Multiple sequence alignment - TraesCS2D01G391700

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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 TraesCS2D01G391700 chr2D 100.000 1851 0 0 972 2822 498805121 498806971 0.000000e+00 3419
1 TraesCS2D01G391700 chr2D 100.000 742 0 0 1 742 498804150 498804891 0.000000e+00 1371
2 TraesCS2D01G391700 chr2B 94.948 871 34 5 973 1837 585936015 585936881 0.000000e+00 1356
3 TraesCS2D01G391700 chr2B 93.424 517 16 4 237 742 585935440 585935949 0.000000e+00 750
4 TraesCS2D01G391700 chr2B 93.333 75 5 0 1821 1895 585936906 585936980 8.260000e-21 111
5 TraesCS2D01G391700 chr2A 93.915 871 36 8 972 1829 643492699 643493565 0.000000e+00 1299
6 TraesCS2D01G391700 chr2A 92.662 477 20 5 237 711 643492148 643492611 0.000000e+00 673
7 TraesCS2D01G391700 chr2A 86.219 566 57 8 1911 2469 744626889 744627440 6.730000e-166 593
8 TraesCS2D01G391700 chr5D 91.640 921 69 2 1909 2822 88473445 88472526 0.000000e+00 1267
9 TraesCS2D01G391700 chr5D 89.924 923 80 6 1909 2822 294346799 294347717 0.000000e+00 1177
10 TraesCS2D01G391700 chrUn 91.309 932 69 6 1898 2822 100223399 100222473 0.000000e+00 1262
11 TraesCS2D01G391700 chr6D 91.422 921 70 3 1909 2822 950953 950035 0.000000e+00 1254
12 TraesCS2D01G391700 chr6D 84.663 163 18 6 1377 1537 343558336 343558179 3.760000e-34 156
13 TraesCS2D01G391700 chr6D 90.000 100 10 0 1 100 471610061 471609962 2.280000e-26 130
14 TraesCS2D01G391700 chr5B 90.997 933 72 4 1897 2822 493514234 493515161 0.000000e+00 1247
15 TraesCS2D01G391700 chr4D 90.685 934 76 4 1896 2822 502030575 502029646 0.000000e+00 1232
16 TraesCS2D01G391700 chr4D 91.753 97 8 0 1 97 400722308 400722212 4.900000e-28 135
17 TraesCS2D01G391700 chr4D 90.722 97 9 0 1 97 38656692 38656788 2.280000e-26 130
18 TraesCS2D01G391700 chr4D 90.722 97 9 0 1 97 260493653 260493557 2.280000e-26 130
19 TraesCS2D01G391700 chr4D 90.722 97 9 0 1 97 305649553 305649649 2.280000e-26 130
20 TraesCS2D01G391700 chr4D 90.722 97 9 0 1 97 358631599 358631503 2.280000e-26 130
21 TraesCS2D01G391700 chr4A 90.889 922 73 4 1909 2822 710173315 710172397 0.000000e+00 1227
22 TraesCS2D01G391700 chr7D 90.435 920 60 10 1911 2822 568946124 568945225 0.000000e+00 1186
23 TraesCS2D01G391700 chr3B 89.902 921 80 5 1909 2822 59219209 59220123 0.000000e+00 1173
24 TraesCS2D01G391700 chr6B 89.174 896 65 10 1935 2822 511708518 511709389 0.000000e+00 1088
25 TraesCS2D01G391700 chr6B 86.567 134 16 2 1377 1509 518392331 518392199 2.270000e-31 147
26 TraesCS2D01G391700 chr6A 84.663 163 18 6 1377 1537 483900976 483900819 3.760000e-34 156
27 TraesCS2D01G391700 chr3D 91.753 97 8 0 1 97 504315184 504315088 4.900000e-28 135
28 TraesCS2D01G391700 chr1A 91.753 97 8 0 1 97 398860202 398860298 4.900000e-28 135
29 TraesCS2D01G391700 chr1D 90.099 101 9 1 1 100 375306441 375306341 2.280000e-26 130


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 TraesCS2D01G391700 chr2D 498804150 498806971 2821 False 2395 3419 100.000000 1 2822 2 chr2D.!!$F1 2821
1 TraesCS2D01G391700 chr2B 585935440 585936980 1540 False 739 1356 93.901667 237 1895 3 chr2B.!!$F1 1658
2 TraesCS2D01G391700 chr2A 643492148 643493565 1417 False 986 1299 93.288500 237 1829 2 chr2A.!!$F2 1592
3 TraesCS2D01G391700 chr2A 744626889 744627440 551 False 593 593 86.219000 1911 2469 1 chr2A.!!$F1 558
4 TraesCS2D01G391700 chr5D 88472526 88473445 919 True 1267 1267 91.640000 1909 2822 1 chr5D.!!$R1 913
5 TraesCS2D01G391700 chr5D 294346799 294347717 918 False 1177 1177 89.924000 1909 2822 1 chr5D.!!$F1 913
6 TraesCS2D01G391700 chrUn 100222473 100223399 926 True 1262 1262 91.309000 1898 2822 1 chrUn.!!$R1 924
7 TraesCS2D01G391700 chr6D 950035 950953 918 True 1254 1254 91.422000 1909 2822 1 chr6D.!!$R1 913
8 TraesCS2D01G391700 chr5B 493514234 493515161 927 False 1247 1247 90.997000 1897 2822 1 chr5B.!!$F1 925
9 TraesCS2D01G391700 chr4D 502029646 502030575 929 True 1232 1232 90.685000 1896 2822 1 chr4D.!!$R4 926
10 TraesCS2D01G391700 chr4A 710172397 710173315 918 True 1227 1227 90.889000 1909 2822 1 chr4A.!!$R1 913
11 TraesCS2D01G391700 chr7D 568945225 568946124 899 True 1186 1186 90.435000 1911 2822 1 chr7D.!!$R1 911
12 TraesCS2D01G391700 chr3B 59219209 59220123 914 False 1173 1173 89.902000 1909 2822 1 chr3B.!!$F1 913
13 TraesCS2D01G391700 chr6B 511708518 511709389 871 False 1088 1088 89.174000 1935 2822 1 chr6B.!!$F1 887

