Multiple sequence alignment - TraesCS3A01G304400

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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 TraesCS3A01G304400 chr3A 100.000 3962 0 0 1 3962 540653670 540657631 0.000000e+00 7317.0
1 TraesCS3A01G304400 chr3A 78.431 255 45 9 3 248 415413582 415413329 1.470000e-34 158.0
2 TraesCS3A01G304400 chr3D 94.687 3388 123 22 261 3629 411005693 411002344 0.000000e+00 5206.0
3 TraesCS3A01G304400 chr3D 90.661 257 18 3 3621 3877 411000901 411000651 1.760000e-88 337.0
4 TraesCS3A01G304400 chr3B 95.301 3022 102 13 261 3262 537470005 537467004 0.000000e+00 4758.0
5 TraesCS3A01G304400 chr3B 90.117 597 47 7 3293 3877 537467003 537466407 0.000000e+00 765.0
6 TraesCS3A01G304400 chr3B 86.250 80 10 1 3883 3962 537464832 537464754 7.050000e-13 86.1
7 TraesCS3A01G304400 chr5B 77.344 256 43 9 3 249 227945157 227944908 1.920000e-28 137.0
8 TraesCS3A01G304400 chr7B 78.873 213 34 9 48 251 54903063 54903273 2.480000e-27 134.0
9 TraesCS3A01G304400 chr7A 75.984 254 43 17 14 254 706117794 706117546 9.000000e-22 115.0
10 TraesCS3A01G304400 chr5A 81.633 98 18 0 3158 3255 320520282 320520185 9.130000e-12 82.4
11 TraesCS3A01G304400 chrUn 94.286 35 2 0 3160 3194 86615127 86615161 2.000000e-03 54.7


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 TraesCS3A01G304400 chr3A 540653670 540657631 3961 False 7317.0 7317 100.000 1 3962 1 chr3A.!!$F1 3961
1 TraesCS3A01G304400 chr3D 411000651 411005693 5042 True 2771.5 5206 92.674 261 3877 2 chr3D.!!$R1 3616
2 TraesCS3A01G304400 chr3B 537464754 537470005 5251 True 1869.7 4758 90.556 261 3962 3 chr3B.!!$R1 3701

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
208 209 0.245539 TCTGTGCCTAAGTACCGTGC 59.754 55.000 0.0 0.0 0.0 5.34 F
213 214 0.390209 GCCTAAGTACCGTGCCGAAA 60.390 55.000 0.0 0.0 0.0 3.46 F
1728 1753 1.003866 GACAACAGCACCAAGAACGTC 60.004 52.381 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1753 1.078567 GAAGGTCTGCAGCCTCCTG 60.079 63.158 24.11 0.00 42.13 3.86 R
1800 1825 5.690997 TGTGATCCTGTATGTAGACGATC 57.309 43.478 0.00 0.00 0.00 3.69 R
3358 3394 0.462581 TCAATAAGCAGGCCGAGCAG 60.463 55.000 22.53 8.91 0.00 4.24 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
22 23 5.574970 CCTAATTCCATTCTTAGCCCTCT 57.425 43.478 0.00 0.00 0.00 3.69
23 24 6.688073 CCTAATTCCATTCTTAGCCCTCTA 57.312 41.667 0.00 0.00 0.00 2.43
24 25 6.468543 CCTAATTCCATTCTTAGCCCTCTAC 58.531 44.000 0.00 0.00 0.00 2.59
25 26 5.975988 AATTCCATTCTTAGCCCTCTACA 57.024 39.130 0.00 0.00 0.00 2.74
26 27 5.975988 ATTCCATTCTTAGCCCTCTACAA 57.024 39.130 0.00 0.00 0.00 2.41
27 28 5.772393 TTCCATTCTTAGCCCTCTACAAA 57.228 39.130 0.00 0.00 0.00 2.83
28 29 5.772393 TCCATTCTTAGCCCTCTACAAAA 57.228 39.130 0.00 0.00 0.00 2.44
29 30 6.134535 TCCATTCTTAGCCCTCTACAAAAA 57.865 37.500 0.00 0.00 0.00 1.94
54 55 9.852091 AAATGAAAGTATCTCTTTTCTGATTGC 57.148 29.630 0.00 0.00 45.15 3.56
55 56 7.984422 TGAAAGTATCTCTTTTCTGATTGCA 57.016 32.000 0.00 0.00 45.15 4.08
56 57 8.571461 TGAAAGTATCTCTTTTCTGATTGCAT 57.429 30.769 0.00 0.00 45.15 3.96
57 58 8.456471 TGAAAGTATCTCTTTTCTGATTGCATG 58.544 33.333 0.00 0.00 45.15 4.06
58 59 7.934855 AAGTATCTCTTTTCTGATTGCATGT 57.065 32.000 0.00 0.00 31.57 3.21
59 60 9.453572 AAAGTATCTCTTTTCTGATTGCATGTA 57.546 29.630 0.00 0.00 42.95 2.29
60 61 9.624373 AAGTATCTCTTTTCTGATTGCATGTAT 57.376 29.630 0.00 0.00 31.57 2.29
61 62 9.270640 AGTATCTCTTTTCTGATTGCATGTATC 57.729 33.333 0.00 0.00 0.00 2.24
62 63 9.270640 GTATCTCTTTTCTGATTGCATGTATCT 57.729 33.333 10.13 0.00 0.00 1.98
63 64 7.783090 TCTCTTTTCTGATTGCATGTATCTC 57.217 36.000 10.13 0.71 0.00 2.75
64 65 7.563020 TCTCTTTTCTGATTGCATGTATCTCT 58.437 34.615 10.13 0.00 0.00 3.10
65 66 8.045507 TCTCTTTTCTGATTGCATGTATCTCTT 58.954 33.333 10.13 0.00 0.00 2.85
66 67 8.206325 TCTTTTCTGATTGCATGTATCTCTTC 57.794 34.615 10.13 0.00 0.00 2.87
67 68 8.045507 TCTTTTCTGATTGCATGTATCTCTTCT 58.954 33.333 10.13 0.00 0.00 2.85
68 69 8.571461 TTTTCTGATTGCATGTATCTCTTCTT 57.429 30.769 10.13 0.00 0.00 2.52
69 70 7.549615 TTCTGATTGCATGTATCTCTTCTTG 57.450 36.000 10.13 0.00 0.00 3.02
70 71 6.647229 TCTGATTGCATGTATCTCTTCTTGT 58.353 36.000 10.13 0.00 0.00 3.16
71 72 6.537660 TCTGATTGCATGTATCTCTTCTTGTG 59.462 38.462 10.13 0.00 0.00 3.33
72 73 5.587443 TGATTGCATGTATCTCTTCTTGTGG 59.413 40.000 10.13 0.00 0.00 4.17
73 74 3.273434 TGCATGTATCTCTTCTTGTGGC 58.727 45.455 0.00 0.00 0.00 5.01
74 75 3.273434 GCATGTATCTCTTCTTGTGGCA 58.727 45.455 0.00 0.00 0.00 4.92
