Multiple sequence alignment - TraesCS1B01G116500

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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 TraesCS1B01G116500 chr1B 100.000 2780 0 0 1 2780 136928871 136926092 0.000000e+00 5134.0
1 TraesCS1B01G116500 chr1B 94.397 232 12 1 1 231 480897755 480897986 3.410000e-94 355.0
2 TraesCS1B01G116500 chr1D 95.139 1584 40 12 625 2193 83916127 83914566 0.000000e+00 2464.0
3 TraesCS1B01G116500 chr1D 89.977 429 13 12 232 631 83918372 83917945 6.820000e-146 527.0
4 TraesCS1B01G116500 chr1D 80.153 524 65 26 2278 2772 41512623 41512110 3.410000e-94 355.0
5 TraesCS1B01G116500 chr1A 93.583 1605 65 15 599 2182 100419353 100417766 0.000000e+00 2359.0
6 TraesCS1B01G116500 chr1A 89.169 397 23 8 232 615 100420401 100420012 6.970000e-131 477.0
7 TraesCS1B01G116500 chr5B 94.828 232 11 1 1 231 598991079 598990848 7.320000e-96 361.0
8 TraesCS1B01G116500 chr5B 93.991 233 13 1 1 232 617043904 617044136 4.410000e-93 351.0
9 TraesCS1B01G116500 chr6B 93.103 232 15 1 1 231 561271305 561271074 3.430000e-89 339.0
10 TraesCS1B01G116500 chr6B 93.074 231 15 1 1 230 676862418 676862188 1.230000e-88 337.0
11 TraesCS1B01G116500 chr6B 91.379 232 20 0 1 232 715476645 715476414 4.470000e-83 318.0
12 TraesCS1B01G116500 chr2B 91.983 237 17 2 1 235 47495662 47495898 5.740000e-87 331.0
13 TraesCS1B01G116500 chr2B 91.845 233 16 3 1 232 714795735 714795505 3.450000e-84 322.0
14 TraesCS1B01G116500 chr2B 79.707 478 68 15 2319 2771 520917084 520917557 4.470000e-83 318.0
15 TraesCS1B01G116500 chr2B 100.000 28 0 0 1255 1282 103794742 103794715 5.000000e-03 52.8
16 TraesCS1B01G116500 chr7B 91.880 234 17 2 1 232 57694403 57694170 2.670000e-85 326.0
17 TraesCS1B01G116500 chr4D 81.250 384 58 11 2277 2650 18685557 18685936 5.820000e-77 298.0
18 TraesCS1B01G116500 chr4D 78.112 466 76 22 2319 2774 187198689 187198240 3.530000e-69 272.0
19 TraesCS1B01G116500 chr7A 76.529 507 83 24 2278 2759 692896333 692895838 7.690000e-61 244.0
20 TraesCS1B01G116500 chr3A 77.843 343 62 11 2317 2650 245403557 245403220 1.690000e-47 200.0
21 TraesCS1B01G116500 chr5A 76.667 330 47 22 2296 2613 642116867 642116556 3.710000e-34 156.0
22 TraesCS1B01G116500 chr2A 73.574 526 88 30 2287 2778 536594590 536594082 1.330000e-33 154.0
23 TraesCS1B01G116500 chr2A 100.000 28 0 0 1255 1282 66914742 66914715 5.000000e-03 52.8
24 TraesCS1B01G116500 chr3D 75.071 353 62 17 2285 2627 531156013 531155677 1.040000e-29 141.0
25 TraesCS1B01G116500 chr7D 77.315 216 34 10 2288 2491 51950471 51950683 2.260000e-21 113.0
26 TraesCS1B01G116500 chr5D 76.543 162 28 5 2319 2471 194087241 194087081 2.300000e-11 80.5
27 TraesCS1B01G116500 chr2D 100.000 28 0 0 1255 1282 67443192 67443219 5.000000e-03 52.8
28 TraesCS1B01G116500 chr2D 100.000 28 0 0 1255 1282 67445822 67445849 5.000000e-03 52.8


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 TraesCS1B01G116500 chr1B 136926092 136928871 2779 True 5134.0 5134 100.000 1 2780 1 chr1B.!!$R1 2779
1 TraesCS1B01G116500 chr1D 83914566 83918372 3806 True 1495.5 2464 92.558 232 2193 2 chr1D.!!$R2 1961
2 TraesCS1B01G116500 chr1D 41512110 41512623 513 True 355.0 355 80.153 2278 2772 1 chr1D.!!$R1 494
3 TraesCS1B01G116500 chr1A 100417766 100420401 2635 True 1418.0 2359 91.376 232 2182 2 chr1A.!!$R1 1950

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
46 47 0.032678 CGCCGATCTACTGGATGCTT 59.967 55.0 0.0 0.0 34.33 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 4001 1.075542 TCGCAACGCACTTTCCATAG 58.924 50.0 0.0 0.0 0.0 2.23 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
23 24 6.371809 TTTTGTATGCCGAACTATTCATCC 57.628 37.500 0.00 0.00 0.00 3.51
24 25 3.649073 TGTATGCCGAACTATTCATCCG 58.351 45.455 0.00 0.00 0.00 4.18
25 26 2.169832 ATGCCGAACTATTCATCCGG 57.830 50.000 0.00 0.00 42.74 5.14
27 28 2.914379 CCGAACTATTCATCCGGCC 58.086 57.895 0.00 0.00 33.47 6.13
28 29 0.944311 CCGAACTATTCATCCGGCCG 60.944 60.000 21.04 21.04 33.47 6.13
29 30 1.557443 CGAACTATTCATCCGGCCGC 61.557 60.000 22.85 0.00 0.00 6.53
30 31 1.227853 AACTATTCATCCGGCCGCC 60.228 57.895 22.85 0.00 0.00 6.13
41 42 3.224324 GGCCGCCGATCTACTGGA 61.224 66.667 0.00 0.00 0.00 3.86
42 43 2.574955 GGCCGCCGATCTACTGGAT 61.575 63.158 0.00 0.00 37.37 3.41
43 44 1.373497 GCCGCCGATCTACTGGATG 60.373 63.158 0.00 0.00 34.33 3.51
44 45 1.373497 CCGCCGATCTACTGGATGC 60.373 63.158 0.00 0.00 34.33 3.91
45 46 1.662608 CGCCGATCTACTGGATGCT 59.337 57.895 0.00 0.00 34.33 3.79
46 47 0.032678 CGCCGATCTACTGGATGCTT 59.967 55.000 0.00 0.00 34.33 3.91