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
24 25 0.323957 AAAGCTAACCCCGGACTGAC 59.676 55.0 0.73 0.00 0.00 3.51 F
271 272 0.461961 AGGCTGCAGTCGAATACTCC 59.538 55.0 16.64 4.27 35.76 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 1042 0.179100 ATCACAGCAACGATCTCCCG 60.179 55.0 0.0 0.0 0.0 5.14 R
2117 2208 0.389025 TCGACAAGTGAAGCTCTGCA 59.611 50.0 0.0 0.0 0.0 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.271055 TGAATAAAGCTAACCCCGGAC 57.729 47.619 0.73 0.00 0.00 4.79
21 22 2.841881 TGAATAAAGCTAACCCCGGACT 59.158 45.455 0.73 0.00 0.00 3.85
22 23 3.203716 GAATAAAGCTAACCCCGGACTG 58.796 50.000 0.73 0.00 0.00 3.51
23 24 1.941377 TAAAGCTAACCCCGGACTGA 58.059 50.000 0.73 0.00 0.00 3.41
24 25 0.323957 AAAGCTAACCCCGGACTGAC 59.676 55.000 0.73 0.00 0.00 3.51
25 26 1.885163 AAGCTAACCCCGGACTGACG 61.885 60.000 0.73 0.00 0.00 4.35
26 27 2.183555 CTAACCCCGGACTGACGC 59.816 66.667 0.73 0.00 0.00 5.19
27 28 2.283388 TAACCCCGGACTGACGCT 60.283 61.111 0.73 0.00 0.00 5.07
28 29 2.558554 CTAACCCCGGACTGACGCTG 62.559 65.000 0.73 0.00 0.00 5.18
30 31 4.003788 CCCCGGACTGACGCTGTT 62.004 66.667 0.73 0.00 0.00 3.16
31 32 2.030562 CCCGGACTGACGCTGTTT 59.969 61.111 0.73 0.00 0.00 2.83
32 33 1.597027 CCCGGACTGACGCTGTTTT 60.597 57.895 0.73 0.00 0.00 2.43
33 34 1.566018 CCCGGACTGACGCTGTTTTC 61.566 60.000 0.73 0.00 0.00 2.29
34 35 0.878523 CCGGACTGACGCTGTTTTCA 60.879 55.000 0.00 0.00 0.00 2.69
49 50 5.499139 TGTTTTCAGCAGAACTTACAAGG 57.501 39.130 0.00 0.00 32.39 3.61
50 51 4.947388 TGTTTTCAGCAGAACTTACAAGGT 59.053 37.500 0.00 0.00 32.39 3.50
51 52 6.116806 TGTTTTCAGCAGAACTTACAAGGTA 58.883 36.000 0.00 0.00 32.39 3.08
52 53 6.770785 TGTTTTCAGCAGAACTTACAAGGTAT 59.229 34.615 0.00 0.00 32.39 2.73
53 54 7.284489 TGTTTTCAGCAGAACTTACAAGGTATT 59.716 33.333 0.00 0.00 32.39 1.89
54 55 8.780249 GTTTTCAGCAGAACTTACAAGGTATTA 58.220 33.333 0.00 0.00 32.39 0.98
55 56 9.515226 TTTTCAGCAGAACTTACAAGGTATTAT 57.485 29.630 0.00 0.00 32.39 1.28
56 57 9.515226 TTTCAGCAGAACTTACAAGGTATTATT 57.485 29.630 0.00 0.00 32.39 1.40
57 58 9.515226 TTCAGCAGAACTTACAAGGTATTATTT 57.485 29.630 0.00 0.00 0.00 1.40
58 59 9.515226 TCAGCAGAACTTACAAGGTATTATTTT 57.485 29.630 0.00 0.00 0.00 1.82
61 62 9.908152 GCAGAACTTACAAGGTATTATTTTTGT 57.092 29.630 0.00 0.00 37.51 2.83
63 64 9.908152 AGAACTTACAAGGTATTATTTTTGTGC 57.092 29.630 0.00 0.00 35.55 4.57
64 65 9.685828 GAACTTACAAGGTATTATTTTTGTGCA 57.314 29.630 0.00 0.00 35.55 4.57
65 66 9.691362 AACTTACAAGGTATTATTTTTGTGCAG 57.309 29.630 0.00 0.00 35.55 4.41
66 67 9.073475 ACTTACAAGGTATTATTTTTGTGCAGA 57.927 29.630 0.00 0.00 35.55 4.26
67 68 9.906660 CTTACAAGGTATTATTTTTGTGCAGAA 57.093 29.630 0.00 0.00 35.55 3.02
80 81 9.701355 ATTTTTGTGCAGAAATAAAAGTTTTCG 57.299 25.926 10.13 0.00 37.98 3.46
81 82 8.467402 TTTTGTGCAGAAATAAAAGTTTTCGA 57.533 26.923 10.13 0.00 37.98 3.71
82 83 8.467402 TTTGTGCAGAAATAAAAGTTTTCGAA 57.533 26.923 4.66 0.00 37.98 3.71
83 84 8.467402 TTGTGCAGAAATAAAAGTTTTCGAAA 57.533 26.923 6.47 6.47 37.98 3.46
84 85 8.641499 TGTGCAGAAATAAAAGTTTTCGAAAT 57.359 26.923 12.12 0.00 37.98 2.17
85 86 8.538856 TGTGCAGAAATAAAAGTTTTCGAAATG 58.461 29.630 12.12 3.50 37.98 2.32
86 87 8.751335 GTGCAGAAATAAAAGTTTTCGAAATGA 58.249 29.630 12.12 0.00 37.98 2.57
87 88 9.307121 TGCAGAAATAAAAGTTTTCGAAATGAA 57.693 25.926 12.12 0.00 37.98 2.57
99 100 4.545823 TCGAAATGAAACGAAACTTGCT 57.454 36.364 0.00 0.00 35.62 3.91
100 101 4.915704 TCGAAATGAAACGAAACTTGCTT 58.084 34.783 0.00 0.00 35.62 3.91
101 102 6.050454 TCGAAATGAAACGAAACTTGCTTA 57.950 33.333 0.00 0.00 35.62 3.09
102 103 6.487960 TCGAAATGAAACGAAACTTGCTTAA 58.512 32.000 0.00 0.00 35.62 1.85
103 104 6.967767 TCGAAATGAAACGAAACTTGCTTAAA 59.032 30.769 0.00 0.00 35.62 1.52
104 105 7.646130 TCGAAATGAAACGAAACTTGCTTAAAT 59.354 29.630 0.00 0.00 35.62 1.40
105 106 8.897809 CGAAATGAAACGAAACTTGCTTAAATA 58.102 29.630 0.00 0.00 0.00 1.40
107 108 9.959749 AAATGAAACGAAACTTGCTTAAATAGA 57.040 25.926 0.00 0.00 0.00 1.98
108 109 9.612620 AATGAAACGAAACTTGCTTAAATAGAG 57.387 29.630 0.00 0.00 0.00 2.43
109 110 8.149973 TGAAACGAAACTTGCTTAAATAGAGT 57.850 30.769 0.00 0.00 0.00 3.24
110 111 8.617809 TGAAACGAAACTTGCTTAAATAGAGTT 58.382 29.630 0.00 0.00 32.33 3.01
111 112 9.104126 GAAACGAAACTTGCTTAAATAGAGTTC 57.896 33.333 0.00 0.00 30.77 3.01
112 113 7.964604 ACGAAACTTGCTTAAATAGAGTTCT 57.035 32.000 0.00 0.00 30.77 3.01
