Multiple sequence alignment - TraesCS5A01G279300

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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 TraesCS5A01G279300 chr5A 100.000 2303 0 0 1 2303 488270689 488268387 0.000000e+00 4253
1 TraesCS5A01G279300 chr5A 98.280 1919 31 2 386 2303 403298132 403296215 0.000000e+00 3360
2 TraesCS5A01G279300 chr5A 99.636 275 1 0 1 275 514011243 514011517 9.500000e-139 503
3 TraesCS5A01G279300 chr5A 99.636 275 1 0 1 275 597067473 597067747 9.500000e-139 503
4 TraesCS5A01G279300 chr5A 99.636 275 1 0 1 275 598310573 598310847 9.500000e-139 503
5 TraesCS5A01G279300 chr7A 98.630 1971 27 0 333 2303 105258958 105260928 0.000000e+00 3491
6 TraesCS5A01G279300 chr7A 98.577 281 4 0 1 281 22967962 22967682 4.420000e-137 497
7 TraesCS5A01G279300 chr1B 98.529 1971 29 0 333 2303 439505655 439507625 0.000000e+00 3480
8 TraesCS5A01G279300 chr2A 98.225 1972 28 3 333 2303 145432477 145434442 0.000000e+00 3441
9 TraesCS5A01G279300 chr2A 98.565 1881 24 3 424 2303 738196634 738198512 0.000000e+00 3321
10 TraesCS5A01G279300 chr3A 97.444 1995 26 7 333 2303 128143645 128145638 0.000000e+00 3378
11 TraesCS5A01G279300 chr4A 98.385 1919 29 2 386 2303 152584306 152582389 0.000000e+00 3371
12 TraesCS5A01G279300 chr4A 99.184 1716 14 0 588 2303 377596841 377595126 0.000000e+00 3092
13 TraesCS5A01G279300 chr4A 86.254 1775 148 53 333 2061 362828958 362827234 0.000000e+00 1838
14 TraesCS5A01G279300 chr4A 99.636 275 1 0 1 275 446477807 446477533 9.500000e-139 503
15 TraesCS5A01G279300 chr1A 97.967 1918 39 0 386 2303 552379371 552377454 0.000000e+00 3326
16 TraesCS5A01G279300 chrUn 99.636 275 1 0 1 275 445689017 445688743 9.500000e-139 503
17 TraesCS5A01G279300 chr3B 99.636 275 1 0 1 275 421086009 421086283 9.500000e-139 503
18 TraesCS5A01G279300 chr2B 99.636 275 1 0 1 275 461108604 461108330 9.500000e-139 503
19 TraesCS5A01G279300 chr2B 99.636 275 1 0 1 275 622707529 622707803 9.500000e-139 503


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 TraesCS5A01G279300 chr5A 488268387 488270689 2302 True 4253 4253 100.000 1 2303 1 chr5A.!!$R2 2302
1 TraesCS5A01G279300 chr5A 403296215 403298132 1917 True 3360 3360 98.280 386 2303 1 chr5A.!!$R1 1917
2 TraesCS5A01G279300 chr7A 105258958 105260928 1970 False 3491 3491 98.630 333 2303 1 chr7A.!!$F1 1970
3 TraesCS5A01G279300 chr1B 439505655 439507625 1970 False 3480 3480 98.529 333 2303 1 chr1B.!!$F1 1970
4 TraesCS5A01G279300 chr2A 145432477 145434442 1965 False 3441 3441 98.225 333 2303 1 chr2A.!!$F1 1970
5 TraesCS5A01G279300 chr2A 738196634 738198512 1878 False 3321 3321 98.565 424 2303 1 chr2A.!!$F2 1879
6 TraesCS5A01G279300 chr3A 128143645 128145638 1993 False 3378 3378 97.444 333 2303 1 chr3A.!!$F1 1970
7 TraesCS5A01G279300 chr4A 152582389 152584306 1917 True 3371 3371 98.385 386 2303 1 chr4A.!!$R1 1917
8 TraesCS5A01G279300 chr4A 377595126 377596841 1715 True 3092 3092 99.184 588 2303 1 chr4A.!!$R3 1715
9 TraesCS5A01G279300 chr4A 362827234 362828958 1724 True 1838 1838 86.254 333 2061 1 chr4A.!!$R2 1728
10 TraesCS5A01G279300 chr1A 552377454 552379371 1917 True 3326 3326 97.967 386 2303 1 chr1A.!!$R1 1917

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
215 216 0.034896 AAGGTGCTCAAGGGTGTACG 59.965 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1502 1.270839 CCTCCAAGCCTCTTCGAAACA 60.271 52.381 0.0 0.0 0.0 2.83 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 3.188895 GGATTGTTGTCTCGCTTTCAC 57.811 47.619 0.00 0.00 0.00 3.18
21 22 2.095718 GGATTGTTGTCTCGCTTTCACC 60.096 50.000 0.00 0.00 0.00 4.02
22 23 2.031258 TTGTTGTCTCGCTTTCACCA 57.969 45.000 0.00 0.00 0.00 4.17
23 24 2.031258 TGTTGTCTCGCTTTCACCAA 57.969 45.000 0.00 0.00 0.00 3.67
24 25 1.668751 TGTTGTCTCGCTTTCACCAAC 59.331 47.619 0.00 0.00 34.32 3.77
25 26 1.668751 GTTGTCTCGCTTTCACCAACA 59.331 47.619 0.00 0.00 34.00 3.33
26 27 2.031258 TGTCTCGCTTTCACCAACAA 57.969 45.000 0.00 0.00 0.00 2.83
27 28 1.939934 TGTCTCGCTTTCACCAACAAG 59.060 47.619 0.00 0.00 0.00 3.16
28 29 1.940613 GTCTCGCTTTCACCAACAAGT 59.059 47.619 0.00 0.00 0.00 3.16
29 30 1.939934 TCTCGCTTTCACCAACAAGTG 59.060 47.619 0.00 0.00 39.20 3.16
50 51 4.125703 TGGTTTTCCACATTGTTCAATGC 58.874 39.130 20.84 6.88 46.22 3.56
51 52 4.125703 GGTTTTCCACATTGTTCAATGCA 58.874 39.130 20.84 0.00 40.31 3.96
52 53 4.756135 GGTTTTCCACATTGTTCAATGCAT 59.244 37.500 20.84 0.00 40.31 3.96
53 54 5.239087 GGTTTTCCACATTGTTCAATGCATT 59.761 36.000 20.84 5.99 40.31 3.56
54 55 5.926214 TTTCCACATTGTTCAATGCATTG 57.074 34.783 29.75 29.75 39.10 2.82
55 56 3.327626 TCCACATTGTTCAATGCATTGC 58.672 40.909 30.57 19.60 37.68 3.56
56 57 3.007074 TCCACATTGTTCAATGCATTGCT 59.993 39.130 30.57 12.16 37.68 3.91
57 58 3.369756 CCACATTGTTCAATGCATTGCTC 59.630 43.478 30.57 24.20 37.68 4.26
58 59 3.991121 CACATTGTTCAATGCATTGCTCA 59.009 39.130 30.57 26.06 37.68 4.26
59 60 4.091365 CACATTGTTCAATGCATTGCTCAG 59.909 41.667 30.57 20.92 37.68 3.35
