Multiple sequence alignment - TraesCS2B01G402200

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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 TraesCS2B01G402200 chr2B 100.000 3161 0 0 926 4086 571042577 571045737 0.000000e+00 5838
1 TraesCS2B01G402200 chr2B 100.000 578 0 0 1 578 571041652 571042229 0.000000e+00 1068
2 TraesCS2B01G402200 chr2B 100.000 83 0 0 4307 4389 571045958 571046040 2.110000e-33 154
3 TraesCS2B01G402200 chr2D 94.486 2938 111 14 927 3836 485999284 486002198 0.000000e+00 4481
4 TraesCS2B01G402200 chr2D 96.861 223 4 1 3867 4086 486002260 486002482 1.930000e-98 370
5 TraesCS2B01G402200 chr2D 89.524 210 8 9 372 578 485999054 485999252 2.030000e-63 254
6 TraesCS2B01G402200 chr2D 92.208 77 2 3 4307 4383 486002511 486002583 6.000000e-19 106
7 TraesCS2B01G402200 chr2A 94.665 2718 83 13 927 3614 631638933 631641618 0.000000e+00 4159
8 TraesCS2B01G402200 chr2A 91.566 498 9 7 3590 4086 631641630 631642095 0.000000e+00 656
9 TraesCS2B01G402200 chr2A 86.182 275 27 6 310 578 631638625 631638894 2.000000e-73 287
10 TraesCS2B01G402200 chr3D 93.839 211 9 3 1 210 475309102 475309309 9.160000e-82 315


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 TraesCS2B01G402200 chr2B 571041652 571046040 4388 False 2353.333333 5838 100.000000 1 4389 3 chr2B.!!$F1 4388
1 TraesCS2B01G402200 chr2D 485999054 486002583 3529 False 1302.750000 4481 93.269750 372 4383 4 chr2D.!!$F1 4011
2 TraesCS2B01G402200 chr2A 631638625 631642095 3470 False 1700.666667 4159 90.804333 310 4086 3 chr2A.!!$F1 3776

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
57 58 0.031616 AGGAGATCCCCAGTCCAGAC 60.032 60.0 0.00 0.0 36.42 3.51 F
176 177 0.032217 AGAGGGCAGAGAGGAAGGAG 60.032 60.0 0.00 0.0 0.00 3.69 F
177 178 0.032615 GAGGGCAGAGAGGAAGGAGA 60.033 60.0 0.00 0.0 0.00 3.71 F
178 179 0.032217 AGGGCAGAGAGGAAGGAGAG 60.032 60.0 0.00 0.0 0.00 3.20 F
186 187 0.041982 GAGGAAGGAGAGGTGGAGGT 59.958 60.0 0.00 0.0 0.00 3.85 F
287 288 0.107214 TGGATCGAATTCCCTGCACC 60.107 55.0 2.62 0.0 34.67 5.01 F
288 289 0.107214 GGATCGAATTCCCTGCACCA 60.107 55.0 0.00 0.0 0.00 4.17 F
1951 1997 0.378962 GTTGCCTGTGCGTGTTTACA 59.621 50.0 0.00 0.0 41.78 2.41 F
2729 2775 0.384669 ATAGAAGCCAGTACGTCCGC 59.615 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1928 0.248843 CACACCTCAGCTCTCTTCCC 59.751 60.000 0.00 0.00 0.00 3.97 R
2027 2073 1.519455 GAGCGTCCAGGTGATTCCG 60.519 63.158 0.00 0.00 41.99 4.30 R
2145 2191 7.333423 CAGAAAGGATGCAACATTTCATTCATT 59.667 33.333 28.13 10.15 41.14 2.57 R
2178 2224 7.444629 AACAGGCACATAATCTGCATAATAG 57.555 36.000 0.00 0.00 36.27 1.73 R
2490 2536 2.686915 CAAAATCCTCCTCTGCATCACC 59.313 50.000 0.00 0.00 0.00 4.02 R
2510 2556 2.880268 CAAGTCAATCTTGCAGTCCACA 59.120 45.455 0.00 0.00 45.37 4.17 R
2619 2665 3.370953 GGGCTACTGACATCTTGGTCATT 60.371 47.826 0.00 0.00 45.97 2.57 R
2872 2918 0.255890 GTTGCTAGGGCCCATCTTCA 59.744 55.000 27.56 11.37 37.74 3.02 R
3804 3897 2.125512 GGTGCTGCCAGGACTACG 60.126 66.667 16.22 0.00 36.73 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.803426 CCGCACCTCTGAGCCGTC 62.803 72.222 0.00 0.00 0.00 4.79
30 31 4.056125 CGCACCTCTGAGCCGTCA 62.056 66.667 0.00 0.00 0.00 4.35
38 39 2.033602 TGAGCCGTCAGACTCCGA 59.966 61.111 0.00 0.00 31.65 4.55
39 40 2.041115 TGAGCCGTCAGACTCCGAG 61.041 63.158 0.00 0.00 31.65 4.63
40 41 2.752238 AGCCGTCAGACTCCGAGG 60.752 66.667 0.00 0.00 0.00 4.63
41 42 2.750637 GCCGTCAGACTCCGAGGA 60.751 66.667 0.00 0.00 0.00 3.71
42 43 2.766400 GCCGTCAGACTCCGAGGAG 61.766 68.421 17.01 17.01 46.91 3.69
43 44 1.078356 CCGTCAGACTCCGAGGAGA 60.078 63.158 24.53 0.39 44.53 3.71
44 45 0.464735 CCGTCAGACTCCGAGGAGAT 60.465 60.000 24.53 10.43 44.53 2.75
45 46 0.941542 CGTCAGACTCCGAGGAGATC 59.058 60.000 24.53 16.88 44.53 2.75
46 47 1.314730 GTCAGACTCCGAGGAGATCC 58.685 60.000 24.53 12.88 44.53 3.36
47 48 0.183971 TCAGACTCCGAGGAGATCCC 59.816 60.000 24.53 10.72 44.53 3.85
48 49 0.825840 CAGACTCCGAGGAGATCCCC 60.826 65.000 24.53 8.59 44.53 4.81
49 50 1.230497 GACTCCGAGGAGATCCCCA 59.770 63.158 24.53 0.00 44.53 4.96
50 51 0.825840 GACTCCGAGGAGATCCCCAG 60.826 65.000 24.53 0.00 44.53 4.45
51 52 1.231641 CTCCGAGGAGATCCCCAGT 59.768 63.158 13.69 0.00 44.53 4.00
52 53 0.825840 CTCCGAGGAGATCCCCAGTC 60.826 65.000 13.69 0.00 44.53 3.51
53 54 1.834822 CCGAGGAGATCCCCAGTCC 60.835 68.421 0.00 0.00 36.42 3.85
54 55 1.075970 CGAGGAGATCCCCAGTCCA 60.076 63.158 0.00 0.00 36.42 4.02
55 56 1.112315 CGAGGAGATCCCCAGTCCAG 61.112 65.000 0.00 0.00 36.42 3.86
56 57 0.263172 GAGGAGATCCCCAGTCCAGA 59.737 60.000 0.00 0.00 36.42 3.86
57 58 0.031616 AGGAGATCCCCAGTCCAGAC 60.032 60.000 0.00 0.00 36.42 3.51
58 59 0.325671 GGAGATCCCCAGTCCAGACA 60.326 60.000 0.00 0.00 0.00 3.41
59 60 0.827368 GAGATCCCCAGTCCAGACAC 59.173 60.000 0.00 0.00 0.00 3.67
60 61 0.618968 AGATCCCCAGTCCAGACACC 60.619 60.000 0.00 0.00 0.00 4.16
61 62 0.909610 GATCCCCAGTCCAGACACCA 60.910 60.000 0.00 0.00 0.00 4.17
