Multiple sequence alignment - TraesCS1B01G003900

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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 TraesCS1B01G003900 chr1B 100.000 3044 0 0 1 3044 2272655 2275698 0.000000e+00 5622
1 TraesCS1B01G003900 chr1B 95.918 98 4 0 170 267 27713411 27713508 3.140000e-35 159
2 TraesCS1B01G003900 chr1B 95.000 100 4 1 168 267 33818895 33818993 4.060000e-34 156
3 TraesCS1B01G003900 chr1B 93.204 103 5 1 167 267 15616822 15616924 1.890000e-32 150
4 TraesCS1B01G003900 chr4B 93.511 2743 174 4 303 3044 184310867 184308128 0.000000e+00 4076
5 TraesCS1B01G003900 chr2A 93.128 2721 186 1 324 3044 114488673 114491392 0.000000e+00 3988
6 TraesCS1B01G003900 chr5B 92.127 2731 213 2 314 3044 241264824 241262096 0.000000e+00 3851
7 TraesCS1B01G003900 chr5B 93.359 1837 121 1 1208 3044 503735225 503737060 0.000000e+00 2715
8 TraesCS1B01G003900 chr5B 95.876 97 4 0 171 267 531200070 531199974 1.130000e-34 158
9 TraesCS1B01G003900 chr5A 91.728 2732 212 2 313 3044 532375161 532377878 0.000000e+00 3781
10 TraesCS1B01G003900 chr1D 86.250 2749 328 27 316 3044 418537001 418534283 0.000000e+00 2937
11 TraesCS1B01G003900 chr2B 86.424 2173 276 10 311 2468 131837090 131834922 0.000000e+00 2361
12 TraesCS1B01G003900 chr2B 86.228 501 61 3 2462 2954 131834738 131834238 1.240000e-148 536
13 TraesCS1B01G003900 chr2B 95.000 100 4 1 168 267 66192231 66192329 4.060000e-34 156
14 TraesCS1B01G003900 chr6D 85.226 1435 182 19 316 1730 346463452 346464876 0.000000e+00 1448
15 TraesCS1B01G003900 chr6D 82.575 1297 220 6 1729 3022 346546407 346547700 0.000000e+00 1138
16 TraesCS1B01G003900 chr3A 77.066 968 218 4 886 1851 332217280 332216315 3.430000e-154 555
17 TraesCS1B01G003900 chr2D 79.056 826 144 8 1017 1842 373345976 373345180 9.600000e-150 540
18 TraesCS1B01G003900 chr2D 93.269 104 6 1 165 267 154110789 154110686 5.260000e-33 152
19 TraesCS1B01G003900 chr6B 80.495 687 91 21 323 991 635273977 635274638 1.270000e-133 486
20 TraesCS1B01G003900 chr7D 72.110 839 212 21 977 1804 75233293 75232466 1.820000e-57 233
21 TraesCS1B01G003900 chr4D 95.000 100 5 0 168 267 127149822 127149723 1.130000e-34 158
22 TraesCS1B01G003900 chr6A 94.898 98 5 0 172 269 521559628 521559725 1.460000e-33 154
23 TraesCS1B01G003900 chr3D 91.589 107 8 1 161 267 326723707 326723602 2.450000e-31 147


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 TraesCS1B01G003900 chr1B 2272655 2275698 3043 False 5622.0 5622 100.000 1 3044 1 chr1B.!!$F1 3043
1 TraesCS1B01G003900 chr4B 184308128 184310867 2739 True 4076.0 4076 93.511 303 3044 1 chr4B.!!$R1 2741
2 TraesCS1B01G003900 chr2A 114488673 114491392 2719 False 3988.0 3988 93.128 324 3044 1 chr2A.!!$F1 2720
3 TraesCS1B01G003900 chr5B 241262096 241264824 2728 True 3851.0 3851 92.127 314 3044 1 chr5B.!!$R1 2730
4 TraesCS1B01G003900 chr5B 503735225 503737060 1835 False 2715.0 2715 93.359 1208 3044 1 chr5B.!!$F1 1836
5 TraesCS1B01G003900 chr5A 532375161 532377878 2717 False 3781.0 3781 91.728 313 3044 1 chr5A.!!$F1 2731
6 TraesCS1B01G003900 chr1D 418534283 418537001 2718 True 2937.0 2937 86.250 316 3044 1 chr1D.!!$R1 2728
7 TraesCS1B01G003900 chr2B 131834238 131837090 2852 True 1448.5 2361 86.326 311 2954 2 chr2B.!!$R1 2643
8 TraesCS1B01G003900 chr6D 346463452 346464876 1424 False 1448.0 1448 85.226 316 1730 1 chr6D.!!$F1 1414
9 TraesCS1B01G003900 chr6D 346546407 346547700 1293 False 1138.0 1138 82.575 1729 3022 1 chr6D.!!$F2 1293
10 TraesCS1B01G003900 chr3A 332216315 332217280 965 True 555.0 555 77.066 886 1851 1 chr3A.!!$R1 965
11 TraesCS1B01G003900 chr2D 373345180 373345976 796 True 540.0 540 79.056 1017 1842 1 chr2D.!!$R2 825
12 TraesCS1B01G003900 chr6B 635273977 635274638 661 False 486.0 486 80.495 323 991 1 chr6B.!!$F1 668
13 TraesCS1B01G003900 chr7D 75232466 75233293 827 True 233.0 233 72.110 977 1804 1 chr7D.!!$R1 827

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
54 55 0.033366 GTGGGCAAATGCGGTTTTCT 59.967 50.0 0.0 0.0 43.26 2.52 F
415 416 0.178921 TCTCAACCTCAGCCTCACCT 60.179 55.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1370 0.179059 TTGTTGACGAGCTGGCTCAA 60.179 50.0 20.39 7.38 42.86 3.02 R
2158 2178 0.106015 AGGCCCAACAGAACTGCTTT 60.106 50.0 0.00 0.00 0.00 3.51 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
30 31 7.812648 TCCTTTTAACAGGATCATTTACAACG 58.187 34.615 6.25 0.00 38.11 4.10
31 32 7.027161 CCTTTTAACAGGATCATTTACAACGG 58.973 38.462 1.00 0.00 35.71 4.44
32 33 7.094549 CCTTTTAACAGGATCATTTACAACGGA 60.095 37.037 1.00 0.00 35.71 4.69
33 34 6.978343 TTAACAGGATCATTTACAACGGAG 57.022 37.500 0.00 0.00 0.00 4.63
35 36 4.253685 ACAGGATCATTTACAACGGAGTG 58.746 43.478 0.00 0.00 45.00 3.51
36 37 4.253685 CAGGATCATTTACAACGGAGTGT 58.746 43.478 0.00 0.00 45.00 3.55
37 38 4.093408 CAGGATCATTTACAACGGAGTGTG 59.907 45.833 0.00 0.00 45.00 3.82
38 39 3.374058 GGATCATTTACAACGGAGTGTGG 59.626 47.826 0.00 0.00 45.00 4.17
39 40 2.773487 TCATTTACAACGGAGTGTGGG 58.227 47.619 0.00 0.00 45.00 4.61
40 41 1.199097 CATTTACAACGGAGTGTGGGC 59.801 52.381 0.00 0.00 45.00 5.36
41 42 0.180642 TTTACAACGGAGTGTGGGCA 59.819 50.000 0.00 0.00 45.00 5.36
42 43 0.180642 TTACAACGGAGTGTGGGCAA 59.819 50.000 0.00 0.00 45.00 4.52
