Multiple sequence alignment - TraesCS5A01G345900

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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 TraesCS5A01G345900 chr5A 100.000 2423 0 0 1 2423 549204033 549201611 0.000000e+00 4475.0
1 TraesCS5A01G345900 chr5A 88.466 867 74 14 417 1280 549213324 549212481 0.000000e+00 1024.0
2 TraesCS5A01G345900 chr5A 88.304 855 75 15 1361 2205 549212478 549211639 0.000000e+00 1002.0
3 TraesCS5A01G345900 chr5A 91.276 619 44 7 1537 2148 9382791 9383406 0.000000e+00 835.0
4 TraesCS5A01G345900 chr5A 81.089 661 105 16 950 1599 549216629 549215978 5.980000e-141 510.0
5 TraesCS5A01G345900 chr5A 87.213 305 33 6 2123 2422 549209028 549208725 2.310000e-90 342.0
6 TraesCS5A01G345900 chr5A 91.391 151 7 4 1402 1549 9375886 9376033 4.080000e-48 202.0
7 TraesCS5A01G345900 chr5D 93.085 1851 97 13 583 2423 435266181 435264352 0.000000e+00 2680.0
8 TraesCS5A01G345900 chr5D 88.697 867 72 14 417 1280 435272326 435271483 0.000000e+00 1035.0
9 TraesCS5A01G345900 chr5D 88.785 856 69 17 1361 2205 435271480 435270641 0.000000e+00 1024.0
10 TraesCS5A01G345900 chr5D 79.666 659 104 18 951 1599 435269657 435269019 4.750000e-122 448.0
11 TraesCS5A01G345900 chr5B 89.915 1993 168 24 417 2390 528577815 528575837 0.000000e+00 2536.0
12 TraesCS5A01G345900 chr5B 88.681 1926 171 26 417 2324 528584543 528582647 0.000000e+00 2305.0
13 TraesCS5A01G345900 chr5B 81.873 662 96 20 951 1599 528581125 528580475 9.860000e-149 536.0
14 TraesCS5A01G345900 chr5B 82.623 610 88 15 1000 1599 528587882 528587281 7.680000e-145 523.0
15 TraesCS5A01G345900 chr3D 93.103 58 3 1 2112 2168 501478905 501478962 1.540000e-12 84.2
16 TraesCS5A01G345900 chr3D 93.103 58 3 1 2112 2168 501513169 501513226 1.540000e-12 84.2


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 TraesCS5A01G345900 chr5A 549201611 549204033 2422 True 4475.00 4475 100.00000 1 2423 1 chr5A.!!$R1 2422
1 TraesCS5A01G345900 chr5A 9382791 9383406 615 False 835.00 835 91.27600 1537 2148 1 chr5A.!!$F2 611
2 TraesCS5A01G345900 chr5A 549208725 549216629 7904 True 719.50 1024 86.26800 417 2422 4 chr5A.!!$R2 2005
3 TraesCS5A01G345900 chr5D 435264352 435272326 7974 True 1296.75 2680 87.55825 417 2423 4 chr5D.!!$R1 2006
4 TraesCS5A01G345900 chr5B 528575837 528587882 12045 True 1475.00 2536 85.77300 417 2390 4 chr5B.!!$R1 1973

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
143 144 0.185901 TCTGCTGAGGGCCAAAAGTT 59.814 50.0 6.18 0.0 40.92 2.66 F
1086 11009 0.613292 AGGAGACTGCAGACACCGAT 60.613 55.0 23.35 4.6 41.13 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 11287 0.662619 TGAAGGCAAACAACTCGCAG 59.337 50.0 0.0 0.0 0.0 5.18 R
2223 14862 1.923356 AACGTTCAAATGGGCAGGAT 58.077 45.0 0.0 0.0 0.0 3.24 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
20 21 3.826236 CCTTGCACAATCACAAGAGAG 57.174 47.619 4.39 0.00 44.89 3.20
21 22 3.144506 CCTTGCACAATCACAAGAGAGT 58.855 45.455 4.39 0.00 44.89 3.24
22 23 4.318332 CCTTGCACAATCACAAGAGAGTA 58.682 43.478 4.39 0.00 44.89 2.59
23 24 4.940046 CCTTGCACAATCACAAGAGAGTAT 59.060 41.667 4.39 0.00 44.89 2.12
24 25 6.108687 CCTTGCACAATCACAAGAGAGTATA 58.891 40.000 4.39 0.00 44.89 1.47
25 26 6.765036 CCTTGCACAATCACAAGAGAGTATAT 59.235 38.462 4.39 0.00 44.89 0.86
29 30 9.264719 TGCACAATCACAAGAGAGTATATATTG 57.735 33.333 0.00 0.00 0.00 1.90
57 58 8.283699 AGAGAGTATACTAAGAAAGTGTGACC 57.716 38.462 5.09 0.00 39.39 4.02
59 60 8.057536 AGAGTATACTAAGAAAGTGTGACCAG 57.942 38.462 5.09 0.00 39.39 4.00
60 61 7.889073 AGAGTATACTAAGAAAGTGTGACCAGA 59.111 37.037 5.09 0.00 39.39 3.86
61 62 8.596781 AGTATACTAAGAAAGTGTGACCAGAT 57.403 34.615 2.75 0.00 39.39 2.90
62 63 8.470805 AGTATACTAAGAAAGTGTGACCAGATG 58.529 37.037 2.75 0.00 39.39 2.90
63 64 4.899502 ACTAAGAAAGTGTGACCAGATGG 58.100 43.478 0.00 0.00 36.93 3.51
64 65 2.191128 AGAAAGTGTGACCAGATGGC 57.809 50.000 0.00 0.00 39.32 4.40
65 66 1.701847 AGAAAGTGTGACCAGATGGCT 59.298 47.619 0.00 0.00 39.32 4.75
