Multiple sequence alignment - TraesCS2A01G247200

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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 TraesCS2A01G247200 chr2A 100.000 2201 0 0 1 2201 365061701 365063901 0.000000e+00 4065.0
1 TraesCS2A01G247200 chr2A 93.899 1885 102 8 328 2201 365070319 365072201 0.000000e+00 2832.0
2 TraesCS2A01G247200 chr2A 86.614 254 29 5 1673 1923 118168861 118168610 2.150000e-70 276.0
3 TraesCS2A01G247200 chr2A 73.506 502 96 23 1592 2068 642963925 642964414 2.930000e-34 156.0
4 TraesCS2A01G247200 chr5A 91.975 1894 125 8 328 2195 433008645 433010537 0.000000e+00 2630.0
5 TraesCS2A01G247200 chr5A 91.144 1897 121 15 329 2198 432991195 432993071 0.000000e+00 2529.0
6 TraesCS2A01G247200 chr5A 88.259 247 26 3 1956 2201 436143661 436143417 2.140000e-75 292.0
7 TraesCS2A01G247200 chr6A 89.335 947 84 9 498 1431 119090948 119091890 0.000000e+00 1173.0
8 TraesCS2A01G247200 chr6A 88.235 1003 87 13 340 1316 119033783 119034780 0.000000e+00 1170.0
9 TraesCS2A01G247200 chr6A 89.956 229 22 1 879 1106 277221362 277221590 5.940000e-76 294.0
10 TraesCS2A01G247200 chr6A 87.179 234 28 2 879 1110 277234393 277234626 4.660000e-67 265.0
11 TraesCS2A01G247200 chr6A 86.631 187 12 6 328 501 119087286 119087472 6.200000e-46 195.0
12 TraesCS2A01G247200 chr2D 93.093 333 20 3 1 332 152087744 152088074 3.290000e-133 484.0
13 TraesCS2A01G247200 chr2D 92.814 334 21 3 1 332 24125970 24125638 4.250000e-132 481.0
14 TraesCS2A01G247200 chr2D 92.814 334 21 3 1 332 591472343 591472011 4.250000e-132 481.0
15 TraesCS2A01G247200 chr2D 86.885 305 36 4 1584 1885 142310898 142310595 2.710000e-89 339.0
16 TraesCS2A01G247200 chr2D 79.394 330 54 12 440 761 566514426 566514103 1.020000e-53 220.0
17 TraesCS2A01G247200 chr2D 82.110 218 36 3 485 701 296124452 296124667 1.340000e-42 183.0
18 TraesCS2A01G247200 chr7D 92.793 333 20 3 1 332 103442643 103442314 1.530000e-131 479.0
19 TraesCS2A01G247200 chr7D 92.814 334 19 4 1 332 506759809 506759479 1.530000e-131 479.0
20 TraesCS2A01G247200 chr7D 88.929 280 28 3 1584 1861 247857417 247857695 2.090000e-90 342.0
21 TraesCS2A01G247200 chr7D 86.792 212 27 1 872 1082 292919365 292919154 3.650000e-58 235.0
22 TraesCS2A01G247200 chr3D 92.793 333 20 3 1 332 408791802 408791473 1.530000e-131 479.0
23 TraesCS2A01G247200 chr5D 92.515 334 22 3 1 332 208487966 208488298 1.980000e-130 475.0
24 TraesCS2A01G247200 chr5D 81.098 164 24 7 1076 1235 13367029 13367189 8.250000e-25 124.0
25 TraesCS2A01G247200 chr4D 92.515 334 21 4 1 332 340623407 340623076 1.980000e-130 475.0
26 TraesCS2A01G247200 chr4D 79.331 329 54 11 440 760 382923957 382924279 3.680000e-53 219.0
27 TraesCS2A01G247200 chr1D 92.515 334 21 4 1 332 384201012 384201343 1.980000e-130 475.0
28 TraesCS2A01G247200 chr1D 89.474 247 25 1 1956 2201 300296642 300296396 5.900000e-81 311.0
29 TraesCS2A01G247200 chr1D 87.854 247 29 1 1956 2201 300303910 300303664 2.760000e-74 289.0
30 TraesCS2A01G247200 chr1D 83.436 163 22 5 1076 1235 200593417 200593577 1.760000e-31 147.0
31 TraesCS2A01G247200 chr6B 89.619 289 25 4 1916 2201 96872864 96873150 1.610000e-96 363.0
32 TraesCS2A01G247200 chr2B 86.348 293 39 1 1076 1368 474361689 474361398 3.530000e-83 318.0
33 TraesCS2A01G247200 chr2B 85.455 275 40 0 1097 1371 765204717 765204991 9.940000e-74 287.0
34 TraesCS2A01G247200 chr3A 87.352 253 26 6 1673 1922 607518267 607518018 3.580000e-73 285.0
35 TraesCS2A01G247200 chr3A 86.561 253 28 6 1673 1922 152633678 152633927 7.740000e-70 274.0
36 TraesCS2A01G247200 chr7B 87.500 248 26 5 1956 2201 461326565 461326809 4.630000e-72 281.0
37 TraesCS2A01G247200 chr7B 87.124 233 28 2 880 1110 490568281 490568049 1.680000e-66 263.0
38 TraesCS2A01G247200 chr7A 87.008 254 28 5 1673 1923 207590849 207590598 4.630000e-72 281.0
39 TraesCS2A01G247200 chr4A 87.149 249 30 2 1954 2201 159141921 159141674 4.630000e-72 281.0
40 TraesCS2A01G247200 chr4A 87.500 72 4 5 444 512 501081776 501081845 6.520000e-11 78.7
41 TraesCS2A01G247200 chr4B 81.373 306 42 14 444 740 59936657 59936956 3.650000e-58 235.0
42 TraesCS2A01G247200 chr4B 81.150 313 42 14 444 747 59978208 59978512 3.650000e-58 235.0
43 TraesCS2A01G247200 chr4B 91.176 68 2 4 444 508 232227606 232227540 3.010000e-14 89.8
44 TraesCS2A01G247200 chr5B 76.432 454 79 22 328 761 442111354 442111799 1.020000e-53 220.0
45 TraesCS2A01G247200 chr5B 78.313 332 56 12 440 761 265065826 265066151 1.330000e-47 200.0


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 TraesCS2A01G247200 chr2A 365061701 365063901 2200 False 4065 4065 100.000 1 2201 1 chr2A.!!$F1 2200
1 TraesCS2A01G247200 chr2A 365070319 365072201 1882 False 2832 2832 93.899 328 2201 1 chr2A.!!$F2 1873
2 TraesCS2A01G247200 chr5A 433008645 433010537 1892 False 2630 2630 91.975 328 2195 1 chr5A.!!$F2 1867
3 TraesCS2A01G247200 chr5A 432991195 432993071 1876 False 2529 2529 91.144 329 2198 1 chr5A.!!$F1 1869
4 TraesCS2A01G247200 chr6A 119033783 119034780 997 False 1170 1170 88.235 340 1316 1 chr6A.!!$F1 976
5 TraesCS2A01G247200 chr6A 119087286 119091890 4604 False 684 1173 87.983 328 1431 2 chr6A.!!$F4 1103

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
77 78 0.043334 AGGACCCACCAGCTACATCT 59.957 55.0 0.0 0.0 42.04 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 4779 0.179094 CGGCTACGGTGATTTAGGCA 60.179 55.0 2.9 0.0 40.13 4.75 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