43 44 0.180642 TACAACGGAGTGTGGGCAAA 59.819 50.000 0.00 0.00 45.00 3.68
44 45 0.467290 ACAACGGAGTGTGGGCAAAT 60.467 50.000 0.00 0.00 45.00 2.32
45 46 0.039256 CAACGGAGTGTGGGCAAATG 60.039 55.000 0.00 0.00 45.00 2.32
46 47 1.805428 AACGGAGTGTGGGCAAATGC 61.805 55.000 0.00 0.00 45.00 3.56
47 48 2.568090 GGAGTGTGGGCAAATGCG 59.432 61.111 0.00 0.00 43.26 4.73
48 49 2.568090 GAGTGTGGGCAAATGCGG 59.432 61.111 0.00 0.00 43.26 5.69
49 50 2.203480 AGTGTGGGCAAATGCGGT 60.203 55.556 0.00 0.00 43.26 5.68
50 51 1.805428 GAGTGTGGGCAAATGCGGTT 61.805 55.000 0.00 0.00 43.26 4.44
51 52 1.068921 GTGTGGGCAAATGCGGTTT 59.931 52.632 0.00 0.00 43.26 3.27
52 53 0.531753 GTGTGGGCAAATGCGGTTTT 60.532 50.000 0.00 0.00 43.26 2.43
53 54 0.249657 TGTGGGCAAATGCGGTTTTC 60.250 50.000 0.00 0.00 43.26 2.29
54 55 0.033366 GTGGGCAAATGCGGTTTTCT 59.967 50.000 0.00 0.00 43.26 2.52
55 56 0.755686 TGGGCAAATGCGGTTTTCTT 59.244 45.000 0.00 0.00 43.26 2.52
56 57 1.964223 TGGGCAAATGCGGTTTTCTTA 59.036 42.857 0.00 0.00 43.26 2.10
57 58 2.564947 TGGGCAAATGCGGTTTTCTTAT 59.435 40.909 0.00 0.00 43.26 1.73
58 59 3.007398 TGGGCAAATGCGGTTTTCTTATT 59.993 39.130 0.00 0.00 43.26 1.40
59 60 3.370672 GGGCAAATGCGGTTTTCTTATTG 59.629 43.478 0.00 0.00 43.26 1.90
60 61 3.181521 GGCAAATGCGGTTTTCTTATTGC 60.182 43.478 0.00 0.00 43.26 3.56
61 62 3.481789 GCAAATGCGGTTTTCTTATTGCG 60.482 43.478 0.00 0.00 33.54 4.85
62 63 2.559998 ATGCGGTTTTCTTATTGCGG 57.440 45.000 0.00 0.00 0.00 5.69
63 64 0.523966 TGCGGTTTTCTTATTGCGGG 59.476 50.000 0.00 0.00 0.00 6.13
64 65 0.806241 GCGGTTTTCTTATTGCGGGA 59.194 50.000 0.00 0.00 0.00 5.14
65 66 1.200484 GCGGTTTTCTTATTGCGGGAA 59.800 47.619 0.00 0.00 0.00 3.97
66 67 2.351932 GCGGTTTTCTTATTGCGGGAAA 60.352 45.455 0.00 0.00 0.00 3.13
67 68 3.857756 GCGGTTTTCTTATTGCGGGAAAA 60.858 43.478 0.00 0.00 36.85 2.29
68 69 4.490743 CGGTTTTCTTATTGCGGGAAAAT 58.509 39.130 0.00 0.00 39.84 1.82
69 70 5.642686 CGGTTTTCTTATTGCGGGAAAATA 58.357 37.500 0.00 0.00 39.84 1.40
70 71 6.094061 CGGTTTTCTTATTGCGGGAAAATAA 58.906 36.000 0.00 0.00 39.84 1.40
71 72 6.586844 CGGTTTTCTTATTGCGGGAAAATAAA 59.413 34.615 0.00 0.00 39.84 1.40
72 73 7.276878 CGGTTTTCTTATTGCGGGAAAATAAAT 59.723 33.333 0.00 0.00 39.84 1.40
73 74 8.387354 GGTTTTCTTATTGCGGGAAAATAAATG 58.613 33.333 0.00 0.00 39.84 2.32
74 75 8.387354 GTTTTCTTATTGCGGGAAAATAAATGG 58.613 33.333 0.00 0.00 39.84 3.16
75 76 7.411486 TTCTTATTGCGGGAAAATAAATGGA 57.589 32.000 0.00 0.00 31.02 3.41
76 77 7.411486 TCTTATTGCGGGAAAATAAATGGAA 57.589 32.000 0.00 0.00 31.02 3.53
77 78 7.488322 TCTTATTGCGGGAAAATAAATGGAAG 58.512 34.615 0.00 0.00 31.02 3.46
78 79 3.518634 TGCGGGAAAATAAATGGAAGC 57.481 42.857 0.00 0.00 0.00 3.86
79 80 2.159310 TGCGGGAAAATAAATGGAAGCG 60.159 45.455 0.00 0.00 0.00 4.68
80 81 2.159296 GCGGGAAAATAAATGGAAGCGT 60.159 45.455 0.00 0.00 0.00 5.07
81 82 3.065648 GCGGGAAAATAAATGGAAGCGTA 59.934 43.478 0.00 0.00 0.00 4.42
82 83 4.261447 GCGGGAAAATAAATGGAAGCGTAT 60.261 41.667 0.00 0.00 0.00 3.06
83 84 5.212194 CGGGAAAATAAATGGAAGCGTATG 58.788 41.667 0.00 0.00 0.00 2.39
84 85 4.982295 GGGAAAATAAATGGAAGCGTATGC 59.018 41.667 0.00 0.00 43.24 3.14
90 91 1.852942 ATGGAAGCGTATGCGTACAG 58.147 50.000 13.36 9.64 46.78 2.74
91 92 1.407618 ATGGAAGCGTATGCGTACAGA 59.592 47.619 13.36 0.00 46.78 3.41
92 93 2.035961 ATGGAAGCGTATGCGTACAGAT 59.964 45.455 13.36 5.07 46.78 2.90
93 94 3.254903 ATGGAAGCGTATGCGTACAGATA 59.745 43.478 13.36 0.00 46.78 1.98
94 95 4.261867 ATGGAAGCGTATGCGTACAGATAA 60.262 41.667 13.36 0.00 46.78 1.75
95 96 6.073747 ATGGAAGCGTATGCGTACAGATAAG 61.074 44.000 13.36 0.00 46.78 1.73
98 99 2.405357 GCGTATGCGTACAGATAAGCAG 59.595 50.000 16.12 0.00 46.79 4.24
99 100 3.852205 GCGTATGCGTACAGATAAGCAGA 60.852 47.826 16.12 0.00 46.79 4.26
100 101 4.287720 CGTATGCGTACAGATAAGCAGAA 58.712 43.478 16.12 0.00 46.79 3.02
101 102 4.738252 CGTATGCGTACAGATAAGCAGAAA 59.262 41.667 16.12 0.00 46.79 2.52
102 103 5.231357 CGTATGCGTACAGATAAGCAGAAAA 59.769 40.000 16.12 0.00 46.79 2.29
103 104 4.921470 TGCGTACAGATAAGCAGAAAAC 57.079 40.909 0.00 0.00 40.33 2.43
104 105 3.682858 TGCGTACAGATAAGCAGAAAACC 59.317 43.478 0.00 0.00 40.33 3.27
105 106 3.933332 GCGTACAGATAAGCAGAAAACCT 59.067 43.478 0.00 0.00 36.00 3.50
106 107 5.107133 GCGTACAGATAAGCAGAAAACCTA 58.893 41.667 0.00 0.00 36.00 3.08
107 108 5.232414 GCGTACAGATAAGCAGAAAACCTAG 59.768 44.000 0.00 0.00 36.00 3.02
108 109 5.232414 CGTACAGATAAGCAGAAAACCTAGC 59.768 44.000 0.00 0.00 0.00 3.42
109 110 5.165961 ACAGATAAGCAGAAAACCTAGCA 57.834 39.130 0.00 0.00 0.00 3.49
110 111 4.938226 ACAGATAAGCAGAAAACCTAGCAC 59.062 41.667 0.00 0.00 0.00 4.40
111 112 5.181748 CAGATAAGCAGAAAACCTAGCACT 58.818 41.667 0.00 0.00 0.00 4.40
112 113 5.645497 CAGATAAGCAGAAAACCTAGCACTT 59.355 40.000 0.00 0.00 0.00 3.16
113 114 5.645497 AGATAAGCAGAAAACCTAGCACTTG 59.355 40.000 0.00 0.00 0.00 3.16
114 115 3.214696 AGCAGAAAACCTAGCACTTGT 57.785 42.857 0.00 0.00 0.00 3.16
115 116 2.880890 AGCAGAAAACCTAGCACTTGTG 59.119 45.455 0.00 0.00 0.00 3.33
116 117 2.618709 GCAGAAAACCTAGCACTTGTGT 59.381 45.455 2.61 0.00 0.00 3.72
117 118 3.304057 GCAGAAAACCTAGCACTTGTGTC 60.304 47.826 2.61 0.00 0.00 3.67
118 119 3.876914 CAGAAAACCTAGCACTTGTGTCA 59.123 43.478 2.61 0.00 0.00 3.58