113 114 9.485206 AACGAAACTTGCTTAAATAGAGTTCTA 57.515 29.630 0.00 0.00 30.77 2.10
114 115 9.654663 ACGAAACTTGCTTAAATAGAGTTCTAT 57.345 29.630 0.00 0.00 40.68 1.98
121 122 8.888579 TGCTTAAATAGAGTTCTATAACAGGC 57.111 34.615 2.26 4.24 38.15 4.85
122 123 8.705594 TGCTTAAATAGAGTTCTATAACAGGCT 58.294 33.333 2.26 0.00 38.15 4.58
123 124 9.198837 GCTTAAATAGAGTTCTATAACAGGCTC 57.801 37.037 2.26 0.00 38.15 4.70
126 127 4.664150 AGAGTTCTATAACAGGCTCTGC 57.336 45.455 2.50 0.00 38.12 4.26
127 128 3.386402 AGAGTTCTATAACAGGCTCTGCC 59.614 47.826 0.00 0.00 40.19 4.85
129 130 7.695554 ATAGAGTTCTATAACAGGCTCTGCCTA 60.696 40.741 11.03 0.00 46.16 3.93
142 143 3.266240 TGCCTAGAGTTCGCAGAGA 57.734 52.632 0.00 0.00 38.43 3.10
143 144 1.769026 TGCCTAGAGTTCGCAGAGAT 58.231 50.000 0.00 0.00 38.43 2.75
144 145 2.932261 TGCCTAGAGTTCGCAGAGATA 58.068 47.619 0.00 0.00 38.43 1.98
145 146 3.288092 TGCCTAGAGTTCGCAGAGATAA 58.712 45.455 0.00 0.00 38.43 1.75
146 147 3.316588 TGCCTAGAGTTCGCAGAGATAAG 59.683 47.826 0.00 0.00 38.43 1.73
147 148 3.855524 GCCTAGAGTTCGCAGAGATAAGC 60.856 52.174 0.00 0.00 38.43 3.09
148 149 3.316588 CCTAGAGTTCGCAGAGATAAGCA 59.683 47.826 0.00 0.00 38.43 3.91
149 150 3.876274 AGAGTTCGCAGAGATAAGCAA 57.124 42.857 0.00 0.00 38.43 3.91
150 151 4.193826 AGAGTTCGCAGAGATAAGCAAA 57.806 40.909 0.00 0.00 38.43 3.68
151 152 4.764172 AGAGTTCGCAGAGATAAGCAAAT 58.236 39.130 0.00 0.00 38.43 2.32
152 153 5.181748 AGAGTTCGCAGAGATAAGCAAATT 58.818 37.500 0.00 0.00 38.43 1.82
153 154 6.341316 AGAGTTCGCAGAGATAAGCAAATTA 58.659 36.000 0.00 0.00 38.43 1.40
154 155 6.818644 AGAGTTCGCAGAGATAAGCAAATTAA 59.181 34.615 0.00 0.00 38.43 1.40
155 156 7.497249 AGAGTTCGCAGAGATAAGCAAATTAAT 59.503 33.333 0.00 0.00 38.43 1.40
156 157 7.989826 AGTTCGCAGAGATAAGCAAATTAATT 58.010 30.769 0.00 0.00 38.43 1.40
157 158 9.109393 AGTTCGCAGAGATAAGCAAATTAATTA 57.891 29.630 0.01 0.00 38.43 1.40
158 159 9.374960 GTTCGCAGAGATAAGCAAATTAATTAG 57.625 33.333 0.01 0.00 38.43 1.73
159 160 8.887036 TCGCAGAGATAAGCAAATTAATTAGA 57.113 30.769 0.01 0.00 0.00 2.10
160 161 8.765219 TCGCAGAGATAAGCAAATTAATTAGAC 58.235 33.333 0.01 0.00 0.00 2.59
161 162 8.012241 CGCAGAGATAAGCAAATTAATTAGACC 58.988 37.037 0.01 0.00 0.00 3.85
162 163 8.840321 GCAGAGATAAGCAAATTAATTAGACCA 58.160 33.333 0.01 0.00 0.00 4.02
164 165 9.061435 AGAGATAAGCAAATTAATTAGACCAGC 57.939 33.333 0.01 0.23 0.00 4.85
165 166 8.986929 AGATAAGCAAATTAATTAGACCAGCT 57.013 30.769 0.01 2.41 0.00 4.24
166 167 9.061435 AGATAAGCAAATTAATTAGACCAGCTC 57.939 33.333 0.01 0.00 0.00 4.09
167 168 5.741388 AGCAAATTAATTAGACCAGCTCG 57.259 39.130 0.01 0.00 0.00 5.03
168 169 4.576463 AGCAAATTAATTAGACCAGCTCGG 59.424 41.667 0.01 1.16 42.50 4.63
169 170 4.574828 GCAAATTAATTAGACCAGCTCGGA 59.425 41.667 0.01 0.00 38.63 4.55
170 171 5.277538 GCAAATTAATTAGACCAGCTCGGAG 60.278 44.000 0.01 0.00 38.63 4.63
171 172 5.871396 AATTAATTAGACCAGCTCGGAGA 57.129 39.130 9.69 0.00 38.63 3.71
172 173 5.871396 ATTAATTAGACCAGCTCGGAGAA 57.129 39.130 9.69 0.00 38.63 2.87
173 174 3.528597 AATTAGACCAGCTCGGAGAAC 57.471 47.619 9.69 0.00 38.63 3.01
174 175 1.183549 TTAGACCAGCTCGGAGAACC 58.816 55.000 9.69 0.00 38.63 3.62
175 176 0.683504 TAGACCAGCTCGGAGAACCC 60.684 60.000 9.69 0.00 38.63 4.11
176 177 3.003763 ACCAGCTCGGAGAACCCC 61.004 66.667 9.69 0.00 38.63 4.95
177 178 2.685380 CCAGCTCGGAGAACCCCT 60.685 66.667 9.69 0.00 36.56 4.79
178 179 2.294078 CCAGCTCGGAGAACCCCTT 61.294 63.158 9.69 0.00 36.56 3.95
179 180 1.679898 CAGCTCGGAGAACCCCTTT 59.320 57.895 9.69 0.00 34.09 3.11
180 181 0.902531 CAGCTCGGAGAACCCCTTTA 59.097 55.000 9.69 0.00 34.09 1.85
181 182 1.278127 CAGCTCGGAGAACCCCTTTAA 59.722 52.381 9.69 0.00 34.09 1.52
182 183 2.092914 CAGCTCGGAGAACCCCTTTAAT 60.093 50.000 9.69 0.00 34.09 1.40
183 184 2.576648 AGCTCGGAGAACCCCTTTAATT 59.423 45.455 9.69 0.00 34.09 1.40
184 185 3.010250 AGCTCGGAGAACCCCTTTAATTT 59.990 43.478 9.69 0.00 34.09 1.82
185 186 3.377485 GCTCGGAGAACCCCTTTAATTTC 59.623 47.826 9.69 0.00 34.09 2.17
186 187 4.585879 CTCGGAGAACCCCTTTAATTTCA 58.414 43.478 0.00 0.00 34.09 2.69
187 188 4.329392 TCGGAGAACCCCTTTAATTTCAC 58.671 43.478 0.00 0.00 0.00 3.18
188 189 3.442625 CGGAGAACCCCTTTAATTTCACC 59.557 47.826 0.00 0.00 0.00 4.02
189 190 4.412843 GGAGAACCCCTTTAATTTCACCA 58.587 43.478 0.00 0.00 31.26 4.17
190 191 5.023452 GGAGAACCCCTTTAATTTCACCAT 58.977 41.667 0.00 0.00 31.26 3.55