17 18 2.174349 CTTCGCACGCAAGGAAGC 59.826 61.111 0.00 0.00 46.39 3.86
25 26 3.423154 GCAAGGAAGCGTGTCCGG 61.423 66.667 0.00 0.00 43.03 5.14
26 27 2.742372 CAAGGAAGCGTGTCCGGG 60.742 66.667 0.00 0.00 43.03 5.73
27 28 4.699522 AAGGAAGCGTGTCCGGGC 62.700 66.667 0.00 0.00 43.03 6.13
30 31 2.975799 GAAGCGTGTCCGGGCAAA 60.976 61.111 12.16 0.00 33.68 3.68
31 32 2.517402 AAGCGTGTCCGGGCAAAA 60.517 55.556 12.16 0.00 33.68 2.44
32 33 2.065906 GAAGCGTGTCCGGGCAAAAA 62.066 55.000 12.16 0.00 33.68 1.94
50 51 4.834911 AAAAACGATTCGCCCCCT 57.165 50.000 5.86 0.00 0.00 4.79
51 52 2.263153 AAAAACGATTCGCCCCCTG 58.737 52.632 5.86 0.00 0.00 4.45
52 53 0.250989 AAAAACGATTCGCCCCCTGA 60.251 50.000 5.86 0.00 0.00 3.86
53 54 0.958876 AAAACGATTCGCCCCCTGAC 60.959 55.000 5.86 0.00 0.00 3.51
54 55 1.838073 AAACGATTCGCCCCCTGACT 61.838 55.000 5.86 0.00 0.00 3.41
55 56 2.202932 CGATTCGCCCCCTGACTG 60.203 66.667 0.00 0.00 0.00 3.51
56 57 2.514824 GATTCGCCCCCTGACTGC 60.515 66.667 0.00 0.00 0.00 4.40
57 58 3.011517 ATTCGCCCCCTGACTGCT 61.012 61.111 0.00 0.00 0.00 4.24
58 59 1.686325 GATTCGCCCCCTGACTGCTA 61.686 60.000 0.00 0.00 0.00 3.49
59 60 1.690219 ATTCGCCCCCTGACTGCTAG 61.690 60.000 0.00 0.00 0.00 3.42
60 61 3.854669 CGCCCCCTGACTGCTAGG 61.855 72.222 0.00 0.00 35.01 3.02
61 62 2.365635 GCCCCCTGACTGCTAGGA 60.366 66.667 0.00 0.00 37.52 2.94
62 63 2.736826 GCCCCCTGACTGCTAGGAC 61.737 68.421 0.00 0.00 37.52 3.85
63 64 2.066999 CCCCCTGACTGCTAGGACC 61.067 68.421 0.00 0.00 37.52 4.46
64 65 2.066999 CCCCTGACTGCTAGGACCC 61.067 68.421 0.00 0.00 37.52 4.46
65 66 1.306141 CCCTGACTGCTAGGACCCA 60.306 63.158 0.00 0.00 37.52 4.51
66 67 1.617947 CCCTGACTGCTAGGACCCAC 61.618 65.000 0.00 0.00 37.52 4.61
67 68 1.617947 CCTGACTGCTAGGACCCACC 61.618 65.000 0.00 0.00 37.52 4.61
68 69 0.904865 CTGACTGCTAGGACCCACCA 60.905 60.000 0.00 0.00 42.04 4.17
69 70 0.904865 TGACTGCTAGGACCCACCAG 60.905 60.000 0.00 0.00 42.04 4.00
70 71 2.245438 GACTGCTAGGACCCACCAGC 62.245 65.000 0.00 0.00 42.04 4.85
71 72 1.992277 CTGCTAGGACCCACCAGCT 60.992 63.158 0.00 0.00 40.67 4.24
72 73 0.687757 CTGCTAGGACCCACCAGCTA 60.688 60.000 0.00 0.00 40.67 3.32
73 74 0.976073 TGCTAGGACCCACCAGCTAC 60.976 60.000 0.00 0.00 40.67 3.58
74 75 0.976073 GCTAGGACCCACCAGCTACA 60.976 60.000 0.00 0.00 42.04 2.74
75 76 1.794714 CTAGGACCCACCAGCTACAT 58.205 55.000 0.00 0.00 42.04 2.29
76 77 1.689273 CTAGGACCCACCAGCTACATC 59.311 57.143 0.00 0.00 42.04 3.06
77 78 0.043334 AGGACCCACCAGCTACATCT 59.957 55.000 0.00 0.00 42.04 2.90
78 79 0.466124 GGACCCACCAGCTACATCTC 59.534 60.000 0.00 0.00 38.79 2.75
79 80 0.466124 GACCCACCAGCTACATCTCC 59.534 60.000 0.00 0.00 0.00 3.71
80 81 1.330655 ACCCACCAGCTACATCTCCG 61.331 60.000 0.00 0.00 0.00 4.63
81 82 1.227380 CCACCAGCTACATCTCCGC 60.227 63.158 0.00 0.00 0.00 5.54
82 83 1.517361 CACCAGCTACATCTCCGCA 59.483 57.895 0.00 0.00 0.00 5.69
83 84 0.529337 CACCAGCTACATCTCCGCAG 60.529 60.000 0.00 0.00 0.00 5.18
84 85 0.684479 ACCAGCTACATCTCCGCAGA 60.684 55.000 0.00 0.00 0.00 4.26
85 86 0.249238 CCAGCTACATCTCCGCAGAC 60.249 60.000 0.00 0.00 0.00 3.51
86 87 0.457443 CAGCTACATCTCCGCAGACA 59.543 55.000 0.00 0.00 0.00 3.41
87 88 1.134995 CAGCTACATCTCCGCAGACAA 60.135 52.381 0.00 0.00 0.00 3.18
88 89 1.135915 AGCTACATCTCCGCAGACAAG 59.864 52.381 0.00 0.00 0.00 3.16
89 90 1.804372 GCTACATCTCCGCAGACAAGG 60.804 57.143 0.00 0.00 0.00 3.61
90 91 1.751351 CTACATCTCCGCAGACAAGGA 59.249 52.381 0.00 0.00 34.93 3.36
91 92 0.976641 ACATCTCCGCAGACAAGGAA 59.023 50.000 0.00 0.00 35.90 3.36
92 93 1.066573 ACATCTCCGCAGACAAGGAAG 60.067 52.381 0.00 0.00 35.90 3.46
93 94 1.066573 CATCTCCGCAGACAAGGAAGT 60.067 52.381 0.00 0.00 35.90 3.01
94 95 0.318441 TCTCCGCAGACAAGGAAGTG 59.682 55.000 0.00 0.00 35.90 3.16
95 96 1.294659 CTCCGCAGACAAGGAAGTGC 61.295 60.000 0.00 0.00 35.90 4.40
96 97 2.328099 CCGCAGACAAGGAAGTGCC 61.328 63.158 0.00 0.00 31.98 5.01
97 98 2.328099 CGCAGACAAGGAAGTGCCC 61.328 63.158 0.00 0.00 37.37 5.36
98 99 2.328099 GCAGACAAGGAAGTGCCCG 61.328 63.158 0.00 0.00 37.37 6.13
99 100 1.371183 CAGACAAGGAAGTGCCCGA 59.629 57.895 0.00 0.00 37.37 5.14
100 101 0.951040 CAGACAAGGAAGTGCCCGAC 60.951 60.000 0.00 0.00 37.37 4.79
101 102 1.070786 GACAAGGAAGTGCCCGACA 59.929 57.895 0.00 0.00 37.37 4.35
102 103 0.951040 GACAAGGAAGTGCCCGACAG 60.951 60.000 0.00 0.00 37.37 3.51
103 104 1.071471 CAAGGAAGTGCCCGACAGT 59.929 57.895 0.00 0.00 37.37 3.55
104 105 0.951040 CAAGGAAGTGCCCGACAGTC 60.951 60.000 0.00 0.00 37.37 3.51
105 106 2.432628 GGAAGTGCCCGACAGTCG 60.433 66.667 16.50 16.50 40.07 4.18
114 115 3.667282 CGACAGTCGGACCCACGT 61.667 66.667 15.64 0.00 36.00 4.49
115 116 2.049433 GACAGTCGGACCCACGTG 60.049 66.667 9.08 9.08 34.94 4.49
116 117 3.569049 GACAGTCGGACCCACGTGG 62.569 68.421 28.26 28.26 41.37 4.94
125 126 2.047274 CCCACGTGGTCGAAGCAT 60.047 61.111 31.80 0.00 40.62 3.79
126 127 1.216977 CCCACGTGGTCGAAGCATA 59.783 57.895 31.80 0.00 40.62 3.14
127 128 0.179084 CCCACGTGGTCGAAGCATAT 60.179 55.000 31.80 0.00 40.62 1.78
128 129 0.930310 CCACGTGGTCGAAGCATATG 59.070 55.000 26.95 0.00 40.62 1.78
129 130 1.640428 CACGTGGTCGAAGCATATGT 58.360 50.000 7.95 0.00 40.62 2.29
130 131 2.480587 CCACGTGGTCGAAGCATATGTA 60.481 50.000 26.95 0.00 40.62 2.29
131 132 2.789339 CACGTGGTCGAAGCATATGTAG 59.211 50.000 7.95 0.00 40.62 2.74
