916 47.619 0.00 0.00 0.00 3.13
10 11 1.003003 TGCAGATCGTGGTTCATGGAA 59.997 47.619 0.00 0.00 0.00 3.53
11 12 0.612744 TGCAGATCGTGGTTCATGGA 59.387 50.000 0.00 0.00 0.00 3.41
12 13 1.012086 CTGCAGATCGTGGTTCATGG 58.988 55.000 8.42 0.00 0.00 3.66
13 14 1.662629 GACTGCAGATCGTGGTTCATG 59.337 52.381 23.35 0.00 0.00 3.07
14 15 1.737029 CGACTGCAGATCGTGGTTCAT 60.737 52.381 23.35 0.00 34.84 2.57
15 16 0.388520 CGACTGCAGATCGTGGTTCA 60.389 55.000 23.35 0.00 34.84 3.18
16 17 0.109272 TCGACTGCAGATCGTGGTTC 60.109 55.000 26.56 11.20 40.50 3.62
17 18 0.109086 CTCGACTGCAGATCGTGGTT 60.109 55.000 26.56 4.10 40.50 3.67
18 19 1.508545 CTCGACTGCAGATCGTGGT 59.491 57.895 26.56 5.55 40.50 4.16
19 20 1.875813 GCTCGACTGCAGATCGTGG 60.876 63.158 26.56 22.18 40.50 4.94
20 21 2.220224 CGCTCGACTGCAGATCGTG 61.220 63.158 26.56 25.15 40.50 4.35
21 22 2.101185 CGCTCGACTGCAGATCGT 59.899 61.111 26.56 7.23 40.50 3.73
22 23 2.653448 CCGCTCGACTGCAGATCG 60.653 66.667 23.35 23.68 41.00 3.69
23 24 1.299014 CTCCGCTCGACTGCAGATC 60.299 63.158 23.35 13.13 0.00 2.75
24 25 2.780094 CCTCCGCTCGACTGCAGAT 61.780 63.158 23.35 4.35 0.00 2.90
25 26 3.443925 CCTCCGCTCGACTGCAGA 61.444 66.667 23.35 0.00 0.00 4.26
36 37 4.527583 CCTGCTGAGAGCCTCCGC 62.528 72.222 10.30 10.30 41.51 5.54
37 38 4.527583 GCCTGCTGAGAGCCTCCG 62.528 72.222 0.00 0.00 41.51 4.63
38 39 3.388703 CTGCCTGCTGAGAGCCTCC 62.389 68.421 0.00 0.00 41.51 4.30
39 40 2.187424 CTGCCTGCTGAGAGCCTC 59.813 66.667 0.00 0.00 41.51 4.70
40 41 2.607134 ACTGCCTGCTGAGAGCCT 60.607 61.111 2.88 0.00 41.51 4.58
41 42 2.436292 CACTGCCTGCTGAGAGCC 60.436 66.667 2.88 0.00 41.51 4.70
42 43 2.436292 CCACTGCCTGCTGAGAGC 60.436 66.667 2.88 0.00 42.82 4.09
43 44 2.436292 GCCACTGCCTGCTGAGAG 60.436 66.667 2.88 0.00 0.00 3.20
44 45 4.383861 CGCCACTGCCTGCTGAGA 62.384 66.667 2.88 0.00 0.00 3.27
50 51 3.376935 CTAGGTCCGCCACTGCCTG 62.377 68.421 0.00 0.00 37.19 4.85
51 52 3.077556 CTAGGTCCGCCACTGCCT 61.078 66.667 0.00 0.00 37.19 4.75
52 53 4.840005 GCTAGGTCCGCCACTGCC 62.840 72.222 0.00 0.00 37.19 4.85
53 54 4.840005 GGCTAGGTCCGCCACTGC 62.840 72.222 3.05 0.00 46.77 4.40
58 59 4.162690 CAGTGGGCTAGGTCCGCC 62.163 72.222 0.00 0.00 46.83 6.13
59 60 4.162690 CCAGTGGGCTAGGTCCGC 62.163 72.222 0.00 0.00 38.20 5.54
60 61 3.470888 CCCAGTGGGCTAGGTCCG 61.471 72.222 17.33 0.00 35.35 4.79