191 192 5.127194 GGAGAACCCCTTTAATTTCACCATC 59.873 44.000 0.00 0.00 31.26 3.51
192 193 5.650283 AGAACCCCTTTAATTTCACCATCA 58.350 37.500 0.00 0.00 0.00 3.07
193 194 6.081356 AGAACCCCTTTAATTTCACCATCAA 58.919 36.000 0.00 0.00 0.00 2.57
194 195 6.730507 AGAACCCCTTTAATTTCACCATCAAT 59.269 34.615 0.00 0.00 0.00 2.57
195 196 6.544928 ACCCCTTTAATTTCACCATCAATC 57.455 37.500 0.00 0.00 0.00 2.67
196 197 5.425217 ACCCCTTTAATTTCACCATCAATCC 59.575 40.000 0.00 0.00 0.00 3.01
197 198 5.163311 CCCCTTTAATTTCACCATCAATCCC 60.163 44.000 0.00 0.00 0.00 3.85
198 199 5.424895 CCCTTTAATTTCACCATCAATCCCA 59.575 40.000 0.00 0.00 0.00 4.37
199 200 6.100134 CCCTTTAATTTCACCATCAATCCCAT 59.900 38.462 0.00 0.00 0.00 4.00
200 201 7.289782 CCCTTTAATTTCACCATCAATCCCATA 59.710 37.037 0.00 0.00 0.00 2.74
201 202 8.873144 CCTTTAATTTCACCATCAATCCCATAT 58.127 33.333 0.00 0.00 0.00 1.78
202 203 9.701098 CTTTAATTTCACCATCAATCCCATATG 57.299 33.333 0.00 0.00 0.00 1.78
203 204 5.733620 ATTTCACCATCAATCCCATATGC 57.266 39.130 0.00 0.00 0.00 3.14
204 205 3.159213 TCACCATCAATCCCATATGCC 57.841 47.619 0.00 0.00 0.00 4.40
205 206 2.446285 TCACCATCAATCCCATATGCCA 59.554 45.455 0.00 0.00 0.00 4.92
206 207 2.559668 CACCATCAATCCCATATGCCAC 59.440 50.000 0.00 0.00 0.00 5.01
207 208 1.814394 CCATCAATCCCATATGCCACG 59.186 52.381 0.00 0.00 0.00 4.94
208 209 2.552809 CCATCAATCCCATATGCCACGA 60.553 50.000 0.00 0.00 0.00 4.35
209 210 2.549064 TCAATCCCATATGCCACGAG 57.451 50.000 0.00 0.00 0.00 4.18
210 211 2.046292 TCAATCCCATATGCCACGAGA 58.954 47.619 0.00 0.00 0.00 4.04
211 212 2.037641 TCAATCCCATATGCCACGAGAG 59.962 50.000 0.00 0.00 0.00 3.20
232 233 4.278678 GTCTGTTGACTTGACACAAAGG 57.721 45.455 0.00 0.00 39.94 3.11
233 234 3.938963 GTCTGTTGACTTGACACAAAGGA 59.061 43.478 0.00 0.00 39.94 3.36
234 235 4.394920 GTCTGTTGACTTGACACAAAGGAA 59.605 41.667 0.00 0.00 39.94 3.36
235 236 5.007034 TCTGTTGACTTGACACAAAGGAAA 58.993 37.500 0.00 0.00 0.00 3.13
271 272 0.461961 AGGCTGCAGTCGAATACTCC 59.538 55.000 16.64 4.27 35.76 3.85
345 347 4.907034 CCATCGGAGCCGTCGACG 62.907 72.222 30.33 30.33 39.55 5.12
347 349 3.129502 ATCGGAGCCGTCGACGAA 61.130 61.111 37.65 15.98 43.02 3.85
487 492 2.439245 GGGAAAGGGGGACACACC 59.561 66.667 0.00 0.00 38.08 4.16
1006 1023 0.609131 CCCGTGAACTCCAGCCATTT 60.609 55.000 0.00 0.00 0.00 2.32
1025 1042 1.129879 TACGCTGCGTCGATCGTTTC 61.130 55.000 32.44 6.35 41.54 2.78
1079 1103 2.050144 GGGAGATGGAGGCTTACATGA 58.950 52.381 0.00 0.00 0.00 3.07
1156 1180 3.060615 CCGTCCGAGTCCGAGGTT 61.061 66.667 0.00 0.00 38.22 3.50
1204 1228 2.400402 GAGGAGCTCGACGACGAC 59.600 66.667 5.75 3.99 43.81 4.34
1289 1313 1.153823 CTCCCGCTCAAGTACGTGG 60.154 63.158 8.98 0.15 0.00 4.94
1316 1340 2.383527 CGGGCACTGCGAGTTCTTC 61.384 63.158 0.00 0.00 0.00 2.87
1317 1341 2.035442 GGGCACTGCGAGTTCTTCC 61.035 63.158 0.00 0.00 0.00 3.46
1323 1347 2.509561 GCGAGTTCTTCCGAGGCC 60.510 66.667 0.00 0.00 0.00 5.19
1356 1384 1.417517 TGAAGCTGTGGTCTGACATGT 59.582 47.619 10.38 0.00 0.00 3.21
1374 1402 5.343249 ACATGTGTGTTCTTTTTCTCTTGC 58.657 37.500 0.00 0.00 34.01 4.01
1829 1860 4.921515 CAGAAATGAGAAACATGCCTTGTG 59.078 41.667 0.00 0.00 38.99 3.33
1845 1917 4.736168 GCCTTGTGCAGTATCTACTCTCAG 60.736 50.000 0.00 0.00 40.77 3.35
1859 1931 4.457834 ACTCTCAGTGCGCTTATAGTTT 57.542 40.909 9.73 0.00 0.00 2.66
1988 2060 0.249114 TACACTCGCTGCGAACAACA 60.249 50.000 25.86 7.50 34.74 3.33
1997 2069 0.165727 TGCGAACAACAAGCATAGCG 59.834 50.000 0.00 0.00 35.81 4.26
2001 2073 2.728846 CGAACAACAAGCATAGCGCAAT 60.729 45.455 11.47 0.00 46.13 3.56
2008 2080 2.260844 AGCATAGCGCAATACCACAT 57.739 45.000 11.47 0.00 46.13 3.21
2080 2171 0.935196 GAAACTCAACACCGCGTCTT 59.065 50.000 4.92 0.00 0.00 3.01
2088 2179 3.598715 ACCGCGTCTTGACCGACA 61.599 61.111 4.92 0.00 33.54 4.35
2117 2208 2.698797 TCTCCGAAGAACACCAACTTCT 59.301 45.455 0.00 0.00 39.90 2.85
2151 2242 2.509336 CGACGCACCATCCACTCC 60.509 66.667 0.00 0.00 0.00 3.85
2320 2422 2.929641 TGTCTCCAAACACAATGCTCA 58.070 42.857 0.00 0.00 0.00 4.26
2453 2568 3.991536 GACGACGCCTCCAAGGAGC 62.992 68.421 10.68 5.67 38.91 4.70
2519 2634 2.095768 CGTGCAAGATTTTCATCCACGT 60.096 45.455 0.00 0.00 37.60 4.49
2530 2645 3.296709 ATCCACGTGTCGCACCTCC 62.297 63.158 15.65 0.00 0.00 4.30
2547 2662 2.370189 CCTCCCCACACCATCTAGAATC 59.630 54.545 0.00 0.00 0.00 2.52
2601 2716 3.434319 CCGCAGCACTTCGCCAAT 61.434 61.111 0.00 0.00 44.04 3.16