132 133 1.787155 CGTGGTCGAAGCATATGTAGC 59.213 52.381 4.29 0.00 39.71 3.58
133 134 2.798145 CGTGGTCGAAGCATATGTAGCA 60.798 50.000 4.29 0.00 39.71 3.49
134 135 3.393800 GTGGTCGAAGCATATGTAGCAT 58.606 45.455 4.29 0.00 0.00 3.79
135 136 3.809832 GTGGTCGAAGCATATGTAGCATT 59.190 43.478 4.29 0.00 0.00 3.56
136 137 3.809279 TGGTCGAAGCATATGTAGCATTG 59.191 43.478 4.29 0.00 0.00 2.82
137 138 3.809832 GGTCGAAGCATATGTAGCATTGT 59.190 43.478 4.29 0.00 0.00 2.71
138 139 4.084328 GGTCGAAGCATATGTAGCATTGTC 60.084 45.833 4.29 0.00 0.00 3.18
139 140 4.507756 GTCGAAGCATATGTAGCATTGTCA 59.492 41.667 4.29 0.00 0.00 3.58
140 141 5.178252 GTCGAAGCATATGTAGCATTGTCAT 59.822 40.000 4.29 0.00 0.00 3.06
141 142 5.759763 TCGAAGCATATGTAGCATTGTCATT 59.240 36.000 4.29 0.00 0.00 2.57
142 143 6.073602 TCGAAGCATATGTAGCATTGTCATTC 60.074 38.462 4.29 0.00 0.00 2.67
143 144 6.073385 CGAAGCATATGTAGCATTGTCATTCT 60.073 38.462 4.29 0.00 0.00 2.40
144 145 6.555812 AGCATATGTAGCATTGTCATTCTG 57.444 37.500 4.29 0.00 0.00 3.02
145 146 5.472478 AGCATATGTAGCATTGTCATTCTGG 59.528 40.000 4.29 0.00 0.00 3.86
146 147 5.240183 GCATATGTAGCATTGTCATTCTGGT 59.760 40.000 4.29 0.00 0.00 4.00
147 148 6.567321 GCATATGTAGCATTGTCATTCTGGTC 60.567 42.308 4.29 0.00 0.00 4.02
148 149 3.261580 TGTAGCATTGTCATTCTGGTCG 58.738 45.455 0.00 0.00 0.00 4.79
149 150 2.479566 AGCATTGTCATTCTGGTCGT 57.520 45.000 0.00 0.00 0.00 4.34
150 151 2.079158 AGCATTGTCATTCTGGTCGTG 58.921 47.619 0.00 0.00 0.00 4.35
151 152 2.076100 GCATTGTCATTCTGGTCGTGA 58.924 47.619 0.00 0.00 0.00 4.35
152 153 2.483877 GCATTGTCATTCTGGTCGTGAA 59.516 45.455 0.00 0.00 0.00 3.18
153 154 3.667960 GCATTGTCATTCTGGTCGTGAAC 60.668 47.826 0.00 0.00 0.00 3.18
154 155 1.778334 TGTCATTCTGGTCGTGAACG 58.222 50.000 0.00 0.00 41.45 3.95
155 156 1.067974 TGTCATTCTGGTCGTGAACGT 59.932 47.619 2.37 0.00 40.80 3.99
156 157 1.455786 GTCATTCTGGTCGTGAACGTG 59.544 52.381 2.37 0.00 40.80 4.49
157 158 1.067974 TCATTCTGGTCGTGAACGTGT 59.932 47.619 2.37 0.00 40.80 4.49
158 159 2.293955 TCATTCTGGTCGTGAACGTGTA 59.706 45.455 2.37 0.00 40.80 2.90
159 160 2.124011 TTCTGGTCGTGAACGTGTAC 57.876 50.000 2.37 0.00 40.80 2.90
160 161 1.023502 TCTGGTCGTGAACGTGTACA 58.976 50.000 2.37 0.00 40.80 2.90
161 162 1.610038 TCTGGTCGTGAACGTGTACAT 59.390 47.619 0.00 0.00 40.80 2.29
162 163 2.813172 TCTGGTCGTGAACGTGTACATA 59.187 45.455 0.00 0.00 40.80 2.29
163 164 2.912967 CTGGTCGTGAACGTGTACATAC 59.087 50.000 0.00 0.00 40.80 2.39
164 165 2.292845 TGGTCGTGAACGTGTACATACA 59.707 45.455 0.00 0.00 40.80 2.29
165 166 3.057386 TGGTCGTGAACGTGTACATACAT 60.057 43.478 0.00 0.00 38.63 2.29
166 167 4.155644 TGGTCGTGAACGTGTACATACATA 59.844 41.667 0.00 0.00 38.63 2.29
167 168 4.496895 GGTCGTGAACGTGTACATACATAC 59.503 45.833 0.00 0.00 38.63 2.39
168 169 5.327091 GTCGTGAACGTGTACATACATACT 58.673 41.667 0.00 0.00 38.63 2.12
169 170 5.226565 GTCGTGAACGTGTACATACATACTG 59.773 44.000 0.00 0.00 38.63 2.74
170 171 4.497966 CGTGAACGTGTACATACATACTGG 59.502 45.833 0.00 0.00 38.63 4.00
171 172 5.404946 GTGAACGTGTACATACATACTGGT 58.595 41.667 0.00 0.00 38.63 4.00
172 173 5.514204 GTGAACGTGTACATACATACTGGTC 59.486 44.000 0.00 0.00 38.63 4.02
173 174 4.282950 ACGTGTACATACATACTGGTCG 57.717 45.455 0.00 0.00 38.63 4.79
174 175 3.940852 ACGTGTACATACATACTGGTCGA 59.059 43.478 0.00 0.00 38.63 4.20
175 176 4.577693 ACGTGTACATACATACTGGTCGAT 59.422 41.667 0.00 0.00 38.63 3.59
176 177 4.909880 CGTGTACATACATACTGGTCGATG 59.090 45.833 0.00 0.00 38.63 3.84
177 178 5.505159 CGTGTACATACATACTGGTCGATGT 60.505 44.000 0.00 0.00 38.63 3.06
178 179 6.293027 CGTGTACATACATACTGGTCGATGTA 60.293 42.308 0.00 0.00 41.50 2.29
179 180 7.076362 GTGTACATACATACTGGTCGATGTAG 58.924 42.308 0.00 0.00 40.80 2.74
180 181 6.993902 TGTACATACATACTGGTCGATGTAGA 59.006 38.462 0.00 0.00 40.80 2.59
181 182 6.561737 ACATACATACTGGTCGATGTAGAG 57.438 41.667 0.00 0.00 40.80 2.43
182 183 5.473846 ACATACATACTGGTCGATGTAGAGG 59.526 44.000 0.00 0.00 40.80 3.69
183 184 2.623889 ACATACTGGTCGATGTAGAGGC 59.376 50.000 0.00 0.00 34.52 4.70
184 185 1.306148 TACTGGTCGATGTAGAGGCG 58.694 55.000 0.00 0.00 0.00 5.52
185 186 1.299468 CTGGTCGATGTAGAGGCGC 60.299 63.158 0.00 0.00 0.00 6.53
186 187 2.353607 GGTCGATGTAGAGGCGCG 60.354 66.667 0.00 0.00 0.00 6.86
187 188 3.025176 GTCGATGTAGAGGCGCGC 61.025 66.667 25.94 25.94 0.00 6.86
188 189 3.514362 TCGATGTAGAGGCGCGCA 61.514 61.111 34.42 11.89 0.00 6.09
189 190 3.323136 CGATGTAGAGGCGCGCAC 61.323 66.667 34.42 25.00 0.00 5.34
190 191 3.323136 GATGTAGAGGCGCGCACG 61.323 66.667 34.42 0.00 44.07 5.34
191 192 4.129737 ATGTAGAGGCGCGCACGT 62.130 61.111 34.42 20.51 42.83 4.49
194 195 4.771356 TAGAGGCGCGCACGTGTC 62.771 66.667 34.42 19.48 42.83 3.67
200 201 2.202209 CGCGCACGTGTCGTAGTA 60.202 61.111 25.33 0.00 38.32 1.82
201 202 2.206487 CGCGCACGTGTCGTAGTAG 61.206 63.158 25.33 13.14 38.32 2.57
202 203 1.133253 GCGCACGTGTCGTAGTAGA 59.867 57.895 25.33 0.00 38.32 2.59
203 204 0.856490 GCGCACGTGTCGTAGTAGAG 60.856 60.000 25.33 0.00 38.32 2.43
204 205 0.247576 CGCACGTGTCGTAGTAGAGG 60.248 60.000 18.38 0.00 38.32 3.69
205 206 0.522915 GCACGTGTCGTAGTAGAGGC 60.523 60.000 18.38 0.00 38.32 4.70
206 207 0.247576 CACGTGTCGTAGTAGAGGCG 60.248 60.000 7.58 0.00 38.32 5.52
207 208 0.671781 ACGTGTCGTAGTAGAGGCGT 60.672 55.000 0.00 0.00 38.73 5.68
208 209 0.247576 CGTGTCGTAGTAGAGGCGTG 60.248 60.000 0.00 0.00 0.00 5.34