68 69 3.788227 AAGTGTGACCAGATGGCTAAA 57.212 42.857 0.00 0.00 39.32 1.85
69 70 4.307032 AAGTGTGACCAGATGGCTAAAT 57.693 40.909 0.00 0.00 39.32 1.40
70 71 3.878778 AGTGTGACCAGATGGCTAAATC 58.121 45.455 0.00 0.00 39.32 2.17
72 73 4.018960 AGTGTGACCAGATGGCTAAATCTT 60.019 41.667 0.00 0.00 39.32 2.40
73 74 4.095483 GTGTGACCAGATGGCTAAATCTTG 59.905 45.833 0.00 0.00 39.32 3.02
75 76 5.045942 TGTGACCAGATGGCTAAATCTTGTA 60.046 40.000 0.00 0.00 33.84 2.41
76 77 5.294552 GTGACCAGATGGCTAAATCTTGTAC 59.705 44.000 0.00 0.00 33.84 2.90
78 79 5.815581 ACCAGATGGCTAAATCTTGTACAA 58.184 37.500 8.28 8.28 39.32 2.41
79 80 5.648092 ACCAGATGGCTAAATCTTGTACAAC 59.352 40.000 3.59 0.00 39.32 3.32
81 82 7.047891 CCAGATGGCTAAATCTTGTACAACTA 58.952 38.462 3.59 0.00 34.60 2.24
82 83 7.716998 CCAGATGGCTAAATCTTGTACAACTAT 59.283 37.037 3.59 0.00 34.60 2.12
83 84 9.113838 CAGATGGCTAAATCTTGTACAACTATT 57.886 33.333 3.59 5.01 34.60 1.73
84 85 9.113838 AGATGGCTAAATCTTGTACAACTATTG 57.886 33.333 3.59 0.00 32.88 1.90
85 86 7.083875 TGGCTAAATCTTGTACAACTATTGC 57.916 36.000 3.59 8.07 0.00 3.56
86 87 6.094881 TGGCTAAATCTTGTACAACTATTGCC 59.905 38.462 20.54 20.54 0.00 4.52
87 88 6.318900 GGCTAAATCTTGTACAACTATTGCCT 59.681 38.462 20.31 8.56 0.00 4.75
88 89 7.189512 GCTAAATCTTGTACAACTATTGCCTG 58.810 38.462 3.59 0.00 0.00 4.85
89 90 5.567138 AATCTTGTACAACTATTGCCTGC 57.433 39.130 3.59 0.00 0.00 4.85
90 91 4.014569 TCTTGTACAACTATTGCCTGCA 57.985 40.909 3.59 0.00 0.00 4.41
93 94 2.039746 TGTACAACTATTGCCTGCAGGT 59.960 45.455 32.81 16.84 37.57 4.00
95 96 3.652057 ACAACTATTGCCTGCAGGTAT 57.348 42.857 32.81 26.18 37.57 2.73
96 97 3.968265 ACAACTATTGCCTGCAGGTATT 58.032 40.909 32.81 25.85 37.57 1.89
97 98 3.947834 ACAACTATTGCCTGCAGGTATTC 59.052 43.478 32.81 17.25 37.57 1.75
100 101 1.668419 ATTGCCTGCAGGTATTCGAC 58.332 50.000 32.81 15.39 37.57 4.20
101 102 0.323302 TTGCCTGCAGGTATTCGACA 59.677 50.000 32.81 17.88 37.57 4.35
102 103 0.391130 TGCCTGCAGGTATTCGACAC 60.391 55.000 32.81 13.92 37.57 3.67
103 104 1.421410 GCCTGCAGGTATTCGACACG 61.421 60.000 32.81 4.20 37.57 4.49
106 107 1.252215 TGCAGGTATTCGACACGGGA 61.252 55.000 0.00 0.00 0.00 5.14
108 109 1.636988 CAGGTATTCGACACGGGAAC 58.363 55.000 0.00 0.00 0.00 3.62
120 121 2.874751 GGGAACGTGGCATTTCCG 59.125 61.111 19.13 8.81 42.10 4.30
124 125 1.369625 GAACGTGGCATTTCCGAGAT 58.630 50.000 2.05 0.00 37.80 2.75
125 126 1.327764 GAACGTGGCATTTCCGAGATC 59.672 52.381 2.05 0.00 37.80 2.75
126 127 0.537188 ACGTGGCATTTCCGAGATCT 59.463 50.000 0.00 0.00 37.80 2.75
127 128 0.933097 CGTGGCATTTCCGAGATCTG 59.067 55.000 0.00 0.00 37.80 2.90
128 129 0.659957 GTGGCATTTCCGAGATCTGC 59.340 55.000 0.00 0.00 37.80 4.26
129 130 0.543277 TGGCATTTCCGAGATCTGCT 59.457 50.000 0.00 0.00 37.80 4.24
131 132 1.473965 GGCATTTCCGAGATCTGCTGA 60.474 52.381 0.00 0.00 33.43 4.26
132 133 1.865970 GCATTTCCGAGATCTGCTGAG 59.134 52.381 0.00 0.00 0.00 3.35
133 134 2.481854 CATTTCCGAGATCTGCTGAGG 58.518 52.381 0.00 0.00 0.00 3.86
134 135 0.826715 TTTCCGAGATCTGCTGAGGG 59.173 55.000 0.00 0.00 0.00 4.30
135 136 1.680522 TTCCGAGATCTGCTGAGGGC 61.681 60.000 0.00 0.00 42.22 5.19
136 137 2.420890 CGAGATCTGCTGAGGGCC 59.579 66.667 0.00 0.00 40.92 5.80
137 138 2.429767 CGAGATCTGCTGAGGGCCA 61.430 63.158 6.18 0.00 40.92 5.36
138 139 1.910722 GAGATCTGCTGAGGGCCAA 59.089 57.895 6.18 0.00 40.92 4.52
139 140 0.254178 GAGATCTGCTGAGGGCCAAA 59.746 55.000 6.18 0.00 40.92 3.28
141 142 1.101331 GATCTGCTGAGGGCCAAAAG 58.899 55.000 6.18 0.30 40.92 2.27
142 143 0.407139 ATCTGCTGAGGGCCAAAAGT 59.593 50.000 6.18 0.00 40.92 2.66
143 144 0.185901 TCTGCTGAGGGCCAAAAGTT 59.814 50.000 6.18 0.00 40.92 2.66
144 145 1.423541 TCTGCTGAGGGCCAAAAGTTA 59.576 47.619 6.18 0.00 40.92 2.24
145 146 1.541588 CTGCTGAGGGCCAAAAGTTAC 59.458 52.381 6.18 0.00 40.92 2.50
146 147 1.144913 TGCTGAGGGCCAAAAGTTACT 59.855 47.619 6.18 0.00 40.92 2.24
147 148 1.813178 GCTGAGGGCCAAAAGTTACTC 59.187 52.381 6.18 0.00 34.27 2.59
148 149 2.553247 GCTGAGGGCCAAAAGTTACTCT 60.553 50.000 6.18 0.00 34.27 3.24