2774 2890 1.296392 CTTGCGATGACTGGACCCA 59.704 57.895 0.00 0.00 0.00 4.51
2814 2930 1.300465 CACCATCGGGAGAGCATCG 60.300 63.158 0.00 0.00 45.48 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.841881 AGTCCGGGGTTAGCTTTATTCA 59.158 45.455 0.00 0.00 0.00 2.57
1 2 3.118519 TCAGTCCGGGGTTAGCTTTATTC 60.119 47.826 0.00 0.00 0.00 1.75
2 3 2.841881 TCAGTCCGGGGTTAGCTTTATT 59.158 45.455 0.00 0.00 0.00 1.40
3 4 2.169978 GTCAGTCCGGGGTTAGCTTTAT 59.830 50.000 0.00 0.00 0.00 1.40
5 6 0.323957 GTCAGTCCGGGGTTAGCTTT 59.676 55.000 0.00 0.00 0.00 3.51
6 7 1.885163 CGTCAGTCCGGGGTTAGCTT 61.885 60.000 0.00 0.00 0.00 3.74
7 8 2.348888 CGTCAGTCCGGGGTTAGCT 61.349 63.158 0.00 0.00 0.00 3.32
8 9 2.183555 CGTCAGTCCGGGGTTAGC 59.816 66.667 0.00 0.00 0.00 3.09
9 10 2.183555 GCGTCAGTCCGGGGTTAG 59.816 66.667 0.00 0.00 0.00 2.34
10 11 2.283388 AGCGTCAGTCCGGGGTTA 60.283 61.111 0.00 0.00 0.00 2.85
11 12 4.003788 CAGCGTCAGTCCGGGGTT 62.004 66.667 0.00 0.00 0.00 4.11
13 14 3.530910 AAACAGCGTCAGTCCGGGG 62.531 63.158 0.00 0.00 0.00 5.73
14 15 1.566018 GAAAACAGCGTCAGTCCGGG 61.566 60.000 0.00 0.00 0.00 5.73
15 16 0.878523 TGAAAACAGCGTCAGTCCGG 60.879 55.000 0.00 0.00 0.00 5.14
16 17 0.508641 CTGAAAACAGCGTCAGTCCG 59.491 55.000 0.00 0.00 37.16 4.79
17 18 0.235926 GCTGAAAACAGCGTCAGTCC 59.764 55.000 6.46 0.00 42.72 3.85
18 19 3.736581 GCTGAAAACAGCGTCAGTC 57.263 52.632 6.46 0.00 42.72 3.51
26 27 5.066505 ACCTTGTAAGTTCTGCTGAAAACAG 59.933 40.000 7.68 5.40 33.52 3.16
27 28 4.947388 ACCTTGTAAGTTCTGCTGAAAACA 59.053 37.500 7.68 9.80 33.52 2.83
28 29 5.500645 ACCTTGTAAGTTCTGCTGAAAAC 57.499 39.130 7.68 7.51 33.52 2.43
29 30 7.817418 AATACCTTGTAAGTTCTGCTGAAAA 57.183 32.000 7.68 0.00 33.52 2.29
30 31 9.515226 AATAATACCTTGTAAGTTCTGCTGAAA 57.485 29.630 7.68 0.00 33.52 2.69
31 32 9.515226 AAATAATACCTTGTAAGTTCTGCTGAA 57.485 29.630 1.33 1.33 0.00 3.02
32 33 9.515226 AAAATAATACCTTGTAAGTTCTGCTGA 57.485 29.630 0.00 0.00 0.00 4.26
35 36 9.908152 ACAAAAATAATACCTTGTAAGTTCTGC 57.092 29.630 0.00 0.00 30.41 4.26
37 38 9.908152 GCACAAAAATAATACCTTGTAAGTTCT 57.092 29.630 0.00 0.00 31.00 3.01
38 39 9.685828 TGCACAAAAATAATACCTTGTAAGTTC 57.314 29.630 0.00 0.00 31.00 3.01
39 40 9.691362 CTGCACAAAAATAATACCTTGTAAGTT 57.309 29.630 0.00 0.00 31.00 2.66
40 41 9.073475 TCTGCACAAAAATAATACCTTGTAAGT 57.927 29.630 0.00 0.00 31.00 2.24
41 42 9.906660 TTCTGCACAAAAATAATACCTTGTAAG 57.093 29.630 0.00 0.00 31.00 2.34
54 55 9.701355 CGAAAACTTTTATTTCTGCACAAAAAT 57.299 25.926 0.00 0.00 35.19 1.82
55 56 8.926710 TCGAAAACTTTTATTTCTGCACAAAAA 58.073 25.926 0.00 0.00 35.19 1.94
56 57 8.467402 TCGAAAACTTTTATTTCTGCACAAAA 57.533 26.923 0.00 0.00 35.19 2.44
57 58 8.467402 TTCGAAAACTTTTATTTCTGCACAAA 57.533 26.923 0.00 0.00 35.19 2.83
58 59 8.467402 TTTCGAAAACTTTTATTTCTGCACAA 57.533 26.923 8.44 0.00 35.19 3.33
59 60 8.538856 CATTTCGAAAACTTTTATTTCTGCACA 58.461 29.630 15.66 0.00 35.19 4.57
60 61 8.751335 TCATTTCGAAAACTTTTATTTCTGCAC 58.249 29.630 15.66 0.00 35.19 4.57
61 62 8.864069 TCATTTCGAAAACTTTTATTTCTGCA 57.136 26.923 15.66 0.00 35.19 4.41
77 78 4.915704 AGCAAGTTTCGTTTCATTTCGAA 58.084 34.783 0.00 0.00 42.82 3.71
78 79 4.545823 AGCAAGTTTCGTTTCATTTCGA 57.454 36.364 0.00 0.00 0.00 3.71
79 80 6.726035 TTAAGCAAGTTTCGTTTCATTTCG 57.274 33.333 0.00 0.00 0.00 3.46
81 82 9.959749 TCTATTTAAGCAAGTTTCGTTTCATTT 57.040 25.926 0.00 0.00 0.00 2.32
82 83 9.612620 CTCTATTTAAGCAAGTTTCGTTTCATT 57.387 29.630 0.00 0.00 0.00 2.57
83 84 8.784043 ACTCTATTTAAGCAAGTTTCGTTTCAT 58.216 29.630 0.00 0.00 0.00 2.57
84 85 8.149973 ACTCTATTTAAGCAAGTTTCGTTTCA 57.850 30.769 0.00 0.00 0.00 2.69
85 86 9.104126 GAACTCTATTTAAGCAAGTTTCGTTTC 57.896 33.333 0.00 0.00 0.00 2.78
86 87 8.837389 AGAACTCTATTTAAGCAAGTTTCGTTT 58.163 29.630 0.00 0.00 0.00 3.60
87 88 8.379457 AGAACTCTATTTAAGCAAGTTTCGTT 57.621 30.769 0.00 0.00 0.00 3.85
88 89 7.964604 AGAACTCTATTTAAGCAAGTTTCGT 57.035 32.000 0.00 0.00 0.00 3.85
95 96 9.326413 GCCTGTTATAGAACTCTATTTAAGCAA 57.674 33.333 4.61 0.00 39.66 3.91
96 97 8.705594 AGCCTGTTATAGAACTCTATTTAAGCA 58.294 33.333 4.61 0.00 39.66 3.91
97 98 9.198837 GAGCCTGTTATAGAACTCTATTTAAGC 57.801 37.037 4.61 3.42 39.66 3.09
100 101 8.361139 GCAGAGCCTGTTATAGAACTCTATTTA 58.639 37.037 4.61 0.00 37.53 1.40
101 102 7.213678 GCAGAGCCTGTTATAGAACTCTATTT 58.786 38.462 4.61 0.00 37.53 1.40
102 103 6.239458 GGCAGAGCCTGTTATAGAACTCTATT 60.239 42.308 4.61 0.00 46.69 1.73