75 76 3.311871 GCATGTATCTCTTCTTGTGGCAG 59.688 47.826 0.00 0.00 0.00 4.85
76 77 4.763073 CATGTATCTCTTCTTGTGGCAGA 58.237 43.478 0.00 0.00 0.00 4.26
77 78 4.890158 TGTATCTCTTCTTGTGGCAGAA 57.110 40.909 0.00 0.00 0.00 3.02
86 87 5.505173 TTCTTGTGGCAGAAGAAGAAAAG 57.495 39.130 29.46 2.76 36.73 2.27
87 88 4.526970 TCTTGTGGCAGAAGAAGAAAAGT 58.473 39.130 23.14 0.00 0.00 2.66
88 89 5.680619 TCTTGTGGCAGAAGAAGAAAAGTA 58.319 37.500 23.14 0.00 0.00 2.24
89 90 6.299141 TCTTGTGGCAGAAGAAGAAAAGTAT 58.701 36.000 23.14 0.00 0.00 2.12
90 91 6.428159 TCTTGTGGCAGAAGAAGAAAAGTATC 59.572 38.462 23.14 0.00 0.00 2.24
91 92 5.869579 TGTGGCAGAAGAAGAAAAGTATCT 58.130 37.500 0.00 0.00 0.00 1.98
92 93 5.934625 TGTGGCAGAAGAAGAAAAGTATCTC 59.065 40.000 0.00 0.00 0.00 2.75
93 94 5.934625 GTGGCAGAAGAAGAAAAGTATCTCA 59.065 40.000 0.00 0.00 0.00 3.27
94 95 5.934625 TGGCAGAAGAAGAAAAGTATCTCAC 59.065 40.000 0.00 0.00 0.00 3.51
95 96 6.169800 GGCAGAAGAAGAAAAGTATCTCACT 58.830 40.000 0.00 0.00 40.05 3.41
96 97 6.312672 GGCAGAAGAAGAAAAGTATCTCACTC 59.687 42.308 0.00 0.00 36.04 3.51
97 98 7.096551 GCAGAAGAAGAAAAGTATCTCACTCT 58.903 38.462 0.00 0.00 36.04 3.24
98 99 7.275560 GCAGAAGAAGAAAAGTATCTCACTCTC 59.724 40.741 0.00 0.00 36.04 3.20
99 100 7.484641 CAGAAGAAGAAAAGTATCTCACTCTCG 59.515 40.741 0.00 0.00 36.04 4.04
100 101 7.392113 AGAAGAAGAAAAGTATCTCACTCTCGA 59.608 37.037 0.00 0.00 36.04 4.04
101 102 7.639113 AGAAGAAAAGTATCTCACTCTCGAT 57.361 36.000 0.00 0.00 36.04 3.59
102 103 8.062065 AGAAGAAAAGTATCTCACTCTCGATT 57.938 34.615 0.00 0.00 36.04 3.34
103 104 7.973388 AGAAGAAAAGTATCTCACTCTCGATTG 59.027 37.037 0.00 0.00 36.04 2.67
104 105 7.164230 AGAAAAGTATCTCACTCTCGATTGT 57.836 36.000 0.00 0.00 36.04 2.71
105 106 7.032580 AGAAAAGTATCTCACTCTCGATTGTG 58.967 38.462 10.52 10.52 36.04 3.33
106 107 5.906113 AAGTATCTCACTCTCGATTGTGT 57.094 39.130 14.70 0.00 36.04 3.72
107 108 5.493133 AGTATCTCACTCTCGATTGTGTC 57.507 43.478 14.70 5.45 35.82 3.67
108 109 5.189928 AGTATCTCACTCTCGATTGTGTCT 58.810 41.667 14.70 6.44 35.82 3.41
109 110 6.350103 AGTATCTCACTCTCGATTGTGTCTA 58.650 40.000 14.70 5.48 35.82 2.59
110 111 6.995686 AGTATCTCACTCTCGATTGTGTCTAT 59.004 38.462 14.70 10.42 35.82 1.98
111 112 5.743026 TCTCACTCTCGATTGTGTCTATC 57.257 43.478 14.70 0.00 35.82 2.08
112 113 5.432645 TCTCACTCTCGATTGTGTCTATCT 58.567 41.667 14.70 0.00 35.82 1.98
113 114 5.525745 TCTCACTCTCGATTGTGTCTATCTC 59.474 44.000 14.70 0.00 35.82 2.75
114 115 5.432645 TCACTCTCGATTGTGTCTATCTCT 58.567 41.667 14.70 0.00 35.82 3.10
115 116 5.883115 TCACTCTCGATTGTGTCTATCTCTT 59.117 40.000 14.70 0.00 35.82 2.85
116 117 6.375736 TCACTCTCGATTGTGTCTATCTCTTT 59.624 38.462 14.70 0.00 35.82 2.52
117 118 7.553044 TCACTCTCGATTGTGTCTATCTCTTTA 59.447 37.037 14.70 0.00 35.82 1.85
118 119 8.349245 CACTCTCGATTGTGTCTATCTCTTTAT 58.651 37.037 9.05 0.00 0.00 1.40
119 120 8.908903 ACTCTCGATTGTGTCTATCTCTTTATT 58.091 33.333 0.00 0.00 0.00 1.40
120 121 9.743057 CTCTCGATTGTGTCTATCTCTTTATTT 57.257 33.333 0.00 0.00 0.00 1.40
121 122 9.521503 TCTCGATTGTGTCTATCTCTTTATTTG 57.478 33.333 0.00 0.00 0.00 2.32
122 123 9.521503 CTCGATTGTGTCTATCTCTTTATTTGA 57.478 33.333 0.00 0.00 0.00 2.69
123 124 9.302345 TCGATTGTGTCTATCTCTTTATTTGAC 57.698 33.333 0.00 0.00 0.00 3.18
124 125 9.307121 CGATTGTGTCTATCTCTTTATTTGACT 57.693 33.333 0.00 0.00 0.00 3.41
157 158 9.685828 TTTACTTGTTACTAACCAATGATTTGC 57.314 29.630 0.00 0.00 0.00 3.68
158 159 7.283625 ACTTGTTACTAACCAATGATTTGCA 57.716 32.000 0.00 0.00 0.00 4.08
159 160 7.721402 ACTTGTTACTAACCAATGATTTGCAA 58.279 30.769 0.00 0.00 0.00 4.08
160 161 7.651704 ACTTGTTACTAACCAATGATTTGCAAC 59.348 33.333 0.00 0.00 0.00 4.17
161 162 6.146216 TGTTACTAACCAATGATTTGCAACG 58.854 36.000 0.00 0.00 0.00 4.10
162 163 4.173036 ACTAACCAATGATTTGCAACGG 57.827 40.909 0.00 0.00 0.00 4.44
163 164 3.572255 ACTAACCAATGATTTGCAACGGT 59.428 39.130 0.00 0.00 36.86 4.83
164 165 4.762765 ACTAACCAATGATTTGCAACGGTA 59.237 37.500 0.00 0.00 34.90 4.02
165 166 4.592485 AACCAATGATTTGCAACGGTAA 57.408 36.364 0.00 0.00 34.90 2.85
166 167 3.908213 ACCAATGATTTGCAACGGTAAC 58.092 40.909 0.00 0.00 34.39 2.50
167 168 3.572255 ACCAATGATTTGCAACGGTAACT 59.428 39.130 0.00 0.00 34.39 2.24
168 169 4.038642 ACCAATGATTTGCAACGGTAACTT 59.961 37.500 0.00 0.00 34.39 2.66
169 170 4.987912 CCAATGATTTGCAACGGTAACTTT 59.012 37.500 0.00 0.00 0.00 2.66
170 171 6.153067 CCAATGATTTGCAACGGTAACTTTA 58.847 36.000 0.00 0.00 0.00 1.85
171 172 6.811170 CCAATGATTTGCAACGGTAACTTTAT 59.189 34.615 0.00 0.00 0.00 1.40