119 120 3.877508 AGAAAACCTAGCACTTGTGTCAC 59.122 43.478 0.00 0.00 0.00 3.67
120 121 3.275617 AAACCTAGCACTTGTGTCACA 57.724 42.857 0.18 0.18 0.00 3.58
121 122 2.240493 ACCTAGCACTTGTGTCACAC 57.760 50.000 4.80 0.00 34.56 3.82
122 123 1.484653 ACCTAGCACTTGTGTCACACA 59.515 47.619 6.50 6.50 43.02 3.72
135 136 5.815850 TGTGTCACACAACATATTTCACAC 58.184 37.500 8.60 0.00 41.69 3.82
136 137 5.355350 TGTGTCACACAACATATTTCACACA 59.645 36.000 8.60 0.00 41.69 3.72
137 138 5.909054 GTGTCACACAACATATTTCACACAG 59.091 40.000 2.00 0.00 34.08 3.66
138 139 5.819901 TGTCACACAACATATTTCACACAGA 59.180 36.000 0.00 0.00 0.00 3.41
139 140 6.486320 TGTCACACAACATATTTCACACAGAT 59.514 34.615 0.00 0.00 0.00 2.90
140 141 7.013178 TGTCACACAACATATTTCACACAGATT 59.987 33.333 0.00 0.00 0.00 2.40
141 142 7.324375 GTCACACAACATATTTCACACAGATTG 59.676 37.037 0.00 0.00 0.00 2.67
142 143 7.013178 TCACACAACATATTTCACACAGATTGT 59.987 33.333 0.00 0.00 39.97 2.71
143 144 7.648908 CACACAACATATTTCACACAGATTGTT 59.351 33.333 0.00 0.00 35.67 2.83
144 145 8.196771 ACACAACATATTTCACACAGATTGTTT 58.803 29.630 0.00 0.00 35.67 2.83
145 146 9.033481 CACAACATATTTCACACAGATTGTTTT 57.967 29.630 0.00 0.00 35.67 2.43
146 147 9.248291 ACAACATATTTCACACAGATTGTTTTC 57.752 29.630 0.00 0.00 35.67 2.29
147 148 9.247126 CAACATATTTCACACAGATTGTTTTCA 57.753 29.630 0.00 0.00 35.67 2.69
148 149 9.985730 AACATATTTCACACAGATTGTTTTCAT 57.014 25.926 0.00 0.00 35.67 2.57
149 150 9.414295 ACATATTTCACACAGATTGTTTTCATG 57.586 29.630 0.00 0.00 35.67 3.07
150 151 9.628746 CATATTTCACACAGATTGTTTTCATGA 57.371 29.630 0.00 0.00 35.67 3.07
153 154 8.945481 TTTCACACAGATTGTTTTCATGAATT 57.055 26.923 9.40 0.00 35.67 2.17
154 155 8.945481 TTCACACAGATTGTTTTCATGAATTT 57.055 26.923 9.40 0.00 35.67 1.82
178 179 9.816787 TTTAAATCCCTTACAAACATACTTCCT 57.183 29.630 0.00 0.00 0.00 3.36
179 180 7.939784 AAATCCCTTACAAACATACTTCCTC 57.060 36.000 0.00 0.00 0.00 3.71
180 181 5.431179 TCCCTTACAAACATACTTCCTCC 57.569 43.478 0.00 0.00 0.00 4.30
181 182 4.081309 TCCCTTACAAACATACTTCCTCCG 60.081 45.833 0.00 0.00 0.00 4.63
182 183 4.323257 CCCTTACAAACATACTTCCTCCGT 60.323 45.833 0.00 0.00 0.00 4.69
183 184 5.243207 CCTTACAAACATACTTCCTCCGTT 58.757 41.667 0.00 0.00 0.00 4.44
184 185 5.704053 CCTTACAAACATACTTCCTCCGTTT 59.296 40.000 0.00 0.00 0.00 3.60
186 187 3.818773 ACAAACATACTTCCTCCGTTTGG 59.181 43.478 15.35 0.00 46.68 3.28
187 188 4.069304 CAAACATACTTCCTCCGTTTGGA 58.931 43.478 0.00 0.00 41.58 3.53
188 189 4.360951 AACATACTTCCTCCGTTTGGAA 57.639 40.909 0.00 0.00 45.87 3.53
189 190 4.569719 ACATACTTCCTCCGTTTGGAAT 57.430 40.909 0.00 0.00 45.87 3.01
190 191 4.918588 ACATACTTCCTCCGTTTGGAATT 58.081 39.130 0.00 0.00 45.87 2.17
191 192 6.057321 ACATACTTCCTCCGTTTGGAATTA 57.943 37.500 0.00 0.00 45.87 1.40
192 193 5.878669 ACATACTTCCTCCGTTTGGAATTAC 59.121 40.000 0.00 0.00 45.87 1.89
193 194 4.635699 ACTTCCTCCGTTTGGAATTACT 57.364 40.909 0.00 0.00 45.87 2.24
194 195 4.981812 ACTTCCTCCGTTTGGAATTACTT 58.018 39.130 0.00 0.00 45.87 2.24
195 196 4.760204 ACTTCCTCCGTTTGGAATTACTTG 59.240 41.667 0.00 0.00 45.87 3.16
196 197 4.360951 TCCTCCGTTTGGAATTACTTGT 57.639 40.909 0.00 0.00 45.87 3.16
197 198 4.320870 TCCTCCGTTTGGAATTACTTGTC 58.679 43.478 0.00 0.00 45.87 3.18
198 199 4.069304 CCTCCGTTTGGAATTACTTGTCA 58.931 43.478 0.00 0.00 45.87 3.58
199 200 4.083484 CCTCCGTTTGGAATTACTTGTCAC 60.083 45.833 0.00 0.00 45.87 3.67
200 201 4.452825 TCCGTTTGGAATTACTTGTCACA 58.547 39.130 0.00 0.00 42.85 3.58
201 202 4.513692 TCCGTTTGGAATTACTTGTCACAG 59.486 41.667 0.00 0.00 42.85 3.66
202 203 4.513692 CCGTTTGGAATTACTTGTCACAGA 59.486 41.667 0.00 0.00 37.49 3.41
203 204 5.008217 CCGTTTGGAATTACTTGTCACAGAA 59.992 40.000 0.00 0.00 37.49 3.02
204 205 6.459024 CCGTTTGGAATTACTTGTCACAGAAA 60.459 38.462 0.00 0.00 37.49 2.52
205 206 7.138736 CGTTTGGAATTACTTGTCACAGAAAT 58.861 34.615 0.00 0.00 0.00 2.17
206 207 7.113404 CGTTTGGAATTACTTGTCACAGAAATG 59.887 37.037 0.00 0.00 0.00 2.32
207 208 6.573664 TGGAATTACTTGTCACAGAAATGG 57.426 37.500 0.00 0.00 0.00 3.16
208 209 6.303054 TGGAATTACTTGTCACAGAAATGGA 58.697 36.000 0.00 0.00 0.00 3.41
209 210 6.947733 TGGAATTACTTGTCACAGAAATGGAT 59.052 34.615 0.00 0.00 0.00 3.41
210 211 7.094248 TGGAATTACTTGTCACAGAAATGGATG 60.094 37.037 0.00 0.00 0.00 3.51
211 212 7.094205 GGAATTACTTGTCACAGAAATGGATGT 60.094 37.037 0.00 0.00 0.00 3.06
212 213 8.862325 AATTACTTGTCACAGAAATGGATGTA 57.138 30.769 0.00 0.00 0.00 2.29
213 214 9.466497 AATTACTTGTCACAGAAATGGATGTAT 57.534 29.630 0.00 0.00 0.00 2.29
214 215 6.992063 ACTTGTCACAGAAATGGATGTATC 57.008 37.500 0.00 0.00 0.00 2.24
215 216 6.715280 ACTTGTCACAGAAATGGATGTATCT 58.285 36.000 0.00 0.00 0.00 1.98
216 217 7.851228 ACTTGTCACAGAAATGGATGTATCTA 58.149 34.615 0.00 0.00 0.00 1.98
217 218 7.984050 ACTTGTCACAGAAATGGATGTATCTAG 59.016 37.037 0.00 0.00 0.00 2.43
218 219 7.660030 TGTCACAGAAATGGATGTATCTAGA 57.340 36.000 0.00 0.00 0.00 2.43
219 220 7.492524 TGTCACAGAAATGGATGTATCTAGAC 58.507 38.462 0.00 0.00 31.82 2.59
220 221 6.638873 GTCACAGAAATGGATGTATCTAGACG 59.361 42.308 0.00 0.00 0.00 4.18
221 222 6.321435 TCACAGAAATGGATGTATCTAGACGT 59.679 38.462 0.00 0.00 0.00 4.34