62 63 1.201429 ATCCCCAGTCCAGACACCAC 61.201 60.000 0.00 0.00 0.00 4.16
63 64 2.750350 CCCAGTCCAGACACCACC 59.250 66.667 0.00 0.00 0.00 4.61
64 65 2.343758 CCAGTCCAGACACCACCG 59.656 66.667 0.00 0.00 0.00 4.94
65 66 2.343758 CAGTCCAGACACCACCGG 59.656 66.667 0.00 0.00 0.00 5.28
66 67 2.923035 AGTCCAGACACCACCGGG 60.923 66.667 6.32 0.00 41.29 5.73
67 68 4.699522 GTCCAGACACCACCGGGC 62.700 72.222 6.32 0.00 37.90 6.13
86 87 4.785453 CTCCCCGCTGGCCAGAAC 62.785 72.222 37.21 18.52 0.00 3.01
92 93 3.123620 GCTGGCCAGAACGCAGAG 61.124 66.667 37.21 7.81 0.00 3.35
93 94 2.435586 CTGGCCAGAACGCAGAGG 60.436 66.667 29.88 0.00 0.00 3.69
94 95 3.241530 TGGCCAGAACGCAGAGGT 61.242 61.111 0.00 0.00 0.00 3.85
95 96 2.435059 GGCCAGAACGCAGAGGTC 60.435 66.667 0.00 0.00 36.63 3.85
96 97 2.343758 GCCAGAACGCAGAGGTCA 59.656 61.111 0.00 0.00 39.61 4.02
97 98 2.029844 GCCAGAACGCAGAGGTCAC 61.030 63.158 0.00 0.00 39.61 3.67
98 99 1.367471 CCAGAACGCAGAGGTCACA 59.633 57.895 0.00 0.00 39.61 3.58
99 100 0.668706 CCAGAACGCAGAGGTCACAG 60.669 60.000 0.00 0.00 39.61 3.66
100 101 0.315251 CAGAACGCAGAGGTCACAGA 59.685 55.000 0.00 0.00 39.61 3.41
101 102 1.067283 CAGAACGCAGAGGTCACAGAT 60.067 52.381 0.00 0.00 39.61 2.90
102 103 1.203523 AGAACGCAGAGGTCACAGATC 59.796 52.381 0.00 0.00 39.61 2.75
103 104 1.203523 GAACGCAGAGGTCACAGATCT 59.796 52.381 0.00 0.00 36.33 2.75
104 105 0.814457 ACGCAGAGGTCACAGATCTC 59.186 55.000 0.00 0.00 39.87 2.75
105 106 0.248417 CGCAGAGGTCACAGATCTCG 60.248 60.000 0.00 0.00 43.86 4.04
106 107 0.102120 GCAGAGGTCACAGATCTCGG 59.898 60.000 0.00 3.51 43.86 4.63
107 108 0.743688 CAGAGGTCACAGATCTCGGG 59.256 60.000 0.00 0.00 43.86 5.14
108 109 1.040339 AGAGGTCACAGATCTCGGGC 61.040 60.000 0.00 0.00 43.86 6.13
109 110 1.000993 AGGTCACAGATCTCGGGCT 59.999 57.895 0.00 0.00 0.00 5.19
110 111 1.040339 AGGTCACAGATCTCGGGCTC 61.040 60.000 0.00 0.00 0.00 4.70
111 112 1.064946 GTCACAGATCTCGGGCTCG 59.935 63.158 0.00 0.00 37.82 5.03
112 113 1.378646 TCACAGATCTCGGGCTCGT 60.379 57.895 5.57 0.00 37.69 4.18
113 114 1.064946 CACAGATCTCGGGCTCGTC 59.935 63.158 5.57 0.00 37.69 4.20
114 115 2.329690 CAGATCTCGGGCTCGTCG 59.670 66.667 5.57 0.00 37.69 5.12
115 116 3.587933 AGATCTCGGGCTCGTCGC 61.588 66.667 5.57 0.00 37.69 5.19
146 147 4.798682 GCGGGAGGGGAAGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
147 148 2.444895 CGGGAGGGGAAGGAGGAG 60.445 72.222 0.00 0.00 0.00 3.69
148 149 2.040359 GGGAGGGGAAGGAGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
149 150 2.040359 GGAGGGGAAGGAGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
150 151 2.040359 GAGGGGAAGGAGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
151 152 4.439901 AGGGGAAGGAGGAGGGGC 62.440 72.222 0.00 0.00 0.00 5.80
153 154 4.798682 GGGAAGGAGGAGGGGCGA 62.799 72.222 0.00 0.00 0.00 5.54
154 155 3.471806 GGAAGGAGGAGGGGCGAC 61.472 72.222 0.00 0.00 0.00 5.19
172 173 4.346049 CGAGAGGGCAGAGAGGAA 57.654 61.111 0.00 0.00 0.00 3.36
173 174 2.114638 CGAGAGGGCAGAGAGGAAG 58.885 63.158 0.00 0.00 0.00 3.46
174 175 1.391157 CGAGAGGGCAGAGAGGAAGG 61.391 65.000 0.00 0.00 0.00 3.46
175 176 0.032615 GAGAGGGCAGAGAGGAAGGA 60.033 60.000 0.00 0.00 0.00 3.36
176 177 0.032217 AGAGGGCAGAGAGGAAGGAG 60.032 60.000 0.00 0.00 0.00 3.69
177 178 0.032615 GAGGGCAGAGAGGAAGGAGA 60.033 60.000 0.00 0.00 0.00 3.71
178 179 0.032217 AGGGCAGAGAGGAAGGAGAG 60.032 60.000 0.00 0.00 0.00 3.20
179 180 1.048160 GGGCAGAGAGGAAGGAGAGG 61.048 65.000 0.00 0.00 0.00 3.69
180 181 0.325203 GGCAGAGAGGAAGGAGAGGT 60.325 60.000 0.00 0.00 0.00 3.85
181 182 0.823460 GCAGAGAGGAAGGAGAGGTG 59.177 60.000 0.00 0.00 0.00 4.00
182 183 1.484038 CAGAGAGGAAGGAGAGGTGG 58.516 60.000 0.00 0.00 0.00 4.61
183 184 1.006519 CAGAGAGGAAGGAGAGGTGGA 59.993 57.143 0.00 0.00 0.00 4.02
184 185 1.287739 AGAGAGGAAGGAGAGGTGGAG 59.712 57.143 0.00 0.00 0.00 3.86
185 186 0.338120 AGAGGAAGGAGAGGTGGAGG 59.662 60.000 0.00 0.00 0.00 4.30
186 187 0.041982 GAGGAAGGAGAGGTGGAGGT 59.958 60.000 0.00 0.00 0.00 3.85
187 188 0.252467 AGGAAGGAGAGGTGGAGGTG 60.252 60.000 0.00 0.00 0.00 4.00
188 189 1.268283 GGAAGGAGAGGTGGAGGTGG 61.268 65.000 0.00 0.00 0.00 4.61
189 190 0.252284 GAAGGAGAGGTGGAGGTGGA 60.252 60.000 0.00 0.00 0.00 4.02
190 191 0.545548 AAGGAGAGGTGGAGGTGGAC 60.546 60.000 0.00 0.00 0.00 4.02
191 192 2.352032 GGAGAGGTGGAGGTGGACG 61.352 68.421 0.00 0.00 0.00 4.79
192 193 2.997897 AGAGGTGGAGGTGGACGC 60.998 66.667 0.00 0.00 0.00 5.19
193 194 4.083862 GAGGTGGAGGTGGACGCC 62.084 72.222 0.00 0.00 39.86 5.68
214 215 4.736896 GCCGGAGTGACCCACGTC 62.737 72.222 5.05 0.00 39.64 4.34
215 216 4.065281 CCGGAGTGACCCACGTCC 62.065 72.222 0.00 0.00 39.64 4.79
216 217 3.299977 CGGAGTGACCCACGTCCA 61.300 66.667 12.53 0.00 39.64 4.02
217 218 2.646175 CGGAGTGACCCACGTCCAT 61.646 63.158 12.53 0.00 39.64 3.41
218 219 1.079127 GGAGTGACCCACGTCCATG 60.079 63.158 0.00 0.00 39.64 3.66
219 220 1.671742 GAGTGACCCACGTCCATGT 59.328 57.895 0.00 0.00 39.64 3.21
220 221 0.670546 GAGTGACCCACGTCCATGTG 60.671 60.000 0.00 0.00 39.64 3.21