172 173 7.009174 CCAATGATTTGCAACGGTAACTTTATC 59.991 37.037 0.00 0.00 0.00 1.75
173 174 5.945155 TGATTTGCAACGGTAACTTTATCC 58.055 37.500 0.00 0.00 0.00 2.59
174 175 5.708230 TGATTTGCAACGGTAACTTTATCCT 59.292 36.000 0.00 0.00 0.00 3.24
175 176 6.207810 TGATTTGCAACGGTAACTTTATCCTT 59.792 34.615 0.00 0.00 0.00 3.36
176 177 7.390996 TGATTTGCAACGGTAACTTTATCCTTA 59.609 33.333 0.00 0.00 0.00 2.69
177 178 7.507733 TTTGCAACGGTAACTTTATCCTTAA 57.492 32.000 0.00 0.00 0.00 1.85
178 179 7.690952 TTGCAACGGTAACTTTATCCTTAAT 57.309 32.000 0.00 0.00 0.00 1.40
179 180 7.690952 TGCAACGGTAACTTTATCCTTAATT 57.309 32.000 0.00 0.00 0.00 1.40
180 181 7.531716 TGCAACGGTAACTTTATCCTTAATTG 58.468 34.615 0.00 0.00 0.00 2.32
181 182 7.390996 TGCAACGGTAACTTTATCCTTAATTGA 59.609 33.333 0.00 0.00 0.00 2.57
182 183 8.403236 GCAACGGTAACTTTATCCTTAATTGAT 58.597 33.333 0.00 0.00 0.00 2.57
197 198 9.866655 TCCTTAATTGATTATAATTCTGTGCCT 57.133 29.630 0.00 0.00 32.79 4.75
204 205 9.555727 TTGATTATAATTCTGTGCCTAAGTACC 57.444 33.333 0.00 0.00 0.00 3.34
205 206 7.870954 TGATTATAATTCTGTGCCTAAGTACCG 59.129 37.037 0.00 0.00 0.00 4.02
206 207 3.975168 AATTCTGTGCCTAAGTACCGT 57.025 42.857 0.00 0.00 0.00 4.83
207 208 2.736144 TTCTGTGCCTAAGTACCGTG 57.264 50.000 0.00 0.00 0.00 4.94
208 209 0.245539 TCTGTGCCTAAGTACCGTGC 59.754 55.000 0.00 0.00 0.00 5.34
209 210 0.739813 CTGTGCCTAAGTACCGTGCC 60.740 60.000 0.00 0.00 0.00 5.01
210 211 1.808390 GTGCCTAAGTACCGTGCCG 60.808 63.158 0.00 0.00 0.00 5.69
211 212 1.978080 TGCCTAAGTACCGTGCCGA 60.978 57.895 0.00 0.00 0.00 5.54
212 213 1.216178 GCCTAAGTACCGTGCCGAA 59.784 57.895 0.00 0.00 0.00 4.30
213 214 0.390209 GCCTAAGTACCGTGCCGAAA 60.390 55.000 0.00 0.00 0.00 3.46
214 215 1.940752 GCCTAAGTACCGTGCCGAAAA 60.941 52.381 0.00 0.00 0.00 2.29
215 216 2.624636 CCTAAGTACCGTGCCGAAAAT 58.375 47.619 0.00 0.00 0.00 1.82
216 217 3.784338 CCTAAGTACCGTGCCGAAAATA 58.216 45.455 0.00 0.00 0.00 1.40
217 218 4.183101 CCTAAGTACCGTGCCGAAAATAA 58.817 43.478 0.00 0.00 0.00 1.40
218 219 4.812626 CCTAAGTACCGTGCCGAAAATAAT 59.187 41.667 0.00 0.00 0.00 1.28
219 220 5.984926 CCTAAGTACCGTGCCGAAAATAATA 59.015 40.000 0.00 0.00 0.00 0.98
220 221 5.723492 AAGTACCGTGCCGAAAATAATAC 57.277 39.130 0.00 0.00 0.00 1.89
221 222 4.757594 AGTACCGTGCCGAAAATAATACA 58.242 39.130 0.00 0.00 0.00 2.29
222 223 4.567959 AGTACCGTGCCGAAAATAATACAC 59.432 41.667 0.00 0.00 0.00 2.90
223 224 2.679336 ACCGTGCCGAAAATAATACACC 59.321 45.455 0.00 0.00 0.00 4.16
224 225 2.940410 CCGTGCCGAAAATAATACACCT 59.060 45.455 0.00 0.00 0.00 4.00
225 226 3.375922 CCGTGCCGAAAATAATACACCTT 59.624 43.478 0.00 0.00 0.00 3.50
226 227 4.571580 CCGTGCCGAAAATAATACACCTTA 59.428 41.667 0.00 0.00 0.00 2.69
227 228 5.495502 CGTGCCGAAAATAATACACCTTAC 58.504 41.667 0.00 0.00 0.00 2.34
228 229 5.495502 GTGCCGAAAATAATACACCTTACG 58.504 41.667 0.00 0.00 0.00 3.18
229 230 5.063817 GTGCCGAAAATAATACACCTTACGT 59.936 40.000 0.00 0.00 0.00 3.57
230 231 6.255453 GTGCCGAAAATAATACACCTTACGTA 59.745 38.462 0.00 0.00 0.00 3.57
231 232 6.815641 TGCCGAAAATAATACACCTTACGTAA 59.184 34.615 7.94 7.94 0.00 3.18
232 233 7.332926 TGCCGAAAATAATACACCTTACGTAAA 59.667 33.333 9.68 0.00 0.00 2.01
233 234 7.847564 GCCGAAAATAATACACCTTACGTAAAG 59.152 37.037 9.68 5.89 34.73 1.85
245 246 4.891260 CTTACGTAAAGGAACAAGGGAGT 58.109 43.478 9.68 0.00 0.00 3.85
246 247 6.029346 CTTACGTAAAGGAACAAGGGAGTA 57.971 41.667 9.68 0.00 0.00 2.59
247 248 6.610075 TTACGTAAAGGAACAAGGGAGTAT 57.390 37.500 5.31 0.00 0.00 2.12
248 249 5.494390 ACGTAAAGGAACAAGGGAGTATT 57.506 39.130 0.00 0.00 0.00 1.89
249 250 6.610075 ACGTAAAGGAACAAGGGAGTATTA 57.390 37.500 0.00 0.00 0.00 0.98
250 251 7.191593 ACGTAAAGGAACAAGGGAGTATTAT 57.808 36.000 0.00 0.00 0.00 1.28
251 252 7.627311 ACGTAAAGGAACAAGGGAGTATTATT 58.373 34.615 0.00 0.00 0.00 1.40
252 253 8.105197 ACGTAAAGGAACAAGGGAGTATTATTT 58.895 33.333 0.00 0.00 0.00 1.40
253 254 8.953313 CGTAAAGGAACAAGGGAGTATTATTTT 58.047 33.333 0.00 0.00 0.00 1.82
255 256 8.950007 AAAGGAACAAGGGAGTATTATTTTCA 57.050 30.769 0.00 0.00 0.00 2.69
256 257 8.950007 AAGGAACAAGGGAGTATTATTTTCAA 57.050 30.769 0.00 0.00 0.00 2.69
257 258 8.950007 AGGAACAAGGGAGTATTATTTTCAAA 57.050 30.769 0.00 0.00 0.00 2.69
258 259 9.025041 AGGAACAAGGGAGTATTATTTTCAAAG 57.975 33.333 0.00 0.00 0.00 2.77
259 260 9.020731 GGAACAAGGGAGTATTATTTTCAAAGA 57.979 33.333 0.00 0.00 0.00 2.52
324 325 3.053291 CGTGCGGGGCTTGCTAAA 61.053 61.111 3.41 0.00 0.00 1.85
389 390 1.064208 AGTCCGTCGACATCAATCTCG 59.936 52.381 17.16 0.00 41.87 4.04