222 223 7.501225 TCACAGAAATGGATGTATCTAGACGTA 59.499 37.037 0.00 0.00 0.00 3.57
223 224 8.300286 CACAGAAATGGATGTATCTAGACGTAT 58.700 37.037 0.00 0.00 0.00 3.06
224 225 8.861086 ACAGAAATGGATGTATCTAGACGTATT 58.139 33.333 0.00 0.00 0.00 1.89
225 226 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
230 231 8.701908 TGGATGTATCTAGACGTATTTTAGGT 57.298 34.615 0.00 0.00 0.00 3.08
231 232 8.790718 TGGATGTATCTAGACGTATTTTAGGTC 58.209 37.037 0.00 0.33 42.28 3.85
243 244 8.701908 ACGTATTTTAGGTCTAGATACATCCA 57.298 34.615 0.00 0.00 0.00 3.41
244 245 9.310449 ACGTATTTTAGGTCTAGATACATCCAT 57.690 33.333 0.00 0.00 0.00 3.41
250 251 9.832445 TTTAGGTCTAGATACATCCATTTTCAC 57.168 33.333 0.00 0.00 0.00 3.18
251 252 6.516718 AGGTCTAGATACATCCATTTTCACG 58.483 40.000 0.00 0.00 0.00 4.35
252 253 6.323996 AGGTCTAGATACATCCATTTTCACGA 59.676 38.462 0.00 0.00 0.00 4.35
253 254 6.421202 GGTCTAGATACATCCATTTTCACGAC 59.579 42.308 0.00 0.00 0.00 4.34
254 255 6.978659 GTCTAGATACATCCATTTTCACGACA 59.021 38.462 0.00 0.00 0.00 4.35
255 256 7.491372 GTCTAGATACATCCATTTTCACGACAA 59.509 37.037 0.00 0.00 0.00 3.18
256 257 6.668541 AGATACATCCATTTTCACGACAAG 57.331 37.500 0.00 0.00 0.00 3.16
257 258 6.173339 AGATACATCCATTTTCACGACAAGT 58.827 36.000 0.00 0.00 0.00 3.16
258 259 7.327975 AGATACATCCATTTTCACGACAAGTA 58.672 34.615 0.00 0.00 0.00 2.24
259 260 7.822334 AGATACATCCATTTTCACGACAAGTAA 59.178 33.333 0.00 0.00 0.00 2.24
260 261 6.817765 ACATCCATTTTCACGACAAGTAAT 57.182 33.333 0.00 0.00 0.00 1.89
261 262 7.214467 ACATCCATTTTCACGACAAGTAATT 57.786 32.000 0.00 0.00 0.00 1.40
262 263 7.305474 ACATCCATTTTCACGACAAGTAATTC 58.695 34.615 0.00 0.00 0.00 2.17
263 264 6.249035 TCCATTTTCACGACAAGTAATTCC 57.751 37.500 0.00 0.00 0.00 3.01
264 265 5.086058 CCATTTTCACGACAAGTAATTCCG 58.914 41.667 0.00 0.00 0.00 4.30
265 266 5.106869 CCATTTTCACGACAAGTAATTCCGA 60.107 40.000 0.00 0.00 0.00 4.55
266 267 5.987777 TTTTCACGACAAGTAATTCCGAA 57.012 34.783 0.00 0.00 0.00 4.30
267 268 6.548441 TTTTCACGACAAGTAATTCCGAAT 57.452 33.333 0.00 0.00 0.00 3.34
268 269 7.655236 TTTTCACGACAAGTAATTCCGAATA 57.345 32.000 0.00 0.00 0.00 1.75
269 270 7.837202 TTTCACGACAAGTAATTCCGAATAT 57.163 32.000 0.00 0.00 0.00 1.28
270 271 7.837202 TTCACGACAAGTAATTCCGAATATT 57.163 32.000 0.00 0.00 0.00 1.28
271 272 7.837202 TCACGACAAGTAATTCCGAATATTT 57.163 32.000 0.00 0.00 0.00 1.40
272 273 8.259049 TCACGACAAGTAATTCCGAATATTTT 57.741 30.769 0.00 0.00 0.00 1.82
273 274 8.385111 TCACGACAAGTAATTCCGAATATTTTC 58.615 33.333 0.00 0.00 0.00 2.29
274 275 7.638683 CACGACAAGTAATTCCGAATATTTTCC 59.361 37.037 0.00 0.00 0.00 3.13
275 276 7.334921 ACGACAAGTAATTCCGAATATTTTCCA 59.665 33.333 0.00 0.00 0.00 3.53
276 277 8.342634 CGACAAGTAATTCCGAATATTTTCCAT 58.657 33.333 0.00 0.00 0.00 3.41
283 284 8.871686 AATTCCGAATATTTTCCATAAACTGC 57.128 30.769 0.00 0.00 0.00 4.40
284 285 6.055231 TCCGAATATTTTCCATAAACTGCG 57.945 37.500 0.00 0.00 0.00 5.18
285 286 5.587043 TCCGAATATTTTCCATAAACTGCGT 59.413 36.000 0.00 0.00 0.00 5.24
286 287 6.762187 TCCGAATATTTTCCATAAACTGCGTA 59.238 34.615 0.00 0.00 0.00 4.42
287 288 6.849305 CCGAATATTTTCCATAAACTGCGTAC 59.151 38.462 0.00 0.00 0.00 3.67
288 289 6.568601 CGAATATTTTCCATAAACTGCGTACG 59.431 38.462 11.84 11.84 0.00 3.67
289 290 7.515528 CGAATATTTTCCATAAACTGCGTACGA 60.516 37.037 21.65 3.19 0.00 3.43
290 291 4.914312 TTTTCCATAAACTGCGTACGAG 57.086 40.909 21.65 15.48 0.00 4.18
291 292 3.853831 TTCCATAAACTGCGTACGAGA 57.146 42.857 21.65 3.04 0.00 4.04
292 293 4.380841 TTCCATAAACTGCGTACGAGAT 57.619 40.909 21.65 5.59 0.00 2.75
293 294 3.702330 TCCATAAACTGCGTACGAGATG 58.298 45.455 21.65 12.14 0.00 2.90
294 295 3.379057 TCCATAAACTGCGTACGAGATGA 59.621 43.478 21.65 2.11 0.00 2.92
295 296 4.037565 TCCATAAACTGCGTACGAGATGAT 59.962 41.667 21.65 4.42 0.00 2.45
296 297 5.239963 TCCATAAACTGCGTACGAGATGATA 59.760 40.000 21.65 4.57 0.00 2.15
297 298 5.918576 CCATAAACTGCGTACGAGATGATAA 59.081 40.000 21.65 0.00 0.00 1.75
298 299 6.088217 CCATAAACTGCGTACGAGATGATAAG 59.912 42.308 21.65 4.96 0.00 1.73
299 300 4.895224 AACTGCGTACGAGATGATAAGA 57.105 40.909 21.65 0.00 0.00 2.10
300 301 5.440234 AACTGCGTACGAGATGATAAGAT 57.560 39.130 21.65 0.00 0.00 2.40
301 302 4.788690 ACTGCGTACGAGATGATAAGATG 58.211 43.478 21.65 0.00 0.00 2.90
302 303 4.160736 TGCGTACGAGATGATAAGATGG 57.839 45.455 21.65 0.00 0.00 3.51
303 304 3.818773 TGCGTACGAGATGATAAGATGGA 59.181 43.478 21.65 0.00 0.00 3.41
304 305 4.159857 GCGTACGAGATGATAAGATGGAC 58.840 47.826 21.65 0.00 0.00 4.02
305 306 4.395656 CGTACGAGATGATAAGATGGACG 58.604 47.826 10.44 0.00 0.00 4.79
306 307 3.290308 ACGAGATGATAAGATGGACGC 57.710 47.619 0.00 0.00 0.00 5.19
307 308 2.623416 ACGAGATGATAAGATGGACGCA 59.377 45.455 0.00 0.00 0.00 5.24
308 309 3.068165 ACGAGATGATAAGATGGACGCAA 59.932 43.478 0.00 0.00 0.00 4.85
309 310 4.240888 CGAGATGATAAGATGGACGCAAT 58.759 43.478 0.00 0.00 0.00 3.56
404 405 1.965754 GCAGCCGATCCTCTCAACCT 61.966 60.000 0.00 0.00 0.00 3.50
415 416 0.178921 TCTCAACCTCAGCCTCACCT 60.179 55.000 0.00 0.00 0.00 4.00
572 573 3.195698 GGATGGGTCGAAGTGCGC 61.196 66.667 0.00 0.00 40.61 6.09
576 577 0.960364 ATGGGTCGAAGTGCGCAATT 60.960 50.000 24.61 24.61 40.61 2.32
729 731 2.899900 TCCTATGATATTCGCTGCCACT 59.100 45.455 0.00 0.00 0.00 4.00