149 150 3.756117 CTGAGGGCCAAAAGTTACTCTT 58.244 45.455 6.18 0.00 38.10 2.85
150 151 3.486383 TGAGGGCCAAAAGTTACTCTTG 58.514 45.455 6.18 0.00 36.40 3.02
152 153 1.960689 GGGCCAAAAGTTACTCTTGCA 59.039 47.619 4.39 0.00 36.40 4.08
154 155 3.006859 GGGCCAAAAGTTACTCTTGCAAT 59.993 43.478 4.39 0.00 36.40 3.56
155 156 3.989817 GGCCAAAAGTTACTCTTGCAATG 59.010 43.478 0.00 0.00 36.40 2.82
157 158 5.049828 GCCAAAAGTTACTCTTGCAATGTT 58.950 37.500 0.00 0.00 36.40 2.71
161 162 7.704472 CCAAAAGTTACTCTTGCAATGTTTGTA 59.296 33.333 0.00 0.00 36.40 2.41
162 163 9.081997 CAAAAGTTACTCTTGCAATGTTTGTAA 57.918 29.630 0.00 3.07 36.40 2.41
168 169 2.437200 TGCAATGTTTGTAAGCTGCC 57.563 45.000 0.00 0.00 0.00 4.85
169 170 1.685517 TGCAATGTTTGTAAGCTGCCA 59.314 42.857 0.00 0.00 0.00 4.92
171 172 2.288395 GCAATGTTTGTAAGCTGCCAGT 60.288 45.455 0.00 0.00 0.00 4.00
172 173 3.057596 GCAATGTTTGTAAGCTGCCAGTA 60.058 43.478 0.00 0.00 0.00 2.74
173 174 4.380867 GCAATGTTTGTAAGCTGCCAGTAT 60.381 41.667 0.00 0.00 0.00 2.12
175 176 4.286297 TGTTTGTAAGCTGCCAGTATCT 57.714 40.909 0.00 0.00 0.00 1.98
179 180 3.365472 TGTAAGCTGCCAGTATCTCTGA 58.635 45.455 0.00 0.00 46.27 3.27
180 181 3.769300 TGTAAGCTGCCAGTATCTCTGAA 59.231 43.478 0.00 0.00 46.27 3.02
183 184 2.368221 AGCTGCCAGTATCTCTGAATCC 59.632 50.000 0.00 0.00 46.27 3.01
185 186 3.181456 GCTGCCAGTATCTCTGAATCCTT 60.181 47.826 0.00 0.00 46.27 3.36
187 188 5.028549 TGCCAGTATCTCTGAATCCTTTC 57.971 43.478 0.00 0.00 46.27 2.62
188 189 4.471025 TGCCAGTATCTCTGAATCCTTTCA 59.529 41.667 0.00 0.00 46.27 2.69
198 199 3.831323 TGAATCCTTTCAGCTTTCCACA 58.169 40.909 0.00 0.00 36.94 4.17
199 200 4.410099 TGAATCCTTTCAGCTTTCCACAT 58.590 39.130 0.00 0.00 36.94 3.21
202 203 4.365514 TCCTTTCAGCTTTCCACATGTA 57.634 40.909 0.00 0.00 0.00 2.29
204 205 6.061022 TCCTTTCAGCTTTCCACATGTATA 57.939 37.500 0.00 0.00 0.00 1.47
205 206 6.480763 TCCTTTCAGCTTTCCACATGTATAA 58.519 36.000 0.00 0.00 0.00 0.98
209 210 6.741992 TCAGCTTTCCACATGTATAAGTTG 57.258 37.500 17.14 17.14 0.00 3.16
210 211 6.472016 TCAGCTTTCCACATGTATAAGTTGA 58.528 36.000 19.74 19.74 34.92 3.18
211 212 7.112122 TCAGCTTTCCACATGTATAAGTTGAT 58.888 34.615 19.74 3.38 33.21 2.57
212 213 7.611467 TCAGCTTTCCACATGTATAAGTTGATT 59.389 33.333 19.74 2.70 33.21 2.57
213 214 8.246180 CAGCTTTCCACATGTATAAGTTGATTT 58.754 33.333 17.83 0.03 31.33 2.17
221 222 9.708222 CACATGTATAAGTTGATTTTAGACTGC 57.292 33.333 0.00 0.00 0.00 4.40
222 223 9.672673 ACATGTATAAGTTGATTTTAGACTGCT 57.327 29.630 0.00 0.00 0.00 4.24
256 257 6.350906 TCATATTCTGTCATGCAATGTCTCA 58.649 36.000 0.00 0.00 46.80 3.27
257 258 6.824704 TCATATTCTGTCATGCAATGTCTCAA 59.175 34.615 0.00 0.00 46.80 3.02
260 261 4.392047 TCTGTCATGCAATGTCTCAAAGT 58.608 39.130 0.00 0.00 46.80 2.66
262 263 5.640783 TCTGTCATGCAATGTCTCAAAGTAG 59.359 40.000 0.00 0.00 46.80 2.57
264 265 4.937620 GTCATGCAATGTCTCAAAGTAGGA 59.062 41.667 0.00 0.00 46.80 2.94
265 266 5.587844 GTCATGCAATGTCTCAAAGTAGGAT 59.412 40.000 0.00 0.00 46.80 3.24
266 267 5.587443 TCATGCAATGTCTCAAAGTAGGATG 59.413 40.000 0.00 0.00 46.80 3.51
267 268 4.910195 TGCAATGTCTCAAAGTAGGATGT 58.090 39.130 0.00 0.00 0.00 3.06
269 270 5.874810 TGCAATGTCTCAAAGTAGGATGTAC 59.125 40.000 0.00 0.00 0.00 2.90
270 271 5.294552 GCAATGTCTCAAAGTAGGATGTACC 59.705 44.000 0.00 0.00 39.35 3.34
281 282 2.024176 GGATGTACCTGTGATTGCGT 57.976 50.000 0.00 0.00 35.41 5.24
284 285 3.190535 GGATGTACCTGTGATTGCGTTTT 59.809 43.478 0.00 0.00 35.41 2.43
285 286 4.393680 GGATGTACCTGTGATTGCGTTTTA 59.606 41.667 0.00 0.00 35.41 1.52
286 287 5.106475 GGATGTACCTGTGATTGCGTTTTAA 60.106 40.000 0.00 0.00 35.41 1.52
289 290 7.618502 TGTACCTGTGATTGCGTTTTAATAT 57.381 32.000 0.00 0.00 0.00 1.28
290 291 7.468441 TGTACCTGTGATTGCGTTTTAATATG 58.532 34.615 0.00 0.00 0.00 1.78
294 295 7.147915 ACCTGTGATTGCGTTTTAATATGGATT 60.148 33.333 0.00 0.00 0.00 3.01
296 297 7.542890 TGTGATTGCGTTTTAATATGGATTGT 58.457 30.769 0.00 0.00 0.00 2.71
297 298 7.700234 TGTGATTGCGTTTTAATATGGATTGTC 59.300 33.333 0.00 0.00 0.00 3.18