399 400 4.084171 CGACATCAATCTCGCATTGCTATT 60.084 41.667 7.12 1.44 0.00 1.73
427 428 6.243551 CAATGCTACAAGTTTGACGATGTAG 58.756 40.000 16.09 16.09 41.75 2.74
494 498 3.404978 CGTTGACGTCGGAATACCA 57.595 52.632 11.62 0.00 33.59 3.25
590 594 4.133078 CTCTCAAAAGCCCCATCAGATAC 58.867 47.826 0.00 0.00 0.00 2.24
591 595 2.874701 CTCAAAAGCCCCATCAGATACG 59.125 50.000 0.00 0.00 0.00 3.06
592 596 2.238646 TCAAAAGCCCCATCAGATACGT 59.761 45.455 0.00 0.00 0.00 3.57
593 597 3.452990 TCAAAAGCCCCATCAGATACGTA 59.547 43.478 0.00 0.00 0.00 3.57
594 598 3.470645 AAAGCCCCATCAGATACGTAC 57.529 47.619 0.00 0.00 0.00 3.67
598 602 2.299013 GCCCCATCAGATACGTACATCA 59.701 50.000 0.00 0.00 0.00 3.07
639 647 1.595357 GACCGTTCCCAATCTCCGT 59.405 57.895 0.00 0.00 0.00 4.69
665 673 6.717986 GAACCTAGGCAGTTAGCGATGGTT 62.718 50.000 9.30 0.00 45.38 3.67
695 703 1.141234 GCCCGCACACTACTAGACC 59.859 63.158 0.00 0.00 0.00 3.85
775 783 5.146010 TCAGCTTCTTCTTCTTCTTCTCC 57.854 43.478 0.00 0.00 0.00 3.71
796 804 6.948309 TCTCCTTTTCTAATCCCTTTTCTTGG 59.052 38.462 0.00 0.00 0.00 3.61
833 841 3.668447 GTTGATGTCATCACTGGTCAGT 58.332 45.455 15.23 0.00 43.61 3.41
865 873 4.459089 GCCTCGCTCGGCCTCTTT 62.459 66.667 0.00 0.00 44.41 2.52
876 884 1.770957 GGCCTCTTTTTCTTGTTGCG 58.229 50.000 0.00 0.00 0.00 4.85
910 918 2.335712 CCGGGCTCTTCTTGTTGCC 61.336 63.158 0.00 0.00 44.22 4.52
928 936 3.861840 TGCCTCTACAAAGTATCTGTGC 58.138 45.455 0.00 0.00 0.00 4.57
1432 1457 2.166459 CCTCTCGGTAAGCAGATCACAA 59.834 50.000 0.00 0.00 0.00 3.33
1433 1458 3.181471 CCTCTCGGTAAGCAGATCACAAT 60.181 47.826 0.00 0.00 0.00 2.71
1434 1459 4.437239 CTCTCGGTAAGCAGATCACAATT 58.563 43.478 0.00 0.00 0.00 2.32
1435 1460 5.451937 CCTCTCGGTAAGCAGATCACAATTA 60.452 44.000 0.00 0.00 0.00 1.40
1542 1567 2.265739 GTGACTGCGATCCTGCCA 59.734 61.111 0.00 0.00 0.00 4.92
1728 1753 1.003866 GACAACAGCACCAAGAACGTC 60.004 52.381 0.00 0.00 0.00 4.34
1800 1825 3.103911 GTCGTTGCGGTCCTCGTG 61.104 66.667 0.00 0.00 41.72 4.35
1818 1843 4.386711 TCGTGATCGTCTACATACAGGAT 58.613 43.478 0.00 0.00 38.33 3.24
2294 2319 4.802051 TCGGCAGATGGGCAAGGC 62.802 66.667 0.00 0.00 43.60 4.35
2296 2321 4.802051 GGCAGATGGGCAAGGCGA 62.802 66.667 0.00 0.00 42.77 5.54
2298 2323 3.056313 GCAGATGGGCAAGGCGAAC 62.056 63.158 0.00 0.00 0.00 3.95
2299 2324 1.675310 CAGATGGGCAAGGCGAACA 60.675 57.895 0.00 0.00 0.00 3.18
2332 2357 1.202973 CTACAGCGTCTTCGGCATCG 61.203 60.000 0.00 0.00 37.56 3.84
2468 2493 0.889186 GTCTTCACCGTTGCCATGGT 60.889 55.000 14.67 0.00 43.94 3.55
2532 2557 2.671682 GAGGGCTTCCAGGACCAC 59.328 66.667 0.00 0.00 36.69 4.16
2536 2561 1.303643 GGCTTCCAGGACCACAAGG 60.304 63.158 0.00 0.00 42.21 3.61
2943 2968 0.820871 CGGAGGAGGAAGAGACCAAG 59.179 60.000 0.00 0.00 0.00 3.61
3009 3034 2.280119 GTGTGCTGGTGTGCTCGA 60.280 61.111 0.00 0.00 0.00 4.04
3017 3042 0.037326 TGGTGTGCTCGATTGACCTC 60.037 55.000 0.00 0.00 0.00 3.85
3071 3104 4.794248 TTGTGATATTGATGTGCTACGC 57.206 40.909 0.00 0.00 0.00 4.42
3084 3117 2.844804 GTGCTACGCTAGTGTAGAAACG 59.155 50.000 36.35 18.12 43.65 3.60
3086 3119 3.376234 TGCTACGCTAGTGTAGAAACGAT 59.624 43.478 36.35 5.22 43.65 3.73
3289 3322 4.448060 GCAAGTACGCCTAGGACATAAATC 59.552 45.833 14.75 0.00 35.65 2.17
3290 3323 4.500603 AGTACGCCTAGGACATAAATCG 57.499 45.455 14.75 6.27 35.65 3.34
3291 3324 2.814280 ACGCCTAGGACATAAATCGG 57.186 50.000 14.75 0.00 0.00 4.18
3292 3325 2.037144 ACGCCTAGGACATAAATCGGT 58.963 47.619 14.75 0.00 0.00 4.69
3293 3326 3.225104 ACGCCTAGGACATAAATCGGTA 58.775 45.455 14.75 0.00 0.00 4.02
3294 3327 3.638160 ACGCCTAGGACATAAATCGGTAA 59.362 43.478 14.75 0.00 0.00 2.85
3295 3328 4.099881 ACGCCTAGGACATAAATCGGTAAA 59.900 41.667 14.75 0.00 0.00 2.01
3296 3329 5.221581 ACGCCTAGGACATAAATCGGTAAAT 60.222 40.000 14.75 0.00 0.00 1.40
3310 3343 7.969536 AATCGGTAAATAGGAGATGAACATG 57.030 36.000 0.00 0.00 0.00 3.21
3334 3367 2.503869 ATCTTCCAGTAGGCCAGGAT 57.496 50.000 5.01 0.00 33.74 3.24
3340 3373 3.460825 TCCAGTAGGCCAGGATAAAGTT 58.539 45.455 5.01 0.00 33.74 2.66
3349 3385 2.407616 GATAAAGTTGCGGCGGCC 59.592 61.111 14.25 9.54 38.85 6.13
3377 3413 0.462581 CTGCTCGGCCTGCTTATTGA 60.463 55.000 16.66 0.00 0.00 2.57
3394 3430 6.684555 GCTTATTGACAGCTTCATAGTTTTCG 59.315 38.462 0.00 0.00 32.84 3.46
3407 3443 7.609760 TCATAGTTTTCGTCAATAGCAATGT 57.390 32.000 0.00 0.00 0.00 2.71
3414 3450 3.447229 TCGTCAATAGCAATGTGGAGAGA 59.553 43.478 0.00 0.00 0.00 3.10
3429 3466 3.392947 TGGAGAGATCGAGGATGTAGTCT 59.607 47.826 0.00 0.00 0.00 3.24
3434 3471 5.995282 AGAGATCGAGGATGTAGTCTAAGTG 59.005 44.000 0.00 0.00 0.00 3.16