209 210 0.522915 GTGTCGTAGTAGAGGCGTGC 60.523 60.000 0.00 0.00 0.00 5.34
210 211 0.956902 TGTCGTAGTAGAGGCGTGCA 60.957 55.000 0.00 0.00 0.00 4.57
211 212 0.522915 GTCGTAGTAGAGGCGTGCAC 60.523 60.000 6.82 6.82 0.00 4.57
212 213 1.582937 CGTAGTAGAGGCGTGCACG 60.583 63.158 34.01 34.01 43.27 5.34
213 214 1.505353 GTAGTAGAGGCGTGCACGT 59.495 57.895 36.80 21.31 42.22 4.49
214 215 0.729116 GTAGTAGAGGCGTGCACGTA 59.271 55.000 36.80 20.63 42.22 3.57
215 216 1.012086 TAGTAGAGGCGTGCACGTAG 58.988 55.000 36.80 13.39 42.22 3.51
216 217 1.872679 GTAGAGGCGTGCACGTAGC 60.873 63.158 36.80 25.49 45.96 3.58
228 229 3.836229 GCACGTAGCATGTACACATAC 57.164 47.619 0.00 0.76 44.79 2.39
229 230 2.215587 GCACGTAGCATGTACACATACG 59.784 50.000 23.89 23.89 44.79 3.06
230 231 3.431856 CACGTAGCATGTACACATACGT 58.568 45.455 24.82 24.82 44.76 3.57
231 232 4.590226 CACGTAGCATGTACACATACGTA 58.410 43.478 27.56 0.00 43.16 3.57
232 233 4.435554 CACGTAGCATGTACACATACGTAC 59.564 45.833 27.56 12.55 43.16 3.67
239 240 4.036567 TGTACACATACGTACATCAGCC 57.963 45.455 0.00 0.00 45.18 4.85
240 241 3.444388 TGTACACATACGTACATCAGCCA 59.556 43.478 0.00 0.00 45.18 4.75
241 242 3.165058 ACACATACGTACATCAGCCAG 57.835 47.619 0.00 0.00 0.00 4.85
242 243 2.496070 ACACATACGTACATCAGCCAGT 59.504 45.455 0.00 0.00 0.00 4.00
243 244 2.860136 CACATACGTACATCAGCCAGTG 59.140 50.000 0.00 0.00 0.00 3.66
244 245 2.496070 ACATACGTACATCAGCCAGTGT 59.504 45.455 0.00 0.00 0.00 3.55
245 246 2.647529 TACGTACATCAGCCAGTGTG 57.352 50.000 0.00 0.00 0.00 3.82
246 247 0.670546 ACGTACATCAGCCAGTGTGC 60.671 55.000 0.00 0.00 0.00 4.57
247 248 0.670239 CGTACATCAGCCAGTGTGCA 60.670 55.000 6.40 0.00 31.54 4.57
248 249 1.522668 GTACATCAGCCAGTGTGCAA 58.477 50.000 6.40 0.00 32.23 4.08
249 250 1.466167 GTACATCAGCCAGTGTGCAAG 59.534 52.381 6.40 0.00 32.23 4.01
250 251 0.109153 ACATCAGCCAGTGTGCAAGA 59.891 50.000 6.40 4.46 0.00 3.02
251 252 1.241165 CATCAGCCAGTGTGCAAGAA 58.759 50.000 6.40 0.00 0.00 2.52
252 253 1.199327 CATCAGCCAGTGTGCAAGAAG 59.801 52.381 6.40 0.00 0.00 2.85
253 254 0.535780 TCAGCCAGTGTGCAAGAAGG 60.536 55.000 6.40 0.00 0.00 3.46
254 255 0.535780 CAGCCAGTGTGCAAGAAGGA 60.536 55.000 6.40 0.00 0.00 3.36
255 256 0.183492 AGCCAGTGTGCAAGAAGGAA 59.817 50.000 6.40 0.00 0.00 3.36
256 257 1.032014 GCCAGTGTGCAAGAAGGAAA 58.968 50.000 0.00 0.00 0.00 3.13
257 258 1.408702 GCCAGTGTGCAAGAAGGAAAA 59.591 47.619 0.00 0.00 0.00 2.29
258 259 2.036346 GCCAGTGTGCAAGAAGGAAAAT 59.964 45.455 0.00 0.00 0.00 1.82
259 260 3.255642 GCCAGTGTGCAAGAAGGAAAATA 59.744 43.478 0.00 0.00 0.00 1.40
260 261 4.798574 CCAGTGTGCAAGAAGGAAAATAC 58.201 43.478 0.00 0.00 0.00 1.89
261 262 4.466828 CAGTGTGCAAGAAGGAAAATACG 58.533 43.478 0.00 0.00 0.00 3.06
262 263 3.502211 AGTGTGCAAGAAGGAAAATACGG 59.498 43.478 0.00 0.00 0.00 4.02
263 264 2.227865 TGTGCAAGAAGGAAAATACGGC 59.772 45.455 0.00 0.00 0.00 5.68
264 265 1.816224 TGCAAGAAGGAAAATACGGCC 59.184 47.619 0.00 0.00 0.00 6.13
265 266 1.816224 GCAAGAAGGAAAATACGGCCA 59.184 47.619 2.24 0.00 0.00 5.36
266 267 2.415491 GCAAGAAGGAAAATACGGCCAC 60.415 50.000 2.24 0.00 0.00 5.01
278 279 2.858729 CGGCCACGTACGTACATAC 58.141 57.895 22.34 10.81 34.81 2.39
288 289 2.953669 CGTACATACGGGCAGTGTC 58.046 57.895 0.00 0.00 45.30 3.67
289 290 0.454600 CGTACATACGGGCAGTGTCT 59.545 55.000 0.00 0.00 45.30 3.41
290 291 1.533338 CGTACATACGGGCAGTGTCTC 60.533 57.143 0.00 0.00 45.30 3.36
291 292 0.736636 TACATACGGGCAGTGTCTCG 59.263 55.000 0.00 5.46 0.00 4.04
292 293 0.963856 ACATACGGGCAGTGTCTCGA 60.964 55.000 12.74 0.00 0.00 4.04
293 294 0.172578 CATACGGGCAGTGTCTCGAA 59.827 55.000 12.74 0.00 0.00 3.71
294 295 0.172803 ATACGGGCAGTGTCTCGAAC 59.827 55.000 12.74 0.00 0.00 3.95
295 296 2.191354 TACGGGCAGTGTCTCGAACG 62.191 60.000 12.74 1.65 0.00 3.95
296 297 3.112709 GGGCAGTGTCTCGAACGC 61.113 66.667 0.00 0.00 38.74 4.84
297 298 3.112709 GGCAGTGTCTCGAACGCC 61.113 66.667 6.05 6.05 39.30 5.68
298 299 2.049063 GCAGTGTCTCGAACGCCT 60.049 61.111 7.40 0.00 39.30 5.52
299 300 1.211969 GCAGTGTCTCGAACGCCTA 59.788 57.895 7.40 0.00 39.30 3.93
300 301 1.071567 GCAGTGTCTCGAACGCCTAC 61.072 60.000 7.40 0.00 39.30 3.18
301 302 0.522180 CAGTGTCTCGAACGCCTACT 59.478 55.000 7.40 0.00 39.30 2.57
302 303 1.736126 CAGTGTCTCGAACGCCTACTA 59.264 52.381 7.40 0.00 39.30 1.82
303 304 2.008329 AGTGTCTCGAACGCCTACTAG 58.992 52.381 7.40 0.00 39.30 2.57
304 305 0.731417 TGTCTCGAACGCCTACTAGC 59.269 55.000 0.00 0.00 0.00 3.42
305 306 0.731417 GTCTCGAACGCCTACTAGCA 59.269 55.000 0.00 0.00 0.00 3.49
306 307 0.731417 TCTCGAACGCCTACTAGCAC 59.269 55.000 0.00 0.00 0.00 4.40
307 308 0.450583 CTCGAACGCCTACTAGCACA 59.549 55.000 0.00 0.00 0.00 4.57
308 309 1.065701 CTCGAACGCCTACTAGCACAT 59.934 52.381 0.00 0.00 0.00 3.21
309 310 2.289820 CTCGAACGCCTACTAGCACATA 59.710 50.000 0.00 0.00 0.00 2.29
310 311 2.032550 TCGAACGCCTACTAGCACATAC 59.967 50.000 0.00 0.00 0.00 2.39
311 312 2.382519 GAACGCCTACTAGCACATACG 58.617 52.381 0.00 0.00 0.00 3.06
312 313 1.386533 ACGCCTACTAGCACATACGT 58.613 50.000 0.00 0.00 0.00 3.57
313 314 2.564771 ACGCCTACTAGCACATACGTA 58.435 47.619 0.00 0.00 0.00 3.57
314 315 3.144506 ACGCCTACTAGCACATACGTAT 58.855 45.455 1.14 1.14 0.00 3.06
315 316 3.058432 ACGCCTACTAGCACATACGTATG 60.058 47.826 29.48 29.48 39.55 2.39
316 317 3.669824 CGCCTACTAGCACATACGTATGG 60.670 52.174 32.83 23.70 38.00 2.74
317 318 3.834610 CCTACTAGCACATACGTATGGC 58.165 50.000 32.83 29.91 38.00 4.40