926 943 2.989253 TCGTGAGCGCTTCCCTGA 60.989 61.111 13.26 2.74 38.14 3.86
939 956 1.182667 TCCCTGATGAGGTGTACACG 58.817 55.000 19.41 4.02 37.73 4.49
1025 1042 2.186903 GCTCGAGGCGGATTTCCA 59.813 61.111 15.58 0.00 35.14 3.53
1056 1073 2.752358 CTGGCCTCAGTGCAAGGA 59.248 61.111 7.13 0.00 35.83 3.36
1057 1074 1.302285 CTGGCCTCAGTGCAAGGAT 59.698 57.895 7.13 0.00 35.83 3.24
1298 1317 2.416162 CCAGTGGTAAGCTCGAGTTCTC 60.416 54.545 15.13 4.80 0.00 2.87
1351 1370 3.063084 GCTCGGAGTGGGAGACGT 61.063 66.667 6.90 0.00 33.27 4.34
1433 1452 2.233271 CTGGCAGGTTGATGTCACTTT 58.767 47.619 6.61 0.00 30.14 2.66
1712 1732 2.224378 CCAGAAGCTGTTTCAGAGGACA 60.224 50.000 7.01 0.00 38.31 4.02
1956 1976 4.735132 TCTTCGGCGGCTTCCACG 62.735 66.667 7.21 0.00 0.00 4.94
2158 2178 1.561643 AGACAATCAGGCTTCGGAGA 58.438 50.000 0.00 0.00 20.59 3.71
2192 2212 4.340246 CCTGGGTGCTGCTCTGCA 62.340 66.667 0.00 0.00 41.05 4.41
2220 2240 2.045926 ATGCCGGACTTGCAGGAC 60.046 61.111 5.05 0.00 42.92 3.85
2252 2272 2.159819 GAGCAGGAGAGCACGGTGAA 62.160 60.000 13.29 0.00 36.85 3.18
2541 2761 0.733909 GGGCGCAAAATGTTCTGCTC 60.734 55.000 10.83 0.00 36.38 4.26
2686 2906 0.468226 AGACGACCAAGCCTTTGACA 59.532 50.000 0.00 0.00 36.36 3.58
2738 2958 0.036732 TTGCCGGAGAATGTTGAGCT 59.963 50.000 5.05 0.00 0.00 4.09
2779 2999 1.847798 TAATCGCTGGGGGTGTGCTT 61.848 55.000 0.00 0.00 0.00 3.91
2911 3132 4.478206 TGGTCTGCTTCCAAGAATCTAG 57.522 45.455 0.00 0.00 31.50 2.43
2924 3145 6.554982 TCCAAGAATCTAGGCTTAATGCTCTA 59.445 38.462 0.00 0.00 42.39 2.43
2943 3164 6.774170 TGCTCTAGATACTTCGGTGGTTAATA 59.226 38.462 0.00 0.00 0.00 0.98
2960 3181 5.497474 GTTAATAAGACTCTTGGCCCAGAA 58.503 41.667 8.09 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.446013 ACTCCGTTGTAAATGATCCTGTTAAAA 59.554 33.333 0.00 0.00 33.73 1.52
9 10 6.938030 ACTCCGTTGTAAATGATCCTGTTAAA 59.062 34.615 0.00 0.00 33.73 1.52
10 11 6.370442 CACTCCGTTGTAAATGATCCTGTTAA 59.630 38.462 0.00 0.00 33.73 2.01
11 12 5.872617 CACTCCGTTGTAAATGATCCTGTTA 59.127 40.000 0.00 0.00 33.73 2.41
12 13 4.695455 CACTCCGTTGTAAATGATCCTGTT 59.305 41.667 0.00 0.00 33.73 3.16
13 14 4.253685 CACTCCGTTGTAAATGATCCTGT 58.746 43.478 0.00 0.00 33.73 4.00
14 15 4.093408 CACACTCCGTTGTAAATGATCCTG 59.907 45.833 0.00 0.00 33.73 3.86
15 16 4.253685 CACACTCCGTTGTAAATGATCCT 58.746 43.478 0.00 0.00 33.73 3.24
16 17 3.374058 CCACACTCCGTTGTAAATGATCC 59.626 47.826 0.00 0.00 33.73 3.36
17 18 3.374058 CCCACACTCCGTTGTAAATGATC 59.626 47.826 0.00 0.00 33.73 2.92
18 19 3.343617 CCCACACTCCGTTGTAAATGAT 58.656 45.455 0.00 0.00 33.73 2.45
19 20 2.773487 CCCACACTCCGTTGTAAATGA 58.227 47.619 0.00 0.00 33.73 2.57
20 21 1.199097 GCCCACACTCCGTTGTAAATG 59.801 52.381 0.00 0.00 0.00 2.32
21 22 1.202830 TGCCCACACTCCGTTGTAAAT 60.203 47.619 0.00 0.00 0.00 1.40
22 23 0.180642 TGCCCACACTCCGTTGTAAA 59.819 50.000 0.00 0.00 0.00 2.01
23 24 0.180642 TTGCCCACACTCCGTTGTAA 59.819 50.000 0.00 0.00 0.00 2.41
24 25 0.180642 TTTGCCCACACTCCGTTGTA 59.819 50.000 0.00 0.00 0.00 2.41
25 26 0.467290 ATTTGCCCACACTCCGTTGT 60.467 50.000 0.00 0.00 0.00 3.32
26 27 0.039256 CATTTGCCCACACTCCGTTG 60.039 55.000 0.00 0.00 0.00 4.10
27 28 1.805428 GCATTTGCCCACACTCCGTT 61.805 55.000 0.00 0.00 34.31 4.44
28 29 2.268076 GCATTTGCCCACACTCCGT 61.268 57.895 0.00 0.00 34.31 4.69
29 30 2.568090 GCATTTGCCCACACTCCG 59.432 61.111 0.00 0.00 34.31 4.63
30 31 2.568090 CGCATTTGCCCACACTCC 59.432 61.111 0.00 0.00 37.91 3.85
31 32 1.805428 AACCGCATTTGCCCACACTC 61.805 55.000 0.00 0.00 37.91 3.51
32 33 1.398958 AAACCGCATTTGCCCACACT 61.399 50.000 0.00 0.00 37.91 3.55
33 34 0.531753 AAAACCGCATTTGCCCACAC 60.532 50.000 0.00 0.00 37.91 3.82
34 35 0.249657 GAAAACCGCATTTGCCCACA 60.250 50.000 0.00 0.00 37.91 4.17
35 36 0.033366 AGAAAACCGCATTTGCCCAC 59.967 50.000 0.00 0.00 37.91 4.61
36 37 0.755686 AAGAAAACCGCATTTGCCCA 59.244 45.000 0.00 0.00 37.91 5.36
37 38 2.734276 TAAGAAAACCGCATTTGCCC 57.266 45.000 0.00 0.00 37.91 5.36
38 39 3.181521 GCAATAAGAAAACCGCATTTGCC 60.182 43.478 0.00 0.00 37.91 4.52
39 40 3.481789 CGCAATAAGAAAACCGCATTTGC 60.482 43.478 0.00 0.00 35.94 3.68
40 41 3.060628 CCGCAATAAGAAAACCGCATTTG 59.939 43.478 0.00 0.00 0.00 2.32
41 42 3.249917 CCGCAATAAGAAAACCGCATTT 58.750 40.909 0.00 0.00 0.00 2.32
42 43 2.416701 CCCGCAATAAGAAAACCGCATT 60.417 45.455 0.00 0.00 0.00 3.56
43 44 1.134175 CCCGCAATAAGAAAACCGCAT 59.866 47.619 0.00 0.00 0.00 4.73
44 45 0.523966 CCCGCAATAAGAAAACCGCA 59.476 50.000 0.00 0.00 0.00 5.69
45 46 0.806241 TCCCGCAATAAGAAAACCGC 59.194 50.000 0.00 0.00 0.00 5.68
46 47 3.562567 TTTCCCGCAATAAGAAAACCG 57.437 42.857 0.00 0.00 0.00 4.44
47 48 7.892778 TTTATTTTCCCGCAATAAGAAAACC 57.107 32.000 0.00 0.00 41.01 3.27
48 49 8.387354 CCATTTATTTTCCCGCAATAAGAAAAC 58.613 33.333 0.00 0.00 41.01 2.43
49 50 8.314751 TCCATTTATTTTCCCGCAATAAGAAAA 58.685 29.630 0.00 0.00 42.04 2.29
50 51 7.841956 TCCATTTATTTTCCCGCAATAAGAAA 58.158 30.769 0.00 0.00 29.79 2.52
51 52 7.411486 TCCATTTATTTTCCCGCAATAAGAA 57.589 32.000 0.00 0.00 29.79 2.52
52 53 7.411486 TTCCATTTATTTTCCCGCAATAAGA 57.589 32.000 0.00 0.00 29.79 2.10
53 54 6.200854 GCTTCCATTTATTTTCCCGCAATAAG 59.799 38.462 0.00 0.00 29.79 1.73
54 55 6.045955 GCTTCCATTTATTTTCCCGCAATAA 58.954 36.000 0.00 0.00 0.00 1.40