3450 3487 1.629043 AGTGGAGGAACAGTAGCGAA 58.371 50.000 0.00 0.00 0.00 4.70
3489 3531 4.465446 CGGCTGAGGAGGGGGAGA 62.465 72.222 0.00 0.00 0.00 3.71
3508 3550 3.134458 AGAAAGAGACCAAGCAAGAACG 58.866 45.455 0.00 0.00 0.00 3.95
3540 3582 4.757355 CAAGGCATTCCCCGGGCA 62.757 66.667 17.73 0.00 0.00 5.36
3560 3602 2.164219 CAGTGTGTTGTGCTTTGACCTT 59.836 45.455 0.00 0.00 0.00 3.50
3578 3620 3.491652 GCACGCGCCTTTCTCTCC 61.492 66.667 5.73 0.00 0.00 3.71
3579 3621 2.048222 CACGCGCCTTTCTCTCCA 60.048 61.111 5.73 0.00 0.00 3.86
3685 5180 5.485209 TCTCAAAACCCTAAGAGTTCCTC 57.515 43.478 0.00 0.00 0.00 3.71
3772 5267 0.618981 ACTAACTACAAGCAGGGGGC 59.381 55.000 0.00 0.00 45.30 5.80
3800 5295 5.268118 TGGTTCTGTAGCTGATGTAGATG 57.732 43.478 0.00 0.00 0.00 2.90
3894 6959 8.543774 AGAAGTATGTCATAATTGTCTCCTTGT 58.456 33.333 10.13 0.00 0.00 3.16
3899 6964 6.166279 TGTCATAATTGTCTCCTTGTCAGTC 58.834 40.000 0.00 0.00 0.00 3.51
3905 6970 2.894126 TGTCTCCTTGTCAGTCTCCTTC 59.106 50.000 0.00 0.00 0.00 3.46
3908 6973 0.969894 CCTTGTCAGTCTCCTTCCGT 59.030 55.000 0.00 0.00 0.00 4.69
3941 7006 4.389077 GGTTTATCCTTGAGAGTGTTGTCG 59.611 45.833 0.00 0.00 0.00 4.35
3942 7007 2.751166 ATCCTTGAGAGTGTTGTCGG 57.249 50.000 0.00 0.00 0.00 4.79
3956 7021 2.084610 TGTCGGAGCTCATGAAACTG 57.915 50.000 17.19 0.23 0.00 3.16
3957 7022 1.344438 TGTCGGAGCTCATGAAACTGT 59.656 47.619 17.19 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.574970 AGAGGGCTAAGAATGGAATTAGG 57.425 43.478 0.00 0.00 36.07 2.69
1 2 7.067496 TGTAGAGGGCTAAGAATGGAATTAG 57.933 40.000 0.00 0.00 36.07 1.73
2 3 7.446106 TTGTAGAGGGCTAAGAATGGAATTA 57.554 36.000 0.00 0.00 36.07 1.40
3 4 5.975988 TGTAGAGGGCTAAGAATGGAATT 57.024 39.130 0.00 0.00 40.93 2.17
4 5 5.975988 TTGTAGAGGGCTAAGAATGGAAT 57.024 39.130 0.00 0.00 0.00 3.01
5 6 5.772393 TTTGTAGAGGGCTAAGAATGGAA 57.228 39.130 0.00 0.00 0.00 3.53
6 7 5.772393 TTTTGTAGAGGGCTAAGAATGGA 57.228 39.130 0.00 0.00 0.00 3.41
28 29 9.852091 GCAATCAGAAAAGAGATACTTTCATTT 57.148 29.630 0.00 0.00 46.55 2.32
29 30 9.017509 TGCAATCAGAAAAGAGATACTTTCATT 57.982 29.630 0.00 0.00 46.55 2.57
30 31 8.571461 TGCAATCAGAAAAGAGATACTTTCAT 57.429 30.769 0.00 0.00 46.55 2.57
31 32 7.984422 TGCAATCAGAAAAGAGATACTTTCA 57.016 32.000 0.00 0.00 46.55 2.69
32 33 8.457261 ACATGCAATCAGAAAAGAGATACTTTC 58.543 33.333 0.00 0.00 46.55 2.62
34 35 7.934855 ACATGCAATCAGAAAAGAGATACTT 57.065 32.000 0.00 0.00 40.98 2.24
35 36 9.270640 GATACATGCAATCAGAAAAGAGATACT 57.729 33.333 0.00 0.00 0.00 2.12
36 37 9.270640 AGATACATGCAATCAGAAAAGAGATAC 57.729 33.333 10.38 0.00 0.00 2.24
37 38 9.486497 GAGATACATGCAATCAGAAAAGAGATA 57.514 33.333 10.38 0.00 0.00 1.98
38 39 8.212312 AGAGATACATGCAATCAGAAAAGAGAT 58.788 33.333 10.38 0.00 0.00 2.75
39 40 7.563020 AGAGATACATGCAATCAGAAAAGAGA 58.437 34.615 10.38 0.00 0.00 3.10
40 41 7.789273 AGAGATACATGCAATCAGAAAAGAG 57.211 36.000 10.38 0.00 0.00 2.85
41 42 8.045507 AGAAGAGATACATGCAATCAGAAAAGA 58.954 33.333 10.38 0.00 0.00 2.52
42 43 8.211116 AGAAGAGATACATGCAATCAGAAAAG 57.789 34.615 10.38 0.00 0.00 2.27
43 44 8.456471 CAAGAAGAGATACATGCAATCAGAAAA 58.544 33.333 10.38 0.00 0.00 2.29
44 45 7.609146 ACAAGAAGAGATACATGCAATCAGAAA 59.391 33.333 10.38 0.00 0.00 2.52
45 46 7.065443 CACAAGAAGAGATACATGCAATCAGAA 59.935 37.037 10.38 0.00 0.00 3.02
46 47 6.537660 CACAAGAAGAGATACATGCAATCAGA 59.462 38.462 10.38 0.00 0.00 3.27
47 48 6.238402 CCACAAGAAGAGATACATGCAATCAG 60.238 42.308 10.38 0.00 0.00 2.90
48 49 5.587443 CCACAAGAAGAGATACATGCAATCA 59.413 40.000 10.38 0.00 0.00 2.57
49 50 5.505324 GCCACAAGAAGAGATACATGCAATC 60.505 44.000 0.00 0.00 0.00 2.67
50 51 4.337555 GCCACAAGAAGAGATACATGCAAT 59.662 41.667 0.00 0.00 0.00 3.56
51 52 3.691118 GCCACAAGAAGAGATACATGCAA 59.309 43.478 0.00 0.00 0.00 4.08
52 53 3.273434 GCCACAAGAAGAGATACATGCA 58.727 45.455 0.00 0.00 0.00 3.96
53 54 3.273434 TGCCACAAGAAGAGATACATGC 58.727 45.455 0.00 0.00 0.00 4.06
54 55 4.763073 TCTGCCACAAGAAGAGATACATG 58.237 43.478 0.00 0.00 0.00 3.21
55 56 5.426689 TTCTGCCACAAGAAGAGATACAT 57.573 39.130 0.00 0.00 32.42 2.29
56 57 4.890158 TTCTGCCACAAGAAGAGATACA 57.110 40.909 0.00 0.00 32.42 2.29
64 65 4.949856 ACTTTTCTTCTTCTGCCACAAGAA 59.050 37.500 0.00 0.00 37.50 2.52
65 66 4.526970 ACTTTTCTTCTTCTGCCACAAGA 58.473 39.130 0.00 0.00 0.00 3.02
66 67 4.907879 ACTTTTCTTCTTCTGCCACAAG 57.092 40.909 0.00 0.00 0.00 3.16
67 68 6.299141 AGATACTTTTCTTCTTCTGCCACAA 58.701 36.000 0.00 0.00 0.00 3.33
68 69 5.869579 AGATACTTTTCTTCTTCTGCCACA 58.130 37.500 0.00 0.00 0.00 4.17