47 48 1.506493 GCCGATCTACTGGATGCTTG 58.494 55.000 0.00 0.00 34.33 4.01
48 49 1.069204 GCCGATCTACTGGATGCTTGA 59.931 52.381 0.00 0.00 34.33 3.02
49 50 2.289320 GCCGATCTACTGGATGCTTGAT 60.289 50.000 0.00 0.00 34.33 2.57
50 51 3.583806 CCGATCTACTGGATGCTTGATC 58.416 50.000 0.00 0.00 34.33 2.92
51 52 3.240884 CGATCTACTGGATGCTTGATCG 58.759 50.000 8.41 8.41 44.13 3.69
52 53 2.515926 TCTACTGGATGCTTGATCGC 57.484 50.000 0.00 0.00 30.87 4.58
53 54 1.069204 TCTACTGGATGCTTGATCGCC 59.931 52.381 0.00 0.00 30.87 5.54
54 55 0.249447 TACTGGATGCTTGATCGCCG 60.249 55.000 0.00 0.00 30.87 6.46
55 56 2.203056 TGGATGCTTGATCGCCGG 60.203 61.111 0.00 0.00 30.87 6.13
56 57 2.108976 GGATGCTTGATCGCCGGA 59.891 61.111 5.05 0.00 30.87 5.14
57 58 1.302033 GGATGCTTGATCGCCGGAT 60.302 57.895 5.05 0.00 34.96 4.18
58 59 0.886490 GGATGCTTGATCGCCGGATT 60.886 55.000 5.05 0.00 31.51 3.01
59 60 0.236711 GATGCTTGATCGCCGGATTG 59.763 55.000 5.05 0.00 31.51 2.67
60 61 0.464373 ATGCTTGATCGCCGGATTGT 60.464 50.000 5.05 0.00 31.51 2.71
61 62 1.353103 GCTTGATCGCCGGATTGTG 59.647 57.895 5.05 0.00 31.51 3.33
62 63 2.016961 CTTGATCGCCGGATTGTGG 58.983 57.895 5.05 0.00 31.51 4.17
74 75 5.467902 CCGGATTGTGGCATTTATTTTTG 57.532 39.130 0.00 0.00 0.00 2.44
75 76 4.332268 CCGGATTGTGGCATTTATTTTTGG 59.668 41.667 0.00 0.00 0.00 3.28
76 77 4.201802 CGGATTGTGGCATTTATTTTTGGC 60.202 41.667 0.00 0.00 38.77 4.52
77 78 4.201802 GGATTGTGGCATTTATTTTTGGCG 60.202 41.667 0.00 0.00 41.00 5.69
78 79 2.072298 TGTGGCATTTATTTTTGGCGC 58.928 42.857 0.00 0.00 45.86 6.53
79 80 1.060409 GTGGCATTTATTTTTGGCGCG 59.940 47.619 0.00 0.00 41.00 6.86
80 81 0.649993 GGCATTTATTTTTGGCGCGG 59.350 50.000 8.83 0.00 0.00 6.46
81 82 0.649993 GCATTTATTTTTGGCGCGGG 59.350 50.000 8.83 0.00 0.00 6.13
82 83 1.737363 GCATTTATTTTTGGCGCGGGA 60.737 47.619 8.83 0.00 0.00 5.14
83 84 2.611518 CATTTATTTTTGGCGCGGGAA 58.388 42.857 8.83 0.00 0.00 3.97
84 85 2.067414 TTTATTTTTGGCGCGGGAAC 57.933 45.000 8.83 0.00 0.00 3.62
85 86 0.959553 TTATTTTTGGCGCGGGAACA 59.040 45.000 8.83 0.00 0.00 3.18
86 87 0.241481 TATTTTTGGCGCGGGAACAC 59.759 50.000 8.83 0.00 0.00 3.32
87 88 1.460273 ATTTTTGGCGCGGGAACACT 61.460 50.000 8.83 0.00 0.00 3.55
88 89 0.818445 TTTTTGGCGCGGGAACACTA 60.818 50.000 8.83 0.00 0.00 2.74
89 90 0.606944 TTTTGGCGCGGGAACACTAT 60.607 50.000 8.83 0.00 0.00 2.12
90 91 1.302383 TTTGGCGCGGGAACACTATG 61.302 55.000 8.83 0.00 0.00 2.23
91 92 2.125269 GGCGCGGGAACACTATGT 60.125 61.111 8.83 0.00 0.00 2.29
92 93 1.743995 GGCGCGGGAACACTATGTT 60.744 57.895 8.83 0.00 44.37 2.71
93 94 1.303091 GGCGCGGGAACACTATGTTT 61.303 55.000 8.83 0.00 41.28 2.83
94 95 0.179200 GCGCGGGAACACTATGTTTG 60.179 55.000 8.83 0.00 41.28 2.93
95 96 1.434555 CGCGGGAACACTATGTTTGA 58.565 50.000 0.00 0.00 41.28 2.69
96 97 1.801771 CGCGGGAACACTATGTTTGAA 59.198 47.619 0.00 0.00 41.28 2.69
97 98 2.418628 CGCGGGAACACTATGTTTGAAT 59.581 45.455 0.00 0.00 41.28 2.57
98 99 3.119990 CGCGGGAACACTATGTTTGAATT 60.120 43.478 0.00 0.00 41.28 2.17
99 100 4.614993 CGCGGGAACACTATGTTTGAATTT 60.615 41.667 0.00 0.00 41.28 1.82
100 101 5.227152 GCGGGAACACTATGTTTGAATTTT 58.773 37.500 0.00 0.00 41.28 1.82
101 102 5.344933 GCGGGAACACTATGTTTGAATTTTC 59.655 40.000 0.00 0.00 41.28 2.29
102 103 5.861787 CGGGAACACTATGTTTGAATTTTCC 59.138 40.000 0.00 0.00 41.28 3.13
103 104 5.861787 GGGAACACTATGTTTGAATTTTCCG 59.138 40.000 0.00 0.00 41.28 4.30
104 105 6.443792 GGAACACTATGTTTGAATTTTCCGT 58.556 36.000 0.00 0.00 41.28 4.69
105 106 6.362283 GGAACACTATGTTTGAATTTTCCGTG 59.638 38.462 0.00 0.00 41.28 4.94
106 107 5.768317 ACACTATGTTTGAATTTTCCGTGG 58.232 37.500 0.00 0.00 0.00 4.94
107 108 4.621034 CACTATGTTTGAATTTTCCGTGGC 59.379 41.667 0.00 0.00 0.00 5.01
108 109 4.522789 ACTATGTTTGAATTTTCCGTGGCT 59.477 37.500 0.00 0.00 0.00 4.75
109 110 3.090952 TGTTTGAATTTTCCGTGGCTG 57.909 42.857 0.00 0.00 0.00 4.85
110 111 2.223923 TGTTTGAATTTTCCGTGGCTGG 60.224 45.455 0.00 0.00 0.00 4.85
111 112 0.965439 TTGAATTTTCCGTGGCTGGG 59.035 50.000 0.00 0.00 0.00 4.45
112 113 0.897863 TGAATTTTCCGTGGCTGGGG 60.898 55.000 0.00 0.00 0.00 4.96
113 114 1.604147 GAATTTTCCGTGGCTGGGGG 61.604 60.000 0.00 0.00 0.00 5.40
136 137 2.496817 GGCTGGAGGCGTGACTAG 59.503 66.667 0.00 0.00 42.94 2.57
137 138 2.496817 GCTGGAGGCGTGACTAGG 59.503 66.667 0.00 0.00 0.00 3.02
138 139 2.052690 GCTGGAGGCGTGACTAGGA 61.053 63.158 0.00 0.00 0.00 2.94
139 140 2.010582 GCTGGAGGCGTGACTAGGAG 62.011 65.000 0.00 0.00 0.00 3.69
140 141 2.010582 CTGGAGGCGTGACTAGGAGC 62.011 65.000 0.00 0.00 0.00 4.70