228 229 2.743636 CACGTCCATGTGGAGTACTT 57.256 50.000 1.07 0.00 46.49 2.24
229 230 3.861276 CACGTCCATGTGGAGTACTTA 57.139 47.619 1.07 0.00 46.49 2.24
230 231 4.182693 CACGTCCATGTGGAGTACTTAA 57.817 45.455 1.07 0.00 46.49 1.85
231 232 4.755411 CACGTCCATGTGGAGTACTTAAT 58.245 43.478 1.07 0.00 46.49 1.40
232 233 5.175859 CACGTCCATGTGGAGTACTTAATT 58.824 41.667 1.07 0.00 46.49 1.40
233 234 5.063438 CACGTCCATGTGGAGTACTTAATTG 59.937 44.000 1.07 0.00 46.49 2.32
234 235 5.046878 ACGTCCATGTGGAGTACTTAATTGA 60.047 40.000 1.07 0.00 46.49 2.57
235 236 5.872617 CGTCCATGTGGAGTACTTAATTGAA 59.127 40.000 1.07 0.00 46.49 2.69
236 237 6.370442 CGTCCATGTGGAGTACTTAATTGAAA 59.630 38.462 1.07 0.00 46.49 2.69
237 238 7.527457 GTCCATGTGGAGTACTTAATTGAAAC 58.473 38.462 1.07 0.00 46.49 2.78
238 239 7.390718 GTCCATGTGGAGTACTTAATTGAAACT 59.609 37.037 1.07 0.00 46.49 2.66
239 240 7.942341 TCCATGTGGAGTACTTAATTGAAACTT 59.058 33.333 0.00 0.00 39.78 2.66
240 241 8.576442 CCATGTGGAGTACTTAATTGAAACTTT 58.424 33.333 0.00 0.00 37.39 2.66
241 242 9.612620 CATGTGGAGTACTTAATTGAAACTTTC 57.387 33.333 0.00 0.00 0.00 2.62
242 243 8.161699 TGTGGAGTACTTAATTGAAACTTTCC 57.838 34.615 0.00 0.00 0.00 3.13
243 244 7.996644 TGTGGAGTACTTAATTGAAACTTTCCT 59.003 33.333 0.00 0.00 0.00 3.36
244 245 8.290325 GTGGAGTACTTAATTGAAACTTTCCTG 58.710 37.037 0.00 0.00 0.00 3.86
245 246 7.040686 TGGAGTACTTAATTGAAACTTTCCTGC 60.041 37.037 0.00 0.00 0.00 4.85
246 247 7.175119 GGAGTACTTAATTGAAACTTTCCTGCT 59.825 37.037 0.00 0.00 0.00 4.24
247 248 8.100508 AGTACTTAATTGAAACTTTCCTGCTC 57.899 34.615 0.00 0.00 0.00 4.26
248 249 7.939588 AGTACTTAATTGAAACTTTCCTGCTCT 59.060 33.333 0.00 0.00 0.00 4.09
249 250 7.588497 ACTTAATTGAAACTTTCCTGCTCTT 57.412 32.000 0.00 0.00 0.00 2.85
250 251 8.011844 ACTTAATTGAAACTTTCCTGCTCTTT 57.988 30.769 0.00 0.00 0.00 2.52
251 252 8.138074 ACTTAATTGAAACTTTCCTGCTCTTTC 58.862 33.333 0.00 0.00 0.00 2.62
252 253 4.918810 TTGAAACTTTCCTGCTCTTTCC 57.081 40.909 0.00 0.00 0.00 3.13
253 254 4.170468 TGAAACTTTCCTGCTCTTTCCT 57.830 40.909 0.00 0.00 0.00 3.36
254 255 4.137543 TGAAACTTTCCTGCTCTTTCCTC 58.862 43.478 0.00 0.00 0.00 3.71
255 256 2.869101 ACTTTCCTGCTCTTTCCTCC 57.131 50.000 0.00 0.00 0.00 4.30
256 257 2.057922 ACTTTCCTGCTCTTTCCTCCA 58.942 47.619 0.00 0.00 0.00 3.86
257 258 2.646798 ACTTTCCTGCTCTTTCCTCCAT 59.353 45.455 0.00 0.00 0.00 3.41
258 259 2.795231 TTCCTGCTCTTTCCTCCATG 57.205 50.000 0.00 0.00 0.00 3.66
259 260 1.661463 TCCTGCTCTTTCCTCCATGT 58.339 50.000 0.00 0.00 0.00 3.21
260 261 1.988107 TCCTGCTCTTTCCTCCATGTT 59.012 47.619 0.00 0.00 0.00 2.71
261 262 2.376518 TCCTGCTCTTTCCTCCATGTTT 59.623 45.455 0.00 0.00 0.00 2.83
262 263 3.160269 CCTGCTCTTTCCTCCATGTTTT 58.840 45.455 0.00 0.00 0.00 2.43
263 264 3.575687 CCTGCTCTTTCCTCCATGTTTTT 59.424 43.478 0.00 0.00 0.00 1.94
264 265 4.766891 CCTGCTCTTTCCTCCATGTTTTTA 59.233 41.667 0.00 0.00 0.00 1.52
265 266 5.243730 CCTGCTCTTTCCTCCATGTTTTTAA 59.756 40.000 0.00 0.00 0.00 1.52
266 267 6.084326 TGCTCTTTCCTCCATGTTTTTAAC 57.916 37.500 0.00 0.00 0.00 2.01
267 268 5.833131 TGCTCTTTCCTCCATGTTTTTAACT 59.167 36.000 0.00 0.00 0.00 2.24
268 269 6.323739 TGCTCTTTCCTCCATGTTTTTAACTT 59.676 34.615 0.00 0.00 0.00 2.66
269 270 6.642540 GCTCTTTCCTCCATGTTTTTAACTTG 59.357 38.462 0.00 0.00 36.58 3.16
280 281 8.173321 CATGTTTTTAACTTGGATCGAATTCC 57.827 34.615 0.00 0.00 34.09 3.01
281 282 6.683715 TGTTTTTAACTTGGATCGAATTCCC 58.316 36.000 2.62 0.00 34.67 3.97
282 283 6.492087 TGTTTTTAACTTGGATCGAATTCCCT 59.508 34.615 2.62 0.00 34.67 4.20
283 284 6.509418 TTTTAACTTGGATCGAATTCCCTG 57.491 37.500 2.62 0.00 34.67 4.45
284 285 2.044123 ACTTGGATCGAATTCCCTGC 57.956 50.000 2.62 0.00 34.67 4.85
285 286 1.281867 ACTTGGATCGAATTCCCTGCA 59.718 47.619 2.62 0.00 34.67 4.41
286 287 1.672881 CTTGGATCGAATTCCCTGCAC 59.327 52.381 2.62 0.00 34.67 4.57
287 288 0.107214 TGGATCGAATTCCCTGCACC 60.107 55.000 2.62 0.00 34.67 5.01
288 289 0.107214 GGATCGAATTCCCTGCACCA 60.107 55.000 0.00 0.00 0.00 4.17
289 290 1.477558 GGATCGAATTCCCTGCACCAT 60.478 52.381 0.00 0.00 0.00 3.55
290 291 1.876156 GATCGAATTCCCTGCACCATC 59.124 52.381 0.00 0.00 0.00 3.51
291 292 0.107214 TCGAATTCCCTGCACCATCC 60.107 55.000 0.00 0.00 0.00 3.51
292 293 0.394216 CGAATTCCCTGCACCATCCA 60.394 55.000 0.00 0.00 0.00 3.41
293 294 1.851304 GAATTCCCTGCACCATCCAA 58.149 50.000 0.00 0.00 0.00 3.53
294 295 2.178580 GAATTCCCTGCACCATCCAAA 58.821 47.619 0.00 0.00 0.00 3.28
295 296 2.555732 ATTCCCTGCACCATCCAAAT 57.444 45.000 0.00 0.00 0.00 2.32
296 297 1.559368 TTCCCTGCACCATCCAAATG 58.441 50.000 0.00 0.00 0.00 2.32
339 340 9.624373 AATCTGTATAATTTGCTTGAGATCACT 57.376 29.630 0.00 0.00 0.00 3.41
340 341 8.429493 TCTGTATAATTTGCTTGAGATCACTG 57.571 34.615 0.00 0.00 0.00 3.66
341 342 7.496920 TCTGTATAATTTGCTTGAGATCACTGG 59.503 37.037 0.00 0.00 0.00 4.00
342 343 7.112122 TGTATAATTTGCTTGAGATCACTGGT 58.888 34.615 0.00 0.00 0.00 4.00
343 344 4.778534 AATTTGCTTGAGATCACTGGTG 57.221 40.909 0.00 0.00 0.00 4.17