69 70 4.684134 CCACCTTGGCCCAGTGGG 62.684 72.222 25.22 25.22 46.01 4.61
78 79 1.322538 GCACTATTGGCCCACCTTGG 61.323 60.000 0.00 0.00 37.25 3.61
79 80 0.611618 TGCACTATTGGCCCACCTTG 60.612 55.000 0.00 0.00 36.63 3.61
80 81 0.114168 TTGCACTATTGGCCCACCTT 59.886 50.000 0.00 0.00 36.63 3.50
81 82 0.336048 ATTGCACTATTGGCCCACCT 59.664 50.000 0.00 0.00 36.63 4.00
82 83 1.194218 AATTGCACTATTGGCCCACC 58.806 50.000 0.00 0.00 0.00 4.61
83 84 3.194542 TGTAAATTGCACTATTGGCCCAC 59.805 43.478 0.00 0.00 0.00 4.61
84 85 3.435275 TGTAAATTGCACTATTGGCCCA 58.565 40.909 0.00 0.00 0.00 5.36
85 86 4.670896 ATGTAAATTGCACTATTGGCCC 57.329 40.909 0.00 0.00 0.00 5.80
86 87 7.881142 TGTATATGTAAATTGCACTATTGGCC 58.119 34.615 0.00 0.00 0.00 5.36
87 88 9.912634 AATGTATATGTAAATTGCACTATTGGC 57.087 29.630 0.00 0.00 0.00 4.52
129 130 9.854668 TGTACTATAGCATAAAGGCCAATAAAA 57.145 29.630 5.01 0.00 0.00 1.52
130 131 9.854668 TTGTACTATAGCATAAAGGCCAATAAA 57.145 29.630 5.01 0.00 0.00 1.40
133 134 9.672673 CTATTGTACTATAGCATAAAGGCCAAT 57.327 33.333 5.01 0.00 0.00 3.16
134 135 8.656806 ACTATTGTACTATAGCATAAAGGCCAA 58.343 33.333 20.05 0.00 32.45 4.52
135 136 8.094548 CACTATTGTACTATAGCATAAAGGCCA 58.905 37.037 20.05 0.00 32.45 5.36
136 137 7.549488 CCACTATTGTACTATAGCATAAAGGCC 59.451 40.741 20.05 0.00 32.45 5.19
137 138 7.064728 GCCACTATTGTACTATAGCATAAAGGC 59.935 40.741 20.05 18.15 32.45 4.35
138 139 8.314751 AGCCACTATTGTACTATAGCATAAAGG 58.685 37.037 20.05 14.10 32.45 3.11
143 144 9.877178 GAAATAGCCACTATTGTACTATAGCAT 57.123 33.333 20.05 9.23 36.85 3.79
144 145 8.311836 GGAAATAGCCACTATTGTACTATAGCA 58.688 37.037 20.05 5.40 36.85 3.49
145 146 8.311836 TGGAAATAGCCACTATTGTACTATAGC 58.688 37.037 20.05 10.41 36.85 2.97
146 147 9.862371 CTGGAAATAGCCACTATTGTACTATAG 57.138 37.037 18.95 18.95 36.85 1.31
147 148 9.596308 TCTGGAAATAGCCACTATTGTACTATA 57.404 33.333 0.81 0.00 36.85 1.31
148 149 8.492415 TCTGGAAATAGCCACTATTGTACTAT 57.508 34.615 0.81 0.00 36.85 2.12
149 150 7.907841 TCTGGAAATAGCCACTATTGTACTA 57.092 36.000 0.81 0.00 36.85 1.82
150 151 6.808321 TCTGGAAATAGCCACTATTGTACT 57.192 37.500 0.81 0.00 36.85 2.73
151 152 7.445945 AGATCTGGAAATAGCCACTATTGTAC 58.554 38.462 0.00 0.00 36.85 2.90
152 153 7.290014 TGAGATCTGGAAATAGCCACTATTGTA 59.710 37.037 0.00 0.00 36.85 2.41
153 154 6.100279 TGAGATCTGGAAATAGCCACTATTGT 59.900 38.462 0.00 0.00 36.85 2.71