103 104 5.245075 GGCAGAGCCTGTTATAGAACTCTAT 59.755 44.000 1.39 4.70 46.69 1.98
104 105 4.585162 GGCAGAGCCTGTTATAGAACTCTA 59.415 45.833 1.39 0.00 46.69 2.43
105 106 3.386402 GGCAGAGCCTGTTATAGAACTCT 59.614 47.826 1.39 0.00 46.69 3.24
106 107 3.723260 GGCAGAGCCTGTTATAGAACTC 58.277 50.000 1.39 0.00 46.69 3.01
107 108 3.828875 GGCAGAGCCTGTTATAGAACT 57.171 47.619 1.39 0.00 46.69 3.01
124 125 1.769026 ATCTCTGCGAACTCTAGGCA 58.231 50.000 0.00 0.00 35.07 4.75
125 126 3.855524 GCTTATCTCTGCGAACTCTAGGC 60.856 52.174 0.00 0.00 0.00 3.93
126 127 3.316588 TGCTTATCTCTGCGAACTCTAGG 59.683 47.826 0.00 0.00 0.00 3.02
127 128 4.560136 TGCTTATCTCTGCGAACTCTAG 57.440 45.455 0.00 0.00 0.00 2.43
128 129 4.983671 TTGCTTATCTCTGCGAACTCTA 57.016 40.909 0.00 0.00 0.00 2.43
129 130 3.876274 TTGCTTATCTCTGCGAACTCT 57.124 42.857 0.00 0.00 0.00 3.24
130 131 5.476752 AATTTGCTTATCTCTGCGAACTC 57.523 39.130 0.00 0.00 35.67 3.01
131 132 6.985188 TTAATTTGCTTATCTCTGCGAACT 57.015 33.333 0.00 0.00 35.67 3.01
132 133 9.374960 CTAATTAATTTGCTTATCTCTGCGAAC 57.625 33.333 5.91 0.00 35.67 3.95
133 134 9.325198 TCTAATTAATTTGCTTATCTCTGCGAA 57.675 29.630 5.91 0.00 37.04 4.70
134 135 8.765219 GTCTAATTAATTTGCTTATCTCTGCGA 58.235 33.333 5.91 0.00 0.00 5.10
135 136 8.012241 GGTCTAATTAATTTGCTTATCTCTGCG 58.988 37.037 5.91 0.00 0.00 5.18
136 137 8.840321 TGGTCTAATTAATTTGCTTATCTCTGC 58.160 33.333 5.91 0.00 0.00 4.26
138 139 9.061435 GCTGGTCTAATTAATTTGCTTATCTCT 57.939 33.333 5.91 0.00 0.00 3.10
139 140 9.061435 AGCTGGTCTAATTAATTTGCTTATCTC 57.939 33.333 5.91 0.00 0.00 2.75
140 141 8.986929 AGCTGGTCTAATTAATTTGCTTATCT 57.013 30.769 5.91 0.00 0.00 1.98
141 142 8.012241 CGAGCTGGTCTAATTAATTTGCTTATC 58.988 37.037 5.91 0.00 0.00 1.75
142 143 7.041098 CCGAGCTGGTCTAATTAATTTGCTTAT 60.041 37.037 5.91 0.00 0.00 1.73
143 144 6.260050 CCGAGCTGGTCTAATTAATTTGCTTA 59.740 38.462 5.91 0.00 0.00 3.09
144 145 5.066505 CCGAGCTGGTCTAATTAATTTGCTT 59.933 40.000 5.91 0.00 0.00 3.91
145 146 4.576463 CCGAGCTGGTCTAATTAATTTGCT 59.424 41.667 5.91 7.02 0.00 3.91
146 147 4.574828 TCCGAGCTGGTCTAATTAATTTGC 59.425 41.667 5.91 1.44 39.52 3.68
147 148 6.049149 TCTCCGAGCTGGTCTAATTAATTTG 58.951 40.000 5.91 4.59 39.52 2.32
148 149 6.235231 TCTCCGAGCTGGTCTAATTAATTT 57.765 37.500 5.91 0.00 39.52 1.82
149 150 5.871396 TCTCCGAGCTGGTCTAATTAATT 57.129 39.130 5.89 5.89 39.52 1.40
150 151 5.453480 GGTTCTCCGAGCTGGTCTAATTAAT 60.453 44.000 5.23 0.00 39.52 1.40
151 152 4.142004 GGTTCTCCGAGCTGGTCTAATTAA 60.142 45.833 5.23 0.00 39.52 1.40
152 153 3.383825 GGTTCTCCGAGCTGGTCTAATTA 59.616 47.826 5.23 0.00 39.52 1.40
153 154 2.168728 GGTTCTCCGAGCTGGTCTAATT 59.831 50.000 5.23 0.00 39.52 1.40
154 155 1.757699 GGTTCTCCGAGCTGGTCTAAT 59.242 52.381 5.23 0.00 39.52 1.73
155 156 1.183549 GGTTCTCCGAGCTGGTCTAA 58.816 55.000 5.23 0.00 39.52 2.10
156 157 0.683504 GGGTTCTCCGAGCTGGTCTA 60.684 60.000 5.23 0.00 39.52 2.59
157 158 1.985116 GGGTTCTCCGAGCTGGTCT 60.985 63.158 5.23 0.00 39.52 3.85
158 159 2.579738 GGGTTCTCCGAGCTGGTC 59.420 66.667 0.00 0.00 39.52 4.02
159 160 3.003763 GGGGTTCTCCGAGCTGGT 61.004 66.667 0.00 0.00 39.52 4.00
160 161 1.842381 AAAGGGGTTCTCCGAGCTGG 61.842 60.000 0.00 0.00 40.09 4.85
161 162 0.902531 TAAAGGGGTTCTCCGAGCTG 59.097 55.000 0.00 0.00 36.01 4.24
162 163 1.652947 TTAAAGGGGTTCTCCGAGCT 58.347 50.000 0.00 0.00 36.01 4.09
163 164 2.711978 ATTAAAGGGGTTCTCCGAGC 57.288 50.000 0.00 0.00 36.01 5.03
164 165 4.395231 GTGAAATTAAAGGGGTTCTCCGAG 59.605 45.833 0.00 0.00 36.01 4.63
165 166 4.329392 GTGAAATTAAAGGGGTTCTCCGA 58.671 43.478 0.00 0.00 36.01 4.55
166 167 3.442625 GGTGAAATTAAAGGGGTTCTCCG 59.557 47.826 0.00 0.00 36.01 4.63
167 168 4.412843 TGGTGAAATTAAAGGGGTTCTCC 58.587 43.478 0.00 0.00 35.28 3.71
168 169 5.714806 TGATGGTGAAATTAAAGGGGTTCTC 59.285 40.000 0.00 0.00 0.00 2.87
169 170 5.650283 TGATGGTGAAATTAAAGGGGTTCT 58.350 37.500 0.00 0.00 0.00 3.01
170 171 5.993748 TGATGGTGAAATTAAAGGGGTTC 57.006 39.130 0.00 0.00 0.00 3.62
171 172 6.070251 GGATTGATGGTGAAATTAAAGGGGTT 60.070 38.462 0.00 0.00 0.00 4.11
172 173 5.425217 GGATTGATGGTGAAATTAAAGGGGT 59.575 40.000 0.00 0.00 0.00 4.95
173 174 5.163311 GGGATTGATGGTGAAATTAAAGGGG 60.163 44.000 0.00 0.00 0.00 4.79
174 175 5.424895 TGGGATTGATGGTGAAATTAAAGGG 59.575 40.000 0.00 0.00 0.00 3.95
175 176 6.543430 TGGGATTGATGGTGAAATTAAAGG 57.457 37.500 0.00 0.00 0.00 3.11