344 345 3.490439 TTTGCTTGAGATCACTGGTGA 57.510 42.857 5.87 5.87 44.59 4.02
345 346 3.490439 TTGCTTGAGATCACTGGTGAA 57.510 42.857 7.53 0.00 43.58 3.18
351 354 3.141398 TGAGATCACTGGTGAAAACAGC 58.859 45.455 7.53 0.00 43.58 4.40
364 367 0.459237 AAACAGCGCTGGAGATCGAG 60.459 55.000 38.27 13.12 34.19 4.04
463 466 2.663188 GCCTCGATCGGCCATCAC 60.663 66.667 16.41 0.00 44.41 3.06
466 469 1.006805 CTCGATCGGCCATCACTCC 60.007 63.158 16.41 0.00 0.00 3.85
467 470 2.029666 CGATCGGCCATCACTCCC 59.970 66.667 7.38 0.00 0.00 4.30
470 473 2.388890 GATCGGCCATCACTCCCCAG 62.389 65.000 2.24 0.00 0.00 4.45
531 542 4.263572 CACGGCTCCACCCCAACA 62.264 66.667 0.00 0.00 33.26 3.33
954 965 2.614057 CGCTCCATTAACAACTCCATCC 59.386 50.000 0.00 0.00 0.00 3.51
1124 1144 3.690460 ACCATGTGAGATTCCTGGTTTC 58.310 45.455 0.00 0.00 36.86 2.78
1174 1201 2.966309 CTTGGTTGCGGCGAGTTCC 61.966 63.158 12.98 7.51 0.00 3.62
1188 1215 2.735762 CGAGTTCCTTCCTGATCGGTTC 60.736 54.545 0.00 0.00 0.00 3.62
1261 1288 1.600916 GGTGGTGAAGCAGGTGTCC 60.601 63.158 0.00 0.00 0.00 4.02
1338 1365 4.475135 GGAGGTTGCGGAGGAGGC 62.475 72.222 0.00 0.00 0.00 4.70
1400 1427 5.220529 GCTTATAACCTACATTGCGTCGTTT 60.221 40.000 0.00 0.00 0.00 3.60
1444 1471 3.677121 GCTCGGATGCTCATGTTATGTAG 59.323 47.826 0.00 0.00 0.00 2.74
1445 1472 4.240888 CTCGGATGCTCATGTTATGTAGG 58.759 47.826 0.00 0.00 0.00 3.18
1446 1473 3.895041 TCGGATGCTCATGTTATGTAGGA 59.105 43.478 0.00 0.00 0.00 2.94
1447 1474 3.990469 CGGATGCTCATGTTATGTAGGAC 59.010 47.826 0.00 0.00 0.00 3.85
1448 1475 4.501400 CGGATGCTCATGTTATGTAGGACA 60.501 45.833 0.00 0.00 0.00 4.02
1449 1476 4.993584 GGATGCTCATGTTATGTAGGACAG 59.006 45.833 0.00 0.00 0.00 3.51
1450 1477 5.453903 GGATGCTCATGTTATGTAGGACAGT 60.454 44.000 0.00 0.00 0.00 3.55
1451 1478 6.239317 GGATGCTCATGTTATGTAGGACAGTA 60.239 42.308 0.00 0.00 0.00 2.74
1452 1479 6.149129 TGCTCATGTTATGTAGGACAGTAG 57.851 41.667 0.00 0.00 0.00 2.57
1453 1480 5.069119 TGCTCATGTTATGTAGGACAGTAGG 59.931 44.000 0.00 0.00 0.00 3.18
1510 1537 3.190874 GACTGGTTAGGAGAGAATTGCG 58.809 50.000 0.00 0.00 0.00 4.85
1538 1565 3.059166 GTGTTTGCTAAAATGCCACAGG 58.941 45.455 0.00 0.00 0.00 4.00
1545 1572 0.971386 AAAATGCCACAGGGAAGCAG 59.029 50.000 0.00 0.00 40.40 4.24
1667 1697 2.802247 CGAGCAGAAAACTGTGACATCA 59.198 45.455 0.00 0.00 0.00 3.07
1784 1815 3.608707 GCTGTCTGTGCATGTTTTCAGAG 60.609 47.826 2.91 1.57 37.56 3.35
1788 1819 4.274459 GTCTGTGCATGTTTTCAGAGTCTT 59.726 41.667 2.91 0.00 37.56 3.01
1897 1928 1.183030 TAGTCACACCACCACTCCCG 61.183 60.000 0.00 0.00 0.00 5.14
1943 1989 1.206578 CCTTTACGTTGCCTGTGCG 59.793 57.895 0.00 0.00 41.78 5.34
1951 1997 0.378962 GTTGCCTGTGCGTGTTTACA 59.621 50.000 0.00 0.00 41.78 2.41
2027 2073 0.533755 AGGCAGTTGAGTGAGCACAC 60.534 55.000 6.11 6.11 46.24 3.82
2178 2224 3.496884 TGTTGCATCCTTTCTGTACGAAC 59.503 43.478 0.00 0.00 0.00 3.95
2490 2536 5.618236 AGGATGACAACTATGGTGATGATG 58.382 41.667 0.00 0.00 0.00 3.07
2510 2556 2.309755 TGGTGATGCAGAGGAGGATTTT 59.690 45.455 0.00 0.00 0.00 1.82
2619 2665 5.606505 TGCCAATGTCTAATTATACGCAGA 58.393 37.500 0.00 0.00 0.00 4.26
2729 2775 0.384669 ATAGAAGCCAGTACGTCCGC 59.615 55.000 0.00 0.00 0.00 5.54
2798 2844 1.821666 GCCCAAGCAGGACCAGTTAAA 60.822 52.381 0.00 0.00 41.22 1.52
2870 2916 6.239176 CCCTTACTTGTAAGGTTGCAAATCAA 60.239 38.462 27.75 2.11 43.89 2.57
2872 2918 7.872483 CCTTACTTGTAAGGTTGCAAATCAAAT 59.128 33.333 24.11 0.00 41.23 2.32
2900 2946 1.065418 GGCCCTAGCAACTCTAGCAAA 60.065 52.381 0.00 0.00 42.73 3.68
3061 3107 5.769662 TGACTGTTGATGACCTTAAGCAATT 59.230 36.000 0.00 0.00 0.00 2.32
3126 3172 1.201429 AGAGGTGCCGATCTTGGGTT 61.201 55.000 0.00 0.00 0.00 4.11
3241 3287 2.417933 GCAAATACAGAGAGGTGCACTG 59.582 50.000 17.98 9.20 40.53 3.66
3295 3341 9.612066 TTGCAATTGTGAGTGATATACTTATCA 57.388 29.630 7.40 0.00 41.50 2.15
3463 3511 7.447374 TGTGTAAAGAATATCCCACTTTGTG 57.553 36.000 0.00 0.00 35.79 3.33
3464 3512 7.001674 TGTGTAAAGAATATCCCACTTTGTGT 58.998 34.615 0.00 0.00 35.79 3.72
3465 3513 8.158132 TGTGTAAAGAATATCCCACTTTGTGTA 58.842 33.333 0.00 0.00 35.79 2.90
3466 3514 8.665685 GTGTAAAGAATATCCCACTTTGTGTAG 58.334 37.037 0.00 0.00 35.79 2.74
3467 3515 6.759497 AAAGAATATCCCACTTTGTGTAGC 57.241 37.500 0.00 0.00 33.49 3.58
3468 3516 5.435686 AGAATATCCCACTTTGTGTAGCA 57.564 39.130 0.00 0.00 0.00 3.49
3469 3517 5.815581 AGAATATCCCACTTTGTGTAGCAA 58.184 37.500 0.00 0.00 34.87 3.91
3470 3518 6.245408 AGAATATCCCACTTTGTGTAGCAAA 58.755 36.000 0.00 0.00 44.05 3.68
3471 3519 6.719370 AGAATATCCCACTTTGTGTAGCAAAA 59.281 34.615 0.00 0.00 45.35 2.44
3472 3520 6.909550 ATATCCCACTTTGTGTAGCAAAAA 57.090 33.333 0.00 0.00 45.35 1.94
3535 3598 4.970860 ATATTGGAGGAGAGATGTGTGG 57.029 45.455 0.00 0.00 0.00 4.17
3547 3610 2.443255 AGATGTGTGGTCCCTTCTTGTT 59.557 45.455 0.00 0.00 0.00 2.83
3586 3649 4.558178 CACAGAATTGGCTTGTTTGCATA 58.442 39.130 0.00 0.00 34.04 3.14
3701 3794 7.359514 GCTTGCTTTCATTTTTCTATGACAACC 60.360 37.037 0.00 0.00 34.41 3.77