318 319 2.814280 ACTAGCACATACGTATGGCC 57.186 50.000 32.83 23.84 38.00 5.36
319 320 2.036387 ACTAGCACATACGTATGGCCA 58.964 47.619 32.83 22.21 38.00 5.36
320 321 2.035961 ACTAGCACATACGTATGGCCAG 59.964 50.000 32.83 29.16 38.00 4.85
321 322 0.106708 AGCACATACGTATGGCCAGG 59.893 55.000 32.83 19.59 38.00 4.45
322 323 0.884704 GCACATACGTATGGCCAGGG 60.885 60.000 32.83 18.17 38.00 4.45
323 324 0.884704 CACATACGTATGGCCAGGGC 60.885 60.000 32.83 5.91 38.00 5.19
324 325 1.054406 ACATACGTATGGCCAGGGCT 61.054 55.000 32.83 11.96 41.60 5.19
325 326 0.320771 CATACGTATGGCCAGGGCTC 60.321 60.000 24.95 4.10 41.60 4.70
326 327 1.816863 ATACGTATGGCCAGGGCTCG 61.817 60.000 13.05 17.31 41.60 5.03
483 497 9.413048 GTCAAATAAAAATGTTCGATGGGTTAA 57.587 29.630 0.00 0.00 0.00 2.01
541 4034 3.441572 ACATCACCTGATTGCTTAGTTGC 59.558 43.478 0.00 0.00 31.21 4.17
651 4147 6.811253 AACTTTTGTGACAGTGTCAGTTAA 57.189 33.333 26.11 17.56 43.57 2.01
720 4216 3.197265 GGCGGCTCAAAATATTGCAAAT 58.803 40.909 1.71 0.00 36.45 2.32
856 4352 0.755698 ATCGGGCACTCGTGGATACT 60.756 55.000 0.00 0.00 37.61 2.12
953 4459 0.546598 AACCCTAGCTCCCAAATCCG 59.453 55.000 0.00 0.00 0.00 4.18
1054 4560 2.109799 CCATTCGCCGCTCCATCT 59.890 61.111 0.00 0.00 0.00 2.90
1069 4575 1.836166 CCATCTTCTTCTGGAGCTCCA 59.164 52.381 33.04 33.04 45.30 3.86
1082 4588 4.778415 CTCCACCGCGTCCGTCTG 62.778 72.222 4.92 0.00 0.00 3.51
1126 4632 0.980231 GAGGAGGACCACCAGCATCT 60.980 60.000 10.90 0.00 38.94 2.90
1272 4779 2.832733 TGTTTTCCCCCTTTGTTTCGTT 59.167 40.909 0.00 0.00 0.00 3.85
1321 4828 2.892425 GCCCACAGCGATCTTCGG 60.892 66.667 0.00 0.00 40.84 4.30
1439 4946 2.743538 GCTGCTGATGCGGTGTCA 60.744 61.111 0.00 0.00 46.77 3.58
1459 4966 2.466982 CGATGTTGCCGCTGCTGAT 61.467 57.895 0.70 0.00 38.71 2.90
1488 4995 4.020617 CTTCCCGCTGCTCCACCA 62.021 66.667 0.00 0.00 0.00 4.17
1525 5032 3.557479 CTCATGTGCGCGCGATGT 61.557 61.111 37.18 13.14 0.00 3.06
1658 5165 2.802816 GTTGCTCGGCTGAATATACTGG 59.197 50.000 0.00 0.00 0.00 4.00
1705 5212 7.222224 GCGACTAGCTAGCTTTTGTATTTCTAA 59.778 37.037 24.88 0.00 44.04 2.10
1926 5435 0.531090 GTGTGCGGGTGTGTGTTCTA 60.531 55.000 0.00 0.00 0.00 2.10
2027 5536 2.343484 CCCCCTCCTCGAAATTTACC 57.657 55.000 0.00 0.00 0.00 2.85
2072 5581 4.422073 TGTTTGAATGACACCTGAGTCT 57.578 40.909 0.00 0.00 39.27 3.24
2116 5625 8.750898 GTCAAACTACTGACTGGGATAACCCC 62.751 50.000 5.46 0.80 44.35 4.95
2135 5644 3.909662 GCAATGACATGCGGGTCT 58.090 55.556 8.74 0.00 38.61 3.85
2150 5659 1.575447 GGTCTCCTGGGCCCTTTGAT 61.575 60.000 25.70 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.174349 GCTTCCTTGCGTGCGAAG 59.826 61.111 0.00 4.30 36.82 3.79
8 9 3.423154 CCGGACACGCTTCCTTGC 61.423 66.667 0.00 0.00 39.22 4.01
9 10 2.742372 CCCGGACACGCTTCCTTG 60.742 66.667 0.73 0.00 39.22 3.61
10 11 4.699522 GCCCGGACACGCTTCCTT 62.700 66.667 0.73 0.00 39.22 3.36
13 14 2.065906 TTTTTGCCCGGACACGCTTC 62.066 55.000 0.73 0.00 39.22 3.86
14 15 2.122167 TTTTTGCCCGGACACGCTT 61.122 52.632 0.73 0.00 39.22 4.68
15 16 2.517402 TTTTTGCCCGGACACGCT 60.517 55.556 0.73 0.00 39.22 5.07
33 34 0.250989 TCAGGGGGCGAATCGTTTTT 60.251 50.000 4.07 0.00 0.00 1.94
34 35 0.958876 GTCAGGGGGCGAATCGTTTT 60.959 55.000 4.07 0.00 0.00 2.43
35 36 1.376812 GTCAGGGGGCGAATCGTTT 60.377 57.895 4.07 0.00 0.00 3.60
36 37 2.267961 GTCAGGGGGCGAATCGTT 59.732 61.111 4.07 0.00 0.00 3.85
37 38 2.683933 AGTCAGGGGGCGAATCGT 60.684 61.111 4.07 0.00 0.00 3.73
38 39 2.202932 CAGTCAGGGGGCGAATCG 60.203 66.667 0.00 0.00 0.00 3.34
39 40 1.686325 TAGCAGTCAGGGGGCGAATC 61.686 60.000 0.00 0.00 0.00 2.52
40 41 1.689233 TAGCAGTCAGGGGGCGAAT 60.689 57.895 0.00 0.00 0.00 3.34
41 42 2.284331 TAGCAGTCAGGGGGCGAA 60.284 61.111 0.00 0.00 0.00 4.70
42 43 2.759973 CTAGCAGTCAGGGGGCGA 60.760 66.667 0.00 0.00 0.00 5.54
43 44 3.854669 CCTAGCAGTCAGGGGGCG 61.855 72.222 0.00 0.00 0.00 6.13
44 45 2.365635 TCCTAGCAGTCAGGGGGC 60.366 66.667 0.00 0.00 33.66 5.80
45 46 2.066999 GGTCCTAGCAGTCAGGGGG 61.067 68.421 0.00 0.00 33.66 5.40
46 47 2.066999 GGGTCCTAGCAGTCAGGGG 61.067 68.421 0.00 0.00 33.66 4.79
47 48 1.306141 TGGGTCCTAGCAGTCAGGG 60.306 63.158 0.00 0.00 33.66 4.45
48 49 1.617947 GGTGGGTCCTAGCAGTCAGG 61.618 65.000 0.00 0.00 34.20 3.86
49 50 0.904865 TGGTGGGTCCTAGCAGTCAG 60.905 60.000 2.51 0.00 37.07 3.51
50 51 0.904865 CTGGTGGGTCCTAGCAGTCA 60.905 60.000 22.65 0.00 38.49 3.41
51 52 1.901085 CTGGTGGGTCCTAGCAGTC 59.099 63.158 22.65 0.00 38.49 3.51
52 53 2.294078 GCTGGTGGGTCCTAGCAGT 61.294 63.158 28.69 0.00 43.58 4.40
53 54 0.687757 TAGCTGGTGGGTCCTAGCAG 60.688 60.000 25.63 25.63 44.28 4.24
54 55 0.976073 GTAGCTGGTGGGTCCTAGCA 60.976 60.000 6.96 6.96 40.35 3.49
55 56 0.976073 TGTAGCTGGTGGGTCCTAGC 60.976 60.000 0.00 0.00 39.16 3.42
56 57 1.689273 GATGTAGCTGGTGGGTCCTAG 59.311 57.143 0.00 0.00 37.07 3.02
57 58 1.291033 AGATGTAGCTGGTGGGTCCTA 59.709 52.381 0.00 0.00 37.07 2.94
58 59 0.043334 AGATGTAGCTGGTGGGTCCT 59.957 55.000 0.00 0.00 37.07 3.85
59 60 0.466124 GAGATGTAGCTGGTGGGTCC 59.534 60.000 0.00 0.00 0.00 4.46
60 61 0.466124 GGAGATGTAGCTGGTGGGTC 59.534 60.000 0.00 0.00 0.00 4.46
61 62 1.330655 CGGAGATGTAGCTGGTGGGT 61.331 60.000 0.00 0.00 0.00 4.51
62 63 1.443407 CGGAGATGTAGCTGGTGGG 59.557 63.158 0.00 0.00 0.00 4.61
63 64 1.227380 GCGGAGATGTAGCTGGTGG 60.227 63.158 0.00 0.00 0.00 4.61
64 65 0.529337 CTGCGGAGATGTAGCTGGTG 60.529 60.000 0.00 0.00 0.00 4.17