55 56 5.596845 GCTTCCATTTATTTTCCCGCAATA 58.403 37.500 0.00 0.00 0.00 1.90
56 57 4.441792 GCTTCCATTTATTTTCCCGCAAT 58.558 39.130 0.00 0.00 0.00 3.56
57 58 3.674682 CGCTTCCATTTATTTTCCCGCAA 60.675 43.478 0.00 0.00 0.00 4.85
58 59 2.159310 CGCTTCCATTTATTTTCCCGCA 60.159 45.455 0.00 0.00 0.00 5.69
59 60 2.159296 ACGCTTCCATTTATTTTCCCGC 60.159 45.455 0.00 0.00 0.00 6.13
60 61 3.775661 ACGCTTCCATTTATTTTCCCG 57.224 42.857 0.00 0.00 0.00 5.14
61 62 4.982295 GCATACGCTTCCATTTATTTTCCC 59.018 41.667 0.00 0.00 34.30 3.97
62 63 4.675114 CGCATACGCTTCCATTTATTTTCC 59.325 41.667 0.00 0.00 35.30 3.13
63 64 5.270853 ACGCATACGCTTCCATTTATTTTC 58.729 37.500 0.00 0.00 45.53 2.29
64 65 5.243426 ACGCATACGCTTCCATTTATTTT 57.757 34.783 0.00 0.00 45.53 1.82
65 66 4.893424 ACGCATACGCTTCCATTTATTT 57.107 36.364 0.00 0.00 45.53 1.40
66 67 4.812091 TGTACGCATACGCTTCCATTTATT 59.188 37.500 0.00 0.00 45.53 1.40
67 68 4.373527 TGTACGCATACGCTTCCATTTAT 58.626 39.130 0.00 0.00 45.53 1.40
68 69 3.783191 TGTACGCATACGCTTCCATTTA 58.217 40.909 0.00 0.00 45.53 1.40
69 70 2.607635 CTGTACGCATACGCTTCCATTT 59.392 45.455 0.00 0.00 45.53 2.32
70 71 2.159156 TCTGTACGCATACGCTTCCATT 60.159 45.455 0.00 0.00 45.53 3.16
71 72 1.407618 TCTGTACGCATACGCTTCCAT 59.592 47.619 0.00 0.00 45.53 3.41
72 73 0.812549 TCTGTACGCATACGCTTCCA 59.187 50.000 0.00 0.00 45.53 3.53
73 74 2.135664 ATCTGTACGCATACGCTTCC 57.864 50.000 0.00 0.00 45.53 3.46
74 75 3.119792 GCTTATCTGTACGCATACGCTTC 59.880 47.826 5.55 0.00 45.53 3.86
75 76 3.050619 GCTTATCTGTACGCATACGCTT 58.949 45.455 5.55 0.00 45.53 4.68
76 77 2.034179 TGCTTATCTGTACGCATACGCT 59.966 45.455 11.37 0.00 45.53 5.07
77 78 2.390938 TGCTTATCTGTACGCATACGC 58.609 47.619 5.75 5.75 45.53 4.42
79 80 6.411652 GTTTTCTGCTTATCTGTACGCATAC 58.588 40.000 0.00 0.00 34.96 2.39
80 81 5.522460 GGTTTTCTGCTTATCTGTACGCATA 59.478 40.000 0.00 0.00 34.96 3.14
81 82 4.332819 GGTTTTCTGCTTATCTGTACGCAT 59.667 41.667 0.00 0.00 34.96 4.73
82 83 3.682858 GGTTTTCTGCTTATCTGTACGCA 59.317 43.478 0.00 0.00 34.39 5.24
83 84 3.933332 AGGTTTTCTGCTTATCTGTACGC 59.067 43.478 0.00 0.00 0.00 4.42
84 85 5.232414 GCTAGGTTTTCTGCTTATCTGTACG 59.768 44.000 0.00 0.00 0.00 3.67
85 86 6.036191 GTGCTAGGTTTTCTGCTTATCTGTAC 59.964 42.308 0.00 0.00 0.00 2.90
86 87 6.070767 AGTGCTAGGTTTTCTGCTTATCTGTA 60.071 38.462 0.00 0.00 0.00 2.74
87 88 4.938226 GTGCTAGGTTTTCTGCTTATCTGT 59.062 41.667 0.00 0.00 0.00 3.41
88 89 5.181748 AGTGCTAGGTTTTCTGCTTATCTG 58.818 41.667 0.00 0.00 0.00 2.90
89 90 5.428184 AGTGCTAGGTTTTCTGCTTATCT 57.572 39.130 0.00 0.00 0.00 1.98
90 91 5.412904 ACAAGTGCTAGGTTTTCTGCTTATC 59.587 40.000 0.00 0.00 0.00 1.75
91 92 5.182001 CACAAGTGCTAGGTTTTCTGCTTAT 59.818 40.000 0.00 0.00 0.00 1.73
92 93 4.515191 CACAAGTGCTAGGTTTTCTGCTTA 59.485 41.667 0.00 0.00 0.00 3.09
93 94 3.316308 CACAAGTGCTAGGTTTTCTGCTT 59.684 43.478 0.00 0.00 0.00 3.91
94 95 2.880890 CACAAGTGCTAGGTTTTCTGCT 59.119 45.455 0.00 0.00 0.00 4.24
95 96 2.618709 ACACAAGTGCTAGGTTTTCTGC 59.381 45.455 0.00 0.00 0.00 4.26
96 97 3.876914 TGACACAAGTGCTAGGTTTTCTG 59.123 43.478 0.00 0.00 0.00 3.02
97 98 3.877508 GTGACACAAGTGCTAGGTTTTCT 59.122 43.478 0.00 0.00 0.00 2.52
98 99 3.625764 TGTGACACAAGTGCTAGGTTTTC 59.374 43.478 5.62 0.00 0.00 2.29
99 100 3.377172 GTGTGACACAAGTGCTAGGTTTT 59.623 43.478 10.50 0.00 34.08 2.43
100 101 2.943033 GTGTGACACAAGTGCTAGGTTT 59.057 45.455 10.50 0.00 34.08 3.27
101 102 2.093181 TGTGTGACACAAGTGCTAGGTT 60.093 45.455 17.13 0.00 41.69 3.50
102 103 1.484653 TGTGTGACACAAGTGCTAGGT 59.515 47.619 17.13 0.00 41.69 3.08
103 104 2.238942 TGTGTGACACAAGTGCTAGG 57.761 50.000 17.13 0.00 41.69 3.02
112 113 5.355350 TGTGTGAAATATGTTGTGTGACACA 59.645 36.000 15.39 15.39 43.02 3.72
113 114 5.815850 TGTGTGAAATATGTTGTGTGACAC 58.184 37.500 9.14 9.14 31.30 3.67
114 115 5.819901 TCTGTGTGAAATATGTTGTGTGACA 59.180 36.000 0.00 0.00 0.00 3.58
115 116 6.299023 TCTGTGTGAAATATGTTGTGTGAC 57.701 37.500 0.00 0.00 0.00 3.67
116 117 7.013178 ACAATCTGTGTGAAATATGTTGTGTGA 59.987 33.333 0.00 0.00 39.72 3.58
117 118 7.140705 ACAATCTGTGTGAAATATGTTGTGTG 58.859 34.615 0.00 0.00 39.72 3.82
118 119 7.275888 ACAATCTGTGTGAAATATGTTGTGT 57.724 32.000 0.00 0.00 39.72 3.72
119 120 8.578308 AAACAATCTGTGTGAAATATGTTGTG 57.422 30.769 0.00 0.00 40.60 3.33
120 121 9.248291 GAAAACAATCTGTGTGAAATATGTTGT 57.752 29.630 0.00 0.00 40.60 3.32
121 122 9.247126 TGAAAACAATCTGTGTGAAATATGTTG 57.753 29.630 0.00 0.00 40.60 3.33
122 123 9.985730 ATGAAAACAATCTGTGTGAAATATGTT 57.014 25.926 0.00 0.00 40.60 2.71
123 124 9.414295 CATGAAAACAATCTGTGTGAAATATGT 57.586 29.630 0.00 0.00 40.60 2.29
124 125 9.628746 TCATGAAAACAATCTGTGTGAAATATG 57.371 29.630 0.00 0.00 40.60 1.78
127 128 9.550406 AATTCATGAAAACAATCTGTGTGAAAT 57.450 25.926 13.09 0.00 40.60 2.17
128 129 8.945481 AATTCATGAAAACAATCTGTGTGAAA 57.055 26.923 13.09 0.00 40.60 2.69
129 130 8.945481 AAATTCATGAAAACAATCTGTGTGAA 57.055 26.923 13.09 0.00 40.60 3.18
152 153 9.816787 AGGAAGTATGTTTGTAAGGGATTTAAA 57.183 29.630 0.00 0.00 0.00 1.52
153 154 9.457436 GAGGAAGTATGTTTGTAAGGGATTTAA 57.543 33.333 0.00 0.00 0.00 1.52
154 155 8.050930 GGAGGAAGTATGTTTGTAAGGGATTTA 58.949 37.037 0.00 0.00 0.00 1.40
155 156 6.890268 GGAGGAAGTATGTTTGTAAGGGATTT 59.110 38.462 0.00 0.00 0.00 2.17