3785 3878 6.700960 TCGATTTCACCGTAAGTTGAGTAAAA 59.299 34.615 0.00 0.00 0.00 1.52
3791 3884 5.292589 CACCGTAAGTTGAGTAAAACACACT 59.707 40.000 0.00 0.00 32.21 3.55
3804 3897 4.632538 AAACACACTAGGCAAGAACAAC 57.367 40.909 0.00 0.00 0.00 3.32
3880 4023 8.487313 TTTTTAAATGCTAGATGCTTACTCGA 57.513 30.769 0.00 0.00 43.37 4.04
3962 4105 8.770828 CCTGTCTTATTGTTTCTTCGAACTAAA 58.229 33.333 0.00 0.00 0.00 1.85
4333 4479 3.837146 ACCAATGGGATTTGTTGCATACA 59.163 39.130 3.55 0.00 38.05 2.29
4367 4513 4.377431 CGCCACATGAGAGTTTTGAAGTAC 60.377 45.833 0.00 0.00 0.00 2.73
4368 4514 4.377431 GCCACATGAGAGTTTTGAAGTACG 60.377 45.833 0.00 0.00 0.00 3.67
4369 4515 4.750098 CCACATGAGAGTTTTGAAGTACGT 59.250 41.667 0.00 0.00 0.00 3.57
4370 4516 5.924254 CCACATGAGAGTTTTGAAGTACGTA 59.076 40.000 0.00 0.00 0.00 3.57
4383 4529 4.099881 TGAAGTACGTAGTGTGACCCTTTT 59.900 41.667 3.10 0.00 45.73 2.27
4384 4530 4.248691 AGTACGTAGTGTGACCCTTTTC 57.751 45.455 1.10 0.00 45.73 2.29
4385 4531 2.538512 ACGTAGTGTGACCCTTTTCC 57.461 50.000 0.00 0.00 42.51 3.13
4386 4532 1.764134 ACGTAGTGTGACCCTTTTCCA 59.236 47.619 0.00 0.00 42.51 3.53
4387 4533 2.370849 ACGTAGTGTGACCCTTTTCCAT 59.629 45.455 0.00 0.00 42.51 3.41
4388 4534 2.742053 CGTAGTGTGACCCTTTTCCATG 59.258 50.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.803426 GACGGCTCAGAGGTGCGG 62.803 72.222 0.00 0.00 39.06 5.69
13 14 3.978723 CTGACGGCTCAGAGGTGCG 62.979 68.421 0.00 0.00 46.32 5.34
14 15 2.125753 CTGACGGCTCAGAGGTGC 60.126 66.667 0.00 0.00 46.32 5.01
15 16 3.686760 TCTGACGGCTCAGAGGTG 58.313 61.111 11.13 0.00 46.79 4.00
20 21 1.987704 CTCGGAGTCTGACGGCTCAG 61.988 65.000 0.00 7.40 44.94 3.35
21 22 2.033602 TCGGAGTCTGACGGCTCA 59.966 61.111 0.00 0.00 33.66 4.26
22 23 2.766400 CCTCGGAGTCTGACGGCTC 61.766 68.421 4.02 0.00 0.00 4.70
23 24 2.752238 CCTCGGAGTCTGACGGCT 60.752 66.667 4.02 0.00 0.00 5.52
24 25 2.750637 TCCTCGGAGTCTGACGGC 60.751 66.667 4.02 0.00 0.00 5.68
25 26 0.464735 ATCTCCTCGGAGTCTGACGG 60.465 60.000 12.43 4.49 42.49 4.79
26 27 0.941542 GATCTCCTCGGAGTCTGACG 59.058 60.000 12.43 0.00 42.49 4.35
27 28 1.314730 GGATCTCCTCGGAGTCTGAC 58.685 60.000 12.43 0.00 42.49 3.51
28 29 0.183971 GGGATCTCCTCGGAGTCTGA 59.816 60.000 12.43 0.74 42.49 3.27
29 30 0.825840 GGGGATCTCCTCGGAGTCTG 60.826 65.000 3.62 0.00 42.49 3.51
30 31 1.289982 TGGGGATCTCCTCGGAGTCT 61.290 60.000 14.22 2.20 40.19 3.24
31 32 0.825840 CTGGGGATCTCCTCGGAGTC 60.826 65.000 14.22 9.23 46.10 3.36
32 33 1.231641 CTGGGGATCTCCTCGGAGT 59.768 63.158 14.22 0.89 46.10 3.85
33 34 0.825840 GACTGGGGATCTCCTCGGAG 60.826 65.000 14.22 3.96 46.10 4.63
34 35 1.230497 GACTGGGGATCTCCTCGGA 59.770 63.158 14.22 0.00 46.10 4.55
36 37 1.075970 TGGACTGGGGATCTCCTCG 60.076 63.158 14.22 6.56 40.19 4.63
37 38 0.263172 TCTGGACTGGGGATCTCCTC 59.737 60.000 14.22 2.32 36.90 3.71
38 39 0.031616 GTCTGGACTGGGGATCTCCT 60.032 60.000 14.22 0.00 35.95 3.69
39 40 0.325671 TGTCTGGACTGGGGATCTCC 60.326 60.000 3.99 3.99 0.00 3.71
40 41 0.827368 GTGTCTGGACTGGGGATCTC 59.173 60.000 2.38 0.00 0.00 2.75
41 42 0.618968 GGTGTCTGGACTGGGGATCT 60.619 60.000 2.38 0.00 0.00 2.75
42 43 0.909610 TGGTGTCTGGACTGGGGATC 60.910 60.000 2.38 0.00 0.00 3.36
43 44 1.160870 TGGTGTCTGGACTGGGGAT 59.839 57.895 2.38 0.00 0.00 3.85
44 45 1.841556 GTGGTGTCTGGACTGGGGA 60.842 63.158 2.38 0.00 0.00 4.81
45 46 2.750350 GTGGTGTCTGGACTGGGG 59.250 66.667 2.38 0.00 0.00 4.96
46 47 2.750350 GGTGGTGTCTGGACTGGG 59.250 66.667 2.38 0.00 0.00 4.45
47 48 2.343758 CGGTGGTGTCTGGACTGG 59.656 66.667 2.38 0.00 0.00 4.00
48 49 2.343758 CCGGTGGTGTCTGGACTG 59.656 66.667 0.00 0.00 36.02 3.51
49 50 2.923035 CCCGGTGGTGTCTGGACT 60.923 66.667 0.00 0.00 36.02 3.85
50 51 4.699522 GCCCGGTGGTGTCTGGAC 62.700 72.222 0.00 0.00 36.02 4.02
69 70 4.785453 GTTCTGGCCAGCGGGGAG 62.785 72.222 28.91 3.31 40.01 4.30
75 76 3.123620 CTCTGCGTTCTGGCCAGC 61.124 66.667 28.91 17.97 0.00 4.85
76 77 2.435586 CCTCTGCGTTCTGGCCAG 60.436 66.667 27.87 27.87 0.00 4.85
77 78 3.240134 GACCTCTGCGTTCTGGCCA 62.240 63.158 4.71 4.71 0.00 5.36
78 79 2.435059 GACCTCTGCGTTCTGGCC 60.435 66.667 0.00 0.00 0.00 5.36
79 80 2.029844 GTGACCTCTGCGTTCTGGC 61.030 63.158 0.00 0.00 0.00 4.85
80 81 0.668706 CTGTGACCTCTGCGTTCTGG 60.669 60.000 0.00 0.00 0.00 3.86
81 82 0.315251 TCTGTGACCTCTGCGTTCTG 59.685 55.000 0.00 0.00 0.00 3.02
82 83 1.203523 GATCTGTGACCTCTGCGTTCT 59.796 52.381 0.00 0.00 0.00 3.01
83 84 1.203523 AGATCTGTGACCTCTGCGTTC 59.796 52.381 0.00 0.00 0.00 3.95
84 85 1.203523 GAGATCTGTGACCTCTGCGTT 59.796 52.381 0.00 0.00 0.00 4.84
85 86 0.814457 GAGATCTGTGACCTCTGCGT 59.186 55.000 0.00 0.00 0.00 5.24
86 87 0.248417 CGAGATCTGTGACCTCTGCG 60.248 60.000 0.00 0.00 0.00 5.18
87 88 0.102120 CCGAGATCTGTGACCTCTGC 59.898 60.000 0.00 0.00 0.00 4.26
88 89 0.743688 CCCGAGATCTGTGACCTCTG 59.256 60.000 0.00 0.00 0.00 3.35
89 90 1.040339 GCCCGAGATCTGTGACCTCT 61.040 60.000 0.00 0.00 0.00 3.69
90 91 1.040339 AGCCCGAGATCTGTGACCTC 61.040 60.000 0.00 0.00 0.00 3.85
91 92 1.000993 AGCCCGAGATCTGTGACCT 59.999 57.895 0.00 0.00 0.00 3.85