65 66 0.684479 TCTGCGGAGATGTAGCTGGT 60.684 55.000 0.98 0.00 0.00 4.00
66 67 0.249238 GTCTGCGGAGATGTAGCTGG 60.249 60.000 10.72 0.00 0.00 4.85
67 68 0.457443 TGTCTGCGGAGATGTAGCTG 59.543 55.000 10.72 0.00 0.00 4.24
68 69 1.135915 CTTGTCTGCGGAGATGTAGCT 59.864 52.381 10.72 0.00 0.00 3.32
69 70 1.565305 CTTGTCTGCGGAGATGTAGC 58.435 55.000 10.72 0.00 0.00 3.58
70 71 1.751351 TCCTTGTCTGCGGAGATGTAG 59.249 52.381 10.72 7.83 0.00 2.74
71 72 1.847328 TCCTTGTCTGCGGAGATGTA 58.153 50.000 10.72 0.00 0.00 2.29
72 73 0.976641 TTCCTTGTCTGCGGAGATGT 59.023 50.000 10.72 0.00 0.00 3.06
73 74 1.066573 ACTTCCTTGTCTGCGGAGATG 60.067 52.381 10.72 3.79 0.00 2.90
74 75 1.066573 CACTTCCTTGTCTGCGGAGAT 60.067 52.381 10.72 0.00 0.00 2.75
75 76 0.318441 CACTTCCTTGTCTGCGGAGA 59.682 55.000 0.98 0.98 0.00 3.71
76 77 1.294659 GCACTTCCTTGTCTGCGGAG 61.295 60.000 0.00 0.00 0.00 4.63
77 78 1.301716 GCACTTCCTTGTCTGCGGA 60.302 57.895 0.00 0.00 0.00 5.54
78 79 2.328099 GGCACTTCCTTGTCTGCGG 61.328 63.158 0.00 0.00 0.00 5.69
79 80 2.328099 GGGCACTTCCTTGTCTGCG 61.328 63.158 0.00 0.00 34.39 5.18
80 81 2.328099 CGGGCACTTCCTTGTCTGC 61.328 63.158 0.00 0.00 34.39 4.26
81 82 0.951040 GTCGGGCACTTCCTTGTCTG 60.951 60.000 0.00 0.00 34.39 3.51
82 83 1.371558 GTCGGGCACTTCCTTGTCT 59.628 57.895 0.00 0.00 34.39 3.41
83 84 0.951040 CTGTCGGGCACTTCCTTGTC 60.951 60.000 0.00 0.00 34.39 3.18
84 85 1.071471 CTGTCGGGCACTTCCTTGT 59.929 57.895 0.00 0.00 34.39 3.16
85 86 0.951040 GACTGTCGGGCACTTCCTTG 60.951 60.000 0.00 0.00 34.39 3.61
86 87 1.371558 GACTGTCGGGCACTTCCTT 59.628 57.895 0.00 0.00 34.39 3.36
87 88 2.932234 CGACTGTCGGGCACTTCCT 61.932 63.158 21.78 0.00 36.00 3.36
88 89 2.432628 CGACTGTCGGGCACTTCC 60.433 66.667 21.78 0.00 36.00 3.46
97 98 3.667282 ACGTGGGTCCGACTGTCG 61.667 66.667 22.49 22.49 40.07 4.35
98 99 2.049433 CACGTGGGTCCGACTGTC 60.049 66.667 7.95 0.00 0.00 3.51
99 100 3.612681 CCACGTGGGTCCGACTGT 61.613 66.667 27.57 0.00 0.00 3.55
108 109 0.179084 ATATGCTTCGACCACGTGGG 60.179 55.000 36.47 20.99 44.81 4.61
109 110 0.930310 CATATGCTTCGACCACGTGG 59.070 55.000 32.83 32.83 40.69 4.94
110 111 1.640428 ACATATGCTTCGACCACGTG 58.360 50.000 9.08 9.08 40.69 4.49
111 112 2.798499 GCTACATATGCTTCGACCACGT 60.798 50.000 1.58 0.00 40.69 4.49
112 113 1.787155 GCTACATATGCTTCGACCACG 59.213 52.381 1.58 0.00 41.26 4.94
113 114 2.821546 TGCTACATATGCTTCGACCAC 58.178 47.619 1.58 0.00 0.00 4.16
114 115 3.751479 ATGCTACATATGCTTCGACCA 57.249 42.857 1.58 0.00 0.00 4.02
115 116 3.809832 ACAATGCTACATATGCTTCGACC 59.190 43.478 1.58 0.00 0.00 4.79
116 117 4.507756 TGACAATGCTACATATGCTTCGAC 59.492 41.667 1.58 0.00 0.00 4.20
117 118 4.692228 TGACAATGCTACATATGCTTCGA 58.308 39.130 1.58 0.00 0.00 3.71
118 119 5.602458 ATGACAATGCTACATATGCTTCG 57.398 39.130 1.58 0.00 0.00 3.79
119 120 7.076362 CAGAATGACAATGCTACATATGCTTC 58.924 38.462 1.58 0.00 39.69 3.86
120 121 6.016527 CCAGAATGACAATGCTACATATGCTT 60.017 38.462 1.58 0.00 39.69 3.91
121 122 5.472478 CCAGAATGACAATGCTACATATGCT 59.528 40.000 1.58 0.00 39.69 3.79
122 123 5.240183 ACCAGAATGACAATGCTACATATGC 59.760 40.000 1.58 0.00 39.69 3.14
123 124 6.347160 CGACCAGAATGACAATGCTACATATG 60.347 42.308 0.00 0.00 39.69 1.78
124 125 5.698089 CGACCAGAATGACAATGCTACATAT 59.302 40.000 0.00 0.00 39.69 1.78
125 126 5.049828 CGACCAGAATGACAATGCTACATA 58.950 41.667 0.00 0.00 39.69 2.29
126 127 3.873361 CGACCAGAATGACAATGCTACAT 59.127 43.478 0.00 0.00 39.69 2.29
127 128 3.261580 CGACCAGAATGACAATGCTACA 58.738 45.455 0.00 0.00 39.69 2.74
128 129 3.062639 CACGACCAGAATGACAATGCTAC 59.937 47.826 0.00 0.00 39.69 3.58
129 130 3.056179 TCACGACCAGAATGACAATGCTA 60.056 43.478 0.00 0.00 39.69 3.49
130 131 2.079158 CACGACCAGAATGACAATGCT 58.921 47.619 0.00 0.00 39.69 3.79
131 132 2.076100 TCACGACCAGAATGACAATGC 58.924 47.619 0.00 0.00 39.69 3.56
132 133 3.423515 CGTTCACGACCAGAATGACAATG 60.424 47.826 0.00 0.00 43.02 2.82
133 134 2.736721 CGTTCACGACCAGAATGACAAT 59.263 45.455 0.00 0.00 43.02 2.71
134 135 2.131972 CGTTCACGACCAGAATGACAA 58.868 47.619 0.00 0.00 43.02 3.18
135 136 1.067974 ACGTTCACGACCAGAATGACA 59.932 47.619 6.30 0.00 43.02 3.58
136 137 1.455786 CACGTTCACGACCAGAATGAC 59.544 52.381 6.30 0.00 43.02 3.06
137 138 1.067974 ACACGTTCACGACCAGAATGA 59.932 47.619 6.30 0.00 43.02 2.57
138 139 1.497991 ACACGTTCACGACCAGAATG 58.502 50.000 6.30 0.00 43.02 2.67
139 140 2.034939 TGTACACGTTCACGACCAGAAT 59.965 45.455 6.30 0.00 43.02 2.40
140 141 1.404748 TGTACACGTTCACGACCAGAA 59.595 47.619 6.30 0.00 43.02 3.02
141 142 1.023502 TGTACACGTTCACGACCAGA 58.976 50.000 6.30 0.00 43.02 3.86
142 143 2.060326 ATGTACACGTTCACGACCAG 57.940 50.000 6.30 0.00 43.02 4.00
143 144 2.292845 TGTATGTACACGTTCACGACCA 59.707 45.455 6.30 0.00 43.02 4.02
144 145 2.932498 TGTATGTACACGTTCACGACC 58.068 47.619 6.30 0.00 43.02 4.79
145 146 5.226565 CAGTATGTATGTACACGTTCACGAC 59.773 44.000 6.30 0.00 43.39 4.34
146 147 5.326292 CAGTATGTATGTACACGTTCACGA 58.674 41.667 6.30 0.00 43.39 4.35
147 148 4.497966 CCAGTATGTATGTACACGTTCACG 59.502 45.833 0.00 0.00 46.33 4.35
148 149 5.404946 ACCAGTATGTATGTACACGTTCAC 58.595 41.667 0.00 0.00 39.30 3.18
149 150 5.643664 GACCAGTATGTATGTACACGTTCA 58.356 41.667 0.00 0.00 39.30 3.18
150 151 4.731961 CGACCAGTATGTATGTACACGTTC 59.268 45.833 0.00 0.00 39.30 3.95
151 152 4.395854 TCGACCAGTATGTATGTACACGTT 59.604 41.667 0.00 0.00 39.30 3.99