60 61 4.021807 ACATTGTTCAATGCATTGCTCAGA 60.022 37.500 30.57 20.17 37.68 3.27
61 62 3.564235 TGTTCAATGCATTGCTCAGAC 57.436 42.857 30.57 21.89 37.68 3.51
62 63 2.885894 TGTTCAATGCATTGCTCAGACA 59.114 40.909 30.57 23.68 37.68 3.41
63 64 3.240069 GTTCAATGCATTGCTCAGACAC 58.760 45.455 30.57 15.22 37.68 3.67
64 65 2.506444 TCAATGCATTGCTCAGACACA 58.494 42.857 30.57 10.62 37.68 3.72
65 66 2.885894 TCAATGCATTGCTCAGACACAA 59.114 40.909 30.57 9.92 37.68 3.33
66 67 3.057806 TCAATGCATTGCTCAGACACAAG 60.058 43.478 30.57 6.40 37.68 3.16
67 68 2.259266 TGCATTGCTCAGACACAAGA 57.741 45.000 10.49 0.00 0.00 3.02
68 69 2.574450 TGCATTGCTCAGACACAAGAA 58.426 42.857 10.49 0.00 0.00 2.52
69 70 2.950975 TGCATTGCTCAGACACAAGAAA 59.049 40.909 10.49 0.00 0.00 2.52
70 71 3.243168 TGCATTGCTCAGACACAAGAAAC 60.243 43.478 10.49 0.00 0.00 2.78
71 72 3.004106 GCATTGCTCAGACACAAGAAACT 59.996 43.478 0.16 0.00 0.00 2.66
72 73 4.498682 GCATTGCTCAGACACAAGAAACTT 60.499 41.667 0.16 0.00 0.00 2.66
73 74 4.621068 TTGCTCAGACACAAGAAACTTG 57.379 40.909 9.51 9.51 0.00 3.16
74 75 3.872696 TGCTCAGACACAAGAAACTTGA 58.127 40.909 16.65 0.00 0.00 3.02
75 76 3.623060 TGCTCAGACACAAGAAACTTGAC 59.377 43.478 16.65 8.51 0.00 3.18
76 77 3.002759 GCTCAGACACAAGAAACTTGACC 59.997 47.826 16.65 6.50 0.00 4.02
77 78 3.541632 TCAGACACAAGAAACTTGACCC 58.458 45.455 16.65 6.22 0.00 4.46
78 79 2.618709 CAGACACAAGAAACTTGACCCC 59.381 50.000 16.65 4.81 0.00 4.95
79 80 1.602377 GACACAAGAAACTTGACCCCG 59.398 52.381 16.65 4.18 0.00 5.73
80 81 0.951558 CACAAGAAACTTGACCCCGG 59.048 55.000 16.65 0.00 0.00 5.73
81 82 0.822121 ACAAGAAACTTGACCCCGGC 60.822 55.000 16.65 0.00 0.00 6.13
82 83 1.599797 AAGAAACTTGACCCCGGCG 60.600 57.895 0.00 0.00 0.00 6.46
83 84 3.053896 GAAACTTGACCCCGGCGG 61.054 66.667 21.46 21.46 37.81 6.13
92 93 4.016706 CCCCGGCGGTCAGAAGTT 62.017 66.667 26.32 0.00 0.00 2.66
93 94 2.032071 CCCGGCGGTCAGAAGTTT 59.968 61.111 26.32 0.00 0.00 2.66
94 95 2.033194 CCCGGCGGTCAGAAGTTTC 61.033 63.158 26.32 0.00 0.00 2.78
95 96 1.004918 CCGGCGGTCAGAAGTTTCT 60.005 57.895 19.97 0.00 38.25 2.52
111 112 7.597386 AGAAGTTTCTGAATAAGAACATTGCC 58.403 34.615 0.00 0.00 44.77 4.52
112 113 5.942872 AGTTTCTGAATAAGAACATTGCCG 58.057 37.500 0.00 0.00 44.77 5.69
113 114 5.705441 AGTTTCTGAATAAGAACATTGCCGA 59.295 36.000 0.00 0.00 44.77 5.54
114 115 6.206634 AGTTTCTGAATAAGAACATTGCCGAA 59.793 34.615 0.00 0.00 44.77 4.30
115 116 6.567687 TTCTGAATAAGAACATTGCCGAAA 57.432 33.333 0.00 0.00 40.09 3.46
116 117 6.182039 TCTGAATAAGAACATTGCCGAAAG 57.818 37.500 0.00 0.00 29.54 2.62
117 118 5.123820 TCTGAATAAGAACATTGCCGAAAGG 59.876 40.000 0.00 0.00 43.54 3.11
118 119 7.022568 TCTGAATAAGAACATTGCCGAAAGGA 61.023 38.462 0.00 0.00 43.43 3.36
119 120 8.441089 TCTGAATAAGAACATTGCCGAAAGGAA 61.441 37.037 0.00 0.00 43.43 3.36
131 132 1.330521 CGAAAGGAATATGTGGGCACG 59.669 52.381 0.00 0.00 0.00 5.34
132 133 2.365582 GAAAGGAATATGTGGGCACGT 58.634 47.619 0.00 0.00 0.00 4.49
133 134 1.750193 AAGGAATATGTGGGCACGTG 58.250 50.000 12.28 12.28 0.00 4.49
134 135 0.748005 AGGAATATGTGGGCACGTGC 60.748 55.000 32.15 32.15 41.14 5.34
135 136 0.748005 GGAATATGTGGGCACGTGCT 60.748 55.000 36.84 21.23 41.70 4.40
136 137 1.094785 GAATATGTGGGCACGTGCTT 58.905 50.000 36.84 22.79 41.70 3.91
137 138 1.472480 GAATATGTGGGCACGTGCTTT 59.528 47.619 36.84 20.09 41.70 3.51
138 139 1.094785 ATATGTGGGCACGTGCTTTC 58.905 50.000 36.84 25.96 41.70 2.62
139 140 1.295357 TATGTGGGCACGTGCTTTCG 61.295 55.000 36.84 1.66 41.70 3.46
140 141 2.970324 GTGGGCACGTGCTTTCGA 60.970 61.111 36.84 17.34 41.70 3.71
141 142 2.031919 TGGGCACGTGCTTTCGAT 59.968 55.556 36.84 0.00 41.70 3.59
142 143 2.324330 TGGGCACGTGCTTTCGATG 61.324 57.895 36.84 0.00 41.70 3.84
143 144 2.032634 GGGCACGTGCTTTCGATGA 61.033 57.895 36.84 0.00 41.70 2.92
144 145 1.573829 GGGCACGTGCTTTCGATGAA 61.574 55.000 36.84 0.00 41.70 2.57
145 146 0.179215 GGCACGTGCTTTCGATGAAG 60.179 55.000 36.84 0.00 41.70 3.02
146 147 0.790207 GCACGTGCTTTCGATGAAGA 59.210 50.000 32.55 0.00 38.21 2.87
147 148 1.394917 GCACGTGCTTTCGATGAAGAT 59.605 47.619 32.55 0.00 38.21 2.40
148 149 2.785681 GCACGTGCTTTCGATGAAGATG 60.786 50.000 32.55 0.00 38.21 2.90
149 150 2.002586 ACGTGCTTTCGATGAAGATGG 58.997 47.619 0.96 0.00 34.70 3.51
150 151 1.267732 CGTGCTTTCGATGAAGATGGC 60.268 52.381 0.96 0.00 0.00 4.40
151 152 1.064654 GTGCTTTCGATGAAGATGGCC 59.935 52.381 0.00 0.00 0.00 5.36
152 153 0.305922 GCTTTCGATGAAGATGGCCG 59.694 55.000 0.00 0.00 0.00 6.13
153 154 0.940126 CTTTCGATGAAGATGGCCGG 59.060 55.000 0.00 0.00 0.00 6.13
154 155 0.539518 TTTCGATGAAGATGGCCGGA 59.460 50.000 5.05 0.00 0.00 5.14
155 156 0.104855 TTCGATGAAGATGGCCGGAG 59.895 55.000 5.05 0.00 0.00 4.63
170 171 1.636988 CGGAGGTACGGTCAAATGAC 58.363 55.000 4.96 4.96 44.04 3.06
171 172 1.067425 CGGAGGTACGGTCAAATGACA 60.067 52.381 14.93 0.00 46.47 3.58
172 173 2.610976 CGGAGGTACGGTCAAATGACAA 60.611 50.000 14.93 0.00 46.47 3.18
173 174 3.000727 GGAGGTACGGTCAAATGACAAG 58.999 50.000 14.93 10.43 46.47 3.16