176 177 9.701098 CATATGGGATTGATGGTGAAATTAAAG 57.299 33.333 0.00 0.00 0.00 1.85
177 178 8.149647 GCATATGGGATTGATGGTGAAATTAAA 58.850 33.333 4.56 0.00 0.00 1.52
178 179 7.256261 GGCATATGGGATTGATGGTGAAATTAA 60.256 37.037 4.56 0.00 0.00 1.40
179 180 6.211184 GGCATATGGGATTGATGGTGAAATTA 59.789 38.462 4.56 0.00 0.00 1.40
180 181 5.012354 GGCATATGGGATTGATGGTGAAATT 59.988 40.000 4.56 0.00 0.00 1.82
181 182 4.529377 GGCATATGGGATTGATGGTGAAAT 59.471 41.667 4.56 0.00 0.00 2.17
182 183 3.896888 GGCATATGGGATTGATGGTGAAA 59.103 43.478 4.56 0.00 0.00 2.69
183 184 3.117208 TGGCATATGGGATTGATGGTGAA 60.117 43.478 4.56 0.00 0.00 3.18
184 185 2.446285 TGGCATATGGGATTGATGGTGA 59.554 45.455 4.56 0.00 0.00 4.02
185 186 2.559668 GTGGCATATGGGATTGATGGTG 59.440 50.000 4.56 0.00 0.00 4.17
186 187 2.815215 CGTGGCATATGGGATTGATGGT 60.815 50.000 4.56 0.00 0.00 3.55
187 188 1.814394 CGTGGCATATGGGATTGATGG 59.186 52.381 4.56 0.00 0.00 3.51
188 189 2.745821 CTCGTGGCATATGGGATTGATG 59.254 50.000 4.56 0.00 0.00 3.07
189 190 2.639347 TCTCGTGGCATATGGGATTGAT 59.361 45.455 4.56 0.00 0.00 2.57
190 191 2.037641 CTCTCGTGGCATATGGGATTGA 59.962 50.000 4.56 0.00 0.00 2.57
191 192 2.224378 ACTCTCGTGGCATATGGGATTG 60.224 50.000 4.56 0.00 0.00 2.67
192 193 2.037772 GACTCTCGTGGCATATGGGATT 59.962 50.000 4.56 0.00 0.00 3.01
193 194 1.620819 GACTCTCGTGGCATATGGGAT 59.379 52.381 4.56 0.00 0.00 3.85
194 195 1.040646 GACTCTCGTGGCATATGGGA 58.959 55.000 4.56 0.00 0.00 4.37
195 196 1.043816 AGACTCTCGTGGCATATGGG 58.956 55.000 4.56 0.00 0.00 4.00
196 197 1.410517 ACAGACTCTCGTGGCATATGG 59.589 52.381 4.56 0.00 0.00 2.74
197 198 2.862536 CAACAGACTCTCGTGGCATATG 59.137 50.000 0.00 0.00 0.00 1.78
198 199 2.760650 TCAACAGACTCTCGTGGCATAT 59.239 45.455 0.00 0.00 0.00 1.78
199 200 2.094700 GTCAACAGACTCTCGTGGCATA 60.095 50.000 0.00 0.00 0.00 3.14
200 201 0.969149 TCAACAGACTCTCGTGGCAT 59.031 50.000 0.00 0.00 0.00 4.40
201 202 0.032130 GTCAACAGACTCTCGTGGCA 59.968 55.000 0.00 0.00 0.00 4.92
202 203 0.315568 AGTCAACAGACTCTCGTGGC 59.684 55.000 0.00 0.00 38.17 5.01
203 204 2.034685 TCAAGTCAACAGACTCTCGTGG 59.965 50.000 0.00 0.00 41.62 4.94
204 205 3.046390 GTCAAGTCAACAGACTCTCGTG 58.954 50.000 0.00 0.00 41.62 4.35
205 206 2.688446 TGTCAAGTCAACAGACTCTCGT 59.312 45.455 0.00 0.00 41.62 4.18
206 207 3.046390 GTGTCAAGTCAACAGACTCTCG 58.954 50.000 0.00 0.00 41.62 4.04
207 208 4.046938 TGTGTCAAGTCAACAGACTCTC 57.953 45.455 0.00 0.00 41.62 3.20
208 209 4.471904 TTGTGTCAAGTCAACAGACTCT 57.528 40.909 0.00 0.00 41.62 3.24
209 210 4.034510 CCTTTGTGTCAAGTCAACAGACTC 59.965 45.833 0.00 0.00 41.62 3.36
210 211 3.941483 CCTTTGTGTCAAGTCAACAGACT 59.059 43.478 0.00 0.00 44.25 3.24
211 212 3.938963 TCCTTTGTGTCAAGTCAACAGAC 59.061 43.478 0.00 0.00 0.00 3.51
212 213 4.214986 TCCTTTGTGTCAAGTCAACAGA 57.785 40.909 0.00 0.00 0.00 3.41
213 214 4.963276 TTCCTTTGTGTCAAGTCAACAG 57.037 40.909 0.00 0.00 0.00 3.16
214 215 5.007034 TCTTTCCTTTGTGTCAAGTCAACA 58.993 37.500 0.00 0.00 0.00 3.33
215 216 5.560966 TCTTTCCTTTGTGTCAAGTCAAC 57.439 39.130 0.00 0.00 0.00 3.18
216 217 7.773224 TCTTATCTTTCCTTTGTGTCAAGTCAA 59.227 33.333 0.00 0.00 0.00 3.18
217 218 7.279615 TCTTATCTTTCCTTTGTGTCAAGTCA 58.720 34.615 0.00 0.00 0.00 3.41
218 219 7.730364 TCTTATCTTTCCTTTGTGTCAAGTC 57.270 36.000 0.00 0.00 0.00 3.01
219 220 8.519799 TTTCTTATCTTTCCTTTGTGTCAAGT 57.480 30.769 0.00 0.00 0.00 3.16
220 221 9.971922 ATTTTCTTATCTTTCCTTTGTGTCAAG 57.028 29.630 0.00 0.00 0.00 3.02
221 222 9.748708 CATTTTCTTATCTTTCCTTTGTGTCAA 57.251 29.630 0.00 0.00 0.00 3.18
222 223 9.130661 TCATTTTCTTATCTTTCCTTTGTGTCA 57.869 29.630 0.00 0.00 0.00 3.58
223 224 9.965824 TTCATTTTCTTATCTTTCCTTTGTGTC 57.034 29.630 0.00 0.00 0.00 3.67
224 225 9.971922 CTTCATTTTCTTATCTTTCCTTTGTGT 57.028 29.630 0.00 0.00 0.00 3.72
225 226 8.919661 GCTTCATTTTCTTATCTTTCCTTTGTG 58.080 33.333 0.00 0.00 0.00 3.33
226 227 8.641541 TGCTTCATTTTCTTATCTTTCCTTTGT 58.358 29.630 0.00 0.00 0.00 2.83
227 228 9.136952 CTGCTTCATTTTCTTATCTTTCCTTTG 57.863 33.333 0.00 0.00 0.00 2.77
228 229 8.309656 CCTGCTTCATTTTCTTATCTTTCCTTT 58.690 33.333 0.00 0.00 0.00 3.11
229 230 7.578380 GCCTGCTTCATTTTCTTATCTTTCCTT 60.578 37.037 0.00 0.00 0.00 3.36
230 231 6.127507 GCCTGCTTCATTTTCTTATCTTTCCT 60.128 38.462 0.00 0.00 0.00 3.36
231 232 6.038985 GCCTGCTTCATTTTCTTATCTTTCC 58.961 40.000 0.00 0.00 0.00 3.13
232 233 6.750963 CAGCCTGCTTCATTTTCTTATCTTTC 59.249 38.462 0.00 0.00 0.00 2.62