154 155 6.528321 TGAGATCTGGAAATAGCCACTATTG 58.472 40.000 0.00 0.00 36.85 1.90
155 156 6.239829 CCTGAGATCTGGAAATAGCCACTATT 60.240 42.308 0.00 0.00 38.17 1.73
156 157 5.248020 CCTGAGATCTGGAAATAGCCACTAT 59.752 44.000 0.00 0.00 37.15 2.12
157 158 4.590647 CCTGAGATCTGGAAATAGCCACTA 59.409 45.833 0.00 0.00 37.15 2.74
158 159 3.390639 CCTGAGATCTGGAAATAGCCACT 59.609 47.826 0.00 0.00 37.15 4.00
159 160 3.495806 CCCTGAGATCTGGAAATAGCCAC 60.496 52.174 0.00 0.00 37.15 5.01
160 161 2.707791 CCCTGAGATCTGGAAATAGCCA 59.292 50.000 0.00 0.00 37.15 4.75
161 162 2.708325 ACCCTGAGATCTGGAAATAGCC 59.292 50.000 0.00 0.00 37.15 3.93
162 163 3.495806 CCACCCTGAGATCTGGAAATAGC 60.496 52.174 0.00 0.00 37.15 2.97
163 164 3.072184 CCCACCCTGAGATCTGGAAATAG 59.928 52.174 0.00 0.00 37.15 1.73
164 165 3.048600 CCCACCCTGAGATCTGGAAATA 58.951 50.000 0.00 0.00 37.15 1.40
165 166 1.849039 CCCACCCTGAGATCTGGAAAT 59.151 52.381 0.00 0.00 37.15 2.17
166 167 1.289160 CCCACCCTGAGATCTGGAAA 58.711 55.000 0.00 0.00 37.15 3.13
167 168 1.274703 GCCCACCCTGAGATCTGGAA 61.275 60.000 0.00 0.00 37.15 3.53
168 169 1.690633 GCCCACCCTGAGATCTGGA 60.691 63.158 0.00 0.00 37.15 3.86
169 170 1.692042 AGCCCACCCTGAGATCTGG 60.692 63.158 0.00 0.00 35.06 3.86
170 171 1.270414 ACAGCCCACCCTGAGATCTG 61.270 60.000 0.00 0.00 36.67 2.90
171 172 1.081833 ACAGCCCACCCTGAGATCT 59.918 57.895 0.00 0.00 36.67 2.75
172 173 1.222936 CACAGCCCACCCTGAGATC 59.777 63.158 0.00 0.00 36.67 2.75
173 174 2.304056 CCACAGCCCACCCTGAGAT 61.304 63.158 0.00 0.00 36.67 2.75
174 175 2.930019 CCACAGCCCACCCTGAGA 60.930 66.667 0.00 0.00 36.67 3.27
175 176 4.729918 GCCACAGCCCACCCTGAG 62.730 72.222 0.00 0.00 36.67 3.35
186 187 4.351054 GGACAGGGTGGGCCACAG 62.351 72.222 35.69 26.03 35.86 3.66
188 189 4.660938 GTGGACAGGGTGGGCCAC 62.661 72.222 28.69 28.69 38.86 5.01
193 194 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
194 195 2.124085 TAGGGGGTGGACAGGGTG 59.876 66.667 0.00 0.00 0.00 4.61
195 196 2.124312 GTAGGGGGTGGACAGGGT 59.876 66.667 0.00 0.00 0.00 4.34
196 197 2.691252 GGTAGGGGGTGGACAGGG 60.691 72.222 0.00 0.00 0.00 4.45
197 198 1.689582 GAGGTAGGGGGTGGACAGG 60.690 68.421 0.00 0.00 0.00 4.00
198 199 1.689582 GGAGGTAGGGGGTGGACAG 60.690 68.421 0.00 0.00 0.00 3.51
199 200 2.453054 GGAGGTAGGGGGTGGACA 59.547 66.667 0.00 0.00 0.00 4.02