174 175 2.415512 GAGGTACGGTCAAATGACAAGC 59.584 50.000 14.93 9.17 46.47 4.01
175 176 2.147958 GGTACGGTCAAATGACAAGCA 58.852 47.619 14.93 0.00 46.47 3.91
176 177 2.550606 GGTACGGTCAAATGACAAGCAA 59.449 45.455 14.93 0.00 46.47 3.91
177 178 3.190535 GGTACGGTCAAATGACAAGCAAT 59.809 43.478 14.93 0.00 46.47 3.56
178 179 4.393680 GGTACGGTCAAATGACAAGCAATA 59.606 41.667 14.93 0.00 46.47 1.90
179 180 5.065988 GGTACGGTCAAATGACAAGCAATAT 59.934 40.000 14.93 0.00 46.47 1.28
180 181 4.985413 ACGGTCAAATGACAAGCAATATG 58.015 39.130 14.93 0.00 46.47 1.78
181 182 4.142403 ACGGTCAAATGACAAGCAATATGG 60.142 41.667 14.93 0.00 46.47 2.74
182 183 4.114794 GGTCAAATGACAAGCAATATGGC 58.885 43.478 14.93 0.00 46.47 4.40
183 184 4.381825 GGTCAAATGACAAGCAATATGGCA 60.382 41.667 14.93 0.00 46.47 4.92
184 185 4.802039 GTCAAATGACAAGCAATATGGCAG 59.198 41.667 4.54 0.00 39.65 4.85
185 186 4.705991 TCAAATGACAAGCAATATGGCAGA 59.294 37.500 4.54 0.00 39.65 4.26
186 187 5.185442 TCAAATGACAAGCAATATGGCAGAA 59.815 36.000 4.54 0.00 39.65 3.02
187 188 5.864418 AATGACAAGCAATATGGCAGAAT 57.136 34.783 4.54 0.00 39.65 2.40
188 189 4.642445 TGACAAGCAATATGGCAGAATG 57.358 40.909 4.54 0.00 40.87 2.67
203 204 4.978083 CAGAATGCTTCAATAAGGTGCT 57.022 40.909 0.00 0.00 32.98 4.40
204 205 4.918037 CAGAATGCTTCAATAAGGTGCTC 58.082 43.478 0.00 0.00 32.98 4.26
205 206 4.397103 CAGAATGCTTCAATAAGGTGCTCA 59.603 41.667 0.00 0.00 32.98 4.26
206 207 5.012239 AGAATGCTTCAATAAGGTGCTCAA 58.988 37.500 0.00 0.00 32.98 3.02
207 208 4.978083 ATGCTTCAATAAGGTGCTCAAG 57.022 40.909 0.00 0.00 32.98 3.02
208 209 3.084039 TGCTTCAATAAGGTGCTCAAGG 58.916 45.455 0.00 0.00 32.98 3.61
209 210 2.424956 GCTTCAATAAGGTGCTCAAGGG 59.575 50.000 0.00 0.00 32.98 3.95
210 211 3.690460 CTTCAATAAGGTGCTCAAGGGT 58.310 45.455 0.00 0.00 0.00 4.34
211 212 3.071874 TCAATAAGGTGCTCAAGGGTG 57.928 47.619 0.00 0.00 0.00 4.61
212 213 2.375174 TCAATAAGGTGCTCAAGGGTGT 59.625 45.455 0.00 0.00 0.00 4.16
213 214 3.585289 TCAATAAGGTGCTCAAGGGTGTA 59.415 43.478 0.00 0.00 0.00 2.90
214 215 3.629142 ATAAGGTGCTCAAGGGTGTAC 57.371 47.619 0.00 0.00 0.00 2.90
215 216 0.034896 AAGGTGCTCAAGGGTGTACG 59.965 55.000 0.00 0.00 0.00 3.67
216 217 1.119574 AGGTGCTCAAGGGTGTACGT 61.120 55.000 0.00 0.00 0.00 3.57
217 218 0.949105 GGTGCTCAAGGGTGTACGTG 60.949 60.000 0.00 0.00 0.00 4.49
218 219 1.301401 TGCTCAAGGGTGTACGTGC 60.301 57.895 0.00 0.00 0.00 5.34
219 220 1.301401 GCTCAAGGGTGTACGTGCA 60.301 57.895 0.82 0.82 0.00 4.57
220 221 0.673644 GCTCAAGGGTGTACGTGCAT 60.674 55.000 10.21 0.00 0.00 3.96
221 222 1.808411 CTCAAGGGTGTACGTGCATT 58.192 50.000 10.21 0.00 0.00 3.56
222 223 2.933492 GCTCAAGGGTGTACGTGCATTA 60.933 50.000 10.21 0.00 0.00 1.90
223 224 2.671396 CTCAAGGGTGTACGTGCATTAC 59.329 50.000 10.21 3.56 0.00 1.89
224 225 1.735571 CAAGGGTGTACGTGCATTACC 59.264 52.381 10.21 12.63 0.00 2.85
225 226 2.771435 GGGTGTACGTGCATTACCC 58.229 57.895 10.21 12.26 43.68 3.69
226 227 1.085501 GGGTGTACGTGCATTACCCG 61.086 60.000 10.21 2.15 41.34 5.28
227 228 0.390209 GGTGTACGTGCATTACCCGT 60.390 55.000 10.21 4.66 38.53 5.28
228 229 0.717224 GTGTACGTGCATTACCCGTG 59.283 55.000 10.21 0.00 36.12 4.94
229 230 0.602060 TGTACGTGCATTACCCGTGA 59.398 50.000 0.82 0.00 36.12 4.35
230 231 0.994263 GTACGTGCATTACCCGTGAC 59.006 55.000 9.31 1.47 36.12 3.67
231 232 0.456482 TACGTGCATTACCCGTGACG 60.456 55.000 9.31 0.00 36.12 4.35
233 234 2.435234 TGCATTACCCGTGACGGC 60.435 61.111 20.39 6.60 46.86 5.68
234 235 2.435234 GCATTACCCGTGACGGCA 60.435 61.111 20.39 5.35 46.86 5.69
235 236 2.036006 GCATTACCCGTGACGGCAA 61.036 57.895 20.39 14.88 46.86 4.52
236 237 1.373590 GCATTACCCGTGACGGCAAT 61.374 55.000 20.39 16.52 46.86 3.56
237 238 1.942677 CATTACCCGTGACGGCAATA 58.057 50.000 20.39 7.65 46.86 1.90
238 239 1.864711 CATTACCCGTGACGGCAATAG 59.135 52.381 20.39 7.12 46.86 1.73
239 240 0.896923 TTACCCGTGACGGCAATAGT 59.103 50.000 20.39 13.23 46.86 2.12
240 241 0.896923 TACCCGTGACGGCAATAGTT 59.103 50.000 20.39 0.00 46.86 2.24
241 242 0.390735 ACCCGTGACGGCAATAGTTC 60.391 55.000 20.39 0.00 46.86 3.01
242 243 0.390603 CCCGTGACGGCAATAGTTCA 60.391 55.000 20.39 0.00 46.86 3.18
243 244 1.434555 CCGTGACGGCAATAGTTCAA 58.565 50.000 12.53 0.00 41.17 2.69
244 245 2.006888 CCGTGACGGCAATAGTTCAAT 58.993 47.619 12.53 0.00 41.17 2.57
245 246 3.191669 CCGTGACGGCAATAGTTCAATA 58.808 45.455 12.53 0.00 41.17 1.90
246 247 3.000925 CCGTGACGGCAATAGTTCAATAC 59.999 47.826 12.53 0.00 41.17 1.89
247 248 3.615056 CGTGACGGCAATAGTTCAATACA 59.385 43.478 0.00 0.00 0.00 2.29
248 249 4.491924 CGTGACGGCAATAGTTCAATACAC 60.492 45.833 0.00 0.00 0.00 2.90
249 250 4.390603 GTGACGGCAATAGTTCAATACACA 59.609 41.667 0.00 0.00 0.00 3.72
250 251 5.064707 GTGACGGCAATAGTTCAATACACAT 59.935 40.000 0.00 0.00 0.00 3.21
251 252 5.645929 TGACGGCAATAGTTCAATACACATT 59.354 36.000 0.00 0.00 0.00 2.71
252 253 6.150307 TGACGGCAATAGTTCAATACACATTT 59.850 34.615 0.00 0.00 0.00 2.32
253 254 6.321717 ACGGCAATAGTTCAATACACATTTG 58.678 36.000 0.00 0.00 0.00 2.32