92 93 1.439644 GAGCCCGAGATCTGTGACC 59.560 63.158 0.00 0.00 0.00 4.02
93 94 1.064946 CGAGCCCGAGATCTGTGAC 59.935 63.158 0.00 0.00 38.22 3.67
94 95 1.377366 GACGAGCCCGAGATCTGTGA 61.377 60.000 0.00 0.00 39.50 3.58
95 96 1.064946 GACGAGCCCGAGATCTGTG 59.935 63.158 0.00 0.00 39.50 3.66
96 97 2.473760 CGACGAGCCCGAGATCTGT 61.474 63.158 0.00 0.00 39.50 3.41
97 98 2.329690 CGACGAGCCCGAGATCTG 59.670 66.667 0.00 0.00 39.50 2.90
98 99 3.587933 GCGACGAGCCCGAGATCT 61.588 66.667 0.00 0.00 40.81 2.75
129 130 4.798682 TCCTCCTTCCCCTCCCGC 62.799 72.222 0.00 0.00 0.00 6.13
130 131 2.444895 CTCCTCCTTCCCCTCCCG 60.445 72.222 0.00 0.00 0.00 5.14
131 132 2.040359 CCTCCTCCTTCCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
132 133 2.040359 CCCTCCTCCTTCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
133 134 2.040359 CCCCTCCTCCTTCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
134 135 4.439901 GCCCCTCCTCCTTCCCCT 62.440 72.222 0.00 0.00 0.00 4.79
136 137 4.798682 TCGCCCCTCCTCCTTCCC 62.799 72.222 0.00 0.00 0.00 3.97
137 138 3.471806 GTCGCCCCTCCTCCTTCC 61.472 72.222 0.00 0.00 0.00 3.46
138 139 3.471806 GGTCGCCCCTCCTCCTTC 61.472 72.222 0.00 0.00 0.00 3.46
142 143 4.816984 TCTCGGTCGCCCCTCCTC 62.817 72.222 0.00 0.00 0.00 3.71
143 144 4.824515 CTCTCGGTCGCCCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
150 151 4.200283 CTCTGCCCTCTCGGTCGC 62.200 72.222 0.00 0.00 0.00 5.19
151 152 2.438614 TCTCTGCCCTCTCGGTCG 60.439 66.667 0.00 0.00 0.00 4.79
152 153 2.124693 CCTCTCTGCCCTCTCGGTC 61.125 68.421 0.00 0.00 0.00 4.79
153 154 2.043450 CCTCTCTGCCCTCTCGGT 60.043 66.667 0.00 0.00 0.00 4.69
154 155 1.380515 TTCCTCTCTGCCCTCTCGG 60.381 63.158 0.00 0.00 0.00 4.63
155 156 1.391157 CCTTCCTCTCTGCCCTCTCG 61.391 65.000 0.00 0.00 0.00 4.04
156 157 0.032615 TCCTTCCTCTCTGCCCTCTC 60.033 60.000 0.00 0.00 0.00 3.20
157 158 0.032217 CTCCTTCCTCTCTGCCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
158 159 0.032615 TCTCCTTCCTCTCTGCCCTC 60.033 60.000 0.00 0.00 0.00 4.30
159 160 0.032217 CTCTCCTTCCTCTCTGCCCT 60.032 60.000 0.00 0.00 0.00 5.19
160 161 1.048160 CCTCTCCTTCCTCTCTGCCC 61.048 65.000 0.00 0.00 0.00 5.36
161 162 0.325203 ACCTCTCCTTCCTCTCTGCC 60.325 60.000 0.00 0.00 0.00 4.85
162 163 0.823460 CACCTCTCCTTCCTCTCTGC 59.177 60.000 0.00 0.00 0.00 4.26
163 164 1.006519 TCCACCTCTCCTTCCTCTCTG 59.993 57.143 0.00 0.00 0.00 3.35
164 165 1.287739 CTCCACCTCTCCTTCCTCTCT 59.712 57.143 0.00 0.00 0.00 3.10
165 166 1.687996 CCTCCACCTCTCCTTCCTCTC 60.688 61.905 0.00 0.00 0.00 3.20
166 167 0.338120 CCTCCACCTCTCCTTCCTCT 59.662 60.000 0.00 0.00 0.00 3.69
167 168 0.041982 ACCTCCACCTCTCCTTCCTC 59.958 60.000 0.00 0.00 0.00 3.71
168 169 0.252467 CACCTCCACCTCTCCTTCCT 60.252 60.000 0.00 0.00 0.00 3.36
169 170 1.268283 CCACCTCCACCTCTCCTTCC 61.268 65.000 0.00 0.00 0.00 3.46
170 171 0.252284 TCCACCTCCACCTCTCCTTC 60.252 60.000 0.00 0.00 0.00 3.46
171 172 0.545548 GTCCACCTCCACCTCTCCTT 60.546 60.000 0.00 0.00 0.00 3.36
172 173 1.079438 GTCCACCTCCACCTCTCCT 59.921 63.158 0.00 0.00 0.00 3.69
173 174 2.352032 CGTCCACCTCCACCTCTCC 61.352 68.421 0.00 0.00 0.00 3.71
174 175 3.007973 GCGTCCACCTCCACCTCTC 62.008 68.421 0.00 0.00 0.00 3.20
175 176 2.997897 GCGTCCACCTCCACCTCT 60.998 66.667 0.00 0.00 0.00 3.69
176 177 4.083862 GGCGTCCACCTCCACCTC 62.084 72.222 0.00 0.00 0.00 3.85
197 198 4.736896 GACGTGGGTCACTCCGGC 62.737 72.222 0.00 0.00 42.91 6.13
198 199 4.065281 GGACGTGGGTCACTCCGG 62.065 72.222 0.00 0.00 45.28 5.14
199 200 2.646175 ATGGACGTGGGTCACTCCG 61.646 63.158 0.00 0.00 45.28 4.63
200 201 1.079127 CATGGACGTGGGTCACTCC 60.079 63.158 0.00 8.54 45.28 3.85
201 202 0.670546 CACATGGACGTGGGTCACTC 60.671 60.000 0.00 0.00 45.28 3.51
202 203 1.371183 CACATGGACGTGGGTCACT 59.629 57.895 0.00 0.00 45.28 3.41
203 204 3.966215 CACATGGACGTGGGTCAC 58.034 61.111 0.00 0.00 45.28 3.67
209 210 2.743636 AAGTACTCCACATGGACGTG 57.256 50.000 0.00 0.00 39.78 4.49
210 211 5.046878 TCAATTAAGTACTCCACATGGACGT 60.047 40.000 0.00 2.76 39.78 4.34
211 212 5.416083 TCAATTAAGTACTCCACATGGACG 58.584 41.667 0.00 0.00 39.78 4.79
212 213 7.390718 AGTTTCAATTAAGTACTCCACATGGAC 59.609 37.037 0.00 0.00 39.78 4.02
213 214 7.458397 AGTTTCAATTAAGTACTCCACATGGA 58.542 34.615 0.00 0.00 43.08 3.41
214 215 7.687941 AGTTTCAATTAAGTACTCCACATGG 57.312 36.000 0.00 0.00 0.00 3.66
215 216 9.612620 GAAAGTTTCAATTAAGTACTCCACATG 57.387 33.333 10.81 0.00 0.00 3.21
216 217 8.793592 GGAAAGTTTCAATTAAGTACTCCACAT 58.206 33.333 17.16 0.00 0.00 3.21
217 218 7.996644 AGGAAAGTTTCAATTAAGTACTCCACA 59.003 33.333 17.16 0.00 0.00 4.17
218 219 8.290325 CAGGAAAGTTTCAATTAAGTACTCCAC 58.710 37.037 17.16 0.00 0.00 4.02
219 220 7.040686 GCAGGAAAGTTTCAATTAAGTACTCCA 60.041 37.037 17.16 0.00 0.00 3.86
220 221 7.175119 AGCAGGAAAGTTTCAATTAAGTACTCC 59.825 37.037 17.16 0.00 0.00 3.85
221 222 8.100508 AGCAGGAAAGTTTCAATTAAGTACTC 57.899 34.615 17.16 0.00 0.00 2.59
222 223 7.939588 AGAGCAGGAAAGTTTCAATTAAGTACT 59.060 33.333 17.16 0.00 0.00 2.73