298 299 7.915397 GTGATTGCGTTTTAATATGGATTGTCT 59.085 33.333 0.00 0.00 0.00 3.41
299 300 8.465999 TGATTGCGTTTTAATATGGATTGTCTT 58.534 29.630 0.00 0.00 0.00 3.01
300 301 9.301153 GATTGCGTTTTAATATGGATTGTCTTT 57.699 29.630 0.00 0.00 0.00 2.52
301 302 8.682128 TTGCGTTTTAATATGGATTGTCTTTC 57.318 30.769 0.00 0.00 0.00 2.62
302 303 8.050778 TGCGTTTTAATATGGATTGTCTTTCT 57.949 30.769 0.00 0.00 0.00 2.52
303 304 8.519526 TGCGTTTTAATATGGATTGTCTTTCTT 58.480 29.630 0.00 0.00 0.00 2.52
304 305 8.798153 GCGTTTTAATATGGATTGTCTTTCTTG 58.202 33.333 0.00 0.00 0.00 3.02
305 306 9.840427 CGTTTTAATATGGATTGTCTTTCTTGT 57.160 29.630 0.00 0.00 0.00 3.16
310 311 3.554934 TGGATTGTCTTTCTTGTGTGCT 58.445 40.909 0.00 0.00 0.00 4.40
311 312 3.316029 TGGATTGTCTTTCTTGTGTGCTG 59.684 43.478 0.00 0.00 0.00 4.41
315 316 4.355543 TGTCTTTCTTGTGTGCTGTTTC 57.644 40.909 0.00 0.00 0.00 2.78
316 317 4.009675 TGTCTTTCTTGTGTGCTGTTTCT 58.990 39.130 0.00 0.00 0.00 2.52
318 319 5.645929 TGTCTTTCTTGTGTGCTGTTTCTTA 59.354 36.000 0.00 0.00 0.00 2.10
319 320 6.183360 TGTCTTTCTTGTGTGCTGTTTCTTAG 60.183 38.462 0.00 0.00 0.00 2.18
320 321 6.037172 GTCTTTCTTGTGTGCTGTTTCTTAGA 59.963 38.462 0.00 0.00 0.00 2.10
321 322 5.991328 TTCTTGTGTGCTGTTTCTTAGAG 57.009 39.130 0.00 0.00 0.00 2.43
323 324 4.100963 TCTTGTGTGCTGTTTCTTAGAGGA 59.899 41.667 0.00 0.00 0.00 3.71
324 325 4.623932 TGTGTGCTGTTTCTTAGAGGAT 57.376 40.909 0.00 0.00 0.00 3.24
325 326 4.569943 TGTGTGCTGTTTCTTAGAGGATC 58.430 43.478 0.00 0.00 0.00 3.36
340 341 4.088823 GAGGATCTGATTTTGCACACAC 57.911 45.455 0.00 0.00 0.00 3.82
341 342 3.489355 AGGATCTGATTTTGCACACACA 58.511 40.909 0.00 0.00 0.00 3.72
342 343 3.504906 AGGATCTGATTTTGCACACACAG 59.495 43.478 0.00 0.00 0.00 3.66
343 344 2.780065 TCTGATTTTGCACACACAGC 57.220 45.000 0.00 0.00 0.00 4.40
345 346 2.033675 TCTGATTTTGCACACACAGCTG 59.966 45.455 13.48 13.48 0.00 4.24
346 347 2.022934 TGATTTTGCACACACAGCTGA 58.977 42.857 23.35 0.00 0.00 4.26
347 348 2.426381 TGATTTTGCACACACAGCTGAA 59.574 40.909 23.35 0.19 0.00 3.02
348 349 3.068448 TGATTTTGCACACACAGCTGAAT 59.932 39.130 23.35 5.92 0.00 2.57
349 350 2.495409 TTTGCACACACAGCTGAATG 57.505 45.000 23.35 19.43 0.00 2.67
350 351 1.677942 TTGCACACACAGCTGAATGA 58.322 45.000 23.35 0.00 0.00 2.57
351 352 1.900245 TGCACACACAGCTGAATGAT 58.100 45.000 23.35 6.06 0.00 2.45
352 353 3.056588 TGCACACACAGCTGAATGATA 57.943 42.857 23.35 7.02 0.00 2.15
353 354 3.613030 TGCACACACAGCTGAATGATAT 58.387 40.909 23.35 0.00 0.00 1.63
355 356 5.370679 TGCACACACAGCTGAATGATATAT 58.629 37.500 23.35 0.00 0.00 0.86
357 358 6.991531 TGCACACACAGCTGAATGATATATAA 59.008 34.615 23.35 0.60 0.00 0.98
358 359 7.172019 TGCACACACAGCTGAATGATATATAAG 59.828 37.037 23.35 4.92 0.00 1.73
359 360 7.516481 CACACACAGCTGAATGATATATAAGC 58.484 38.462 23.35 0.00 0.00 3.09
360 361 7.172019 CACACACAGCTGAATGATATATAAGCA 59.828 37.037 23.35 0.00 33.08 3.91
361 362 7.716560 ACACACAGCTGAATGATATATAAGCAA 59.283 33.333 23.35 0.00 33.08 3.91
362 363 8.727910 CACACAGCTGAATGATATATAAGCAAT 58.272 33.333 23.35 0.00 33.08 3.56
380 381 7.524717 AAGCAATTAGGTAACACTTTGACAT 57.475 32.000 0.00 0.00 41.41 3.06
381 382 7.145932 AGCAATTAGGTAACACTTTGACATC 57.854 36.000 0.00 0.00 41.41 3.06
383 384 6.072175 GCAATTAGGTAACACTTTGACATCCA 60.072 38.462 0.00 0.00 41.41 3.41
384 385 7.523052 GCAATTAGGTAACACTTTGACATCCAA 60.523 37.037 0.00 0.00 41.41 3.53
386 387 9.747898 AATTAGGTAACACTTTGACATCCAATA 57.252 29.630 0.00 0.00 41.41 1.90
387 388 8.786826 TTAGGTAACACTTTGACATCCAATAG 57.213 34.615 0.00 0.00 41.41 1.73
388 389 7.016153 AGGTAACACTTTGACATCCAATAGA 57.984 36.000 0.00 0.00 41.41 1.98
389 390 7.633789 AGGTAACACTTTGACATCCAATAGAT 58.366 34.615 0.00 0.00 41.41 1.98
405 406 7.526041 TCCAATAGATGCACTATATTTTGGGT 58.474 34.615 17.20 0.40 40.49 4.51
408 409 9.725019 CAATAGATGCACTATATTTTGGGTCTA 57.275 33.333 8.59 0.00 40.49 2.59
410 411 6.773638 AGATGCACTATATTTTGGGTCTAGG 58.226 40.000 0.00 0.00 0.00 3.02