254 255 6.150307 ACGGCAATAGTTCAATACACATTTGA 59.850 34.615 0.00 0.00 0.00 2.69
255 256 6.468956 CGGCAATAGTTCAATACACATTTGAC 59.531 38.462 0.00 0.00 33.03 3.18
256 257 7.312154 GGCAATAGTTCAATACACATTTGACA 58.688 34.615 0.00 0.00 33.03 3.58
257 258 7.812191 GGCAATAGTTCAATACACATTTGACAA 59.188 33.333 0.00 0.00 33.03 3.18
258 259 8.853345 GCAATAGTTCAATACACATTTGACAAG 58.147 33.333 0.00 0.00 33.03 3.16
259 260 9.897744 CAATAGTTCAATACACATTTGACAAGT 57.102 29.630 0.00 0.00 33.03 3.16
261 262 9.897744 ATAGTTCAATACACATTTGACAAGTTG 57.102 29.630 0.00 0.00 33.03 3.16
262 263 7.995289 AGTTCAATACACATTTGACAAGTTGA 58.005 30.769 10.54 0.00 33.03 3.18
263 264 8.465999 AGTTCAATACACATTTGACAAGTTGAA 58.534 29.630 10.54 0.00 33.03 2.69
264 265 9.248291 GTTCAATACACATTTGACAAGTTGAAT 57.752 29.630 10.54 0.00 36.05 2.57
265 266 8.800231 TCAATACACATTTGACAAGTTGAATG 57.200 30.769 10.54 11.49 36.00 2.67
266 267 8.628280 TCAATACACATTTGACAAGTTGAATGA 58.372 29.630 17.89 2.08 34.47 2.57
267 268 9.247126 CAATACACATTTGACAAGTTGAATGAA 57.753 29.630 17.89 5.77 34.47 2.57
268 269 9.985730 AATACACATTTGACAAGTTGAATGAAT 57.014 25.926 17.89 10.23 34.47 2.57
270 271 8.801715 ACACATTTGACAAGTTGAATGAATAC 57.198 30.769 17.89 0.00 34.47 1.89
271 272 8.632679 ACACATTTGACAAGTTGAATGAATACT 58.367 29.630 17.89 0.00 34.47 2.12
272 273 9.467258 CACATTTGACAAGTTGAATGAATACTT 57.533 29.630 17.89 0.00 34.47 2.24
277 278 9.515020 TTGACAAGTTGAATGAATACTTTTGAC 57.485 29.630 10.54 0.00 30.08 3.18
278 279 8.681806 TGACAAGTTGAATGAATACTTTTGACA 58.318 29.630 10.54 0.00 30.08 3.58
279 280 9.515020 GACAAGTTGAATGAATACTTTTGACAA 57.485 29.630 10.54 0.00 30.08 3.18
280 281 9.520204 ACAAGTTGAATGAATACTTTTGACAAG 57.480 29.630 10.54 0.00 30.08 3.16
281 282 9.520204 CAAGTTGAATGAATACTTTTGACAAGT 57.480 29.630 0.00 0.00 30.08 3.16
283 284 9.520204 AGTTGAATGAATACTTTTGACAAGTTG 57.480 29.630 0.00 0.00 0.00 3.16
284 285 9.515020 GTTGAATGAATACTTTTGACAAGTTGA 57.485 29.630 10.54 0.00 0.00 3.18
294 295 8.856490 ACTTTTGACAAGTTGAATCAATACAC 57.144 30.769 10.54 0.00 32.61 2.90
295 296 8.465999 ACTTTTGACAAGTTGAATCAATACACA 58.534 29.630 10.54 0.00 32.61 3.72
296 297 9.467258 CTTTTGACAAGTTGAATCAATACACAT 57.533 29.630 10.54 0.00 32.61 3.21
297 298 9.814899 TTTTGACAAGTTGAATCAATACACATT 57.185 25.926 10.54 0.00 32.61 2.71
298 299 9.814899 TTTGACAAGTTGAATCAATACACATTT 57.185 25.926 10.54 0.00 32.61 2.32
299 300 8.800231 TGACAAGTTGAATCAATACACATTTG 57.200 30.769 10.54 0.00 0.00 2.32
300 301 8.628280 TGACAAGTTGAATCAATACACATTTGA 58.372 29.630 10.54 0.00 37.49 2.69
301 302 8.801715 ACAAGTTGAATCAATACACATTTGAC 57.198 30.769 10.54 0.00 36.02 3.18
302 303 8.412456 ACAAGTTGAATCAATACACATTTGACA 58.588 29.630 10.54 0.00 36.02 3.58
303 304 9.247126 CAAGTTGAATCAATACACATTTGACAA 57.753 29.630 0.00 0.00 36.02 3.18
304 305 9.467258 AAGTTGAATCAATACACATTTGACAAG 57.533 29.630 0.00 0.00 36.02 3.16
305 306 8.632679 AGTTGAATCAATACACATTTGACAAGT 58.367 29.630 0.00 0.00 36.02 3.16
306 307 9.248291 GTTGAATCAATACACATTTGACAAGTT 57.752 29.630 0.00 0.00 36.02 2.66
307 308 8.800231 TGAATCAATACACATTTGACAAGTTG 57.200 30.769 0.00 0.00 36.02 3.16
308 309 8.628280 TGAATCAATACACATTTGACAAGTTGA 58.372 29.630 10.54 0.00 36.02 3.18
309 310 9.462174 GAATCAATACACATTTGACAAGTTGAA 57.538 29.630 10.54 0.00 36.02 2.69
310 311 9.985730 AATCAATACACATTTGACAAGTTGAAT 57.014 25.926 10.54 0.00 36.02 2.57
311 312 9.630098 ATCAATACACATTTGACAAGTTGAATC 57.370 29.630 10.54 0.00 36.02 2.52
312 313 8.628280 TCAATACACATTTGACAAGTTGAATCA 58.372 29.630 10.54 0.49 0.00 2.57
313 314 9.247126 CAATACACATTTGACAAGTTGAATCAA 57.753 29.630 10.54 7.33 0.00 2.57
314 315 9.985730 AATACACATTTGACAAGTTGAATCAAT 57.014 25.926 10.54 0.00 32.61 2.57
316 317 8.801715 ACACATTTGACAAGTTGAATCAATAC 57.198 30.769 10.54 0.00 32.61 1.89
317 318 8.412456 ACACATTTGACAAGTTGAATCAATACA 58.588 29.630 10.54 0.00 32.61 2.29
318 319 8.693504 CACATTTGACAAGTTGAATCAATACAC 58.306 33.333 10.54 0.00 32.61 2.90
319 320 8.412456 ACATTTGACAAGTTGAATCAATACACA 58.588 29.630 10.54 0.00 32.61 3.72
320 321 9.414295 CATTTGACAAGTTGAATCAATACACAT 57.586 29.630 10.54 0.00 32.61 3.21
321 322 9.985730 ATTTGACAAGTTGAATCAATACACATT 57.014 25.926 10.54 0.00 32.61 2.71
322 323 9.814899 TTTGACAAGTTGAATCAATACACATTT 57.185 25.926 10.54 0.00 32.61 2.32
323 324 8.800231 TGACAAGTTGAATCAATACACATTTG 57.200 30.769 10.54 0.00 0.00 2.32
324 325 8.628280 TGACAAGTTGAATCAATACACATTTGA 58.372 29.630 10.54 0.00 37.49 2.69
325 326 8.801715 ACAAGTTGAATCAATACACATTTGAC 57.198 30.769 10.54 0.00 36.02 3.18
326 327 8.412456 ACAAGTTGAATCAATACACATTTGACA 58.588 29.630 10.54 0.00 36.02 3.58
327 328 9.247126 CAAGTTGAATCAATACACATTTGACAA 57.753 29.630 0.00 0.00 36.02 3.18
328 329 9.467258 AAGTTGAATCAATACACATTTGACAAG 57.533 29.630 0.00 0.00 36.02 3.16
329 330 8.632679 AGTTGAATCAATACACATTTGACAAGT 58.367 29.630 0.00 0.00 36.02 3.16
330 331 9.248291 GTTGAATCAATACACATTTGACAAGTT 57.752 29.630 0.00 0.00 36.02 2.66