200 201 2.762875 CGGAGGTAGGGGGTGGAC 60.763 72.222 0.00 0.00 0.00 4.02
201 202 4.791069 GCGGAGGTAGGGGGTGGA 62.791 72.222 0.00 0.00 0.00 4.02
205 206 4.798682 AGTGGCGGAGGTAGGGGG 62.799 72.222 0.00 0.00 0.00 5.40
206 207 3.470888 CAGTGGCGGAGGTAGGGG 61.471 72.222 0.00 0.00 0.00 4.79
207 208 2.683933 ACAGTGGCGGAGGTAGGG 60.684 66.667 0.00 0.00 0.00 3.53
208 209 1.949847 CTGACAGTGGCGGAGGTAGG 61.950 65.000 0.00 0.00 0.00 3.18
209 210 1.513158 CTGACAGTGGCGGAGGTAG 59.487 63.158 0.00 0.00 0.00 3.18
210 211 2.646175 GCTGACAGTGGCGGAGGTA 61.646 63.158 9.70 0.00 0.00 3.08
211 212 4.008933 GCTGACAGTGGCGGAGGT 62.009 66.667 9.70 0.00 0.00 3.85
212 213 3.947132 CTGCTGACAGTGGCGGAGG 62.947 68.421 9.70 0.00 39.22 4.30
213 214 2.433838 CTGCTGACAGTGGCGGAG 60.434 66.667 9.70 1.60 39.22 4.63
214 215 4.007644 CCTGCTGACAGTGGCGGA 62.008 66.667 9.70 0.00 42.81 5.54
217 218 0.677731 TATTGCCTGCTGACAGTGGC 60.678 55.000 24.96 24.96 42.81 5.01
218 219 1.470098 GTTATTGCCTGCTGACAGTGG 59.530 52.381 3.99 8.15 42.81 4.00
219 220 2.430465 AGTTATTGCCTGCTGACAGTG 58.570 47.619 3.99 0.00 42.81 3.66
220 221 2.816087 CAAGTTATTGCCTGCTGACAGT 59.184 45.455 3.99 0.00 42.81 3.55
221 222 2.816087 ACAAGTTATTGCCTGCTGACAG 59.184 45.455 0.00 0.00 40.27 3.51
222 223 2.553602 CACAAGTTATTGCCTGCTGACA 59.446 45.455 0.00 0.00 40.27 3.58
223 224 2.554032 ACACAAGTTATTGCCTGCTGAC 59.446 45.455 0.00 0.00 40.27 3.51
269 270 3.775654 CTGTCTCCCACCGCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
270 271 2.060980 ATCTGTCTCCCACCGCCTC 61.061 63.158 0.00 0.00 0.00 4.70
271 272 2.039624 ATCTGTCTCCCACCGCCT 59.960 61.111 0.00 0.00 0.00 5.52
272 273 1.690219 ATCATCTGTCTCCCACCGCC 61.690 60.000 0.00 0.00 0.00 6.13
273 274 0.179000 AATCATCTGTCTCCCACCGC 59.821 55.000 0.00 0.00 0.00 5.68
274 275 1.208052 ACAATCATCTGTCTCCCACCG 59.792 52.381 0.00 0.00 0.00 4.94
275 276 2.026822 ACACAATCATCTGTCTCCCACC 60.027 50.000 0.00 0.00 0.00 4.61
286 287 6.029346 AGAAAAACATCCCACACAATCATC 57.971 37.500 0.00 0.00 0.00 2.92
291 292 5.656416 AGAGAAAGAAAAACATCCCACACAA 59.344 36.000 0.00 0.00 0.00 3.33
375 376 1.070786 GCCGTTCTTCTCCCACACA 59.929 57.895 0.00 0.00 0.00 3.72
390 391 3.243201 GGCCATCTTCAATTCTAAAGCCG 60.243 47.826 0.00 0.00 0.00 5.52
402 403 5.711976 CCTTTTCTTTCTTAGGCCATCTTCA 59.288 40.000 5.01 0.00 0.00 3.02