156 157 6.424032 GGAGGAAGTATGTTTGTAAGGGATT 58.576 40.000 0.00 0.00 0.00 3.01
157 158 5.396436 CGGAGGAAGTATGTTTGTAAGGGAT 60.396 44.000 0.00 0.00 0.00 3.85
158 159 4.081309 CGGAGGAAGTATGTTTGTAAGGGA 60.081 45.833 0.00 0.00 0.00 4.20
159 160 4.189231 CGGAGGAAGTATGTTTGTAAGGG 58.811 47.826 0.00 0.00 0.00 3.95
160 161 4.828829 ACGGAGGAAGTATGTTTGTAAGG 58.171 43.478 0.00 0.00 0.00 2.69
161 162 6.348213 CCAAACGGAGGAAGTATGTTTGTAAG 60.348 42.308 13.17 0.00 44.75 2.34
162 163 5.470777 CCAAACGGAGGAAGTATGTTTGTAA 59.529 40.000 13.17 0.00 44.75 2.41
163 164 4.998672 CCAAACGGAGGAAGTATGTTTGTA 59.001 41.667 13.17 0.00 44.75 2.41
164 165 3.818773 CCAAACGGAGGAAGTATGTTTGT 59.181 43.478 13.17 0.00 44.75 2.83
165 166 4.069304 TCCAAACGGAGGAAGTATGTTTG 58.931 43.478 8.68 8.68 45.42 2.93
166 167 4.360951 TCCAAACGGAGGAAGTATGTTT 57.639 40.909 0.00 0.00 33.34 2.83
167 168 4.360951 TTCCAAACGGAGGAAGTATGTT 57.639 40.909 1.90 0.00 40.11 2.71
175 176 4.202377 TGACAAGTAATTCCAAACGGAGGA 60.202 41.667 0.00 0.00 32.88 3.71
176 177 4.069304 TGACAAGTAATTCCAAACGGAGG 58.931 43.478 0.00 0.00 32.88 4.30
177 178 4.513692 TGTGACAAGTAATTCCAAACGGAG 59.486 41.667 0.00 0.00 32.88 4.63
178 179 4.452825 TGTGACAAGTAATTCCAAACGGA 58.547 39.130 0.00 0.00 0.00 4.69
179 180 4.513692 TCTGTGACAAGTAATTCCAAACGG 59.486 41.667 0.00 0.00 0.00 4.44
180 181 5.666969 TCTGTGACAAGTAATTCCAAACG 57.333 39.130 0.00 0.00 0.00 3.60
181 182 7.382218 CCATTTCTGTGACAAGTAATTCCAAAC 59.618 37.037 0.00 0.00 0.00 2.93
182 183 7.286546 TCCATTTCTGTGACAAGTAATTCCAAA 59.713 33.333 0.00 0.00 0.00 3.28
183 184 6.775142 TCCATTTCTGTGACAAGTAATTCCAA 59.225 34.615 0.00 0.00 0.00 3.53
184 185 6.303054 TCCATTTCTGTGACAAGTAATTCCA 58.697 36.000 0.00 0.00 0.00 3.53
185 186 6.817765 TCCATTTCTGTGACAAGTAATTCC 57.182 37.500 0.00 0.00 0.00 3.01
186 187 7.820648 ACATCCATTTCTGTGACAAGTAATTC 58.179 34.615 0.00 0.00 0.00 2.17
187 188 7.765695 ACATCCATTTCTGTGACAAGTAATT 57.234 32.000 0.00 0.00 0.00 1.40
188 189 9.113838 GATACATCCATTTCTGTGACAAGTAAT 57.886 33.333 0.00 0.00 0.00 1.89
189 190 8.321353 AGATACATCCATTTCTGTGACAAGTAA 58.679 33.333 0.00 0.00 0.00 2.24
190 191 7.851228 AGATACATCCATTTCTGTGACAAGTA 58.149 34.615 0.00 0.00 0.00 2.24
191 192 6.715280 AGATACATCCATTTCTGTGACAAGT 58.285 36.000 0.00 0.00 0.00 3.16
192 193 8.200120 TCTAGATACATCCATTTCTGTGACAAG 58.800 37.037 0.00 0.00 0.00 3.16
193 194 7.981789 GTCTAGATACATCCATTTCTGTGACAA 59.018 37.037 0.00 0.00 0.00 3.18
194 195 7.492524 GTCTAGATACATCCATTTCTGTGACA 58.507 38.462 0.00 0.00 0.00 3.58
195 196 6.638873 CGTCTAGATACATCCATTTCTGTGAC 59.361 42.308 0.00 0.00 0.00 3.67
196 197 6.321435 ACGTCTAGATACATCCATTTCTGTGA 59.679 38.462 0.00 0.00 0.00 3.58
197 198 6.507900 ACGTCTAGATACATCCATTTCTGTG 58.492 40.000 0.00 0.00 0.00 3.66
198 199 6.716934 ACGTCTAGATACATCCATTTCTGT 57.283 37.500 0.00 0.00 0.00 3.41
199 200 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
204 205 9.310449 ACCTAAAATACGTCTAGATACATCCAT 57.690 33.333 0.00 0.00 0.00 3.41
205 206 8.701908 ACCTAAAATACGTCTAGATACATCCA 57.298 34.615 0.00 0.00 0.00 3.41
206 207 9.012161 AGACCTAAAATACGTCTAGATACATCC 57.988 37.037 0.00 0.00 35.12 3.51
216 217 9.012161 GGATGTATCTAGACCTAAAATACGTCT 57.988 37.037 14.68 0.00 38.23 4.18
217 218 8.790718 TGGATGTATCTAGACCTAAAATACGTC 58.209 37.037 0.00 3.02 37.78 4.34
218 219 8.701908 TGGATGTATCTAGACCTAAAATACGT 57.298 34.615 0.00 0.00 0.00 3.57
224 225 9.832445 GTGAAAATGGATGTATCTAGACCTAAA 57.168 33.333 0.00 0.00 0.00 1.85
225 226 8.141909 CGTGAAAATGGATGTATCTAGACCTAA 58.858 37.037 0.00 0.00 0.00 2.69
226 227 7.504574 TCGTGAAAATGGATGTATCTAGACCTA 59.495 37.037 0.00 0.00 0.00 3.08
227 228 6.323996 TCGTGAAAATGGATGTATCTAGACCT 59.676 38.462 0.00 0.00 0.00 3.85
228 229 6.421202 GTCGTGAAAATGGATGTATCTAGACC 59.579 42.308 0.00 0.00 0.00 3.85
229 230 6.978659 TGTCGTGAAAATGGATGTATCTAGAC 59.021 38.462 0.00 0.00 0.00 2.59
230 231 7.107639 TGTCGTGAAAATGGATGTATCTAGA 57.892 36.000 0.00 0.00 0.00 2.43
231 232 7.492669 ACTTGTCGTGAAAATGGATGTATCTAG 59.507 37.037 0.00 0.00 0.00 2.43
232 233 7.327975 ACTTGTCGTGAAAATGGATGTATCTA 58.672 34.615 0.00 0.00 0.00 1.98
233 234 6.173339 ACTTGTCGTGAAAATGGATGTATCT 58.827 36.000 0.00 0.00 0.00 1.98
234 235 6.422776 ACTTGTCGTGAAAATGGATGTATC 57.577 37.500 0.00 0.00 0.00 2.24
235 236 7.915293 TTACTTGTCGTGAAAATGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
236 237 7.915293 ATTACTTGTCGTGAAAATGGATGTA 57.085 32.000 0.00 0.00 0.00 2.29
237 238 6.817765 ATTACTTGTCGTGAAAATGGATGT 57.182 33.333 0.00 0.00 0.00 3.06
238 239 6.747280 GGAATTACTTGTCGTGAAAATGGATG 59.253 38.462 0.00 0.00 0.00 3.51
239 240 6.403200 CGGAATTACTTGTCGTGAAAATGGAT 60.403 38.462 0.00 0.00 0.00 3.41
240 241 5.106869 CGGAATTACTTGTCGTGAAAATGGA 60.107 40.000 0.00 0.00 0.00 3.41
241 242 5.086058 CGGAATTACTTGTCGTGAAAATGG 58.914 41.667 0.00 0.00 0.00 3.16
242 243 5.922546 TCGGAATTACTTGTCGTGAAAATG 58.077 37.500 0.00 0.00 0.00 2.32
243 244 6.548441 TTCGGAATTACTTGTCGTGAAAAT 57.452 33.333 0.00 0.00 0.00 1.82
244 245 5.987777 TTCGGAATTACTTGTCGTGAAAA 57.012 34.783 0.00 0.00 0.00 2.29
245 246 7.837202 ATATTCGGAATTACTTGTCGTGAAA 57.163 32.000 8.76 0.00 0.00 2.69