331 332 8.800231 TGAATCAATACACATTTGACAAGTTG 57.200 30.769 0.00 0.00 36.02 3.16
354 355 3.923017 AAATTGCTAAGTCAGTGTGCC 57.077 42.857 0.00 0.00 0.00 5.01
398 399 2.167693 ACTATACAGTGCAGCGCCTAAA 59.832 45.455 2.29 0.00 32.25 1.85
441 466 3.647771 GGCGTCCTTCCCTTGGGT 61.648 66.667 5.51 0.00 0.00 4.51
735 761 4.537751 TCTCAGATCCGGAGTATTTGACT 58.462 43.478 11.34 0.00 42.90 3.41
923 965 8.276453 AGGTTTTCATAGTATGCTAGGGTTAT 57.724 34.615 5.18 0.00 30.61 1.89
1081 1150 0.321653 GTGGGAGGACGCATCTTTGT 60.322 55.000 0.00 0.00 40.82 2.83
1433 1502 2.161609 GGCAATGACGGTTCGAAGAATT 59.838 45.455 0.00 0.00 45.90 2.17
1809 1878 7.739295 TGAATTGTCTTAAGTTATGAACTCGC 58.261 34.615 1.63 0.00 41.91 5.03
2287 2356 7.280428 TCACAAGTTCGTCAACCTAATTAAACA 59.720 33.333 0.00 0.00 32.22 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.095718 GGTGAAAGCGAGACAACAATCC 60.096 50.000 0.00 0.00 0.00 3.01
3 4 2.031258 TGGTGAAAGCGAGACAACAA 57.969 45.000 0.00 0.00 36.92 2.83
4 5 1.668751 GTTGGTGAAAGCGAGACAACA 59.331 47.619 0.00 0.00 38.37 3.33
6 7 2.031258 TGTTGGTGAAAGCGAGACAA 57.969 45.000 0.00 0.00 36.92 3.18
7 8 1.939934 CTTGTTGGTGAAAGCGAGACA 59.060 47.619 0.00 0.00 36.92 3.41
8 9 1.940613 ACTTGTTGGTGAAAGCGAGAC 59.059 47.619 0.00 0.00 36.92 3.36
9 10 1.939934 CACTTGTTGGTGAAAGCGAGA 59.060 47.619 0.00 0.00 39.34 4.04
10 11 1.002468 CCACTTGTTGGTGAAAGCGAG 60.002 52.381 0.00 0.00 41.10 5.03
11 12 1.021202 CCACTTGTTGGTGAAAGCGA 58.979 50.000 0.00 0.00 41.10 4.93
12 13 3.549997 CCACTTGTTGGTGAAAGCG 57.450 52.632 0.00 0.00 41.10 4.68
21 22 4.502962 ACAATGTGGAAAACCACTTGTTG 58.497 39.130 18.10 19.04 40.92 3.33
22 23 4.817318 ACAATGTGGAAAACCACTTGTT 57.183 36.364 18.10 9.23 40.92 2.83
23 24 4.221703 TGAACAATGTGGAAAACCACTTGT 59.778 37.500 18.10 19.34 40.92 3.16
24 25 4.753233 TGAACAATGTGGAAAACCACTTG 58.247 39.130 18.10 18.87 40.92 3.16
25 26 5.413309 TTGAACAATGTGGAAAACCACTT 57.587 34.783 18.10 10.61 40.92 3.16
26 27 5.358922 CATTGAACAATGTGGAAAACCACT 58.641 37.500 18.10 3.90 42.32 4.00
27 28 5.655893 CATTGAACAATGTGGAAAACCAC 57.344 39.130 16.43 11.82 42.32 4.16
39 40 4.021807 TGTCTGAGCAATGCATTGAACAAT 60.022 37.500 37.36 19.19 40.14 2.71
40 41 3.318557 TGTCTGAGCAATGCATTGAACAA 59.681 39.130 37.36 21.99 40.14 2.83
41 42 2.885894 TGTCTGAGCAATGCATTGAACA 59.114 40.909 37.36 30.52 40.14 3.18
42 43 3.240069 GTGTCTGAGCAATGCATTGAAC 58.760 45.455 37.36 28.24 40.14 3.18
43 44 2.885894 TGTGTCTGAGCAATGCATTGAA 59.114 40.909 37.36 22.22 40.14 2.69
44 45 2.506444 TGTGTCTGAGCAATGCATTGA 58.494 42.857 37.36 19.23 40.14 2.57
45 46 3.057806 TCTTGTGTCTGAGCAATGCATTG 60.058 43.478 30.92 30.92 40.66 2.82
46 47 3.151554 TCTTGTGTCTGAGCAATGCATT 58.848 40.909 5.99 5.99 0.00 3.56
47 48 2.786777 TCTTGTGTCTGAGCAATGCAT 58.213 42.857 8.35 0.00 0.00 3.96
48 49 2.259266 TCTTGTGTCTGAGCAATGCA 57.741 45.000 8.35 0.00 0.00 3.96
49 50 3.004106 AGTTTCTTGTGTCTGAGCAATGC 59.996 43.478 0.00 0.00 0.00 3.56
50 51 4.825546 AGTTTCTTGTGTCTGAGCAATG 57.174 40.909 0.00 0.00 0.00 2.82
51 52 4.883585 TCAAGTTTCTTGTGTCTGAGCAAT 59.116 37.500 8.93 0.00 0.00 3.56
52 53 4.094887 GTCAAGTTTCTTGTGTCTGAGCAA 59.905 41.667 8.93 0.00 0.00 3.91
53 54 3.623060 GTCAAGTTTCTTGTGTCTGAGCA 59.377 43.478 8.93 0.00 0.00 4.26
54 55 3.002759 GGTCAAGTTTCTTGTGTCTGAGC 59.997 47.826 8.93 0.00 0.00 4.26
55 56 3.561725 GGGTCAAGTTTCTTGTGTCTGAG 59.438 47.826 8.93 0.00 0.00 3.35
56 57 3.541632 GGGTCAAGTTTCTTGTGTCTGA 58.458 45.455 8.93 0.00 0.00 3.27
57 58 2.618709 GGGGTCAAGTTTCTTGTGTCTG 59.381 50.000 8.93 0.00 0.00 3.51
58 59 2.745152 CGGGGTCAAGTTTCTTGTGTCT 60.745 50.000 8.93 0.00 0.00 3.41
59 60 1.602377 CGGGGTCAAGTTTCTTGTGTC 59.398 52.381 8.93 2.89 0.00 3.67
60 61 1.675552 CGGGGTCAAGTTTCTTGTGT 58.324 50.000 8.93 0.00 0.00 3.72
61 62 0.951558 CCGGGGTCAAGTTTCTTGTG 59.048 55.000 8.93 0.00 0.00 3.33
62 63 0.822121 GCCGGGGTCAAGTTTCTTGT 60.822 55.000 2.18 0.00 0.00 3.16
63 64 1.852067 CGCCGGGGTCAAGTTTCTTG 61.852 60.000 11.01 3.44 0.00 3.02
64 65 1.599797 CGCCGGGGTCAAGTTTCTT 60.600 57.895 11.01 0.00 0.00 2.52
65 66 2.032071 CGCCGGGGTCAAGTTTCT 59.968 61.111 11.01 0.00 0.00 2.52
66 67 3.053896 CCGCCGGGGTCAAGTTTC 61.054 66.667 18.27 0.00 0.00 2.78
75 76 3.546714 AAACTTCTGACCGCCGGGG 62.547 63.158 12.43 12.43 43.62 5.73
76 77 2.032071 AAACTTCTGACCGCCGGG 59.968 61.111 8.57 0.00 40.11 5.73
77 78 1.004918 AGAAACTTCTGACCGCCGG 60.005 57.895 0.00 0.00 35.89 6.13
78 79 4.675404 AGAAACTTCTGACCGCCG 57.325 55.556 0.00 0.00 35.89 6.46
86 87 7.573843 CGGCAATGTTCTTATTCAGAAACTTCT 60.574 37.037 0.00 0.00 43.52 2.85
87 88 6.524586 CGGCAATGTTCTTATTCAGAAACTTC 59.475 38.462 0.00 0.00 43.52 3.01
88 89 6.206634 TCGGCAATGTTCTTATTCAGAAACTT 59.793 34.615 0.00 0.00 43.52 2.66
89 90 5.705441 TCGGCAATGTTCTTATTCAGAAACT 59.295 36.000 0.00 0.00 43.52 2.66
90 91 5.938322 TCGGCAATGTTCTTATTCAGAAAC 58.062 37.500 0.00 0.00 43.52 2.78
91 92 6.567687 TTCGGCAATGTTCTTATTCAGAAA 57.432 33.333 0.00 0.00 43.52 2.52
92 93 6.349280 CCTTTCGGCAATGTTCTTATTCAGAA 60.349 38.462 0.00 0.00 39.39 3.02