441 443 8.201242 TGCTCATTTAGAAAAACCCCTTTAAT 57.799 30.769 0.00 0.00 0.00 1.40
447 449 5.047377 TCACATGCTCATTTAGAAAAACCCC 60.047 40.000 0.00 0.00 0.00 4.95
486 489 6.001460 CCCGCCAATAAAAAGAGGTGATATA 58.999 40.000 0.00 0.00 33.57 0.86
578 581 9.090692 GGATGACATTTGAATGGTTTCTTATTG 57.909 33.333 8.44 0.00 40.70 1.90
667 670 7.471539 CGGAGAGACTATATTTTTAGCTCCCAA 60.472 40.741 0.00 0.00 36.84 4.12
699 702 8.892723 TGATGATCTAAACGCACTCATATTTTT 58.107 29.630 0.00 0.00 0.00 1.94
700 703 8.338259 GTGATGATCTAAACGCACTCATATTTT 58.662 33.333 0.00 0.00 0.00 1.82
733 736 6.893020 ATTAACAAGTACTCCCTCCATCTT 57.107 37.500 0.00 0.00 0.00 2.40
803 806 9.838339 AGATCACCCTTATATTTCTTTACAGTG 57.162 33.333 0.00 0.00 0.00 3.66
821 824 9.797556 AAAAATATAAAAGCGTTTAGATCACCC 57.202 29.630 11.74 0.00 31.44 4.61
862 885 8.145122 CCTTCTCTCTATGTTCCCATTAACTAC 58.855 40.741 0.00 0.00 32.29 2.73
870 893 4.061131 TGTCCTTCTCTCTATGTTCCCA 57.939 45.455 0.00 0.00 0.00 4.37
880 903 4.383226 GGGTCAGGTATTTGTCCTTCTCTC 60.383 50.000 0.00 0.00 32.37 3.20
1063 1094 4.135153 CTGAGGGTCCTCGCCGTG 62.135 72.222 11.89 0.00 45.48 4.94
1116 1147 0.523072 GCGGAAGGTAGTCGTACACA 59.477 55.000 0.00 0.00 0.00 3.72
1527 1570 2.451493 TCTTGGACCCCCTTGGCA 60.451 61.111 0.00 0.00 37.83 4.92
1848 1891 2.270352 TGTCCTCCAACATGGTGAAC 57.730 50.000 13.74 5.50 39.03 3.18
1969 2069 1.119574 ACACGGAGGTTAGGTGCACT 61.120 55.000 17.98 5.41 35.11 4.40
2062 2251 4.672587 TTGGGAGTATCAGCACAGATAC 57.327 45.455 13.11 13.11 46.82 2.24
2063 2252 5.150715 AGATTGGGAGTATCAGCACAGATA 58.849 41.667 0.00 0.00 36.25 1.98
2064 2253 3.972638 AGATTGGGAGTATCAGCACAGAT 59.027 43.478 0.00 0.00 36.25 2.90
2065 2254 3.378512 AGATTGGGAGTATCAGCACAGA 58.621 45.455 0.00 0.00 36.25 3.41
2066 2255 3.834489 AGATTGGGAGTATCAGCACAG 57.166 47.619 0.00 0.00 36.25 3.66
2067 2256 4.901250 TCATAGATTGGGAGTATCAGCACA 59.099 41.667 0.00 0.00 36.25 4.57
2068 2257 5.474578 TCATAGATTGGGAGTATCAGCAC 57.525 43.478 0.00 0.00 36.25 4.40
2069 2258 5.188555 GGATCATAGATTGGGAGTATCAGCA 59.811 44.000 0.00 0.00 36.25 4.41
2070 2259 5.396213 GGGATCATAGATTGGGAGTATCAGC 60.396 48.000 0.00 0.00 36.25 4.26
2071 2260 5.723405 TGGGATCATAGATTGGGAGTATCAG 59.277 44.000 0.00 0.00 36.25 2.90
2072 2261 5.664665 TGGGATCATAGATTGGGAGTATCA 58.335 41.667 0.00 0.00 36.25 2.15
2073 2262 6.627087 TTGGGATCATAGATTGGGAGTATC 57.373 41.667 0.00 0.00 0.00 2.24