141 142 1.755008 GGAGGCGTGACTAGGAGCT 60.755 63.158 0.00 0.00 0.00 4.09
142 143 0.465824 GGAGGCGTGACTAGGAGCTA 60.466 60.000 0.00 0.00 0.00 3.32
143 144 0.948678 GAGGCGTGACTAGGAGCTAG 59.051 60.000 0.00 0.00 39.72 3.42
144 145 0.466555 AGGCGTGACTAGGAGCTAGG 60.467 60.000 0.00 0.00 38.30 3.02
145 146 1.360911 GCGTGACTAGGAGCTAGGC 59.639 63.158 0.00 0.00 42.13 3.93
146 147 2.034607 CGTGACTAGGAGCTAGGCC 58.965 63.158 0.00 0.00 41.15 5.19
147 148 1.787057 CGTGACTAGGAGCTAGGCCG 61.787 65.000 0.00 0.00 41.15 6.13
148 149 0.465824 GTGACTAGGAGCTAGGCCGA 60.466 60.000 0.00 0.00 41.15 5.54
149 150 0.465824 TGACTAGGAGCTAGGCCGAC 60.466 60.000 0.00 0.00 41.15 4.79
150 151 1.152715 ACTAGGAGCTAGGCCGACC 60.153 63.158 0.00 0.00 38.30 4.79
151 152 1.904378 CTAGGAGCTAGGCCGACCC 60.904 68.421 0.00 0.00 36.11 4.46
152 153 3.447933 TAGGAGCTAGGCCGACCCC 62.448 68.421 0.00 0.00 36.11 4.95
154 155 3.541713 GAGCTAGGCCGACCCCAG 61.542 72.222 0.00 0.00 36.11 4.45
166 167 3.480133 CCCCAGGGGCCGAACTAG 61.480 72.222 13.35 0.00 35.35 2.57
167 168 4.176752 CCCAGGGGCCGAACTAGC 62.177 72.222 0.00 0.00 0.00 3.42
168 169 4.530857 CCAGGGGCCGAACTAGCG 62.531 72.222 0.00 0.00 0.00 4.26
194 195 2.917227 CCCCAGGCCGCAGTTTTT 60.917 61.111 0.00 0.00 0.00 1.94
195 196 2.650778 CCCAGGCCGCAGTTTTTC 59.349 61.111 0.00 0.00 0.00 2.29
196 197 2.255252 CCAGGCCGCAGTTTTTCG 59.745 61.111 0.00 0.00 0.00 3.46
203 204 3.670377 GCAGTTTTTCGGCGCCCT 61.670 61.111 23.46 8.01 0.00 5.19
204 205 2.255252 CAGTTTTTCGGCGCCCTG 59.745 61.111 23.46 17.24 0.00 4.45
205 206 2.983592 AGTTTTTCGGCGCCCTGG 60.984 61.111 23.46 7.26 0.00 4.45
206 207 4.050934 GTTTTTCGGCGCCCTGGG 62.051 66.667 23.46 8.86 0.00 4.45
227 228 2.892425 CCGAACGGCTGGAGATGC 60.892 66.667 0.00 0.00 0.00 3.91
228 229 2.185350 CGAACGGCTGGAGATGCT 59.815 61.111 0.00 0.00 0.00 3.79
229 230 1.880340 CGAACGGCTGGAGATGCTC 60.880 63.158 0.00 0.00 0.00 4.26
230 231 1.519719 GAACGGCTGGAGATGCTCT 59.480 57.895 0.00 0.00 0.00 4.09
288 289 1.379044 CCTCCCATCACAACCTGGC 60.379 63.158 0.00 0.00 0.00 4.85
303 304 1.600957 CCTGGCGAGCTATGAAACATG 59.399 52.381 0.00 0.00 0.00 3.21
305 306 1.065491 TGGCGAGCTATGAAACATGGT 60.065 47.619 0.00 0.00 0.00 3.55
309 310 4.095782 GGCGAGCTATGAAACATGGTTTTA 59.904 41.667 0.00 0.00 0.00 1.52
310 311 5.266242 GCGAGCTATGAAACATGGTTTTAG 58.734 41.667 0.00 3.83 0.00 1.85
332 335 0.598065 GGCAGCATTCACTCGGTTTT 59.402 50.000 0.00 0.00 0.00 2.43
333 336 1.810151 GGCAGCATTCACTCGGTTTTA 59.190 47.619 0.00 0.00 0.00 1.52
334 337 2.159517 GGCAGCATTCACTCGGTTTTAG 60.160 50.000 0.00 0.00 0.00 1.85
335 338 2.484264 GCAGCATTCACTCGGTTTTAGT 59.516 45.455 0.00 0.00 0.00 2.24
336 339 3.058224 GCAGCATTCACTCGGTTTTAGTT 60.058 43.478 0.00 0.00 0.00 2.24
337 340 4.466828 CAGCATTCACTCGGTTTTAGTTG 58.533 43.478 0.00 0.00 0.00 3.16
373 383 5.782047 TCCTTGAAAGTTGTTAATGCATGG 58.218 37.500 0.00 0.00 0.00 3.66
406 416 0.403271 ATTGGTGGACAGAAGCTGCT 59.597 50.000 0.00 0.00 34.37 4.24
434 444 8.982685 CAATATATGCGGATTGTATGGATCTAC 58.017 37.037 0.00 0.00 0.00 2.59
452 462 5.560722 TCTACTTGTGGAGATTGGAAACA 57.439 39.130 0.00 0.00 39.83 2.83
507 522 4.958509 ACCACTCATGAGATTGCTAGATG 58.041 43.478 29.27 12.77 0.00 2.90
568 584 9.783081 GATGGGCATCCTGATTTTATTTTTAAT 57.217 29.630 0.00 0.00 31.76 1.40
570 586 9.972106 TGGGCATCCTGATTTTATTTTTAATTT 57.028 25.926 0.00 0.00 0.00 1.82
761 2840 6.816140 CAGCAAAAAGACCCTAAAACTTTTGA 59.184 34.615 8.77 0.00 41.09 2.69
762 2841 7.495606 CAGCAAAAAGACCCTAAAACTTTTGAT 59.504 33.333 8.77 0.50 41.09 2.57
791 2870 2.374170 ACCCACTAAACTAACCACCAGG 59.626 50.000 0.00 0.00 42.21 4.45
816 2895 1.078708 ATTGCAACCCTACGACCCG 60.079 57.895 0.00 0.00 0.00 5.28
872 2951 2.959707 AGCCTCCAAGATCTACTTACCG 59.040 50.000 0.00 0.00 37.03 4.02
903 2982 4.655649 TCATTCTTAGCTTGCTCCTCCATA 59.344 41.667 0.00 0.00 0.00 2.74
1787 3878 2.103042 GCTGCTTCTGATCCGCGTT 61.103 57.895 4.92 0.00 0.00 4.84
1899 3990 0.681733 AGCATCAGACCAACTCGTGT 59.318 50.000 0.00 0.00 0.00 4.49
2027 4124 3.307762 CCACTCTCCTTCTAGGGGTTTTG 60.308 52.174 0.00 0.00 37.09 2.44
2055 4154 9.950680 AATAAATAAACTAGTTCATTGCCATCG 57.049 29.630 8.95 0.00 0.00 3.84
2089 4192 3.664798 CGATCTCGTTCGAGGTACATAGC 60.665 52.174 19.65 3.99 41.62 2.97
2128 4232 3.113322 GCTGCGAGTGATATCGTTTACA 58.887 45.455 0.00 0.00 44.53 2.41
2132 4236 6.469139 TGCGAGTGATATCGTTTACAAAAA 57.531 33.333 0.00 0.00 44.53 1.94
2133 4237 7.067532 TGCGAGTGATATCGTTTACAAAAAT 57.932 32.000 0.00 0.00 44.53 1.82
2134 4238 6.958752 TGCGAGTGATATCGTTTACAAAAATG 59.041 34.615 0.00 0.00 44.53 2.32