93 94 5.123820 CCTTTCGGCAATGTTCTTATTCAGA 59.876 40.000 0.00 0.00 0.00 3.27
94 95 5.123820 TCCTTTCGGCAATGTTCTTATTCAG 59.876 40.000 0.00 0.00 0.00 3.02
95 96 5.007034 TCCTTTCGGCAATGTTCTTATTCA 58.993 37.500 0.00 0.00 0.00 2.57
96 97 5.560966 TCCTTTCGGCAATGTTCTTATTC 57.439 39.130 0.00 0.00 0.00 1.75
97 98 5.975693 TTCCTTTCGGCAATGTTCTTATT 57.024 34.783 0.00 0.00 0.00 1.40
98 99 7.285401 ACATATTCCTTTCGGCAATGTTCTTAT 59.715 33.333 0.00 0.00 0.00 1.73
99 100 6.601613 ACATATTCCTTTCGGCAATGTTCTTA 59.398 34.615 0.00 0.00 0.00 2.10
100 101 5.418840 ACATATTCCTTTCGGCAATGTTCTT 59.581 36.000 0.00 0.00 0.00 2.52
101 102 4.949856 ACATATTCCTTTCGGCAATGTTCT 59.050 37.500 0.00 0.00 0.00 3.01
102 103 5.036737 CACATATTCCTTTCGGCAATGTTC 58.963 41.667 0.00 0.00 29.69 3.18
103 104 4.142182 CCACATATTCCTTTCGGCAATGTT 60.142 41.667 0.00 0.00 29.69 2.71
104 105 3.381272 CCACATATTCCTTTCGGCAATGT 59.619 43.478 0.00 0.00 31.20 2.71
105 106 3.243501 CCCACATATTCCTTTCGGCAATG 60.244 47.826 0.00 0.00 0.00 2.82
106 107 2.958355 CCCACATATTCCTTTCGGCAAT 59.042 45.455 0.00 0.00 0.00 3.56
107 108 2.374184 CCCACATATTCCTTTCGGCAA 58.626 47.619 0.00 0.00 0.00 4.52
108 109 2.021723 GCCCACATATTCCTTTCGGCA 61.022 52.381 0.00 0.00 35.20 5.69
109 110 0.668535 GCCCACATATTCCTTTCGGC 59.331 55.000 0.00 0.00 0.00 5.54
110 111 1.676006 GTGCCCACATATTCCTTTCGG 59.324 52.381 0.00 0.00 0.00 4.30
111 112 1.330521 CGTGCCCACATATTCCTTTCG 59.669 52.381 0.00 0.00 0.00 3.46
112 113 2.097466 CACGTGCCCACATATTCCTTTC 59.903 50.000 0.82 0.00 0.00 2.62
113 114 2.091541 CACGTGCCCACATATTCCTTT 58.908 47.619 0.82 0.00 0.00 3.11
114 115 1.750193 CACGTGCCCACATATTCCTT 58.250 50.000 0.82 0.00 0.00 3.36
115 116 0.748005 GCACGTGCCCACATATTCCT 60.748 55.000 30.12 0.00 34.31 3.36
116 117 0.748005 AGCACGTGCCCACATATTCC 60.748 55.000 35.51 5.06 43.38 3.01
117 118 1.094785 AAGCACGTGCCCACATATTC 58.905 50.000 35.51 5.62 43.38 1.75
118 119 1.472480 GAAAGCACGTGCCCACATATT 59.528 47.619 35.51 19.18 43.38 1.28
119 120 1.094785 GAAAGCACGTGCCCACATAT 58.905 50.000 35.51 13.87 43.38 1.78
120 121 1.295357 CGAAAGCACGTGCCCACATA 61.295 55.000 35.51 0.00 43.38 2.29
121 122 2.616330 CGAAAGCACGTGCCCACAT 61.616 57.895 35.51 15.48 43.38 3.21
122 123 3.276091 CGAAAGCACGTGCCCACA 61.276 61.111 35.51 0.00 43.38 4.17
123 124 2.325082 ATCGAAAGCACGTGCCCAC 61.325 57.895 35.51 24.01 43.38 4.61
124 125 2.031919 ATCGAAAGCACGTGCCCA 59.968 55.556 35.51 16.11 43.38 5.36
125 126 1.573829 TTCATCGAAAGCACGTGCCC 61.574 55.000 35.51 23.20 43.38 5.36
126 127 0.179215 CTTCATCGAAAGCACGTGCC 60.179 55.000 35.51 20.11 43.38 5.01
127 128 0.790207 TCTTCATCGAAAGCACGTGC 59.210 50.000 32.79 32.79 42.49 5.34
128 129 2.222886 CCATCTTCATCGAAAGCACGTG 60.223 50.000 12.28 12.28 34.70 4.49
129 130 2.002586 CCATCTTCATCGAAAGCACGT 58.997 47.619 0.00 0.00 34.70 4.49
130 131 1.267732 GCCATCTTCATCGAAAGCACG 60.268 52.381 0.00 0.00 0.00 5.34
131 132 1.064654 GGCCATCTTCATCGAAAGCAC 59.935 52.381 0.00 0.00 0.00 4.40
132 133 1.382522 GGCCATCTTCATCGAAAGCA 58.617 50.000 0.00 0.00 0.00 3.91
133 134 0.305922 CGGCCATCTTCATCGAAAGC 59.694 55.000 2.24 0.00 0.00 3.51
134 135 0.940126 CCGGCCATCTTCATCGAAAG 59.060 55.000 2.24 0.00 0.00 2.62
135 136 0.539518 TCCGGCCATCTTCATCGAAA 59.460 50.000 2.24 0.00 0.00 3.46
136 137 0.104855 CTCCGGCCATCTTCATCGAA 59.895 55.000 2.24 0.00 0.00 3.71
137 138 1.742146 CTCCGGCCATCTTCATCGA 59.258 57.895 2.24 0.00 0.00 3.59
138 139 1.301244 CCTCCGGCCATCTTCATCG 60.301 63.158 2.24 0.00 0.00 3.84
139 140 1.048601 TACCTCCGGCCATCTTCATC 58.951 55.000 2.24 0.00 0.00 2.92
140 141 0.759346 GTACCTCCGGCCATCTTCAT 59.241 55.000 2.24 0.00 0.00 2.57
141 142 1.672854 CGTACCTCCGGCCATCTTCA 61.673 60.000 2.24 0.00 0.00 3.02
142 143 1.067582 CGTACCTCCGGCCATCTTC 59.932 63.158 2.24 0.00 0.00 2.87
143 144 2.432300 CCGTACCTCCGGCCATCTT 61.432 63.158 2.24 0.00 41.78 2.40
144 145 2.838225 CCGTACCTCCGGCCATCT 60.838 66.667 2.24 0.00 41.78 2.90
151 152 1.067425 TGTCATTTGACCGTACCTCCG 60.067 52.381 8.16 0.00 44.15 4.63
152 153 2.754946 TGTCATTTGACCGTACCTCC 57.245 50.000 8.16 0.00 44.15 4.30
153 154 2.415512 GCTTGTCATTTGACCGTACCTC 59.584 50.000 8.16 0.00 44.15 3.85
154 155 2.224426 TGCTTGTCATTTGACCGTACCT 60.224 45.455 8.16 0.00 44.15 3.08
155 156 2.147958 TGCTTGTCATTTGACCGTACC 58.852 47.619 8.16 0.00 44.15 3.34
156 157 3.889196 TTGCTTGTCATTTGACCGTAC 57.111 42.857 8.16 0.00 44.15 3.67
157 158 5.065859 CCATATTGCTTGTCATTTGACCGTA 59.934 40.000 8.16 0.00 44.15 4.02
158 159 4.142403 CCATATTGCTTGTCATTTGACCGT 60.142 41.667 8.16 0.00 44.15 4.83
159 160 4.353737 CCATATTGCTTGTCATTTGACCG 58.646 43.478 8.16 1.29 44.15 4.79
160 161 4.114794 GCCATATTGCTTGTCATTTGACC 58.885 43.478 8.16 0.00 44.15 4.02
161 162 4.746729 TGCCATATTGCTTGTCATTTGAC 58.253 39.130 3.72 3.72 44.97 3.18
162 163 4.705991 TCTGCCATATTGCTTGTCATTTGA 59.294 37.500 0.00 0.00 0.00 2.69
163 164 5.001237 TCTGCCATATTGCTTGTCATTTG 57.999 39.130 0.00 0.00 0.00 2.32