223 224 8.100508 AGAGCAGGAAAGTTTCAATTAAGTAC 57.899 34.615 17.16 0.00 0.00 2.73
224 225 8.691661 AAGAGCAGGAAAGTTTCAATTAAGTA 57.308 30.769 17.16 0.00 0.00 2.24
225 226 7.588497 AAGAGCAGGAAAGTTTCAATTAAGT 57.412 32.000 17.16 0.00 0.00 2.24
226 227 7.596621 GGAAAGAGCAGGAAAGTTTCAATTAAG 59.403 37.037 17.16 1.79 0.00 1.85
227 228 7.287696 AGGAAAGAGCAGGAAAGTTTCAATTAA 59.712 33.333 17.16 0.00 0.00 1.40
228 229 6.777580 AGGAAAGAGCAGGAAAGTTTCAATTA 59.222 34.615 17.16 0.00 0.00 1.40
229 230 5.600069 AGGAAAGAGCAGGAAAGTTTCAATT 59.400 36.000 17.16 0.00 0.00 2.32
230 231 5.143369 AGGAAAGAGCAGGAAAGTTTCAAT 58.857 37.500 17.16 2.53 0.00 2.57
231 232 4.536765 AGGAAAGAGCAGGAAAGTTTCAA 58.463 39.130 17.16 0.00 0.00 2.69
232 233 4.137543 GAGGAAAGAGCAGGAAAGTTTCA 58.862 43.478 17.16 0.00 0.00 2.69
233 234 3.504134 GGAGGAAAGAGCAGGAAAGTTTC 59.496 47.826 7.09 7.09 0.00 2.78
234 235 3.117512 TGGAGGAAAGAGCAGGAAAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
235 236 2.443255 TGGAGGAAAGAGCAGGAAAGTT 59.557 45.455 0.00 0.00 0.00 2.66
236 237 2.057922 TGGAGGAAAGAGCAGGAAAGT 58.942 47.619 0.00 0.00 0.00 2.66
237 238 2.867109 TGGAGGAAAGAGCAGGAAAG 57.133 50.000 0.00 0.00 0.00 2.62
238 239 2.376518 ACATGGAGGAAAGAGCAGGAAA 59.623 45.455 0.00 0.00 0.00 3.13
239 240 1.988107 ACATGGAGGAAAGAGCAGGAA 59.012 47.619 0.00 0.00 0.00 3.36
240 241 1.661463 ACATGGAGGAAAGAGCAGGA 58.339 50.000 0.00 0.00 0.00 3.86
241 242 2.503895 AACATGGAGGAAAGAGCAGG 57.496 50.000 0.00 0.00 0.00 4.85
242 243 4.861102 AAAAACATGGAGGAAAGAGCAG 57.139 40.909 0.00 0.00 0.00 4.24
243 244 5.833131 AGTTAAAAACATGGAGGAAAGAGCA 59.167 36.000 0.00 0.00 0.00 4.26
244 245 6.332735 AGTTAAAAACATGGAGGAAAGAGC 57.667 37.500 0.00 0.00 0.00 4.09
255 256 7.275560 GGGAATTCGATCCAAGTTAAAAACATG 59.724 37.037 7.35 0.00 41.55 3.21
256 257 7.178451 AGGGAATTCGATCCAAGTTAAAAACAT 59.822 33.333 7.35 0.00 41.55 2.71
257 258 6.492087 AGGGAATTCGATCCAAGTTAAAAACA 59.508 34.615 7.35 0.00 41.55 2.83
258 259 6.806739 CAGGGAATTCGATCCAAGTTAAAAAC 59.193 38.462 7.35 0.00 41.55 2.43
259 260 6.571537 GCAGGGAATTCGATCCAAGTTAAAAA 60.572 38.462 7.35 0.00 41.55 1.94
260 261 5.105917 GCAGGGAATTCGATCCAAGTTAAAA 60.106 40.000 7.35 0.00 41.55 1.52
261 262 4.398044 GCAGGGAATTCGATCCAAGTTAAA 59.602 41.667 7.35 0.00 41.55 1.52
262 263 3.945285 GCAGGGAATTCGATCCAAGTTAA 59.055 43.478 7.35 0.00 41.55 2.01
263 264 3.054728 TGCAGGGAATTCGATCCAAGTTA 60.055 43.478 7.35 0.00 41.55 2.24
264 265 2.290896 TGCAGGGAATTCGATCCAAGTT 60.291 45.455 7.35 0.00 41.55 2.66
265 266 1.281867 TGCAGGGAATTCGATCCAAGT 59.718 47.619 7.35 0.00 41.55 3.16
266 267 1.672881 GTGCAGGGAATTCGATCCAAG 59.327 52.381 7.35 0.37 41.55 3.61
267 268 1.681780 GGTGCAGGGAATTCGATCCAA 60.682 52.381 7.35 0.00 41.55 3.53
268 269 0.107214 GGTGCAGGGAATTCGATCCA 60.107 55.000 7.35 0.00 41.55 3.41
269 270 0.107214 TGGTGCAGGGAATTCGATCC 60.107 55.000 0.00 0.00 38.86 3.36
270 271 1.876156 GATGGTGCAGGGAATTCGATC 59.124 52.381 0.00 0.00 0.00 3.69
271 272 1.477558 GGATGGTGCAGGGAATTCGAT 60.478 52.381 0.00 0.00 0.00 3.59
272 273 0.107214 GGATGGTGCAGGGAATTCGA 60.107 55.000 0.00 0.00 0.00 3.71
273 274 0.394216 TGGATGGTGCAGGGAATTCG 60.394 55.000 0.00 0.00 0.00 3.34
274 275 1.851304 TTGGATGGTGCAGGGAATTC 58.149 50.000 0.00 0.00 0.00 2.17
275 276 2.323999 TTTGGATGGTGCAGGGAATT 57.676 45.000 0.00 0.00 0.00 2.17
276 277 2.112998 CATTTGGATGGTGCAGGGAAT 58.887 47.619 0.00 0.00 0.00 3.01
277 278 1.559368 CATTTGGATGGTGCAGGGAA 58.441 50.000 0.00 0.00 0.00 3.97
278 279 0.324552 CCATTTGGATGGTGCAGGGA 60.325 55.000 0.00 0.00 46.48 4.20
279 280 2.204748 CCATTTGGATGGTGCAGGG 58.795 57.895 0.00 0.00 46.48 4.45
319 320 7.337938 TCACCAGTGATCTCAAGCAAATTATA 58.662 34.615 0.00 0.00 34.14 0.98
322 323 4.401022 TCACCAGTGATCTCAAGCAAATT 58.599 39.130 0.00 0.00 34.14 1.82
324 325 3.490439 TCACCAGTGATCTCAAGCAAA 57.510 42.857 0.00 0.00 34.14 3.68
328 329 4.320057 GCTGTTTTCACCAGTGATCTCAAG 60.320 45.833 0.48 0.00 39.64 3.02
338 339 1.165907 TCCAGCGCTGTTTTCACCAG 61.166 55.000 33.75 16.41 0.00 4.00
339 340 1.153066 TCCAGCGCTGTTTTCACCA 60.153 52.632 33.75 6.11 0.00 4.17
340 341 0.884704 TCTCCAGCGCTGTTTTCACC 60.885 55.000 33.75 0.00 0.00 4.02
341 342 1.129437 GATCTCCAGCGCTGTTTTCAC 59.871 52.381 33.75 17.18 0.00 3.18
342 343 1.442769 GATCTCCAGCGCTGTTTTCA 58.557 50.000 33.75 14.52 0.00 2.69
343 344 0.371645 CGATCTCCAGCGCTGTTTTC 59.628 55.000 33.75 22.38 0.00 2.29
344 345 0.037326 TCGATCTCCAGCGCTGTTTT 60.037 50.000 33.75 16.79 0.00 2.43
345 346 0.459237 CTCGATCTCCAGCGCTGTTT 60.459 55.000 33.75 16.44 0.00 2.83
351 354 1.220169 CCAATGCTCGATCTCCAGCG 61.220 60.000 0.00 0.00 38.59 5.18
364 367 0.033366 AAGTTTGAACGGGCCAATGC 59.967 50.000 4.39 0.00 0.00 3.56
517 528 2.561037 CGTTTGTTGGGGTGGAGCC 61.561 63.158 0.00 0.00 0.00 4.70
518 529 2.561037 CCGTTTGTTGGGGTGGAGC 61.561 63.158 0.00 0.00 0.00 4.70
520 531 1.152922 GACCGTTTGTTGGGGTGGA 60.153 57.895 0.00 0.00 33.28 4.02
521 532 1.452145 CTGACCGTTTGTTGGGGTGG 61.452 60.000 0.00 0.00 33.28 4.61