411 412 5.968676 TGCACTATATTTTGGGTCTAGGT 57.031 39.130 0.00 0.00 0.00 3.08
412 413 5.925509 TGCACTATATTTTGGGTCTAGGTC 58.074 41.667 0.00 0.00 0.00 3.85
413 414 5.665812 TGCACTATATTTTGGGTCTAGGTCT 59.334 40.000 0.00 0.00 0.00 3.85
414 415 6.183360 TGCACTATATTTTGGGTCTAGGTCTC 60.183 42.308 0.00 0.00 0.00 3.36
415 416 6.183360 GCACTATATTTTGGGTCTAGGTCTCA 60.183 42.308 0.00 0.00 0.00 3.27
417 418 8.432805 CACTATATTTTGGGTCTAGGTCTCATT 58.567 37.037 0.00 0.00 0.00 2.57
418 419 9.004231 ACTATATTTTGGGTCTAGGTCTCATTT 57.996 33.333 0.00 0.00 0.00 2.32
419 420 9.853177 CTATATTTTGGGTCTAGGTCTCATTTT 57.147 33.333 0.00 0.00 0.00 1.82
436 3452 9.567848 GTCTCATTTTAAGTTGAAACAAGACAA 57.432 29.630 20.52 0.00 34.40 3.18
437 3453 9.787532 TCTCATTTTAAGTTGAAACAAGACAAG 57.212 29.630 0.00 0.00 0.00 3.16
438 3454 9.573133 CTCATTTTAAGTTGAAACAAGACAAGT 57.427 29.630 0.00 0.00 0.00 3.16
443 3459 8.850454 TTAAGTTGAAACAAGACAAGTAATGC 57.150 30.769 0.00 0.00 0.00 3.56
453 3469 2.488153 GACAAGTAATGCCCACAGGAAC 59.512 50.000 0.00 0.00 33.47 3.62
459 3475 1.843368 ATGCCCACAGGAACATGAAG 58.157 50.000 0.00 0.00 33.47 3.02
476 3492 2.087646 GAAGACCAGGAAACATGGCTC 58.912 52.381 0.00 0.00 41.87 4.70
492 3508 2.029739 TGGCTCGAACGAAGTAATCACA 60.030 45.455 0.00 0.00 45.00 3.58
497 3513 3.849708 TCGAACGAAGTAATCACATGACG 59.150 43.478 0.00 0.00 45.00 4.35
504 3521 1.731709 GTAATCACATGACGCACTGCA 59.268 47.619 0.00 0.00 0.00 4.41
550 3567 5.086104 AGTTGCTTGTACTGAATACCGAT 57.914 39.130 0.00 0.00 32.16 4.18
567 3585 2.158900 CCGATATGTTCAGGCCAGAAGT 60.159 50.000 11.39 5.92 0.00 3.01
572 3590 6.071896 CGATATGTTCAGGCCAGAAGTATAGA 60.072 42.308 11.39 0.00 0.00 1.98
573 3591 4.737855 TGTTCAGGCCAGAAGTATAGAC 57.262 45.455 11.39 0.00 0.00 2.59
574 3592 4.093743 TGTTCAGGCCAGAAGTATAGACA 58.906 43.478 11.39 1.48 0.00 3.41
577 3595 3.701542 TCAGGCCAGAAGTATAGACAGTG 59.298 47.826 5.01 0.00 0.00 3.66
607 3625 2.702478 CCATGGGCTCTATCAGTCTTCA 59.298 50.000 2.85 0.00 0.00 3.02
614 3632 3.674682 GCTCTATCAGTCTTCACACGCTT 60.675 47.826 0.00 0.00 0.00 4.68
649 3667 1.070604 ATGGTGATATGGAGGGCTGG 58.929 55.000 0.00 0.00 0.00 4.85
688 3706 2.812011 AGCTTTTCTAACCATTTCGCGT 59.188 40.909 5.77 0.00 0.00 6.01
699 3717 1.588404 CATTTCGCGTGCCAGTACTAG 59.412 52.381 5.77 0.00 0.00 2.57
754 3772 0.620030 TCACATGCCATACAGCTGGT 59.380 50.000 19.93 6.35 38.63 4.00
778 3796 9.727627 GGTCTCATCAAAATCTTATCAAATCAC 57.272 33.333 0.00 0.00 0.00 3.06
814 3832 4.209703 GCATTGCACATGCCATGTTTATAC 59.790 41.667 7.80 0.00 43.60 1.47
824 3842 4.018870 TGCCATGTTTATACCCTTGTCTCA 60.019 41.667 0.00 0.00 0.00 3.27
850 3868 1.224069 CCTGTCCACACTTGTGCTCG 61.224 60.000 3.68 0.00 44.34 5.03
855 3873 1.291877 CCACACTTGTGCTCGTAGCC 61.292 60.000 3.68 0.00 44.34 3.93
928 3949 1.352017 TCACACAGCCACTTCATCCAT 59.648 47.619 0.00 0.00 0.00 3.41
932 3953 3.021695 CACAGCCACTTCATCCATGAAT 58.978 45.455 2.45 0.00 44.92 2.57
986 4007 7.219484 TGAGAAAAAGAGCATTTTAGGAAGG 57.781 36.000 0.69 0.00 32.85 3.46
998 4019 4.993705 TTTAGGAAGGACACCACAGAAT 57.006 40.909 0.00 0.00 0.00 2.40
1086 11009 0.613292 AGGAGACTGCAGACACCGAT 60.613 55.000 23.35 4.60 41.13 4.18
1230 11153 3.008485 GGATGTCTCAAGAGGAGTTTGGT 59.992 47.826 0.00 0.00 44.40 3.67
1242 11165 1.002792 GAGTTTGGTTTCACCTGCGAC 60.003 52.381 0.00 0.00 39.58 5.19
1276 11199 1.748122 CCCTGTGATGCCTCTGTGC 60.748 63.158 0.00 0.00 0.00 4.57
1308 11231 6.950842 TGTGATGTGTTTGATTAGGAGAGAT 58.049 36.000 0.00 0.00 0.00 2.75
1332 11255 0.891373 CTGAAGAGGTCGAGAAGGCA 59.109 55.000 0.00 0.00 0.00 4.75
1364 11287 2.555199 CATAGTGAGGCCTTGCTACAC 58.445 52.381 6.77 10.40 35.96 2.90
1380 11303 0.748005 ACACTGCGAGTTGTTTGCCT 60.748 50.000 0.00 0.00 35.11 4.75
1381 11304 0.381801 CACTGCGAGTTGTTTGCCTT 59.618 50.000 0.00 0.00 35.11 4.35
1482 11406 4.701651 TCAGGACAATAGGAAATGCAACAG 59.298 41.667 0.00 0.00 0.00 3.16
1752 11682 6.218019 CCAAATTCTCAAGCACTGATGAAAA 58.782 36.000 0.00 0.00 32.14 2.29
1836 11768 3.244561 ACTGGAACCAACCACTGTATGAG 60.245 47.826 0.00 0.00 35.91 2.90