233 234 6.628185 CAGCCTGCTTCATTTTCTTATCTTT 58.372 36.000 0.00 0.00 0.00 2.52
234 235 5.393896 GCAGCCTGCTTCATTTTCTTATCTT 60.394 40.000 10.04 0.00 40.96 2.40
235 236 4.097589 GCAGCCTGCTTCATTTTCTTATCT 59.902 41.667 10.04 0.00 40.96 1.98
263 264 1.784525 CTCGGATTGGCGGAGTATTC 58.215 55.000 0.00 0.00 38.68 1.75
271 272 2.586079 ACGATGCTCGGATTGGCG 60.586 61.111 9.75 0.00 45.59 5.69
297 298 6.335777 GGGTCGAGTAAAATAGAGTGCTTTA 58.664 40.000 0.00 0.00 0.00 1.85
333 334 0.665369 TCTTTTTCGTCGACGGCTCC 60.665 55.000 35.05 0.00 40.29 4.70
345 347 3.247886 GCCGTCGGATCCTTATCTTTTTC 59.752 47.826 17.49 0.00 32.29 2.29
347 349 2.484947 GGCCGTCGGATCCTTATCTTTT 60.485 50.000 17.49 0.00 32.29 2.27
487 492 4.284550 CACTGTGGTGGGGGTGGG 62.285 72.222 0.00 0.00 39.59 4.61
488 493 4.974721 GCACTGTGGTGGGGGTGG 62.975 72.222 10.21 0.00 43.18 4.61
1006 1023 1.129879 GAAACGATCGACGCAGCGTA 61.130 55.000 23.04 6.66 46.94 4.42
1025 1042 0.179100 ATCACAGCAACGATCTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
1027 1044 1.203928 CGATCACAGCAACGATCTCC 58.796 55.000 0.00 0.00 36.66 3.71
1028 1045 1.585668 CACGATCACAGCAACGATCTC 59.414 52.381 0.00 0.00 36.66 2.75
1029 1046 1.067565 ACACGATCACAGCAACGATCT 60.068 47.619 0.00 0.00 36.66 2.75
1031 1048 1.070821 CACACGATCACAGCAACGAT 58.929 50.000 0.00 0.00 0.00 3.73
1079 1103 2.114670 CATTGCTCCGCGGGAACAT 61.115 57.895 27.83 10.19 27.33 2.71
1204 1228 4.463879 CTGGAGCTGGAGGTGGCG 62.464 72.222 0.00 0.00 0.00 5.69
1301 1325 1.347817 CTCGGAAGAACTCGCAGTGC 61.348 60.000 4.58 4.58 41.32 4.40
1305 1329 2.261671 GCCTCGGAAGAACTCGCA 59.738 61.111 0.00 0.00 41.32 5.10
1323 1347 0.393537 AGCTTCAAGATCAAGGCCGG 60.394 55.000 0.00 0.00 0.00 6.13
1326 1350 1.471684 CCACAGCTTCAAGATCAAGGC 59.528 52.381 0.00 0.00 0.00 4.35
1327 1351 2.746362 GACCACAGCTTCAAGATCAAGG 59.254 50.000 0.00 0.00 0.00 3.61
1330 1354 2.634453 TCAGACCACAGCTTCAAGATCA 59.366 45.455 0.00 0.00 0.00 2.92
1356 1384 2.223479 GCGGCAAGAGAAAAAGAACACA 60.223 45.455 0.00 0.00 0.00 3.72
1374 1402 3.775654 GACAGACCCCTCCTGCGG 61.776 72.222 0.00 0.00 35.14 5.69
1829 1860 2.856720 GCGCACTGAGAGTAGATACTGC 60.857 54.545 0.30 0.00 36.50 4.40
1845 1917 4.317418 CGAGTGATGAAACTATAAGCGCAC 60.317 45.833 11.47 0.00 0.00 5.34
1859 1931 6.025749 ACTTGAACAATAGACGAGTGATGA 57.974 37.500 0.00 0.00 0.00 2.92
1891 1963 9.968870 ATACTCTCGAGGAAAGAAAACATATAC 57.031 33.333 13.56 0.00 0.00 1.47
1895 1967 5.582665 GCATACTCTCGAGGAAAGAAAACAT 59.417 40.000 13.56 0.00 0.00 2.71
1896 1968 4.929808 GCATACTCTCGAGGAAAGAAAACA 59.070 41.667 13.56 0.00 0.00 2.83
1897 1969 4.330347 GGCATACTCTCGAGGAAAGAAAAC 59.670 45.833 13.56 0.00 0.00 2.43
1898 1970 4.223032 AGGCATACTCTCGAGGAAAGAAAA 59.777 41.667 13.56 0.00 0.00 2.29
1899 1971 3.769844 AGGCATACTCTCGAGGAAAGAAA 59.230 43.478 13.56 0.00 0.00 2.52
1900 1972 3.366396 AGGCATACTCTCGAGGAAAGAA 58.634 45.455 13.56 0.00 0.00 2.52
1901 1973 2.952978 GAGGCATACTCTCGAGGAAAGA 59.047 50.000 13.56 0.00 43.14 2.52
1902 1974 3.363341 GAGGCATACTCTCGAGGAAAG 57.637 52.381 13.56 5.26 43.14 2.62
1988 2060 2.036958 TGTGGTATTGCGCTATGCTT 57.963 45.000 17.83 0.00 46.63 3.91
1997 2069 1.064060 GTTGCTCGGATGTGGTATTGC 59.936 52.381 0.00 0.00 0.00 3.56
2001 2073 1.070914 TGTTGTTGCTCGGATGTGGTA 59.929 47.619 0.00 0.00 0.00 3.25
2008 2080 2.970324 GCGGTGTTGTTGCTCGGA 60.970 61.111 0.00 0.00 0.00 4.55
2117 2208 0.389025 TCGACAAGTGAAGCTCTGCA 59.611 50.000 0.00 0.00 0.00 4.41
2151 2242 2.288518 GCCACTTCCTCTTAGGCGATAG 60.289 54.545 0.00 0.00 34.61 2.08
2231 2329 4.307443 TGATCCTCTACAACGCTATGTG 57.693 45.455 1.88 0.00 34.75 3.21
2240 2342 4.081420 GCTGTCCTTCTTGATCCTCTACAA 60.081 45.833 0.00 0.00 0.00 2.41
2241 2343 3.449018 GCTGTCCTTCTTGATCCTCTACA 59.551 47.826 0.00 0.00 0.00 2.74
2291 2393 3.936772 TTTGGAGACATGGCCGGCC 62.937 63.158 39.40 39.40 42.32 6.13
2320 2422 1.213094 CGACGTCGTTCCTTTGCTGT 61.213 55.000 29.08 0.00 34.11 4.40
2326 2428 3.468780 GTCTTCGACGTCGTTCCTT 57.531 52.632 34.40 0.00 40.80 3.36
2497 2612 3.829886 GTGGATGAAAATCTTGCACGA 57.170 42.857 0.00 0.00 34.38 4.35
2519 2634 3.936203 GTGTGGGGAGGTGCGACA 61.936 66.667 0.00 0.00 0.00 4.35
2530 2645 1.070758 CCCGATTCTAGATGGTGTGGG 59.929 57.143 0.00 0.00 0.00 4.61
2601 2716 2.265739 CTCGGCTTGGCAGCTACA 59.734 61.111 8.45 0.00 46.44 2.74
2774 2890 0.737715 GCTTGGCTTCGTCGAGATGT 60.738 55.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.