152 153 3.940852 TCGACCAGTATGTATGTACACGT 59.059 43.478 0.00 0.00 39.30 4.49
153 154 4.541085 TCGACCAGTATGTATGTACACG 57.459 45.455 0.00 0.00 39.30 4.49
154 155 5.828747 ACATCGACCAGTATGTATGTACAC 58.171 41.667 0.00 0.00 39.30 2.90
155 156 6.993902 TCTACATCGACCAGTATGTATGTACA 59.006 38.462 0.00 0.00 37.79 2.90
156 157 7.361031 CCTCTACATCGACCAGTATGTATGTAC 60.361 44.444 0.00 0.00 37.79 2.90
157 158 6.653740 CCTCTACATCGACCAGTATGTATGTA 59.346 42.308 0.00 0.00 37.79 2.29
158 159 5.473846 CCTCTACATCGACCAGTATGTATGT 59.526 44.000 0.00 0.00 37.79 2.29
159 160 5.620205 GCCTCTACATCGACCAGTATGTATG 60.620 48.000 0.00 0.00 37.79 2.39
160 161 4.459685 GCCTCTACATCGACCAGTATGTAT 59.540 45.833 0.00 0.00 37.79 2.29
161 162 3.819337 GCCTCTACATCGACCAGTATGTA 59.181 47.826 0.00 0.00 37.50 2.29
162 163 2.623889 GCCTCTACATCGACCAGTATGT 59.376 50.000 0.00 0.00 39.56 2.29
163 164 2.350868 CGCCTCTACATCGACCAGTATG 60.351 54.545 0.00 0.00 0.00 2.39
164 165 1.880675 CGCCTCTACATCGACCAGTAT 59.119 52.381 0.00 0.00 0.00 2.12
165 166 1.306148 CGCCTCTACATCGACCAGTA 58.694 55.000 0.00 0.00 0.00 2.74
166 167 2.005960 GCGCCTCTACATCGACCAGT 62.006 60.000 0.00 0.00 0.00 4.00
167 168 1.299468 GCGCCTCTACATCGACCAG 60.299 63.158 0.00 0.00 0.00 4.00
168 169 2.805546 GCGCCTCTACATCGACCA 59.194 61.111 0.00 0.00 0.00 4.02
169 170 2.353607 CGCGCCTCTACATCGACC 60.354 66.667 0.00 0.00 0.00 4.79
170 171 3.025176 GCGCGCCTCTACATCGAC 61.025 66.667 23.24 0.00 0.00 4.20
171 172 3.514362 TGCGCGCCTCTACATCGA 61.514 61.111 30.77 1.61 0.00 3.59
172 173 3.323136 GTGCGCGCCTCTACATCG 61.323 66.667 30.77 0.00 0.00 3.84
173 174 3.323136 CGTGCGCGCCTCTACATC 61.323 66.667 30.77 7.51 0.00 3.06
174 175 4.129737 ACGTGCGCGCCTCTACAT 62.130 61.111 30.77 5.08 42.83 2.29
177 178 4.771356 GACACGTGCGCGCCTCTA 62.771 66.667 30.77 6.71 42.83 2.43
183 184 2.202209 TACTACGACACGTGCGCG 60.202 61.111 25.05 24.62 41.39 6.86
184 185 0.856490 CTCTACTACGACACGTGCGC 60.856 60.000 25.05 14.00 41.39 6.09
185 186 0.247576 CCTCTACTACGACACGTGCG 60.248 60.000 24.02 24.02 41.39 5.34
186 187 0.522915 GCCTCTACTACGACACGTGC 60.523 60.000 17.22 7.72 41.39 5.34
187 188 0.247576 CGCCTCTACTACGACACGTG 60.248 60.000 15.48 15.48 41.39 4.49
188 189 0.671781 ACGCCTCTACTACGACACGT 60.672 55.000 1.91 1.91 44.35 4.49
189 190 0.247576 CACGCCTCTACTACGACACG 60.248 60.000 0.00 0.00 0.00 4.49
190 191 0.522915 GCACGCCTCTACTACGACAC 60.523 60.000 0.00 0.00 0.00 3.67
191 192 0.956902 TGCACGCCTCTACTACGACA 60.957 55.000 0.00 0.00 0.00 4.35
192 193 0.522915 GTGCACGCCTCTACTACGAC 60.523 60.000 0.00 0.00 0.00 4.34
193 194 1.798735 GTGCACGCCTCTACTACGA 59.201 57.895 0.00 0.00 0.00 3.43
194 195 1.582937 CGTGCACGCCTCTACTACG 60.583 63.158 28.16 0.00 0.00 3.51
195 196 0.729116 TACGTGCACGCCTCTACTAC 59.271 55.000 37.35 0.00 44.43 2.73
196 197 1.012086 CTACGTGCACGCCTCTACTA 58.988 55.000 37.35 19.56 44.43 1.82
197 198 1.801332 CTACGTGCACGCCTCTACT 59.199 57.895 37.35 19.49 44.43 2.57
198 199 1.872679 GCTACGTGCACGCCTCTAC 60.873 63.158 37.35 17.90 44.43 2.59
199 200 2.488355 GCTACGTGCACGCCTCTA 59.512 61.111 37.35 21.34 44.43 2.43
208 209 2.215587 CGTATGTGTACATGCTACGTGC 59.784 50.000 18.78 0.00 36.91 5.34
209 210 3.431856 ACGTATGTGTACATGCTACGTG 58.568 45.455 26.01 10.40 43.29 4.49
210 211 3.770263 ACGTATGTGTACATGCTACGT 57.230 42.857 23.36 23.36 41.44 3.57
219 220 4.036567 TGGCTGATGTACGTATGTGTAC 57.963 45.455 0.00 3.16 43.95 2.90
220 221 3.697542 ACTGGCTGATGTACGTATGTGTA 59.302 43.478 0.00 0.00 0.00 2.90
221 222 2.496070 ACTGGCTGATGTACGTATGTGT 59.504 45.455 0.00 0.00 0.00 3.72
222 223 2.860136 CACTGGCTGATGTACGTATGTG 59.140 50.000 0.00 0.00 0.00 3.21
223 224 2.496070 ACACTGGCTGATGTACGTATGT 59.504 45.455 0.00 0.00 0.00 2.29
224 225 2.860136 CACACTGGCTGATGTACGTATG 59.140 50.000 0.00 0.00 0.00 2.39
225 226 2.738643 GCACACTGGCTGATGTACGTAT 60.739 50.000 0.00 0.00 0.00 3.06
226 227 1.403647 GCACACTGGCTGATGTACGTA 60.404 52.381 0.00 0.00 0.00 3.57
227 228 0.670546 GCACACTGGCTGATGTACGT 60.671 55.000 0.00 0.00 0.00 3.57
228 229 0.670239 TGCACACTGGCTGATGTACG 60.670 55.000 0.00 0.00 34.04 3.67
229 230 1.466167 CTTGCACACTGGCTGATGTAC 59.534 52.381 0.00 0.00 34.04 2.90
230 231 1.347378 TCTTGCACACTGGCTGATGTA 59.653 47.619 0.00 0.00 34.04 2.29
231 232 0.109153 TCTTGCACACTGGCTGATGT 59.891 50.000 0.00 0.00 34.04 3.06
232 233 1.199327 CTTCTTGCACACTGGCTGATG 59.801 52.381 0.00 0.00 34.04 3.07
233 234 1.531423 CTTCTTGCACACTGGCTGAT 58.469 50.000 0.00 0.00 34.04 2.90
234 235 0.535780 CCTTCTTGCACACTGGCTGA 60.536 55.000 0.00 0.00 34.04 4.26
235 236 0.535780 TCCTTCTTGCACACTGGCTG 60.536 55.000 0.00 0.00 34.04 4.85
236 237 0.183492 TTCCTTCTTGCACACTGGCT 59.817 50.000 0.00 0.00 34.04 4.75
237 238 1.032014 TTTCCTTCTTGCACACTGGC 58.968 50.000 0.00 0.00 0.00 4.85
238 239 4.613622 CGTATTTTCCTTCTTGCACACTGG 60.614 45.833 0.00 0.00 0.00 4.00
239 240 4.466828 CGTATTTTCCTTCTTGCACACTG 58.533 43.478 0.00 0.00 0.00 3.66
240 241 3.502211 CCGTATTTTCCTTCTTGCACACT 59.498 43.478 0.00 0.00 0.00 3.55
241 242 3.821841 CCGTATTTTCCTTCTTGCACAC 58.178 45.455 0.00 0.00 0.00 3.82
242 243 2.227865 GCCGTATTTTCCTTCTTGCACA 59.772 45.455 0.00 0.00 0.00 4.57
243 244 2.415491 GGCCGTATTTTCCTTCTTGCAC 60.415 50.000 0.00 0.00 0.00 4.57
244 245 1.816224 GGCCGTATTTTCCTTCTTGCA 59.184 47.619 0.00 0.00 0.00 4.08
245 246 1.816224 TGGCCGTATTTTCCTTCTTGC 59.184 47.619 0.00 0.00 0.00 4.01