1851 11791 1.826385 ATGAGCCTCCTTTTGTTCCG 58.174 50.000 0.00 0.00 0.00 4.30
2107 12049 6.946009 AGCTACTCTCCTCATAGAATCCTAAC 59.054 42.308 0.00 0.00 0.00 2.34
2110 12052 6.001460 ACTCTCCTCATAGAATCCTAACGAG 58.999 44.000 0.00 0.00 32.51 4.18
2138 12080 1.816074 TTTTGTACTGGATCGGGCAC 58.184 50.000 0.00 0.00 0.00 5.01
2161 12104 7.502561 GCACTCTATTAGTAAACCCATTTGGAT 59.497 37.037 0.00 0.00 35.76 3.41
2233 14872 4.870636 TGAGAAACATTTATCCTGCCCAT 58.129 39.130 0.00 0.00 0.00 4.00
2278 14918 1.014564 GTCTGAGGCCACGTAACTGC 61.015 60.000 5.01 0.00 0.00 4.40
2324 14964 4.058817 CTGTTCAAGTCCTAAAAGCGACT 58.941 43.478 0.00 0.00 41.10 4.18
2363 15003 6.765036 CGCAGAAATATATATGCTGGAGGAAT 59.235 38.462 19.54 0.00 36.52 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.783090 ATATACTCTCTTGTGATTGTGCAAG 57.217 36.000 0.00 0.00 42.32 4.01
4 5 9.481340 TCAATATATACTCTCTTGTGATTGTGC 57.519 33.333 0.00 0.00 0.00 4.57
31 32 9.393512 GGTCACACTTTCTTAGTATACTCTCTA 57.606 37.037 9.12 0.00 34.56 2.43
32 33 7.889073 TGGTCACACTTTCTTAGTATACTCTCT 59.111 37.037 9.12 0.00 34.56 3.10
33 34 8.053026 TGGTCACACTTTCTTAGTATACTCTC 57.947 38.462 9.12 0.00 34.56 3.20
35 36 8.053026 TCTGGTCACACTTTCTTAGTATACTC 57.947 38.462 9.12 0.00 34.56 2.59
36 37 8.470805 CATCTGGTCACACTTTCTTAGTATACT 58.529 37.037 10.87 10.87 34.56 2.12
37 38 7.707035 CCATCTGGTCACACTTTCTTAGTATAC 59.293 40.741 0.00 0.00 34.56 1.47
38 39 7.632898 GCCATCTGGTCACACTTTCTTAGTATA 60.633 40.741 0.00 0.00 34.46 1.47
39 40 6.644347 CCATCTGGTCACACTTTCTTAGTAT 58.356 40.000 0.00 0.00 34.56 2.12
40 41 5.568825 GCCATCTGGTCACACTTTCTTAGTA 60.569 44.000 0.00 0.00 34.46 1.82
41 42 4.804261 GCCATCTGGTCACACTTTCTTAGT 60.804 45.833 0.00 0.00 35.87 2.24
42 43 3.686726 GCCATCTGGTCACACTTTCTTAG 59.313 47.826 0.00 0.00 37.57 2.18
46 47 2.191128 AGCCATCTGGTCACACTTTC 57.809 50.000 0.00 0.00 37.57 2.62
48 49 3.788227 TTTAGCCATCTGGTCACACTT 57.212 42.857 0.00 0.00 37.57 3.16
49 50 3.521126 AGATTTAGCCATCTGGTCACACT 59.479 43.478 0.00 0.00 37.57 3.55
50 51 3.878778 AGATTTAGCCATCTGGTCACAC 58.121 45.455 0.00 0.00 37.57 3.82
51 52 4.263462 ACAAGATTTAGCCATCTGGTCACA 60.263 41.667 0.00 0.00 32.66 3.58
52 53 4.265073 ACAAGATTTAGCCATCTGGTCAC 58.735 43.478 0.00 0.00 32.66 3.67
53 54 4.574674 ACAAGATTTAGCCATCTGGTCA 57.425 40.909 0.00 0.00 32.66 4.02
54 55 5.428253 TGTACAAGATTTAGCCATCTGGTC 58.572 41.667 0.00 0.00 38.29 4.02
55 56 5.435686 TGTACAAGATTTAGCCATCTGGT 57.564 39.130 0.00 4.13 40.16 4.00
57 58 6.992063 AGTTGTACAAGATTTAGCCATCTG 57.008 37.500 8.98 0.00 33.52 2.90
59 60 7.857885 GCAATAGTTGTACAAGATTTAGCCATC 59.142 37.037 8.98 0.00 0.00 3.51
60 61 7.201821 GGCAATAGTTGTACAAGATTTAGCCAT 60.202 37.037 23.62 3.74 35.15 4.40
61 62 6.094881 GGCAATAGTTGTACAAGATTTAGCCA 59.905 38.462 23.62 2.01 35.15 4.75
62 63 6.318900 AGGCAATAGTTGTACAAGATTTAGCC 59.681 38.462 22.40 22.40 35.26 3.93
63 64 7.189512 CAGGCAATAGTTGTACAAGATTTAGC 58.810 38.462 8.98 11.44 0.00 3.09
64 65 7.148255 TGCAGGCAATAGTTGTACAAGATTTAG 60.148 37.037 8.98 2.97 0.00 1.85
65 66 6.657117 TGCAGGCAATAGTTGTACAAGATTTA 59.343 34.615 8.98 0.34 0.00 1.40
68 69 4.588899 TGCAGGCAATAGTTGTACAAGAT 58.411 39.130 8.98 2.74 0.00 2.40
69 70 4.002982 CTGCAGGCAATAGTTGTACAAGA 58.997 43.478 8.98 0.04 0.00 3.02
70 71 3.127548 CCTGCAGGCAATAGTTGTACAAG 59.872 47.826 22.33 0.00 0.00 3.16
72 73 2.039746 ACCTGCAGGCAATAGTTGTACA 59.960 45.455 33.06 0.00 39.32 2.90
73 74 2.711542 ACCTGCAGGCAATAGTTGTAC 58.288 47.619 33.06 0.00 39.32 2.90
75 76 3.652057 ATACCTGCAGGCAATAGTTGT 57.348 42.857 33.06 12.32 39.32 3.32
76 77 3.002656 CGAATACCTGCAGGCAATAGTTG 59.997 47.826 33.06 16.27 39.32 3.16
78 79 2.434336 TCGAATACCTGCAGGCAATAGT 59.566 45.455 33.06 16.88 39.32 2.12
79 80 2.802816 GTCGAATACCTGCAGGCAATAG 59.197 50.000 33.06 20.50 39.32 1.73
81 82 1.065491 TGTCGAATACCTGCAGGCAAT 60.065 47.619 33.06 22.73 39.32 3.56
82 83 0.323302 TGTCGAATACCTGCAGGCAA 59.677 50.000 33.06 21.42 39.32 4.52