2136 4240 7.480542 GCGAGTGATATCGTTTACAAAAATGTT 59.519 33.333 0.00 0.00 44.53 2.71
2137 4241 8.775884 CGAGTGATATCGTTTACAAAAATGTTG 58.224 33.333 0.00 0.00 37.91 3.33
2138 4242 8.964420 AGTGATATCGTTTACAAAAATGTTGG 57.036 30.769 0.00 0.00 33.95 3.77
2139 4243 8.026607 AGTGATATCGTTTACAAAAATGTTGGG 58.973 33.333 0.00 0.00 33.95 4.12
2140 4244 6.809196 TGATATCGTTTACAAAAATGTTGGGC 59.191 34.615 0.00 0.00 33.95 5.36
2155 4259 0.389817 TGGGCGAACTGATGAAGTCG 60.390 55.000 0.00 0.00 38.56 4.18
2157 4261 1.272781 GGCGAACTGATGAAGTCGAG 58.727 55.000 0.00 0.00 38.56 4.04
2190 4294 8.474025 CAGGACTCTTTAGTTGTATCAGAGATT 58.526 37.037 1.55 0.00 35.56 2.40
2210 4314 9.586435 AGAGATTTTTATTTTATCTTTTGCGGG 57.414 29.630 0.00 0.00 0.00 6.13
2211 4315 8.716646 AGATTTTTATTTTATCTTTTGCGGGG 57.283 30.769 0.00 0.00 0.00 5.73
2212 4316 8.536175 AGATTTTTATTTTATCTTTTGCGGGGA 58.464 29.630 0.00 0.00 0.00 4.81
2213 4317 9.157104 GATTTTTATTTTATCTTTTGCGGGGAA 57.843 29.630 0.00 0.00 0.00 3.97
2214 4318 9.679661 ATTTTTATTTTATCTTTTGCGGGGAAT 57.320 25.926 0.00 0.00 0.00 3.01
2215 4319 9.508642 TTTTTATTTTATCTTTTGCGGGGAATT 57.491 25.926 0.00 0.00 0.00 2.17
2216 4320 8.485976 TTTATTTTATCTTTTGCGGGGAATTG 57.514 30.769 0.00 0.00 0.00 2.32
2217 4321 5.476091 TTTTATCTTTTGCGGGGAATTGT 57.524 34.783 0.00 0.00 0.00 2.71
2218 4322 6.591750 TTTTATCTTTTGCGGGGAATTGTA 57.408 33.333 0.00 0.00 0.00 2.41
2219 4323 6.783708 TTTATCTTTTGCGGGGAATTGTAT 57.216 33.333 0.00 0.00 0.00 2.29
2220 4324 7.883391 TTTATCTTTTGCGGGGAATTGTATA 57.117 32.000 0.00 0.00 0.00 1.47
2221 4325 7.883391 TTATCTTTTGCGGGGAATTGTATAA 57.117 32.000 0.00 0.00 0.00 0.98
2222 4326 5.828299 TCTTTTGCGGGGAATTGTATAAG 57.172 39.130 0.00 0.00 0.00 1.73
2223 4327 5.502079 TCTTTTGCGGGGAATTGTATAAGA 58.498 37.500 0.00 0.00 0.00 2.10
2224 4328 5.588648 TCTTTTGCGGGGAATTGTATAAGAG 59.411 40.000 0.00 0.00 0.00 2.85
2225 4329 4.764050 TTGCGGGGAATTGTATAAGAGA 57.236 40.909 0.00 0.00 0.00 3.10
2226 4330 4.974645 TGCGGGGAATTGTATAAGAGAT 57.025 40.909 0.00 0.00 0.00 2.75
2227 4331 4.894784 TGCGGGGAATTGTATAAGAGATC 58.105 43.478 0.00 0.00 0.00 2.75
2228 4332 4.593206 TGCGGGGAATTGTATAAGAGATCT 59.407 41.667 0.00 0.00 0.00 2.75
2229 4333 5.071788 TGCGGGGAATTGTATAAGAGATCTT 59.928 40.000 0.00 0.07 39.85 2.40
2230 4334 6.269077 TGCGGGGAATTGTATAAGAGATCTTA 59.731 38.462 4.84 4.84 42.04 2.10
2231 4335 6.590677 GCGGGGAATTGTATAAGAGATCTTAC 59.409 42.308 4.47 0.00 40.81 2.34
2232 4336 7.667557 CGGGGAATTGTATAAGAGATCTTACA 58.332 38.462 4.47 0.00 40.81 2.41
2233 4337 8.148351 CGGGGAATTGTATAAGAGATCTTACAA 58.852 37.037 16.31 16.31 40.81 2.41
2403 4508 9.810545 ATGGTATTAAATTTTTATGGGTTCGTG 57.189 29.630 0.00 0.00 0.00 4.35
2408 4513 5.968528 AATTTTTATGGGTTCGTGTGCTA 57.031 34.783 0.00 0.00 0.00 3.49
2409 4514 5.560966 ATTTTTATGGGTTCGTGTGCTAG 57.439 39.130 0.00 0.00 0.00 3.42
2437 4542 9.524106 AAAAAGGTTTTTCCAGAATTTAGTACG 57.476 29.630 0.00 0.00 35.61 3.67
2438 4543 8.454570 AAAGGTTTTTCCAGAATTTAGTACGA 57.545 30.769 0.00 0.00 39.02 3.43
2444 4549 2.470821 CAGAATTTAGTACGAGGGCCG 58.529 52.381 0.00 0.00 45.44 6.13
2445 4550 1.202498 AGAATTTAGTACGAGGGCCGC 60.202 52.381 0.00 0.00 43.32 6.53
2471 4578 2.682494 CCAGCAAAGCCAGCCCAT 60.682 61.111 0.00 0.00 0.00 4.00
2474 4581 0.035739 CAGCAAAGCCAGCCCATTTT 59.964 50.000 0.00 0.00 0.00 1.82
2476 4583 1.977129 AGCAAAGCCAGCCCATTTTTA 59.023 42.857 0.00 0.00 0.00 1.52
2489 4596 4.068599 CCCATTTTTATTTTTGCCCACGT 58.931 39.130 0.00 0.00 0.00 4.49
2490 4597 5.238583 CCCATTTTTATTTTTGCCCACGTA 58.761 37.500 0.00 0.00 0.00 3.57
2491 4598 5.120986 CCCATTTTTATTTTTGCCCACGTAC 59.879 40.000 0.00 0.00 0.00 3.67
2493 4600 5.532664 TTTTTATTTTTGCCCACGTACCT 57.467 34.783 0.00 0.00 0.00 3.08
2495 4602 0.601057 ATTTTTGCCCACGTACCTGC 59.399 50.000 0.00 0.00 0.00 4.85
2496 4603 0.466555 TTTTTGCCCACGTACCTGCT 60.467 50.000 0.00 0.00 0.00 4.24
2512 4620 7.827729 ACGTACCTGCTAAAATTCTATTTTCCT 59.172 33.333 0.99 0.00 0.00 3.36
2514 4622 9.174166 GTACCTGCTAAAATTCTATTTTCCTCA 57.826 33.333 0.99 0.00 0.00 3.86
2520 4628 8.523658 GCTAAAATTCTATTTTCCTCACAAGGT 58.476 33.333 0.99 0.00 43.82 3.50
2531 4639 5.304686 TCCTCACAAGGTGACAAATAGTT 57.695 39.130 0.00 0.00 43.82 2.24
2533 4641 4.216257 CCTCACAAGGTGACAAATAGTTGG 59.784 45.833 7.93 0.00 37.67 3.77
2541 4649 3.746492 GTGACAAATAGTTGGAGCTTCGT 59.254 43.478 7.93 0.00 39.22 3.85
2543 4651 5.062308 GTGACAAATAGTTGGAGCTTCGTAG 59.938 44.000 7.93 0.00 39.22 3.51
2547 4655 2.217510 AGTTGGAGCTTCGTAGAGGA 57.782 50.000 0.00 0.00 38.43 3.71
2552 4660 1.819903 GGAGCTTCGTAGAGGACAACT 59.180 52.381 0.00 0.00 38.43 3.16