246 247 2.159572 CGTGGCCGTATTTTCCTTCTTG 60.160 50.000 0.00 0.00 0.00 3.02
247 248 2.081462 CGTGGCCGTATTTTCCTTCTT 58.919 47.619 0.00 0.00 0.00 2.52
248 249 1.734163 CGTGGCCGTATTTTCCTTCT 58.266 50.000 0.00 0.00 0.00 2.85
258 259 4.173802 CGTATGTACGTACGTGGCCGTA 62.174 54.545 30.61 18.67 44.20 4.02
259 260 3.500013 CGTATGTACGTACGTGGCCGT 62.500 57.143 30.61 19.60 44.67 5.68
260 261 0.925267 CGTATGTACGTACGTGGCCG 60.925 60.000 30.61 21.00 44.13 6.13
261 262 2.858729 CGTATGTACGTACGTGGCC 58.141 57.895 30.61 17.58 44.13 5.36
271 272 1.533338 CGAGACACTGCCCGTATGTAC 60.533 57.143 0.00 0.00 0.00 2.90
272 273 0.736636 CGAGACACTGCCCGTATGTA 59.263 55.000 0.00 0.00 0.00 2.29
273 274 0.963856 TCGAGACACTGCCCGTATGT 60.964 55.000 0.00 0.00 0.00 2.29
274 275 0.172578 TTCGAGACACTGCCCGTATG 59.827 55.000 0.00 0.00 0.00 2.39
275 276 0.172803 GTTCGAGACACTGCCCGTAT 59.827 55.000 0.00 0.00 0.00 3.06
276 277 1.582968 GTTCGAGACACTGCCCGTA 59.417 57.895 0.00 0.00 0.00 4.02
277 278 2.338984 GTTCGAGACACTGCCCGT 59.661 61.111 0.00 0.00 0.00 5.28
278 279 2.805353 CGTTCGAGACACTGCCCG 60.805 66.667 0.00 0.00 0.00 6.13
279 280 3.112709 GCGTTCGAGACACTGCCC 61.113 66.667 0.00 0.00 0.00 5.36
280 281 2.209064 TAGGCGTTCGAGACACTGCC 62.209 60.000 11.27 11.27 42.76 4.85
281 282 1.071567 GTAGGCGTTCGAGACACTGC 61.072 60.000 0.00 0.00 0.00 4.40
282 283 0.522180 AGTAGGCGTTCGAGACACTG 59.478 55.000 0.00 0.00 0.00 3.66
283 284 2.008329 CTAGTAGGCGTTCGAGACACT 58.992 52.381 0.00 0.00 0.00 3.55
284 285 1.531470 GCTAGTAGGCGTTCGAGACAC 60.531 57.143 0.00 0.00 0.00 3.67
285 286 0.731417 GCTAGTAGGCGTTCGAGACA 59.269 55.000 0.00 0.00 0.00 3.41
286 287 0.731417 TGCTAGTAGGCGTTCGAGAC 59.269 55.000 0.00 0.00 34.52 3.36
287 288 0.731417 GTGCTAGTAGGCGTTCGAGA 59.269 55.000 0.00 0.00 34.52 4.04
288 289 0.450583 TGTGCTAGTAGGCGTTCGAG 59.549 55.000 0.00 0.00 34.52 4.04
289 290 1.100510 ATGTGCTAGTAGGCGTTCGA 58.899 50.000 0.00 0.00 34.52 3.71
290 291 2.382519 GTATGTGCTAGTAGGCGTTCG 58.617 52.381 0.00 0.00 34.52 3.95
291 292 2.223433 ACGTATGTGCTAGTAGGCGTTC 60.223 50.000 0.00 0.00 34.52 3.95
292 293 1.747355 ACGTATGTGCTAGTAGGCGTT 59.253 47.619 0.00 0.00 34.52 4.84
293 294 1.386533 ACGTATGTGCTAGTAGGCGT 58.613 50.000 0.00 0.00 34.52 5.68
294 295 3.489444 CATACGTATGTGCTAGTAGGCG 58.511 50.000 24.46 0.00 34.52 5.52
295 296 3.834610 CCATACGTATGTGCTAGTAGGC 58.165 50.000 28.80 0.00 31.82 3.93
296 297 3.367087 GGCCATACGTATGTGCTAGTAGG 60.367 52.174 30.57 18.10 33.38 3.18
297 298 3.254903 TGGCCATACGTATGTGCTAGTAG 59.745 47.826 30.57 18.27 33.38 2.57
298 299 3.224269 TGGCCATACGTATGTGCTAGTA 58.776 45.455 30.57 19.63 33.38 1.82
299 300 2.035961 CTGGCCATACGTATGTGCTAGT 59.964 50.000 31.26 5.14 35.67 2.57
300 301 2.610479 CCTGGCCATACGTATGTGCTAG 60.610 54.545 31.93 31.93 37.76 3.42
301 302 1.343142 CCTGGCCATACGTATGTGCTA 59.657 52.381 30.57 27.05 33.38 3.49
302 303 0.106708 CCTGGCCATACGTATGTGCT 59.893 55.000 30.57 4.74 33.38 4.40
303 304 0.884704 CCCTGGCCATACGTATGTGC 60.885 60.000 28.80 27.92 31.82 4.57
304 305 0.884704 GCCCTGGCCATACGTATGTG 60.885 60.000 28.80 21.75 34.56 3.21
305 306 1.054406 AGCCCTGGCCATACGTATGT 61.054 55.000 28.80 9.55 43.17 2.29
306 307 0.320771 GAGCCCTGGCCATACGTATG 60.321 60.000 25.55 25.55 43.17 2.39
307 308 1.816863 CGAGCCCTGGCCATACGTAT 61.817 60.000 5.51 1.14 43.17 3.06
308 309 2.495409 CGAGCCCTGGCCATACGTA 61.495 63.158 5.51 0.00 43.17 3.57
309 310 3.849951 CGAGCCCTGGCCATACGT 61.850 66.667 5.51 0.00 43.17 3.57
310 311 3.385749 AACGAGCCCTGGCCATACG 62.386 63.158 5.51 10.59 43.17 3.06
311 312 1.819632 CAACGAGCCCTGGCCATAC 60.820 63.158 5.51 0.00 43.17 2.39
312 313 0.978667 TACAACGAGCCCTGGCCATA 60.979 55.000 5.51 0.00 43.17 2.74
313 314 1.847798 TTACAACGAGCCCTGGCCAT 61.848 55.000 5.51 0.00 43.17 4.40
314 315 2.521451 TTACAACGAGCCCTGGCCA 61.521 57.895 4.71 4.71 43.17 5.36
315 316 2.038837 GTTACAACGAGCCCTGGCC 61.039 63.158 4.13 0.00 43.17 5.36
316 317 3.574780 GTTACAACGAGCCCTGGC 58.425 61.111 0.00 0.00 42.33 4.85
326 327 6.540205 AGCTTAATTTTCCGATCGTTACAAC 58.460 36.000 15.09 0.00 0.00 3.32
335 336 9.262358 GAGATTACTGTAGCTTAATTTTCCGAT 57.738 33.333 0.00 0.00 0.00 4.18
336 337 8.475639 AGAGATTACTGTAGCTTAATTTTCCGA 58.524 33.333 0.00 0.00 0.00 4.55
541 4034 7.709269 TGGTACTATTTTAAATGCTAGAGCG 57.291 36.000 0.00 0.00 45.83 5.03
598 4093 8.837788 AGGAGTTTGAATTGATTTGGATTTTC 57.162 30.769 0.00 0.00 0.00 2.29
759 4255 5.542251 GGCCTCCTCTATCATTTCTCTTACT 59.458 44.000 0.00 0.00 0.00 2.24
1272 4779 0.179094 CGGCTACGGTGATTTAGGCA 60.179 55.000 2.90 0.00 40.13 4.75
1308 4815 1.982395 TGTCCCCGAAGATCGCTGT 60.982 57.895 0.00 0.00 38.82 4.40
1439 4946 4.704833 AGCAGCGGCAACATCGGT 62.705 61.111 12.44 0.00 44.61 4.69
1459 4966 3.470888 GGGAAGGAGCTAGCGGCA 61.471 66.667 9.55 0.00 44.79 5.69
1627 5134 2.176546 CGAGCAACAACGGCATGG 59.823 61.111 0.00 0.00 0.00 3.66
1705 5212 4.518249 GCTGTTTAGAGGGCTAGTGATTT 58.482 43.478 0.00 0.00 0.00 2.17
1709 5216 1.134371 GGGCTGTTTAGAGGGCTAGTG 60.134 57.143 0.00 0.00 0.00 2.74
1926 5435 4.722700 GGCCGGCCTCACACACAT 62.723 66.667 38.76 0.00 0.00 3.21
2116 5625 3.112126 GACCCGCATGTCATTGCCG 62.112 63.158 0.00 0.00 39.52 5.69
2135 5644 1.564348 GACTAATCAAAGGGCCCAGGA 59.436 52.381 27.56 18.63 0.00 3.86
2150 5659 1.689813 TCAACTGAGGCCGTTGACTAA 59.310 47.619 17.62 0.06 44.03 2.24


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

AutoCloner maintained by Alex Coulton.