523 534 0.476771 ATCTGACCGTTTGTTGGGGT 59.523 50.000 0.00 0.00 36.58 4.95
524 535 1.539827 GAATCTGACCGTTTGTTGGGG 59.460 52.381 0.00 0.00 0.00 4.96
525 536 1.539827 GGAATCTGACCGTTTGTTGGG 59.460 52.381 0.00 0.00 0.00 4.12
526 537 2.484264 GAGGAATCTGACCGTTTGTTGG 59.516 50.000 0.00 0.00 0.00 3.77
527 538 3.058914 GTGAGGAATCTGACCGTTTGTTG 60.059 47.826 0.00 0.00 0.00 3.33
528 539 3.139077 GTGAGGAATCTGACCGTTTGTT 58.861 45.455 0.00 0.00 0.00 2.83
529 540 2.767505 GTGAGGAATCTGACCGTTTGT 58.232 47.619 0.00 0.00 0.00 2.83
530 541 1.726791 CGTGAGGAATCTGACCGTTTG 59.273 52.381 0.00 0.00 0.00 2.93
531 542 1.616865 TCGTGAGGAATCTGACCGTTT 59.383 47.619 0.00 0.00 0.00 3.60
925 936 1.076332 GTTAATGGAGCGTGCTTCGT 58.924 50.000 0.00 0.00 42.13 3.85
954 965 0.740737 GGGCTGTGGGATTCGATTTG 59.259 55.000 0.00 0.00 0.00 2.32
1174 1201 0.905357 ACCCAGAACCGATCAGGAAG 59.095 55.000 10.05 0.00 45.00 3.46
1267 1294 2.435059 GCCCTCGTCTCTGGCAAC 60.435 66.667 0.00 0.00 44.70 4.17
1317 1344 3.691342 CCTCCGCAACCTCCACGA 61.691 66.667 0.00 0.00 0.00 4.35
1355 1382 3.075005 CCTCGGCTCCTTTCCGGA 61.075 66.667 0.00 0.00 46.43 5.14
1400 1427 1.959226 GGAGCGACCGTGAGCAAAA 60.959 57.895 0.00 0.00 35.48 2.44
1444 1471 3.825014 TCACACAAGTACTCCTACTGTCC 59.175 47.826 0.00 0.00 33.14 4.02
1445 1472 4.519730 ACTCACACAAGTACTCCTACTGTC 59.480 45.833 0.00 0.00 33.14 3.51
1446 1473 4.278669 CACTCACACAAGTACTCCTACTGT 59.721 45.833 0.00 0.00 33.14 3.55
1447 1474 4.278669 ACACTCACACAAGTACTCCTACTG 59.721 45.833 0.00 0.00 33.14 2.74
1448 1475 4.278669 CACACTCACACAAGTACTCCTACT 59.721 45.833 0.00 0.00 34.38 2.57
1449 1476 4.547532 CACACTCACACAAGTACTCCTAC 58.452 47.826 0.00 0.00 0.00 3.18
1450 1477 3.005472 GCACACTCACACAAGTACTCCTA 59.995 47.826 0.00 0.00 0.00 2.94
1451 1478 2.224066 GCACACTCACACAAGTACTCCT 60.224 50.000 0.00 0.00 0.00 3.69
1452 1479 2.135933 GCACACTCACACAAGTACTCC 58.864 52.381 0.00 0.00 0.00 3.85
1453 1480 1.787155 CGCACACTCACACAAGTACTC 59.213 52.381 0.00 0.00 0.00 2.59
1510 1537 3.578688 CATTTTAGCAAACACCAGAGCC 58.421 45.455 0.00 0.00 0.00 4.70
1538 1565 5.698545 CCAGTAATTCTACTATGCTGCTTCC 59.301 44.000 0.00 0.00 36.14 3.46
1545 1572 7.667557 TGTATCCACCAGTAATTCTACTATGC 58.332 38.462 0.00 0.00 36.14 3.14
1597 1627 1.009829 AGAACGGCAATTCGCATCTC 58.990 50.000 0.00 0.00 45.17 2.75
1667 1697 2.879233 ATCCACTGTCGGCGTTGGT 61.879 57.895 6.85 0.91 0.00 3.67
1784 1815 5.739161 CAGCAAACACAAGTTACTGAAAGAC 59.261 40.000 0.00 0.00 41.23 3.01
1788 1819 4.674101 GCACAGCAAACACAAGTTACTGAA 60.674 41.667 14.41 0.00 41.23 3.02
1897 1928 0.248843 CACACCTCAGCTCTCTTCCC 59.751 60.000 0.00 0.00 0.00 3.97
1951 1997 7.067494 AGCAAACACAAGTTACTGAAAGAATCT 59.933 33.333 0.00 0.00 36.84 2.40
2027 2073 1.519455 GAGCGTCCAGGTGATTCCG 60.519 63.158 0.00 0.00 41.99 4.30
2145 2191 7.333423 CAGAAAGGATGCAACATTTCATTCATT 59.667 33.333 28.13 10.15 41.14 2.57
2178 2224 7.444629 AACAGGCACATAATCTGCATAATAG 57.555 36.000 0.00 0.00 36.27 1.73
2490 2536 2.686915 CAAAATCCTCCTCTGCATCACC 59.313 50.000 0.00 0.00 0.00 4.02
2510 2556 2.880268 CAAGTCAATCTTGCAGTCCACA 59.120 45.455 0.00 0.00 45.37 4.17
2619 2665 3.370953 GGGCTACTGACATCTTGGTCATT 60.371 47.826 0.00 0.00 45.97 2.57
2636 2682 2.971598 GCTCTTGGGCACAGGGCTA 61.972 63.158 0.00 0.00 44.01 3.93
2798 2844 8.747538 AGTTTACATTCTCCTTGTACAACTTT 57.252 30.769 3.59 0.00 32.89 2.66
2870 2916 1.225373 TGCTAGGGCCCATCTTCATT 58.775 50.000 27.56 2.06 37.74 2.57
2872 2918 0.255890 GTTGCTAGGGCCCATCTTCA 59.744 55.000 27.56 11.37 37.74 3.02
2900 2946 1.272147 GCATCCACAGAAACTTCCCCT 60.272 52.381 0.00 0.00 0.00 4.79
3061 3107 2.099756 CGTGGAGATGATGTAGCTGACA 59.900 50.000 0.00 0.00 43.97 3.58
3126 3172 1.263356 CTCCAGTAACTTCCCACCGA 58.737 55.000 0.00 0.00 0.00 4.69
3295 3341 5.769662 TCTGTCCTGCAACAAATCATTAACT 59.230 36.000 0.00 0.00 0.00 2.24
3442 3490 7.335924 TGCTACACAAAGTGGGATATTCTTTAC 59.664 37.037 1.93 0.00 37.94 2.01
3471 3519 9.543783 GGATTCAGTTATAAATCTACGGACTTT 57.456 33.333 0.00 0.00 33.36 2.66
3472 3520 8.701895 TGGATTCAGTTATAAATCTACGGACTT 58.298 33.333 0.00 0.00 33.36 3.01
3473 3521 8.246430 TGGATTCAGTTATAAATCTACGGACT 57.754 34.615 0.00 0.00 33.36 3.85
3474 3522 8.522178 CTGGATTCAGTTATAAATCTACGGAC 57.478 38.462 0.00 0.00 36.30 4.79
3535 3598 3.840124 ATATCCGGAACAAGAAGGGAC 57.160 47.619 9.01 0.00 0.00 4.46
3547 3610 2.628178 CTGTGGCACTTCTATATCCGGA 59.372 50.000 19.83 6.61 0.00 5.14
3701 3794 2.672996 CAGAACCCACAAGGCCCG 60.673 66.667 0.00 0.00 40.58 6.13
3785 3878 2.210116 CGTTGTTCTTGCCTAGTGTGT 58.790 47.619 0.00 0.00 0.00 3.72
3791 3884 2.895404 AGGACTACGTTGTTCTTGCCTA 59.105 45.455 5.00 0.00 0.00 3.93
3804 3897 2.125512 GGTGCTGCCAGGACTACG 60.126 66.667 16.22 0.00 36.73 3.51
3880 4023 7.710907 ACATAATGCGTTTGTATAGTGTGAGAT 59.289 33.333 0.00 0.00 0.00 2.75
3962 4105 6.787957 AGCAGTAGTCCCAAGTATATATTGGT 59.212 38.462 15.01 3.89 44.81 3.67
4367 4513 2.536761 TGGAAAAGGGTCACACTACG 57.463 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.