2553 4661 2.416162 GGAGCTTCGTAGAGGACAACTG 60.416 54.545 0.00 0.00 38.43 3.16
2554 4662 2.488545 GAGCTTCGTAGAGGACAACTGA 59.511 50.000 0.00 0.00 38.43 3.41
2559 4667 6.043411 GCTTCGTAGAGGACAACTGATAATT 58.957 40.000 0.00 0.00 38.43 1.40
2562 4670 4.508124 CGTAGAGGACAACTGATAATTGGC 59.492 45.833 0.00 0.00 34.03 4.52
2627 4735 6.917208 ATTCTCCTTCCCCTATCTCTTTTT 57.083 37.500 0.00 0.00 0.00 1.94
2721 4851 8.895737 AGAAAATGTTCAGATTTGCAAAATTGT 58.104 25.926 17.19 4.46 36.09 2.71
2722 4852 8.844441 AAAATGTTCAGATTTGCAAAATTGTG 57.156 26.923 17.19 9.67 0.00 3.33
2724 4854 6.981762 TGTTCAGATTTGCAAAATTGTGTT 57.018 29.167 17.19 0.00 0.00 3.32
2726 4856 5.886715 TCAGATTTGCAAAATTGTGTTCG 57.113 34.783 17.19 4.48 0.00 3.95
2727 4857 5.347342 TCAGATTTGCAAAATTGTGTTCGT 58.653 33.333 17.19 0.00 0.00 3.85
2728 4858 6.499172 TCAGATTTGCAAAATTGTGTTCGTA 58.501 32.000 17.19 0.00 0.00 3.43
2729 4859 7.144661 TCAGATTTGCAAAATTGTGTTCGTAT 58.855 30.769 17.19 0.00 0.00 3.06
2733 4863 8.765044 ATTTGCAAAATTGTGTTCGTATTTTG 57.235 26.923 17.19 12.66 45.35 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.007234 CGGATGAATAGTTCGGCATACAAAA 59.993 40.000 0.00 0.00 0.00 2.44
1 2 4.509970 CGGATGAATAGTTCGGCATACAAA 59.490 41.667 0.00 0.00 0.00 2.83
2 3 4.055360 CGGATGAATAGTTCGGCATACAA 58.945 43.478 0.00 0.00 0.00 2.41
3 4 3.554129 CCGGATGAATAGTTCGGCATACA 60.554 47.826 0.00 0.00 34.17 2.29
4 5 2.993899 CCGGATGAATAGTTCGGCATAC 59.006 50.000 0.00 0.00 34.17 2.39
5 6 3.313012 CCGGATGAATAGTTCGGCATA 57.687 47.619 0.00 0.00 34.17 3.14
6 7 2.169832 CCGGATGAATAGTTCGGCAT 57.830 50.000 0.00 0.00 34.17 4.40
7 8 3.678921 CCGGATGAATAGTTCGGCA 57.321 52.632 0.00 0.00 34.17 5.69
9 10 0.944311 CGGCCGGATGAATAGTTCGG 60.944 60.000 20.10 0.00 43.13 4.30
10 11 1.557443 GCGGCCGGATGAATAGTTCG 61.557 60.000 29.38 0.00 0.00 3.95
11 12 1.228657 GGCGGCCGGATGAATAGTTC 61.229 60.000 29.38 4.68 0.00 3.01
12 13 1.227853 GGCGGCCGGATGAATAGTT 60.228 57.895 29.38 0.00 0.00 2.24
13 14 2.426023 GGCGGCCGGATGAATAGT 59.574 61.111 29.38 0.00 0.00 2.12
14 15 2.738521 CGGCGGCCGGATGAATAG 60.739 66.667 32.80 1.55 44.15 1.73
24 25 2.574955 ATCCAGTAGATCGGCGGCC 61.575 63.158 9.54 9.54 0.00 6.13
25 26 1.373497 CATCCAGTAGATCGGCGGC 60.373 63.158 7.21 0.00 30.59 6.53
26 27 1.373497 GCATCCAGTAGATCGGCGG 60.373 63.158 7.21 0.00 30.59 6.13
27 28 0.032678 AAGCATCCAGTAGATCGGCG 59.967 55.000 0.00 0.00 30.92 6.46
28 29 1.069204 TCAAGCATCCAGTAGATCGGC 59.931 52.381 0.00 0.00 30.59 5.54
29 30 3.583806 GATCAAGCATCCAGTAGATCGG 58.416 50.000 0.00 0.00 30.59 4.18
30 31 3.240884 CGATCAAGCATCCAGTAGATCG 58.759 50.000 8.01 8.01 45.51 3.69
31 32 2.992543 GCGATCAAGCATCCAGTAGATC 59.007 50.000 0.00 0.00 37.05 2.75
32 33 2.289320 GGCGATCAAGCATCCAGTAGAT 60.289 50.000 0.00 0.00 39.27 1.98
33 34 1.069204 GGCGATCAAGCATCCAGTAGA 59.931 52.381 0.00 0.00 39.27 2.59
34 35 1.506493 GGCGATCAAGCATCCAGTAG 58.494 55.000 0.00 0.00 39.27 2.57
35 36 0.249447 CGGCGATCAAGCATCCAGTA 60.249 55.000 0.00 0.00 39.27 2.74
36 37 1.522355 CGGCGATCAAGCATCCAGT 60.522 57.895 0.00 0.00 39.27 4.00
37 38 2.249535 CCGGCGATCAAGCATCCAG 61.250 63.158 9.30 0.00 39.27 3.86
38 39 2.043604 ATCCGGCGATCAAGCATCCA 62.044 55.000 9.30 0.00 39.27 3.41
39 40 0.886490 AATCCGGCGATCAAGCATCC 60.886 55.000 9.30 0.00 39.27 3.51
40 41 0.236711 CAATCCGGCGATCAAGCATC 59.763 55.000 9.30 0.00 39.27 3.91
41 42 0.464373 ACAATCCGGCGATCAAGCAT 60.464 50.000 9.30 0.00 39.27 3.79
42 43 1.078497 ACAATCCGGCGATCAAGCA 60.078 52.632 9.30 0.00 39.27 3.91
43 44 1.353103 CACAATCCGGCGATCAAGC 59.647 57.895 9.30 0.00 0.00 4.01
44 45 2.016961 CCACAATCCGGCGATCAAG 58.983 57.895 9.30 0.00 0.00 3.02
45 46 2.112198 GCCACAATCCGGCGATCAA 61.112 57.895 9.30 0.00 40.35 2.57
46 47 2.513666 GCCACAATCCGGCGATCA 60.514 61.111 9.30 0.00 40.35 2.92
52 53 4.332268 CCAAAAATAAATGCCACAATCCGG 59.668 41.667 0.00 0.00 0.00 5.14
53 54 4.201802 GCCAAAAATAAATGCCACAATCCG 60.202 41.667 0.00 0.00 0.00 4.18
54 55 4.201802 CGCCAAAAATAAATGCCACAATCC 60.202 41.667 0.00 0.00 0.00 3.01
55 56 4.727448 GCGCCAAAAATAAATGCCACAATC 60.727 41.667 0.00 0.00 0.00 2.67
56 57 3.126686 GCGCCAAAAATAAATGCCACAAT 59.873 39.130 0.00 0.00 0.00 2.71
57 58 2.481952 GCGCCAAAAATAAATGCCACAA 59.518 40.909 0.00 0.00 0.00 3.33
58 59 2.072298 GCGCCAAAAATAAATGCCACA 58.928 42.857 0.00 0.00 0.00 4.17
59 60 1.060409 CGCGCCAAAAATAAATGCCAC 59.940 47.619 0.00 0.00 0.00 5.01
60 61 1.354040 CGCGCCAAAAATAAATGCCA 58.646 45.000 0.00 0.00 0.00 4.92
61 62 0.649993 CCGCGCCAAAAATAAATGCC 59.350 50.000 0.00 0.00 0.00 4.40