164 165 5.664294 TTCTGCCATATTGCTTGTCATTT 57.336 34.783 0.00 0.00 0.00 2.32
165 166 5.597806 CATTCTGCCATATTGCTTGTCATT 58.402 37.500 0.00 0.00 0.00 2.57
166 167 4.500887 GCATTCTGCCATATTGCTTGTCAT 60.501 41.667 0.00 0.00 37.42 3.06
167 168 3.181484 GCATTCTGCCATATTGCTTGTCA 60.181 43.478 0.00 0.00 37.42 3.58
168 169 3.067742 AGCATTCTGCCATATTGCTTGTC 59.932 43.478 0.00 0.00 46.52 3.18
169 170 3.028850 AGCATTCTGCCATATTGCTTGT 58.971 40.909 0.00 0.00 46.52 3.16
170 171 3.728076 AGCATTCTGCCATATTGCTTG 57.272 42.857 0.00 0.00 46.52 4.01
185 186 4.159135 CCTTGAGCACCTTATTGAAGCATT 59.841 41.667 0.00 0.00 0.00 3.56
186 187 3.698040 CCTTGAGCACCTTATTGAAGCAT 59.302 43.478 0.00 0.00 0.00 3.79
187 188 3.084039 CCTTGAGCACCTTATTGAAGCA 58.916 45.455 0.00 0.00 0.00 3.91
188 189 2.424956 CCCTTGAGCACCTTATTGAAGC 59.575 50.000 0.00 0.00 0.00 3.86
189 190 3.441572 CACCCTTGAGCACCTTATTGAAG 59.558 47.826 0.00 0.00 0.00 3.02
190 191 3.181434 ACACCCTTGAGCACCTTATTGAA 60.181 43.478 0.00 0.00 0.00 2.69
191 192 2.375174 ACACCCTTGAGCACCTTATTGA 59.625 45.455 0.00 0.00 0.00 2.57
192 193 2.795329 ACACCCTTGAGCACCTTATTG 58.205 47.619 0.00 0.00 0.00 1.90
193 194 3.618997 CGTACACCCTTGAGCACCTTATT 60.619 47.826 0.00 0.00 0.00 1.40
194 195 2.093658 CGTACACCCTTGAGCACCTTAT 60.094 50.000 0.00 0.00 0.00 1.73
195 196 1.274167 CGTACACCCTTGAGCACCTTA 59.726 52.381 0.00 0.00 0.00 2.69
196 197 0.034896 CGTACACCCTTGAGCACCTT 59.965 55.000 0.00 0.00 0.00 3.50
197 198 1.119574 ACGTACACCCTTGAGCACCT 61.120 55.000 0.00 0.00 0.00 4.00
198 199 0.949105 CACGTACACCCTTGAGCACC 60.949 60.000 0.00 0.00 0.00 5.01
199 200 1.566018 GCACGTACACCCTTGAGCAC 61.566 60.000 0.00 0.00 0.00 4.40
200 201 1.301401 GCACGTACACCCTTGAGCA 60.301 57.895 0.00 0.00 0.00 4.26
201 202 0.673644 ATGCACGTACACCCTTGAGC 60.674 55.000 0.00 0.00 0.00 4.26
202 203 1.808411 AATGCACGTACACCCTTGAG 58.192 50.000 0.00 0.00 0.00 3.02
203 204 2.613474 GGTAATGCACGTACACCCTTGA 60.613 50.000 10.64 0.00 0.00 3.02
204 205 1.735571 GGTAATGCACGTACACCCTTG 59.264 52.381 10.64 0.00 0.00 3.61
205 206 1.339342 GGGTAATGCACGTACACCCTT 60.339 52.381 13.22 0.00 44.62 3.95
206 207 0.251073 GGGTAATGCACGTACACCCT 59.749 55.000 13.22 0.00 44.62 4.34
207 208 1.085501 CGGGTAATGCACGTACACCC 61.086 60.000 11.28 11.28 44.59 4.61
208 209 2.375981 CGGGTAATGCACGTACACC 58.624 57.895 10.64 8.47 39.58 4.16
215 216 3.481661 CCGTCACGGGTAATGCAC 58.518 61.111 8.94 0.00 44.15 4.57
225 226 3.615056 TGTATTGAACTATTGCCGTCACG 59.385 43.478 0.00 0.00 0.00 4.35
226 227 4.390603 TGTGTATTGAACTATTGCCGTCAC 59.609 41.667 0.00 0.00 0.00 3.67
227 228 4.570930 TGTGTATTGAACTATTGCCGTCA 58.429 39.130 0.00 0.00 0.00 4.35
228 229 5.734855 ATGTGTATTGAACTATTGCCGTC 57.265 39.130 0.00 0.00 0.00 4.79
229 230 6.150307 TCAAATGTGTATTGAACTATTGCCGT 59.850 34.615 0.00 0.00 34.04 5.68
230 231 6.468956 GTCAAATGTGTATTGAACTATTGCCG 59.531 38.462 0.00 0.00 38.44 5.69
231 232 7.312154 TGTCAAATGTGTATTGAACTATTGCC 58.688 34.615 0.00 0.00 38.44 4.52
232 233 8.741101 TTGTCAAATGTGTATTGAACTATTGC 57.259 30.769 0.00 0.00 38.44 3.56
233 234 9.897744 ACTTGTCAAATGTGTATTGAACTATTG 57.102 29.630 0.00 0.00 38.44 1.90
235 236 9.897744 CAACTTGTCAAATGTGTATTGAACTAT 57.102 29.630 0.00 0.00 38.44 2.12
236 237 9.114952 TCAACTTGTCAAATGTGTATTGAACTA 57.885 29.630 0.00 0.00 38.44 2.24
237 238 7.995289 TCAACTTGTCAAATGTGTATTGAACT 58.005 30.769 0.00 0.00 38.44 3.01
238 239 8.627487 TTCAACTTGTCAAATGTGTATTGAAC 57.373 30.769 0.00 0.00 38.44 3.18
239 240 9.247126 CATTCAACTTGTCAAATGTGTATTGAA 57.753 29.630 0.00 0.00 38.44 2.69
240 241 8.628280 TCATTCAACTTGTCAAATGTGTATTGA 58.372 29.630 0.00 0.00 34.56 2.57
241 242 8.800231 TCATTCAACTTGTCAAATGTGTATTG 57.200 30.769 0.00 0.00 32.31 1.90
242 243 9.985730 ATTCATTCAACTTGTCAAATGTGTATT 57.014 25.926 0.00 0.00 32.31 1.89
244 245 9.891828 GTATTCATTCAACTTGTCAAATGTGTA 57.108 29.630 0.00 0.00 32.31 2.90
245 246 8.632679 AGTATTCATTCAACTTGTCAAATGTGT 58.367 29.630 0.00 0.00 32.31 3.72
246 247 9.467258 AAGTATTCATTCAACTTGTCAAATGTG 57.533 29.630 0.00 0.00 32.38 3.21
251 252 9.515020 GTCAAAAGTATTCATTCAACTTGTCAA 57.485 29.630 0.00 0.00 33.85 3.18
252 253 8.681806 TGTCAAAAGTATTCATTCAACTTGTCA 58.318 29.630 0.00 0.00 33.85 3.58
253 254 9.515020 TTGTCAAAAGTATTCATTCAACTTGTC 57.485 29.630 0.00 0.00 33.85 3.18
254 255 9.520204 CTTGTCAAAAGTATTCATTCAACTTGT 57.480 29.630 0.00 0.00 33.85 3.16
255 256 9.520204 ACTTGTCAAAAGTATTCATTCAACTTG 57.480 29.630 0.00 0.00 33.85 3.16
257 258 9.520204 CAACTTGTCAAAAGTATTCATTCAACT 57.480 29.630 0.00 0.00 0.00 3.16
258 259 9.515020 TCAACTTGTCAAAAGTATTCATTCAAC 57.485 29.630 0.00 0.00 0.00 3.18
268 269 9.944663 GTGTATTGATTCAACTTGTCAAAAGTA 57.055 29.630 0.15 0.00 35.70 2.24
269 270 8.465999 TGTGTATTGATTCAACTTGTCAAAAGT 58.534 29.630 0.15 0.00 35.70 2.66
270 271 8.854979 TGTGTATTGATTCAACTTGTCAAAAG 57.145 30.769 0.15 0.00 35.70 2.27
271 272 9.814899 AATGTGTATTGATTCAACTTGTCAAAA 57.185 25.926 0.15 0.00 35.70 2.44
272 273 9.814899 AAATGTGTATTGATTCAACTTGTCAAA 57.185 25.926 0.15 0.00 35.70 2.69