69 70 5.934625 TGAGATACTTTTCTTCTTCTGCCAC 59.065 40.000 0.00 0.00 0.00 5.01
70 71 5.934625 GTGAGATACTTTTCTTCTTCTGCCA 59.065 40.000 0.00 0.00 0.00 4.92
71 72 6.169800 AGTGAGATACTTTTCTTCTTCTGCC 58.830 40.000 0.00 0.00 35.67 4.85
72 73 7.096551 AGAGTGAGATACTTTTCTTCTTCTGC 58.903 38.462 0.00 0.00 40.53 4.26
73 74 7.484641 CGAGAGTGAGATACTTTTCTTCTTCTG 59.515 40.741 0.00 0.00 40.53 3.02
74 75 7.392113 TCGAGAGTGAGATACTTTTCTTCTTCT 59.608 37.037 0.00 0.00 40.53 2.85
75 76 7.531716 TCGAGAGTGAGATACTTTTCTTCTTC 58.468 38.462 0.00 0.00 40.53 2.87
76 77 7.455641 TCGAGAGTGAGATACTTTTCTTCTT 57.544 36.000 0.00 0.00 40.53 2.52
77 78 7.639113 ATCGAGAGTGAGATACTTTTCTTCT 57.361 36.000 0.00 0.00 40.53 2.85
78 79 7.757624 ACAATCGAGAGTGAGATACTTTTCTTC 59.242 37.037 7.57 0.00 40.53 2.87
79 80 7.543868 CACAATCGAGAGTGAGATACTTTTCTT 59.456 37.037 13.13 0.00 40.53 2.52
80 81 7.032580 CACAATCGAGAGTGAGATACTTTTCT 58.967 38.462 13.13 0.00 40.53 2.52
81 82 6.809196 ACACAATCGAGAGTGAGATACTTTTC 59.191 38.462 22.25 0.00 40.53 2.29
82 83 6.692486 ACACAATCGAGAGTGAGATACTTTT 58.308 36.000 22.25 0.00 40.53 2.27
83 84 6.151985 AGACACAATCGAGAGTGAGATACTTT 59.848 38.462 22.25 2.11 40.53 2.66
84 85 5.650266 AGACACAATCGAGAGTGAGATACTT 59.350 40.000 22.25 2.73 40.53 2.24
85 86 5.189928 AGACACAATCGAGAGTGAGATACT 58.810 41.667 22.25 11.91 44.02 2.12
86 87 5.493133 AGACACAATCGAGAGTGAGATAC 57.507 43.478 22.25 10.41 39.03 2.24
87 88 7.220740 AGATAGACACAATCGAGAGTGAGATA 58.779 38.462 22.25 13.26 39.03 1.98
88 89 6.061441 AGATAGACACAATCGAGAGTGAGAT 58.939 40.000 22.25 13.32 39.03 2.75
89 90 5.432645 AGATAGACACAATCGAGAGTGAGA 58.567 41.667 22.25 10.03 39.03 3.27
90 91 5.527214 AGAGATAGACACAATCGAGAGTGAG 59.473 44.000 22.25 7.92 39.03 3.51
91 92 5.432645 AGAGATAGACACAATCGAGAGTGA 58.567 41.667 22.25 5.06 39.03 3.41
92 93 5.749596 AGAGATAGACACAATCGAGAGTG 57.250 43.478 15.94 15.94 41.40 3.51
93 94 6.767524 AAAGAGATAGACACAATCGAGAGT 57.232 37.500 0.00 0.00 0.00 3.24
94 95 9.743057 AAATAAAGAGATAGACACAATCGAGAG 57.257 33.333 0.00 0.00 0.00 3.20
95 96 9.521503 CAAATAAAGAGATAGACACAATCGAGA 57.478 33.333 0.00 0.00 0.00 4.04
96 97 9.521503 TCAAATAAAGAGATAGACACAATCGAG 57.478 33.333 0.00 0.00 0.00 4.04
97 98 9.302345 GTCAAATAAAGAGATAGACACAATCGA 57.698 33.333 0.00 0.00 0.00 3.59
98 99 9.307121 AGTCAAATAAAGAGATAGACACAATCG 57.693 33.333 0.00 0.00 0.00 3.34
131 132 9.685828 GCAAATCATTGGTTAGTAACAAGTAAA 57.314 29.630 14.81 1.99 37.02 2.01
132 133 8.851145 TGCAAATCATTGGTTAGTAACAAGTAA 58.149 29.630 14.81 4.90 37.02 2.24
133 134 8.397575 TGCAAATCATTGGTTAGTAACAAGTA 57.602 30.769 14.81 0.00 37.02 2.24
134 135 7.283625 TGCAAATCATTGGTTAGTAACAAGT 57.716 32.000 14.81 0.00 37.02 3.16
135 136 7.148983 CGTTGCAAATCATTGGTTAGTAACAAG 60.149 37.037 14.81 1.88 37.02 3.16
136 137 6.638873 CGTTGCAAATCATTGGTTAGTAACAA 59.361 34.615 14.81 0.06 37.02 2.83
137 138 6.146216 CGTTGCAAATCATTGGTTAGTAACA 58.854 36.000 14.81 0.00 37.02 2.41
138 139 5.571357 CCGTTGCAAATCATTGGTTAGTAAC 59.429 40.000 0.00 4.32 37.02 2.50
139 140 5.241949 ACCGTTGCAAATCATTGGTTAGTAA 59.758 36.000 0.00 0.00 37.02 2.24
140 141 4.762765 ACCGTTGCAAATCATTGGTTAGTA 59.237 37.500 0.00 0.00 37.02 1.82
141 142 3.572255 ACCGTTGCAAATCATTGGTTAGT 59.428 39.130 0.00 0.00 37.02 2.24
142 143 4.173036 ACCGTTGCAAATCATTGGTTAG 57.827 40.909 0.00 0.00 37.02 2.34
143 144 5.241949 AGTTACCGTTGCAAATCATTGGTTA 59.758 36.000 0.00 0.00 37.02 2.85
144 145 4.038642 AGTTACCGTTGCAAATCATTGGTT 59.961 37.500 0.00 0.00 37.02 3.67
145 146 3.572255 AGTTACCGTTGCAAATCATTGGT 59.428 39.130 0.00 5.40 37.02 3.67
146 147 4.173036 AGTTACCGTTGCAAATCATTGG 57.827 40.909 0.00 0.00 37.02 3.16
147 148 7.009174 GGATAAAGTTACCGTTGCAAATCATTG 59.991 37.037 0.00 0.00 39.65 2.82
148 149 7.033185 GGATAAAGTTACCGTTGCAAATCATT 58.967 34.615 0.00 0.00 0.00 2.57
149 150 6.377146 AGGATAAAGTTACCGTTGCAAATCAT 59.623 34.615 0.00 0.00 0.00 2.45
150 151 5.708230 AGGATAAAGTTACCGTTGCAAATCA 59.292 36.000 0.00 0.00 0.00 2.57
151 152 6.190954 AGGATAAAGTTACCGTTGCAAATC 57.809 37.500 0.00 0.00 0.00 2.17
152 153 6.584185 AAGGATAAAGTTACCGTTGCAAAT 57.416 33.333 0.00 0.00 0.00 2.32
153 154 7.507733 TTAAGGATAAAGTTACCGTTGCAAA 57.492 32.000 0.00 0.00 0.00 3.68
154 155 7.690952 ATTAAGGATAAAGTTACCGTTGCAA 57.309 32.000 0.00 0.00 0.00 4.08
155 156 7.390996 TCAATTAAGGATAAAGTTACCGTTGCA 59.609 33.333 0.00 0.00 0.00 4.08
156 157 7.754625 TCAATTAAGGATAAAGTTACCGTTGC 58.245 34.615 0.00 0.00 0.00 4.17
171 172 9.866655 AGGCACAGAATTATAATCAATTAAGGA 57.133 29.630 0.00 0.00 0.00 3.36