62 63 0.649993 CCCGCGCCAAAAATAAATGC 59.350 50.000 0.00 0.00 0.00 3.56
63 64 2.285827 TCCCGCGCCAAAAATAAATG 57.714 45.000 0.00 0.00 0.00 2.32
64 65 2.028930 TGTTCCCGCGCCAAAAATAAAT 60.029 40.909 0.00 0.00 0.00 1.40
65 66 1.340248 TGTTCCCGCGCCAAAAATAAA 59.660 42.857 0.00 0.00 0.00 1.40
66 67 0.959553 TGTTCCCGCGCCAAAAATAA 59.040 45.000 0.00 0.00 0.00 1.40
67 68 0.241481 GTGTTCCCGCGCCAAAAATA 59.759 50.000 0.00 0.00 0.00 1.40
68 69 1.006688 GTGTTCCCGCGCCAAAAAT 60.007 52.632 0.00 0.00 0.00 1.82
69 70 0.818445 TAGTGTTCCCGCGCCAAAAA 60.818 50.000 0.00 0.00 0.00 1.94
70 71 0.606944 ATAGTGTTCCCGCGCCAAAA 60.607 50.000 0.00 0.00 0.00 2.44
71 72 1.003112 ATAGTGTTCCCGCGCCAAA 60.003 52.632 0.00 0.00 0.00 3.28
72 73 1.743623 CATAGTGTTCCCGCGCCAA 60.744 57.895 0.00 0.00 0.00 4.52
73 74 2.125310 CATAGTGTTCCCGCGCCA 60.125 61.111 0.00 0.00 0.00 5.69
74 75 1.303091 AAACATAGTGTTCCCGCGCC 61.303 55.000 0.00 0.00 40.14 6.53
75 76 0.179200 CAAACATAGTGTTCCCGCGC 60.179 55.000 0.00 0.00 40.14 6.86
76 77 1.434555 TCAAACATAGTGTTCCCGCG 58.565 50.000 0.00 0.00 40.14 6.46
77 78 4.434713 AATTCAAACATAGTGTTCCCGC 57.565 40.909 0.00 0.00 40.14 6.13
78 79 5.861787 GGAAAATTCAAACATAGTGTTCCCG 59.138 40.000 0.00 0.00 40.14 5.14
79 80 5.861787 CGGAAAATTCAAACATAGTGTTCCC 59.138 40.000 0.00 0.00 40.14 3.97
80 81 6.362283 CACGGAAAATTCAAACATAGTGTTCC 59.638 38.462 0.00 0.00 40.14 3.62
81 82 6.362283 CCACGGAAAATTCAAACATAGTGTTC 59.638 38.462 0.00 0.00 40.14 3.18
82 83 6.212955 CCACGGAAAATTCAAACATAGTGTT 58.787 36.000 0.00 0.00 43.41 3.32
83 84 5.768317 CCACGGAAAATTCAAACATAGTGT 58.232 37.500 0.00 0.00 0.00 3.55
84 85 4.621034 GCCACGGAAAATTCAAACATAGTG 59.379 41.667 0.00 0.00 0.00 2.74
85 86 4.522789 AGCCACGGAAAATTCAAACATAGT 59.477 37.500 0.00 0.00 0.00 2.12
86 87 4.858692 CAGCCACGGAAAATTCAAACATAG 59.141 41.667 0.00 0.00 0.00 2.23
87 88 4.321601 CCAGCCACGGAAAATTCAAACATA 60.322 41.667 0.00 0.00 0.00 2.29
88 89 3.554752 CCAGCCACGGAAAATTCAAACAT 60.555 43.478 0.00 0.00 0.00 2.71
89 90 2.223923 CCAGCCACGGAAAATTCAAACA 60.224 45.455 0.00 0.00 0.00 2.83
90 91 2.403259 CCAGCCACGGAAAATTCAAAC 58.597 47.619 0.00 0.00 0.00 2.93
91 92 1.342819 CCCAGCCACGGAAAATTCAAA 59.657 47.619 0.00 0.00 0.00 2.69
92 93 0.965439 CCCAGCCACGGAAAATTCAA 59.035 50.000 0.00 0.00 0.00 2.69
93 94 0.897863 CCCCAGCCACGGAAAATTCA 60.898 55.000 0.00 0.00 0.00 2.57
94 95 1.604147 CCCCCAGCCACGGAAAATTC 61.604 60.000 0.00 0.00 0.00 2.17
95 96 1.609210 CCCCCAGCCACGGAAAATT 60.609 57.895 0.00 0.00 0.00 1.82
96 97 2.037208 CCCCCAGCCACGGAAAAT 59.963 61.111 0.00 0.00 0.00 1.82
118 119 3.417275 CTAGTCACGCCTCCAGCCG 62.417 68.421 0.00 0.00 38.78 5.52
119 120 2.496817 CTAGTCACGCCTCCAGCC 59.503 66.667 0.00 0.00 38.78 4.85
120 121 2.010582 CTCCTAGTCACGCCTCCAGC 62.011 65.000 0.00 0.00 38.52 4.85
121 122 2.010582 GCTCCTAGTCACGCCTCCAG 62.011 65.000 0.00 0.00 0.00 3.86
122 123 2.052690 GCTCCTAGTCACGCCTCCA 61.053 63.158 0.00 0.00 0.00 3.86
123 124 0.465824 TAGCTCCTAGTCACGCCTCC 60.466 60.000 0.00 0.00 0.00 4.30
124 125 0.948678 CTAGCTCCTAGTCACGCCTC 59.051 60.000 0.00 0.00 30.16 4.70
125 126 0.466555 CCTAGCTCCTAGTCACGCCT 60.467 60.000 0.00 0.00 32.62 5.52
126 127 2.034607 CCTAGCTCCTAGTCACGCC 58.965 63.158 0.00 0.00 32.62 5.68
127 128 1.360911 GCCTAGCTCCTAGTCACGC 59.639 63.158 0.00 0.00 32.62 5.34
128 129 1.787057 CGGCCTAGCTCCTAGTCACG 61.787 65.000 0.00 0.00 32.62 4.35
129 130 0.465824 TCGGCCTAGCTCCTAGTCAC 60.466 60.000 0.00 0.00 32.62 3.67
130 131 0.465824 GTCGGCCTAGCTCCTAGTCA 60.466 60.000 0.00 0.00 32.62 3.41
131 132 1.174078 GGTCGGCCTAGCTCCTAGTC 61.174 65.000 0.00 0.00 32.62 2.59
132 133 1.152715 GGTCGGCCTAGCTCCTAGT 60.153 63.158 0.00 0.00 32.62 2.57
133 134 1.904378 GGGTCGGCCTAGCTCCTAG 60.904 68.421 5.77 0.00 34.16 3.02
134 135 2.197875 GGGTCGGCCTAGCTCCTA 59.802 66.667 5.77 0.00 34.45 2.94
135 136 4.862823 GGGGTCGGCCTAGCTCCT 62.863 72.222 5.77 0.00 34.45 3.69
137 138 3.541713 CTGGGGTCGGCCTAGCTC 61.542 72.222 5.77 2.45 34.45 4.09
148 149 4.342086 TAGTTCGGCCCCTGGGGT 62.342 66.667 31.95 14.37 46.51 4.95
150 151 4.176752 GCTAGTTCGGCCCCTGGG 62.177 72.222 5.50 5.50 38.57 4.45
151 152 4.530857 CGCTAGTTCGGCCCCTGG 62.531 72.222 0.00 0.00 0.00 4.45
177 178 2.917227 AAAAACTGCGGCCTGGGG 60.917 61.111 0.00 0.00 0.00 4.96
178 179 2.650778 GAAAAACTGCGGCCTGGG 59.349 61.111 0.00 0.00 0.00 4.45
179 180 2.255252 CGAAAAACTGCGGCCTGG 59.745 61.111 0.00 0.00 0.00 4.45
180 181 2.255252 CCGAAAAACTGCGGCCTG 59.745 61.111 0.00 0.00 41.17 4.85
186 187 3.670377 AGGGCGCCGAAAAACTGC 61.670 61.111 22.54 2.36 0.00 4.40