273 274 9.247126 CAAATGTGTATTGATTCAACTTGTCAA 57.753 29.630 0.15 0.00 36.42 3.18
274 275 8.628280 TCAAATGTGTATTGATTCAACTTGTCA 58.372 29.630 0.15 0.00 32.10 3.58
275 276 8.905702 GTCAAATGTGTATTGATTCAACTTGTC 58.094 33.333 0.15 0.00 38.89 3.18
276 277 8.412456 TGTCAAATGTGTATTGATTCAACTTGT 58.588 29.630 0.15 0.00 38.89 3.16
277 278 8.800231 TGTCAAATGTGTATTGATTCAACTTG 57.200 30.769 0.15 0.00 38.89 3.16
278 279 9.467258 CTTGTCAAATGTGTATTGATTCAACTT 57.533 29.630 0.15 0.00 38.89 2.66
279 280 8.632679 ACTTGTCAAATGTGTATTGATTCAACT 58.367 29.630 0.15 0.00 38.89 3.16
280 281 8.801715 ACTTGTCAAATGTGTATTGATTCAAC 57.198 30.769 0.15 0.00 38.89 3.18
281 282 9.247126 CAACTTGTCAAATGTGTATTGATTCAA 57.753 29.630 0.75 0.75 38.89 2.69
282 283 8.628280 TCAACTTGTCAAATGTGTATTGATTCA 58.372 29.630 0.00 0.00 38.89 2.57
283 284 9.462174 TTCAACTTGTCAAATGTGTATTGATTC 57.538 29.630 0.00 0.00 38.89 2.52
284 285 9.985730 ATTCAACTTGTCAAATGTGTATTGATT 57.014 25.926 0.00 0.00 38.89 2.57
285 286 9.630098 GATTCAACTTGTCAAATGTGTATTGAT 57.370 29.630 0.00 0.00 38.89 2.57
286 287 8.628280 TGATTCAACTTGTCAAATGTGTATTGA 58.372 29.630 0.00 0.00 34.56 2.57
287 288 8.800231 TGATTCAACTTGTCAAATGTGTATTG 57.200 30.769 0.00 0.00 0.00 1.90
288 289 9.985730 ATTGATTCAACTTGTCAAATGTGTATT 57.014 25.926 0.15 0.00 35.70 1.89
290 291 9.891828 GTATTGATTCAACTTGTCAAATGTGTA 57.108 29.630 0.15 0.00 35.70 2.90
291 292 8.412456 TGTATTGATTCAACTTGTCAAATGTGT 58.588 29.630 0.15 0.00 35.70 3.72
292 293 8.693504 GTGTATTGATTCAACTTGTCAAATGTG 58.306 33.333 0.15 0.00 35.70 3.21
293 294 8.412456 TGTGTATTGATTCAACTTGTCAAATGT 58.588 29.630 0.15 0.00 35.70 2.71
294 295 8.800231 TGTGTATTGATTCAACTTGTCAAATG 57.200 30.769 0.15 0.00 35.70 2.32
295 296 9.985730 AATGTGTATTGATTCAACTTGTCAAAT 57.014 25.926 0.15 0.00 35.70 2.32
296 297 9.814899 AAATGTGTATTGATTCAACTTGTCAAA 57.185 25.926 0.15 0.00 35.70 2.69
297 298 9.247126 CAAATGTGTATTGATTCAACTTGTCAA 57.753 29.630 0.15 0.00 36.42 3.18
298 299 8.628280 TCAAATGTGTATTGATTCAACTTGTCA 58.372 29.630 0.15 0.00 32.10 3.58
299 300 8.905702 GTCAAATGTGTATTGATTCAACTTGTC 58.094 33.333 0.15 0.00 38.89 3.18
300 301 8.412456 TGTCAAATGTGTATTGATTCAACTTGT 58.588 29.630 0.15 0.00 38.89 3.16
301 302 8.800231 TGTCAAATGTGTATTGATTCAACTTG 57.200 30.769 0.15 0.00 38.89 3.16
302 303 9.467258 CTTGTCAAATGTGTATTGATTCAACTT 57.533 29.630 0.15 0.00 38.89 2.66
303 304 8.632679 ACTTGTCAAATGTGTATTGATTCAACT 58.367 29.630 0.15 0.00 38.89 3.16
304 305 8.801715 ACTTGTCAAATGTGTATTGATTCAAC 57.198 30.769 0.15 0.00 38.89 3.18
305 306 9.247126 CAACTTGTCAAATGTGTATTGATTCAA 57.753 29.630 0.75 0.75 38.89 2.69
306 307 8.628280 TCAACTTGTCAAATGTGTATTGATTCA 58.372 29.630 0.00 0.00 38.89 2.57
307 308 9.462174 TTCAACTTGTCAAATGTGTATTGATTC 57.538 29.630 0.00 0.00 38.89 2.52
308 309 9.814899 TTTCAACTTGTCAAATGTGTATTGATT 57.185 25.926 0.00 0.00 38.89 2.57
309 310 9.814899 TTTTCAACTTGTCAAATGTGTATTGAT 57.185 25.926 0.00 0.00 38.89 2.57
310 311 9.645059 TTTTTCAACTTGTCAAATGTGTATTGA 57.355 25.926 0.00 0.00 34.56 2.57
314 315 8.386606 GCAATTTTTCAACTTGTCAAATGTGTA 58.613 29.630 0.00 0.00 0.00 2.90
315 316 7.119553 AGCAATTTTTCAACTTGTCAAATGTGT 59.880 29.630 0.00 0.00 0.00 3.72
316 317 7.465989 AGCAATTTTTCAACTTGTCAAATGTG 58.534 30.769 0.00 0.00 0.00 3.21
317 318 7.614124 AGCAATTTTTCAACTTGTCAAATGT 57.386 28.000 0.00 0.00 0.00 2.71
318 319 9.640974 CTTAGCAATTTTTCAACTTGTCAAATG 57.359 29.630 0.00 0.00 0.00 2.32
319 320 9.382275 ACTTAGCAATTTTTCAACTTGTCAAAT 57.618 25.926 0.00 0.00 0.00 2.32
320 321 8.770438 ACTTAGCAATTTTTCAACTTGTCAAA 57.230 26.923 0.00 0.00 0.00 2.69
321 322 8.031864 TGACTTAGCAATTTTTCAACTTGTCAA 58.968 29.630 0.00 0.00 0.00 3.18
322 323 7.542890 TGACTTAGCAATTTTTCAACTTGTCA 58.457 30.769 0.00 0.00 0.00 3.58
323 324 7.702348 ACTGACTTAGCAATTTTTCAACTTGTC 59.298 33.333 0.00 0.00 0.00 3.18
324 325 7.489113 CACTGACTTAGCAATTTTTCAACTTGT 59.511 33.333 0.00 0.00 0.00 3.16
325 326 7.489113 ACACTGACTTAGCAATTTTTCAACTTG 59.511 33.333 0.00 0.00 0.00 3.16
326 327 7.489113 CACACTGACTTAGCAATTTTTCAACTT 59.511 33.333 0.00 0.00 0.00 2.66
327 328 6.974622 CACACTGACTTAGCAATTTTTCAACT 59.025 34.615 0.00 0.00 0.00 3.16
328 329 6.291796 GCACACTGACTTAGCAATTTTTCAAC 60.292 38.462 0.00 0.00 0.00 3.18
329 330 5.748152 GCACACTGACTTAGCAATTTTTCAA 59.252 36.000 0.00 0.00 0.00 2.69
330 331 5.280945 GCACACTGACTTAGCAATTTTTCA 58.719 37.500 0.00 0.00 0.00 2.69
331 332 4.681483 GGCACACTGACTTAGCAATTTTTC 59.319 41.667 0.00 0.00 0.00 2.29
441 466 0.106521 TGCTAAGTCAGTGTGCAGCA 59.893 50.000 0.00 0.00 36.72 4.41
735 761 1.243902 GGTTGGCTTCGAAATCCACA 58.756 50.000 15.89 7.31 0.00 4.17
923 965 4.145807 CAACCCTAACACCAACATAACCA 58.854 43.478 0.00 0.00 0.00 3.67
1081 1150 5.306937 TGACATCTTTCTCCTTCACCTTGTA 59.693 40.000 0.00 0.00 0.00 2.41
1433 1502 1.270839 CCTCCAAGCCTCTTCGAAACA 60.271 52.381 0.00 0.00 0.00 2.83
1809 1878 7.644986 TGAACAAACATAAATTTTAAGCCGG 57.355 32.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.