178 179 9.555727 GGTACTTAGGCACAGAATTATAATCAA 57.444 33.333 0.00 0.00 0.00 2.57
179 180 7.870954 CGGTACTTAGGCACAGAATTATAATCA 59.129 37.037 0.00 0.00 0.00 2.57
180 181 7.871463 ACGGTACTTAGGCACAGAATTATAATC 59.129 37.037 0.00 0.00 0.00 1.75
181 182 7.656137 CACGGTACTTAGGCACAGAATTATAAT 59.344 37.037 0.00 0.00 0.00 1.28
182 183 6.982141 CACGGTACTTAGGCACAGAATTATAA 59.018 38.462 0.00 0.00 0.00 0.98
183 184 6.509656 CACGGTACTTAGGCACAGAATTATA 58.490 40.000 0.00 0.00 0.00 0.98
184 185 5.357257 CACGGTACTTAGGCACAGAATTAT 58.643 41.667 0.00 0.00 0.00 1.28
185 186 4.751060 CACGGTACTTAGGCACAGAATTA 58.249 43.478 0.00 0.00 0.00 1.40
186 187 3.596214 CACGGTACTTAGGCACAGAATT 58.404 45.455 0.00 0.00 0.00 2.17
187 188 2.677037 GCACGGTACTTAGGCACAGAAT 60.677 50.000 0.00 0.00 0.00 2.40
188 189 1.337447 GCACGGTACTTAGGCACAGAA 60.337 52.381 0.00 0.00 0.00 3.02
189 190 0.245539 GCACGGTACTTAGGCACAGA 59.754 55.000 0.00 0.00 0.00 3.41
190 191 0.739813 GGCACGGTACTTAGGCACAG 60.740 60.000 0.00 0.00 0.00 3.66
191 192 1.294138 GGCACGGTACTTAGGCACA 59.706 57.895 0.00 0.00 0.00 4.57
192 193 4.196965 GGCACGGTACTTAGGCAC 57.803 61.111 0.00 0.00 0.00 5.01
205 206 5.063817 ACGTAAGGTGTATTATTTTCGGCAC 59.936 40.000 0.00 0.00 46.39 5.01
206 207 5.177326 ACGTAAGGTGTATTATTTTCGGCA 58.823 37.500 0.00 0.00 46.39 5.69
207 208 5.723492 ACGTAAGGTGTATTATTTTCGGC 57.277 39.130 0.00 0.00 46.39 5.54
224 225 4.961438 ACTCCCTTGTTCCTTTACGTAA 57.039 40.909 3.29 3.29 0.00 3.18
225 226 6.610075 AATACTCCCTTGTTCCTTTACGTA 57.390 37.500 0.00 0.00 0.00 3.57
226 227 5.494390 AATACTCCCTTGTTCCTTTACGT 57.506 39.130 0.00 0.00 0.00 3.57
227 228 8.502105 AAATAATACTCCCTTGTTCCTTTACG 57.498 34.615 0.00 0.00 0.00 3.18
230 231 8.950007 TGAAAATAATACTCCCTTGTTCCTTT 57.050 30.769 0.00 0.00 0.00 3.11
231 232 8.950007 TTGAAAATAATACTCCCTTGTTCCTT 57.050 30.769 0.00 0.00 0.00 3.36
232 233 8.950007 TTTGAAAATAATACTCCCTTGTTCCT 57.050 30.769 0.00 0.00 0.00 3.36
233 234 9.020731 TCTTTGAAAATAATACTCCCTTGTTCC 57.979 33.333 0.00 0.00 0.00 3.62
249 250 9.635520 CTTTCTGACTGCATAATCTTTGAAAAT 57.364 29.630 0.00 0.00 0.00 1.82
250 251 8.849168 TCTTTCTGACTGCATAATCTTTGAAAA 58.151 29.630 0.00 0.00 0.00 2.29
251 252 8.394971 TCTTTCTGACTGCATAATCTTTGAAA 57.605 30.769 0.00 0.00 0.00 2.69
252 253 7.663081 ACTCTTTCTGACTGCATAATCTTTGAA 59.337 33.333 0.00 0.00 0.00 2.69
253 254 7.164122 ACTCTTTCTGACTGCATAATCTTTGA 58.836 34.615 0.00 0.00 0.00 2.69
254 255 7.375106 ACTCTTTCTGACTGCATAATCTTTG 57.625 36.000 0.00 0.00 0.00 2.77
255 256 6.597280 GGACTCTTTCTGACTGCATAATCTTT 59.403 38.462 0.00 0.00 0.00 2.52
256 257 6.112058 GGACTCTTTCTGACTGCATAATCTT 58.888 40.000 0.00 0.00 0.00 2.40
257 258 5.188555 TGGACTCTTTCTGACTGCATAATCT 59.811 40.000 0.00 0.00 0.00 2.40
258 259 5.293079 GTGGACTCTTTCTGACTGCATAATC 59.707 44.000 0.00 0.00 0.00 1.75
259 260 5.181748 GTGGACTCTTTCTGACTGCATAAT 58.818 41.667 0.00 0.00 0.00 1.28
266 267 0.318762 GGCGTGGACTCTTTCTGACT 59.681 55.000 0.00 0.00 0.00 3.41
296 297 1.209127 CCCGCACGGTCATTTTCAC 59.791 57.895 8.49 0.00 0.00 3.18
399 400 3.547813 CGTCAAACTTGTAGCATTGCACA 60.548 43.478 11.91 10.20 0.00 4.57
427 428 0.598065 AGAGGATTTGGTTGCGCAAC 59.402 50.000 38.71 38.71 40.45 4.17
485 489 2.675844 TCGTTGAAATGCTGGTATTCCG 59.324 45.455 0.00 0.00 36.30 4.30
489 493 3.378112 CCATGTCGTTGAAATGCTGGTAT 59.622 43.478 0.00 0.00 0.00 2.73
494 498 4.094887 GTGTATCCATGTCGTTGAAATGCT 59.905 41.667 0.00 0.00 0.00 3.79
516 520 2.438975 CGGCAGGGATGTGCATGT 60.439 61.111 0.00 0.00 45.93 3.21
554 558 0.401738 TGAGAGAAGCTTTGGGTGGG 59.598 55.000 0.00 0.00 0.00 4.61
555 559 2.276732 TTGAGAGAAGCTTTGGGTGG 57.723 50.000 0.00 0.00 0.00 4.61
556 560 3.551659 GCTTTTGAGAGAAGCTTTGGGTG 60.552 47.826 0.00 0.00 44.63 4.61
557 561 2.625314 GCTTTTGAGAGAAGCTTTGGGT 59.375 45.455 0.00 0.00 44.63 4.51
590 594 0.966179 TGATCCCCGGATGATGTACG 59.034 55.000 0.73 0.00 34.60 3.67
591 595 3.403038 CTTTGATCCCCGGATGATGTAC 58.597 50.000 0.73 0.00 34.60 2.90
592 596 2.371841 CCTTTGATCCCCGGATGATGTA 59.628 50.000 0.73 0.00 34.60 2.29
593 597 1.143684 CCTTTGATCCCCGGATGATGT 59.856 52.381 0.73 0.00 34.60 3.06
594 598 1.901591 CCTTTGATCCCCGGATGATG 58.098 55.000 0.73 0.00 34.60 3.07
598 602 1.533711 CTGCCTTTGATCCCCGGAT 59.466 57.895 0.73 0.00 37.59 4.18
622 630 1.595357 GACGGAGATTGGGAACGGT 59.405 57.895 0.00 0.00 0.00 4.83
639 647 0.822164 GCTAACTGCCTAGGTTCCGA 59.178 55.000 11.31 0.00 35.15 4.55
663 671 1.912371 GCGGGCTAGCTGTGAACAAC 61.912 60.000 15.72 0.00 0.00 3.32