187 188 2.255252 CAGGGCGCCGAAAAACTG 59.745 61.111 22.54 16.90 0.00 3.16
188 189 2.983592 CCAGGGCGCCGAAAAACT 60.984 61.111 22.54 7.71 0.00 2.66
189 190 4.050934 CCCAGGGCGCCGAAAAAC 62.051 66.667 22.54 4.96 0.00 2.43
210 211 2.892425 GCATCTCCAGCCGTTCGG 60.892 66.667 6.90 6.90 0.00 4.30
211 212 1.880340 GAGCATCTCCAGCCGTTCG 60.880 63.158 0.00 0.00 0.00 3.95
212 213 4.116878 GAGCATCTCCAGCCGTTC 57.883 61.111 0.00 0.00 0.00 3.95
223 224 0.244721 GCAAACCCACCAAGAGCATC 59.755 55.000 0.00 0.00 0.00 3.91
224 225 0.469705 TGCAAACCCACCAAGAGCAT 60.470 50.000 0.00 0.00 0.00 3.79
225 226 1.076412 TGCAAACCCACCAAGAGCA 60.076 52.632 0.00 0.00 0.00 4.26
226 227 0.823356 TCTGCAAACCCACCAAGAGC 60.823 55.000 0.00 0.00 0.00 4.09
227 228 0.954452 GTCTGCAAACCCACCAAGAG 59.046 55.000 0.00 0.00 0.00 2.85
228 229 0.257328 TGTCTGCAAACCCACCAAGA 59.743 50.000 0.00 0.00 0.00 3.02
229 230 1.000060 CATGTCTGCAAACCCACCAAG 60.000 52.381 0.00 0.00 0.00 3.61
230 231 1.039068 CATGTCTGCAAACCCACCAA 58.961 50.000 0.00 0.00 0.00 3.67
288 289 6.422776 ACTAAAACCATGTTTCATAGCTCG 57.577 37.500 0.00 0.00 0.00 5.03
303 304 3.005791 AGTGAATGCTGCCAACTAAAACC 59.994 43.478 0.00 0.00 0.00 3.27
305 306 3.058293 CGAGTGAATGCTGCCAACTAAAA 60.058 43.478 0.00 0.00 0.00 1.52
309 310 0.957395 CCGAGTGAATGCTGCCAACT 60.957 55.000 0.00 0.00 0.00 3.16
310 311 1.237285 ACCGAGTGAATGCTGCCAAC 61.237 55.000 0.00 0.00 0.00 3.77
332 335 4.640771 AGGAGTTTGATTCTGCCAACTA 57.359 40.909 0.00 0.00 0.00 2.24
333 336 3.515602 AGGAGTTTGATTCTGCCAACT 57.484 42.857 0.00 0.00 0.00 3.16
334 337 3.569701 TCAAGGAGTTTGATTCTGCCAAC 59.430 43.478 0.00 0.00 40.82 3.77
335 338 3.831323 TCAAGGAGTTTGATTCTGCCAA 58.169 40.909 0.00 0.00 40.82 4.52
336 339 3.507162 TCAAGGAGTTTGATTCTGCCA 57.493 42.857 0.00 0.00 40.82 4.92
337 340 4.279420 ACTTTCAAGGAGTTTGATTCTGCC 59.721 41.667 0.00 0.00 44.90 4.85
373 383 5.240623 TGTCCACCAATAGTTTGTTCATGTC 59.759 40.000 0.00 0.00 0.00 3.06
434 444 7.925483 TGTTTAAATGTTTCCAATCTCCACAAG 59.075 33.333 0.00 0.00 0.00 3.16
507 522 7.251281 ACAAGAAAGCTTACTCTCAAAACAAC 58.749 34.615 0.00 0.00 31.81 3.32
587 622 8.000709 TCATGGCTACCTTATTGATCTCAAATT 58.999 33.333 0.00 0.00 39.55 1.82
761 2840 8.799367 GTGGTTAGTTTAGTGGGTAATTTTGAT 58.201 33.333 0.00 0.00 0.00 2.57
762 2841 7.231115 GGTGGTTAGTTTAGTGGGTAATTTTGA 59.769 37.037 0.00 0.00 0.00 2.69
791 2870 1.668628 CGTAGGGTTGCAATGTTTGGC 60.669 52.381 0.59 0.00 0.00 4.52
816 2895 1.202428 GGAGATGGCTAGTGACGGTTC 60.202 57.143 0.00 0.00 0.00 3.62
872 2951 6.434018 AGCAAGCTAAGAATGATTCTCAAC 57.566 37.500 8.32 1.03 39.61 3.18
886 2965 2.100916 GACGTATGGAGGAGCAAGCTAA 59.899 50.000 0.00 0.00 0.00 3.09
1060 3142 1.291877 ACGCGCATCTTGGAGAACAC 61.292 55.000 5.73 0.00 0.00 3.32
1539 3621 2.350458 GGGGTTGTAGCCGTACGGA 61.350 63.158 37.62 15.62 36.39 4.69
1787 3878 3.478394 GCATGCAAGACGCGTCGA 61.478 61.111 31.56 18.03 46.97 4.20
1868 3959 1.414181 TCTGATGCTTCGAAGGGATCC 59.586 52.381 25.77 1.92 31.89 3.36
1910 4001 1.075542 TCGCAACGCACTTTCCATAG 58.924 50.000 0.00 0.00 0.00 2.23
1914 4005 1.713932 GAAAATCGCAACGCACTTTCC 59.286 47.619 0.00 0.00 0.00 3.13
1915 4006 2.650608 AGAAAATCGCAACGCACTTTC 58.349 42.857 0.00 0.00 0.00 2.62
1916 4007 2.774439 AGAAAATCGCAACGCACTTT 57.226 40.000 0.00 0.00 0.00 2.66
2027 4124 8.925161 TGGCAATGAACTAGTTTATTTATTGC 57.075 30.769 26.29 26.29 44.91 3.56
2068 4171 3.365164 GGCTATGTACCTCGAACGAGATC 60.365 52.174 22.96 13.50 44.53 2.75
2114 4218 7.201401 GCCCAACATTTTTGTAAACGATATCAC 60.201 37.037 3.12 0.00 0.00 3.06
2128 4232 3.320541 TCATCAGTTCGCCCAACATTTTT 59.679 39.130 0.00 0.00 37.48 1.94
2132 4236 2.086869 CTTCATCAGTTCGCCCAACAT 58.913 47.619 0.00 0.00 37.48 2.71
2133 4237 1.202758 ACTTCATCAGTTCGCCCAACA 60.203 47.619 0.00 0.00 37.48 3.33
2134 4238 1.464997 GACTTCATCAGTTCGCCCAAC 59.535 52.381 0.00 0.00 35.01 3.77
2136 4240 0.389817 CGACTTCATCAGTTCGCCCA 60.390 55.000 0.00 0.00 35.01 5.36
2137 4241 0.108804 TCGACTTCATCAGTTCGCCC 60.109 55.000 0.00 0.00 35.01 6.13
2138 4242 1.272781 CTCGACTTCATCAGTTCGCC 58.727 55.000 0.00 0.00 35.01 5.54
2139 4243 0.642800 GCTCGACTTCATCAGTTCGC 59.357 55.000 0.00 0.00 35.01 4.70
2140 4244 2.270275 AGCTCGACTTCATCAGTTCG 57.730 50.000 0.00 0.00 35.01 3.95
2155 4259 7.100409 ACAACTAAAGAGTCCTGATAAAGCTC 58.900 38.462 0.00 0.00 33.58 4.09
2157 4261 8.950208 ATACAACTAAAGAGTCCTGATAAAGC 57.050 34.615 0.00 0.00 33.58 3.51
2190 4294 8.940952 CAATTCCCCGCAAAAGATAAAATAAAA 58.059 29.630 0.00 0.00 0.00 1.52
2193 4297 7.176589 ACAATTCCCCGCAAAAGATAAAATA 57.823 32.000 0.00 0.00 0.00 1.40
2194 4298 6.048732 ACAATTCCCCGCAAAAGATAAAAT 57.951 33.333 0.00 0.00 0.00 1.82