83 84 0.391130 GTGTCGAATACCTGCAGGCA 60.391 55.000 33.06 21.93 39.32 4.75
84 85 1.421410 CGTGTCGAATACCTGCAGGC 61.421 60.000 33.06 15.27 39.32 4.85
85 86 0.806102 CCGTGTCGAATACCTGCAGG 60.806 60.000 31.60 31.60 42.17 4.85
86 87 0.806102 CCCGTGTCGAATACCTGCAG 60.806 60.000 6.78 6.78 0.00 4.41
87 88 1.216977 CCCGTGTCGAATACCTGCA 59.783 57.895 0.00 0.00 0.00 4.41
88 89 0.108520 TTCCCGTGTCGAATACCTGC 60.109 55.000 0.00 0.00 0.00 4.85
89 90 1.636988 GTTCCCGTGTCGAATACCTG 58.363 55.000 0.00 0.00 0.00 4.00
90 91 0.171903 CGTTCCCGTGTCGAATACCT 59.828 55.000 0.00 0.00 0.00 3.08
102 103 2.874751 GGAAATGCCACGTTCCCG 59.125 61.111 0.00 0.00 37.87 5.14
103 104 1.644786 CTCGGAAATGCCACGTTCCC 61.645 60.000 3.94 0.00 40.27 3.97
106 107 1.066143 AGATCTCGGAAATGCCACGTT 60.066 47.619 0.00 0.00 35.94 3.99
108 109 0.933097 CAGATCTCGGAAATGCCACG 59.067 55.000 0.00 0.00 35.94 4.94
109 110 0.659957 GCAGATCTCGGAAATGCCAC 59.340 55.000 0.00 0.00 35.94 5.01
113 114 2.481854 CCTCAGCAGATCTCGGAAATG 58.518 52.381 0.00 0.00 0.00 2.32
114 115 1.415659 CCCTCAGCAGATCTCGGAAAT 59.584 52.381 0.00 0.00 0.00 2.17
115 116 0.826715 CCCTCAGCAGATCTCGGAAA 59.173 55.000 0.00 0.00 0.00 3.13
116 117 1.680522 GCCCTCAGCAGATCTCGGAA 61.681 60.000 0.00 0.00 42.97 4.30
117 118 2.130426 GCCCTCAGCAGATCTCGGA 61.130 63.158 0.00 0.00 42.97 4.55
118 119 2.420890 GCCCTCAGCAGATCTCGG 59.579 66.667 0.00 0.00 42.97 4.63
119 120 1.964608 TTGGCCCTCAGCAGATCTCG 61.965 60.000 0.00 0.00 46.50 4.04
120 121 0.254178 TTTGGCCCTCAGCAGATCTC 59.746 55.000 0.00 0.00 46.50 2.75
124 125 0.185901 AACTTTTGGCCCTCAGCAGA 59.814 50.000 0.00 0.00 46.50 4.26
125 126 1.541588 GTAACTTTTGGCCCTCAGCAG 59.458 52.381 0.00 0.00 46.50 4.24
126 127 1.144913 AGTAACTTTTGGCCCTCAGCA 59.855 47.619 0.00 0.00 46.50 4.41
127 128 1.813178 GAGTAACTTTTGGCCCTCAGC 59.187 52.381 0.00 0.00 42.60 4.26
128 129 3.425162 AGAGTAACTTTTGGCCCTCAG 57.575 47.619 0.00 0.00 0.00 3.35
129 130 3.486383 CAAGAGTAACTTTTGGCCCTCA 58.514 45.455 0.00 0.00 36.61 3.86
131 132 2.239400 GCAAGAGTAACTTTTGGCCCT 58.761 47.619 0.00 0.00 36.61 5.19
132 133 1.960689 TGCAAGAGTAACTTTTGGCCC 59.039 47.619 0.00 0.00 36.61 5.80
133 134 3.726291 TTGCAAGAGTAACTTTTGGCC 57.274 42.857 0.00 0.00 36.61 5.36
134 135 4.620982 ACATTGCAAGAGTAACTTTTGGC 58.379 39.130 4.94 0.00 36.61 4.52
135 136 6.534793 ACAAACATTGCAAGAGTAACTTTTGG 59.465 34.615 4.94 0.00 36.61 3.28
136 137 7.524294 ACAAACATTGCAAGAGTAACTTTTG 57.476 32.000 4.94 9.38 36.61 2.44
137 138 9.301153 CTTACAAACATTGCAAGAGTAACTTTT 57.699 29.630 4.94 0.00 36.36 2.27
138 139 7.435192 GCTTACAAACATTGCAAGAGTAACTTT 59.565 33.333 4.94 0.00 36.36 2.66
139 140 6.918022 GCTTACAAACATTGCAAGAGTAACTT 59.082 34.615 4.94 0.00 36.36 2.66
141 142 6.360681 CAGCTTACAAACATTGCAAGAGTAAC 59.639 38.462 4.94 5.08 36.36 2.50
142 143 6.437928 CAGCTTACAAACATTGCAAGAGTAA 58.562 36.000 4.94 8.23 36.36 2.24
143 144 5.562696 GCAGCTTACAAACATTGCAAGAGTA 60.563 40.000 4.94 0.48 36.36 2.59
144 145 4.794003 GCAGCTTACAAACATTGCAAGAGT 60.794 41.667 4.94 3.12 36.36 3.24
145 146 3.671928 GCAGCTTACAAACATTGCAAGAG 59.328 43.478 4.94 2.40 36.36 2.85
146 147 3.552684 GGCAGCTTACAAACATTGCAAGA 60.553 43.478 4.94 0.00 36.36 3.02
147 148 2.733026 GGCAGCTTACAAACATTGCAAG 59.267 45.455 4.94 0.00 37.15 4.01
148 149 2.102084 TGGCAGCTTACAAACATTGCAA 59.898 40.909 0.00 0.00 33.42 4.08
149 150 1.685517 TGGCAGCTTACAAACATTGCA 59.314 42.857 0.00 0.00 33.42 4.08
150 151 2.288395 ACTGGCAGCTTACAAACATTGC 60.288 45.455 15.89 0.00 0.00 3.56
152 153 5.256474 AGATACTGGCAGCTTACAAACATT 58.744 37.500 15.89 0.00 0.00 2.71
154 155 4.020218 AGAGATACTGGCAGCTTACAAACA 60.020 41.667 15.89 0.00 0.00 2.83
155 156 4.331168 CAGAGATACTGGCAGCTTACAAAC 59.669 45.833 15.89 0.00 42.39 2.93
157 158 3.769300 TCAGAGATACTGGCAGCTTACAA 59.231 43.478 15.89 0.00 45.76 2.41
161 162 3.181456 GGATTCAGAGATACTGGCAGCTT 60.181 47.826 15.89 1.17 45.76 3.74
162 163 2.368221 GGATTCAGAGATACTGGCAGCT 59.632 50.000 15.89 3.23 45.76 4.24
163 164 2.368221 AGGATTCAGAGATACTGGCAGC 59.632 50.000 15.89 0.00 45.76 5.25