664 672 1.671054 GCGGGCTAGCTGTGAACAA 60.671 57.895 15.72 0.00 0.00 2.83
665 673 2.047274 GCGGGCTAGCTGTGAACA 60.047 61.111 15.72 0.00 0.00 3.18
721 729 1.537135 GCACGAGGGATAGAGACAAGC 60.537 57.143 0.00 0.00 0.00 4.01
833 841 2.422597 CGAGGCGATTTATATGGGCAA 58.577 47.619 4.80 0.00 37.48 4.52
865 873 5.425577 TGCTTTGTATACGCAACAAGAAA 57.574 34.783 1.93 0.00 38.05 2.52
876 884 2.767505 CCCGGGAGATGCTTTGTATAC 58.232 52.381 18.48 0.00 0.00 1.47
928 936 5.007234 CGACGGAGAGAGCAAGATATATAGG 59.993 48.000 0.00 0.00 0.00 2.57
988 1008 1.146485 CCTCCATGCTCTCTGCCTG 59.854 63.158 0.00 0.00 42.00 4.85
989 1009 1.306825 ACCTCCATGCTCTCTGCCT 60.307 57.895 0.00 0.00 42.00 4.75
990 1010 1.145819 GACCTCCATGCTCTCTGCC 59.854 63.158 0.00 0.00 42.00 4.85
1394 1419 2.887568 GCTGACGACGCATCCCAG 60.888 66.667 0.00 0.00 0.00 4.45
1442 1467 4.388499 GCAAGAGGAACGGGCGGA 62.388 66.667 0.00 0.00 0.00 5.54
1542 1567 1.893801 CCCGGAGTCTTCTTGTACACT 59.106 52.381 0.73 0.00 0.00 3.55
1728 1753 1.078567 GAAGGTCTGCAGCCTCCTG 60.079 63.158 24.11 0.00 42.13 3.86
1800 1825 5.690997 TGTGATCCTGTATGTAGACGATC 57.309 43.478 0.00 0.00 0.00 3.69
2332 2357 2.430921 CCAGACGGTGAGCGTGAC 60.431 66.667 16.53 0.12 0.00 3.67
2455 2480 2.668212 CACGACCATGGCAACGGT 60.668 61.111 23.38 11.41 42.51 4.83
2536 2561 4.088762 CATGTGCACCACCGCGTC 62.089 66.667 15.69 0.00 32.73 5.19
2916 2941 4.507916 TCCTCCTCCGCCTCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
2943 2968 4.418392 CCTATCATTTGTGCTGTTCTTGC 58.582 43.478 0.00 0.00 0.00 4.01
3017 3042 4.341240 GAGATAAAGGCGCGCGCG 62.341 66.667 45.73 45.73 43.06 6.86
3071 3104 6.207213 GGTGTATCCATCGTTTCTACACTAG 58.793 44.000 10.04 0.00 41.08 2.57
3084 3117 2.930826 ATTGACCGGGTGTATCCATC 57.069 50.000 3.30 0.00 38.11 3.51
3086 3119 5.088026 TGATATATTGACCGGGTGTATCCA 58.912 41.667 3.30 0.00 38.11 3.41
3101 3134 9.895138 TGACCGAATGATGAATGATGATATATT 57.105 29.630 0.00 0.00 0.00 1.28
3245 3278 4.215399 TGCTGCTGTTCTTACATGTTTACC 59.785 41.667 2.30 0.00 32.86 2.85
3289 3322 6.280643 TGACATGTTCATCTCCTATTTACCG 58.719 40.000 0.00 0.00 0.00 4.02
3290 3323 9.950496 ATATGACATGTTCATCTCCTATTTACC 57.050 33.333 12.23 0.00 41.53 2.85
3294 3327 9.941325 GAAGATATGACATGTTCATCTCCTATT 57.059 33.333 14.51 7.03 41.53 1.73
3295 3328 8.538701 GGAAGATATGACATGTTCATCTCCTAT 58.461 37.037 14.51 4.97 41.53 2.57
3296 3329 7.510343 TGGAAGATATGACATGTTCATCTCCTA 59.490 37.037 14.51 2.33 41.53 2.94
3310 3343 3.007398 CCTGGCCTACTGGAAGATATGAC 59.993 52.174 3.32 0.00 40.42 3.06
3358 3394 0.462581 TCAATAAGCAGGCCGAGCAG 60.463 55.000 22.53 8.91 0.00 4.24
3377 3413 6.183360 GCTATTGACGAAAACTATGAAGCTGT 60.183 38.462 0.00 0.00 0.00 4.40
3394 3430 4.447054 CGATCTCTCCACATTGCTATTGAC 59.553 45.833 0.00 0.00 0.00 3.18
3407 3443 3.392947 AGACTACATCCTCGATCTCTCCA 59.607 47.826 0.00 0.00 0.00 3.86
3414 3450 5.050126 TCCACTTAGACTACATCCTCGAT 57.950 43.478 0.00 0.00 0.00 3.59
3429 3466 2.799017 TCGCTACTGTTCCTCCACTTA 58.201 47.619 0.00 0.00 0.00 2.24
3434 3471 2.094182 TGATGTTCGCTACTGTTCCTCC 60.094 50.000 0.00 0.00 0.00 4.30
3467 3504 3.801997 CCCTCCTCAGCCGCCAAT 61.802 66.667 0.00 0.00 0.00 3.16
3489 3531 2.222027 CCGTTCTTGCTTGGTCTCTTT 58.778 47.619 0.00 0.00 0.00 2.52
3540 3582 2.128771 AGGTCAAAGCACAACACACT 57.871 45.000 0.00 0.00 0.00 3.55
3560 3602 2.738521 GAGAGAAAGGCGCGTGCA 60.739 61.111 24.18 0.00 45.35 4.57
3685 5180 6.506500 AAGCATCAACTAATTCTTCAGGTG 57.493 37.500 0.00 0.00 0.00 4.00
3744 5239 8.867097 CCCCTGCTTGTAGTTAGTAGATATAAA 58.133 37.037 0.00 0.00 0.00 1.40
3764 5259 4.603535 ACCAACAGTGCCCCCTGC 62.604 66.667 0.00 0.00 41.77 4.85
3772 5267 3.111853 TCAGCTACAGAACCAACAGTG 57.888 47.619 0.00 0.00 0.00 3.66
3800 5295 4.457257 ACAAAGCCTAGATTTGAGAGCAAC 59.543 41.667 20.60 0.00 40.76 4.17
3833 5328 3.206150 ACACCAATTATGACATCGGCTC 58.794 45.455 0.00 0.00 0.00 4.70
3835 5330 4.370364 AAACACCAATTATGACATCGGC 57.630 40.909 0.00 0.00 0.00 5.54
3871 5367 7.851228 TGACAAGGAGACAATTATGACATACT 58.149 34.615 0.00 0.00 0.00 2.12
3877 5373 6.351371 GGAGACTGACAAGGAGACAATTATGA 60.351 42.308 0.00 0.00 0.00 2.15
3881 6946 3.906846 AGGAGACTGACAAGGAGACAATT 59.093 43.478 0.00 0.00 41.13 2.32
3890 6955 1.613925 TCACGGAAGGAGACTGACAAG 59.386 52.381 0.00 0.00 42.68 3.16
3891 6956 1.613925 CTCACGGAAGGAGACTGACAA 59.386 52.381 0.00 0.00 42.68 3.18
3894 6959 0.612174 CCCTCACGGAAGGAGACTGA 60.612 60.000 6.91 0.00 42.68 3.41
3941 7006 2.479566 TGGACAGTTTCATGAGCTCC 57.520 50.000 12.15 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.