246 247 7.837202 AATATTCGGAATTACTTGTCGTGAA 57.163 32.000 8.76 0.00 0.00 3.18
247 248 7.837202 AAATATTCGGAATTACTTGTCGTGA 57.163 32.000 8.76 0.00 0.00 4.35
248 249 7.638683 GGAAAATATTCGGAATTACTTGTCGTG 59.361 37.037 8.76 0.00 36.36 4.35
249 250 7.334921 TGGAAAATATTCGGAATTACTTGTCGT 59.665 33.333 8.76 0.00 36.36 4.34
250 251 7.690228 TGGAAAATATTCGGAATTACTTGTCG 58.310 34.615 8.76 0.00 36.36 4.35
257 258 9.959749 GCAGTTTATGGAAAATATTCGGAATTA 57.040 29.630 8.76 0.00 36.36 1.40
258 259 7.647715 CGCAGTTTATGGAAAATATTCGGAATT 59.352 33.333 8.76 0.00 36.36 2.17
259 260 7.138736 CGCAGTTTATGGAAAATATTCGGAAT 58.861 34.615 8.49 8.49 36.36 3.01
260 261 6.094325 ACGCAGTTTATGGAAAATATTCGGAA 59.906 34.615 0.00 0.00 37.78 4.30
261 262 5.587043 ACGCAGTTTATGGAAAATATTCGGA 59.413 36.000 0.00 0.00 37.78 4.55
262 263 5.816919 ACGCAGTTTATGGAAAATATTCGG 58.183 37.500 0.00 0.00 37.78 4.30
263 264 6.568601 CGTACGCAGTTTATGGAAAATATTCG 59.431 38.462 0.52 0.00 37.78 3.34
264 265 7.623770 TCGTACGCAGTTTATGGAAAATATTC 58.376 34.615 11.24 0.00 37.78 1.75
265 266 7.493320 TCTCGTACGCAGTTTATGGAAAATATT 59.507 33.333 11.24 0.00 37.78 1.28
266 267 6.982141 TCTCGTACGCAGTTTATGGAAAATAT 59.018 34.615 11.24 0.00 37.78 1.28
267 268 6.331845 TCTCGTACGCAGTTTATGGAAAATA 58.668 36.000 11.24 0.00 37.78 1.40
268 269 5.172934 TCTCGTACGCAGTTTATGGAAAAT 58.827 37.500 11.24 0.00 37.78 1.82
269 270 4.558178 TCTCGTACGCAGTTTATGGAAAA 58.442 39.130 11.24 0.00 37.78 2.29
270 271 4.177165 TCTCGTACGCAGTTTATGGAAA 57.823 40.909 11.24 0.00 37.78 3.13
271 272 3.853831 TCTCGTACGCAGTTTATGGAA 57.146 42.857 11.24 0.00 37.78 3.53
272 273 3.379057 TCATCTCGTACGCAGTTTATGGA 59.621 43.478 11.24 0.00 37.78 3.41
273 274 3.702330 TCATCTCGTACGCAGTTTATGG 58.298 45.455 11.24 0.00 37.78 2.74
274 275 6.856426 TCTTATCATCTCGTACGCAGTTTATG 59.144 38.462 11.24 8.89 37.78 1.90
275 276 6.967135 TCTTATCATCTCGTACGCAGTTTAT 58.033 36.000 11.24 2.49 37.78 1.40
276 277 6.367686 TCTTATCATCTCGTACGCAGTTTA 57.632 37.500 11.24 0.00 37.78 2.01
277 278 5.244785 TCTTATCATCTCGTACGCAGTTT 57.755 39.130 11.24 0.00 37.78 2.66
278 279 4.895224 TCTTATCATCTCGTACGCAGTT 57.105 40.909 11.24 1.71 37.78 3.16
280 281 4.083271 TCCATCTTATCATCTCGTACGCAG 60.083 45.833 11.24 9.26 0.00 5.18
281 282 3.818773 TCCATCTTATCATCTCGTACGCA 59.181 43.478 11.24 0.00 0.00 5.24
282 283 4.159857 GTCCATCTTATCATCTCGTACGC 58.840 47.826 11.24 0.00 0.00 4.42
283 284 4.395656 CGTCCATCTTATCATCTCGTACG 58.604 47.826 9.53 9.53 0.00 3.67
284 285 4.159857 GCGTCCATCTTATCATCTCGTAC 58.840 47.826 0.00 0.00 0.00 3.67
285 286 3.818773 TGCGTCCATCTTATCATCTCGTA 59.181 43.478 0.00 0.00 0.00 3.43
286 287 2.623416 TGCGTCCATCTTATCATCTCGT 59.377 45.455 0.00 0.00 0.00 4.18
287 288 3.288809 TGCGTCCATCTTATCATCTCG 57.711 47.619 0.00 0.00 0.00 4.04
288 289 4.629200 GGATTGCGTCCATCTTATCATCTC 59.371 45.833 3.24 0.00 46.96 2.75
289 290 4.573900 GGATTGCGTCCATCTTATCATCT 58.426 43.478 3.24 0.00 46.96 2.90
290 291 4.935885 GGATTGCGTCCATCTTATCATC 57.064 45.455 3.24 0.00 46.96 2.92
302 303 1.376609 AAGCCATTCGGGATTGCGTC 61.377 55.000 0.00 0.00 45.48 5.19
303 304 1.378514 AAGCCATTCGGGATTGCGT 60.379 52.632 0.00 0.00 45.48 5.24
304 305 3.513225 AAGCCATTCGGGATTGCG 58.487 55.556 0.00 0.00 45.48 4.85
308 309 0.395724 GTTGGGAAGCCATTCGGGAT 60.396 55.000 0.00 0.00 40.01 3.85
309 310 1.001393 GTTGGGAAGCCATTCGGGA 60.001 57.895 0.00 0.00 40.01 5.14
380 381 3.620785 GAGGATCGGCTGCGGGAT 61.621 66.667 7.38 5.98 0.00 3.85
381 382 4.841617 AGAGGATCGGCTGCGGGA 62.842 66.667 7.38 0.83 42.67 5.14
711 713 2.037641 AGCAGTGGCAGCGAATATCATA 59.962 45.455 0.00 0.00 44.61 2.15
712 714 1.202734 AGCAGTGGCAGCGAATATCAT 60.203 47.619 0.00 0.00 44.61 2.45
926 943 0.107703 CCCATGCGTGTACACCTCAT 60.108 55.000 20.11 18.72 0.00 2.90
975 992 1.744639 GGAGCGAGAGATGATGCCA 59.255 57.895 0.00 0.00 0.00 4.92
1298 1317 1.476471 CCTCTATTCCCAGCTTGCAGG 60.476 57.143 0.00 0.00 0.00 4.85
1337 1356 1.213013 CTCAACGTCTCCCACTCCG 59.787 63.158 0.00 0.00 0.00 4.63
1351 1370 0.179059 TTGTTGACGAGCTGGCTCAA 60.179 50.000 20.39 7.38 42.86 3.02
1554 1574 3.062466 AGAGTGCGGCGCTCAGTA 61.062 61.111 36.40 9.45 42.72 2.74
2041 2061 0.695924 AACCCATGATCCGGTGTTCA 59.304 50.000 0.00 4.02 30.96 3.18
2158 2178 0.106015 AGGCCCAACAGAACTGCTTT 60.106 50.000 0.00 0.00 0.00 3.51
2168 2188 4.601794 CAGCACCCAGGCCCAACA 62.602 66.667 0.00 0.00 0.00 3.33
2192 2212 2.270205 CCGGCATCTTGAGTGGCT 59.730 61.111 0.00 0.00 39.73 4.75
2220 2240 3.978723 CTGCTCTCCAGACCGCACG 62.979 68.421 0.00 0.00 44.64 5.34
2453 2473 2.847234 TCCTGCGTGGGGTGAAGT 60.847 61.111 0.00 0.00 36.20 3.01
2541 2761 3.792053 GATCACGCCTAGGCCACGG 62.792 68.421 28.09 16.11 37.98 4.94
2686 2906 1.531739 AAACCATCATGCGCCGGTTT 61.532 50.000 17.12 17.12 44.82 3.27
2779 2999 7.224753 GTCTGACTGTCATGACTAACAGAAAAA 59.775 37.037 30.38 17.79 44.54 1.94
2924 3145 7.560626 AGAGTCTTATTAACCACCGAAGTATCT 59.439 37.037 0.00 0.00 0.00 1.98
2943 3164 3.160269 CAAATTCTGGGCCAAGAGTCTT 58.840 45.455 10.51 0.00 0.00 3.01
2960 3181 2.101640 AAGCCTCAAACCCACCAAAT 57.898 45.000 0.00 0.00 0.00 2.32
2965 3186 1.367471 GGCAAAGCCTCAAACCCAC 59.633 57.895 0.00 0.00 46.69 4.61
3001 3222 3.846588 TCTCCAGGCTAACAGAATTCCTT 59.153 43.478 0.65 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.