2074 2263 7.594849 ATTTGGGATCATAGATTGGGAGTAT 57.405 36.000 0.00 0.00 0.00 2.12
2075 2264 7.739444 ACTATTTGGGATCATAGATTGGGAGTA 59.261 37.037 5.12 0.00 0.00 2.59
2076 2265 5.937492 ATTTGGGATCATAGATTGGGAGT 57.063 39.130 0.00 0.00 0.00 3.85
2077 2266 7.025520 ACTATTTGGGATCATAGATTGGGAG 57.974 40.000 5.12 0.00 0.00 4.30
2078 2267 7.406620 AACTATTTGGGATCATAGATTGGGA 57.593 36.000 5.12 0.00 0.00 4.37
2079 2268 9.759473 ATAAACTATTTGGGATCATAGATTGGG 57.241 33.333 5.12 0.00 0.00 4.12
2085 2274 9.442047 GGTCAGATAAACTATTTGGGATCATAG 57.558 37.037 0.00 0.00 0.00 2.23
2086 2275 9.170890 AGGTCAGATAAACTATTTGGGATCATA 57.829 33.333 0.00 0.00 0.00 2.15
2087 2276 8.050316 AGGTCAGATAAACTATTTGGGATCAT 57.950 34.615 0.00 0.00 0.00 2.45
2097 2286 4.227300 TGCACCCAAGGTCAGATAAACTAT 59.773 41.667 0.00 0.00 31.02 2.12
2166 2603 2.762327 CTGCACCTCTATGGCCAAAATT 59.238 45.455 10.96 0.00 40.22 1.82
2345 2981 6.976934 TCTGACCATGCTAGATACACAATA 57.023 37.500 0.00 0.00 0.00 1.90
2397 3155 6.920569 TTAGTCTCAAACAAGTTCAGGAAC 57.079 37.500 4.00 4.00 41.45 3.62
2452 3246 7.564793 TCAGTGCATACATTAGTTCAGGTATT 58.435 34.615 0.00 0.00 0.00 1.89
2494 3289 1.669115 CTTCAGATATGCGGCGGGG 60.669 63.158 9.78 0.00 0.00 5.73
2571 3366 0.725686 CCTTCTTCATGCTCTGCACG 59.274 55.000 0.00 0.00 43.04 5.34
2630 3425 1.128692 CCGCGATGAACTTGAGGAAAC 59.871 52.381 8.23 0.00 29.81 2.78
2673 3468 0.480690 TGGCCACCACAACTACCATT 59.519 50.000 0.00 0.00 0.00 3.16
2679 3474 0.760189 ATTTGCTGGCCACCACAACT 60.760 50.000 0.00 0.00 29.43 3.16
2809 3604 5.012664 TGTTGCTGTAAATAGGACTTCCAGA 59.987 40.000 0.00 0.00 38.89 3.86
3012 3828 5.626955 GCTGAGCTTGAATGAGTTTTGTTAC 59.373 40.000 0.00 0.00 0.00 2.50
3153 3969 1.613437 GTGAATGTTTGTGGAGTGGGG 59.387 52.381 0.00 0.00 0.00 4.96
3186 4002 5.164620 TGTAACCCATATCGCATGATCAT 57.835 39.130 1.18 1.18 35.99 2.45
3188 4004 4.142816 GCTTGTAACCCATATCGCATGATC 60.143 45.833 0.00 0.00 35.99 2.92
3197 4013 4.705023 GTCAGGTTTGCTTGTAACCCATAT 59.295 41.667 0.00 0.00 44.96 1.78
3204 4020 3.271729 TGTTCGTCAGGTTTGCTTGTAA 58.728 40.909 0.00 0.00 0.00 2.41
3345 4161 1.038130 AGTAGGAGCTGGTACGCCTG 61.038 60.000 0.00 0.00 40.41 4.85
3741 4570 1.911357 AGTGAGGATGGCAGAATGTGA 59.089 47.619 0.00 0.00 39.31 3.58


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

AutoCloner maintained by Alex Coulton.