2195 4299 5.476091 ACAATTCCCCGCAAAAGATAAAA 57.524 34.783 0.00 0.00 0.00 1.52
2196 4300 6.783708 ATACAATTCCCCGCAAAAGATAAA 57.216 33.333 0.00 0.00 0.00 1.40
2197 4301 7.776030 TCTTATACAATTCCCCGCAAAAGATAA 59.224 33.333 0.00 0.00 0.00 1.75
2198 4302 7.284074 TCTTATACAATTCCCCGCAAAAGATA 58.716 34.615 0.00 0.00 0.00 1.98
2199 4303 6.126409 TCTTATACAATTCCCCGCAAAAGAT 58.874 36.000 0.00 0.00 0.00 2.40
2200 4304 5.502079 TCTTATACAATTCCCCGCAAAAGA 58.498 37.500 0.00 0.00 0.00 2.52
2201 4305 5.588648 TCTCTTATACAATTCCCCGCAAAAG 59.411 40.000 0.00 0.00 0.00 2.27
2202 4306 5.502079 TCTCTTATACAATTCCCCGCAAAA 58.498 37.500 0.00 0.00 0.00 2.44
2203 4307 5.105567 TCTCTTATACAATTCCCCGCAAA 57.894 39.130 0.00 0.00 0.00 3.68
2204 4308 4.764050 TCTCTTATACAATTCCCCGCAA 57.236 40.909 0.00 0.00 0.00 4.85
2205 4309 4.593206 AGATCTCTTATACAATTCCCCGCA 59.407 41.667 0.00 0.00 0.00 5.69
2206 4310 5.153950 AGATCTCTTATACAATTCCCCGC 57.846 43.478 0.00 0.00 0.00 6.13
2207 4311 7.667557 TGTAAGATCTCTTATACAATTCCCCG 58.332 38.462 0.00 0.00 40.20 5.73
2305 4409 7.031372 TGGCGAAACACACTTAGTAAGTATAG 58.969 38.462 15.13 10.31 40.46 1.31
2306 4410 6.923012 TGGCGAAACACACTTAGTAAGTATA 58.077 36.000 15.13 0.00 40.46 1.47
2307 4411 5.786311 TGGCGAAACACACTTAGTAAGTAT 58.214 37.500 15.13 1.02 40.46 2.12
2308 4412 5.199024 TGGCGAAACACACTTAGTAAGTA 57.801 39.130 15.13 0.00 40.46 2.24
2310 4414 5.607119 ATTGGCGAAACACACTTAGTAAG 57.393 39.130 8.41 8.41 0.00 2.34
2311 4415 6.380095 AAATTGGCGAAACACACTTAGTAA 57.620 33.333 0.00 0.00 0.00 2.24
2312 4416 6.380095 AAAATTGGCGAAACACACTTAGTA 57.620 33.333 0.00 0.00 0.00 1.82
2383 4488 6.750148 AGCACACGAACCCATAAAAATTTAA 58.250 32.000 0.00 0.00 0.00 1.52
2390 4495 3.965379 TCTAGCACACGAACCCATAAA 57.035 42.857 0.00 0.00 0.00 1.40
2416 4521 6.128090 CCCTCGTACTAAATTCTGGAAAAACC 60.128 42.308 0.00 0.00 39.54 3.27
2418 4523 5.413523 GCCCTCGTACTAAATTCTGGAAAAA 59.586 40.000 0.00 0.00 0.00 1.94
2419 4524 4.939439 GCCCTCGTACTAAATTCTGGAAAA 59.061 41.667 0.00 0.00 0.00 2.29
2430 4535 4.197498 GCGCGGCCCTCGTACTAA 62.197 66.667 8.83 0.00 41.72 2.24
2445 4550 3.437795 CTTTGCTGGGCCAGAGCG 61.438 66.667 37.07 16.84 39.47 5.03
2459 4566 5.278907 GCAAAAATAAAAATGGGCTGGCTTT 60.279 36.000 0.00 0.00 0.00 3.51
2471 4578 5.290386 CAGGTACGTGGGCAAAAATAAAAA 58.710 37.500 7.69 0.00 0.00 1.94
2474 4581 2.229302 GCAGGTACGTGGGCAAAAATAA 59.771 45.455 16.75 0.00 0.00 1.40
2476 4583 0.601057 GCAGGTACGTGGGCAAAAAT 59.399 50.000 16.75 0.00 0.00 1.82
2489 4596 9.174166 GTGAGGAAAATAGAATTTTAGCAGGTA 57.826 33.333 0.00 0.00 0.00 3.08
2490 4597 7.669722 TGTGAGGAAAATAGAATTTTAGCAGGT 59.330 33.333 0.00 0.00 0.00 4.00
2491 4598 8.055279 TGTGAGGAAAATAGAATTTTAGCAGG 57.945 34.615 0.00 0.00 0.00 4.85
2493 4600 8.522830 CCTTGTGAGGAAAATAGAATTTTAGCA 58.477 33.333 0.00 0.00 46.74 3.49
2495 4602 9.846248 CACCTTGTGAGGAAAATAGAATTTTAG 57.154 33.333 0.00 0.00 46.74 1.85
2496 4603 9.581289 TCACCTTGTGAGGAAAATAGAATTTTA 57.419 29.630 0.00 0.00 46.74 1.52
2512 4620 5.042463 TCCAACTATTTGTCACCTTGTGA 57.958 39.130 0.00 0.00 40.50 3.58
2514 4622 3.821033 GCTCCAACTATTTGTCACCTTGT 59.179 43.478 0.00 0.00 0.00 3.16
2520 4628 4.002906 ACGAAGCTCCAACTATTTGTCA 57.997 40.909 0.00 0.00 0.00 3.58
2531 4639 1.544691 GTTGTCCTCTACGAAGCTCCA 59.455 52.381 0.00 0.00 0.00 3.86
2533 4641 2.488545 TCAGTTGTCCTCTACGAAGCTC 59.511 50.000 0.00 0.00 0.00 4.09
2541 4649 5.396772 CCAGCCAATTATCAGTTGTCCTCTA 60.397 44.000 0.00 0.00 0.00 2.43
2543 4651 3.629398 CCAGCCAATTATCAGTTGTCCTC 59.371 47.826 0.00 0.00 0.00 3.71
2547 4655 2.102578 GGCCAGCCAATTATCAGTTGT 58.897 47.619 3.12 0.00 35.81 3.32
2552 4660 2.475339 AATGGGCCAGCCAATTATCA 57.525 45.000 13.78 0.00 37.94 2.15
2553 4661 3.843893 AAAATGGGCCAGCCAATTATC 57.156 42.857 13.78 0.00 38.73 1.75
2554 4662 3.781965 AGAAAAATGGGCCAGCCAATTAT 59.218 39.130 13.78 4.40 38.73 1.28
2559 4667 1.072015 CAAAGAAAAATGGGCCAGCCA 59.928 47.619 13.78 0.00 37.98 4.75
2562 4670 4.512571 CAGAAACAAAGAAAAATGGGCCAG 59.487 41.667 13.78 0.00 0.00 4.85
2598 4706 8.588642 AGAGATAGGGGAAGGAGAATAAAATT 57.411 34.615 0.00 0.00 0.00 1.82
2599 4707 8.588642 AAGAGATAGGGGAAGGAGAATAAAAT 57.411 34.615 0.00 0.00 0.00 1.82
2705 4835 5.640218 ACGAACACAATTTTGCAAATCTG 57.360 34.783 13.65 14.96 0.00 2.90
2709 4839 7.963981 TCAAAATACGAACACAATTTTGCAAA 58.036 26.923 8.05 8.05 44.51 3.68
2712 4842 8.813263 TTTTCAAAATACGAACACAATTTTGC 57.187 26.923 12.58 0.00 44.51 3.68


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

AutoCloner maintained by Alex Coulton.