164 165 4.686191 AAGGATTCAGAGATACTGGCAG 57.314 45.455 14.16 14.16 45.76 4.85
165 166 4.471025 TGAAAGGATTCAGAGATACTGGCA 59.529 41.667 0.00 0.00 45.76 4.92
166 167 5.028549 TGAAAGGATTCAGAGATACTGGC 57.971 43.478 0.00 0.00 45.76 4.85
179 180 4.154942 ACATGTGGAAAGCTGAAAGGATT 58.845 39.130 0.00 0.00 0.00 3.01
180 181 3.771216 ACATGTGGAAAGCTGAAAGGAT 58.229 40.909 0.00 0.00 0.00 3.24
183 184 7.383102 ACTTATACATGTGGAAAGCTGAAAG 57.617 36.000 9.11 0.32 0.00 2.62
185 186 6.939730 TCAACTTATACATGTGGAAAGCTGAA 59.060 34.615 9.11 0.12 0.00 3.02
187 188 6.741992 TCAACTTATACATGTGGAAAGCTG 57.258 37.500 9.11 10.41 0.00 4.24
188 189 7.944729 AATCAACTTATACATGTGGAAAGCT 57.055 32.000 9.11 0.00 0.00 3.74
189 190 8.986477 AAAATCAACTTATACATGTGGAAAGC 57.014 30.769 9.11 0.00 0.00 3.51
195 196 9.708222 GCAGTCTAAAATCAACTTATACATGTG 57.292 33.333 9.11 0.00 0.00 3.21
229 230 9.163899 GAGACATTGCATGACAGAATATGATAT 57.836 33.333 0.00 0.00 0.00 1.63
231 232 6.996282 TGAGACATTGCATGACAGAATATGAT 59.004 34.615 0.00 0.00 0.00 2.45
232 233 6.350906 TGAGACATTGCATGACAGAATATGA 58.649 36.000 0.00 0.00 0.00 2.15
235 236 6.656270 ACTTTGAGACATTGCATGACAGAATA 59.344 34.615 0.00 0.00 0.00 1.75
237 238 4.823442 ACTTTGAGACATTGCATGACAGAA 59.177 37.500 0.00 0.00 0.00 3.02
239 240 4.761235 ACTTTGAGACATTGCATGACAG 57.239 40.909 0.00 0.00 0.00 3.51
240 241 4.696877 CCTACTTTGAGACATTGCATGACA 59.303 41.667 0.00 0.00 0.00 3.58
241 242 4.937620 TCCTACTTTGAGACATTGCATGAC 59.062 41.667 0.00 0.00 0.00 3.06
242 243 5.164620 TCCTACTTTGAGACATTGCATGA 57.835 39.130 0.00 0.00 0.00 3.07
243 244 5.356190 ACATCCTACTTTGAGACATTGCATG 59.644 40.000 0.00 0.00 0.00 4.06
244 245 5.503927 ACATCCTACTTTGAGACATTGCAT 58.496 37.500 0.00 0.00 0.00 3.96
245 246 4.910195 ACATCCTACTTTGAGACATTGCA 58.090 39.130 0.00 0.00 0.00 4.08
247 248 6.536582 CAGGTACATCCTACTTTGAGACATTG 59.463 42.308 0.00 0.00 46.24 2.82
248 249 6.213600 ACAGGTACATCCTACTTTGAGACATT 59.786 38.462 0.00 0.00 46.24 2.71
249 250 5.721960 ACAGGTACATCCTACTTTGAGACAT 59.278 40.000 0.00 0.00 46.24 3.06
250 251 5.047306 CACAGGTACATCCTACTTTGAGACA 60.047 44.000 0.00 0.00 46.24 3.41
252 253 5.330233 TCACAGGTACATCCTACTTTGAGA 58.670 41.667 0.00 0.00 46.24 3.27
253 254 5.661056 TCACAGGTACATCCTACTTTGAG 57.339 43.478 0.00 0.00 46.24 3.02
254 255 6.406370 CAATCACAGGTACATCCTACTTTGA 58.594 40.000 0.00 0.00 46.24 2.69
256 257 5.186198 GCAATCACAGGTACATCCTACTTT 58.814 41.667 0.00 0.00 46.24 2.66
257 258 4.680708 CGCAATCACAGGTACATCCTACTT 60.681 45.833 0.00 0.00 46.24 2.24
260 261 2.764010 ACGCAATCACAGGTACATCCTA 59.236 45.455 0.00 0.00 46.24 2.94
262 263 2.024176 ACGCAATCACAGGTACATCC 57.976 50.000 0.00 0.00 0.00 3.51
264 265 5.950758 TTAAAACGCAATCACAGGTACAT 57.049 34.783 0.00 0.00 0.00 2.29
265 266 5.950758 ATTAAAACGCAATCACAGGTACA 57.049 34.783 0.00 0.00 0.00 2.90
266 267 6.910433 CCATATTAAAACGCAATCACAGGTAC 59.090 38.462 0.00 0.00 0.00 3.34
267 268 6.824196 TCCATATTAAAACGCAATCACAGGTA 59.176 34.615 0.00 0.00 0.00 3.08
269 270 6.130298 TCCATATTAAAACGCAATCACAGG 57.870 37.500 0.00 0.00 0.00 4.00
270 271 7.701924 ACAATCCATATTAAAACGCAATCACAG 59.298 33.333 0.00 0.00 0.00 3.66
271 272 7.542890 ACAATCCATATTAAAACGCAATCACA 58.457 30.769 0.00 0.00 0.00 3.58
273 274 7.995289 AGACAATCCATATTAAAACGCAATCA 58.005 30.769 0.00 0.00 0.00 2.57
274 275 8.856490 AAGACAATCCATATTAAAACGCAATC 57.144 30.769 0.00 0.00 0.00 2.67
278 279 8.798153 CAAGAAAGACAATCCATATTAAAACGC 58.202 33.333 0.00 0.00 0.00 4.84
279 280 9.840427 ACAAGAAAGACAATCCATATTAAAACG 57.160 29.630 0.00 0.00 0.00 3.60
284 285 7.611467 AGCACACAAGAAAGACAATCCATATTA 59.389 33.333 0.00 0.00 0.00 0.98
285 286 6.435277 AGCACACAAGAAAGACAATCCATATT 59.565 34.615 0.00 0.00 0.00 1.28
286 287 5.948162 AGCACACAAGAAAGACAATCCATAT 59.052 36.000 0.00 0.00 0.00 1.78
289 290 3.316029 CAGCACACAAGAAAGACAATCCA 59.684 43.478 0.00 0.00 0.00 3.41
290 291 3.316308 ACAGCACACAAGAAAGACAATCC 59.684 43.478 0.00 0.00 0.00 3.01
294 295 4.009675 AGAAACAGCACACAAGAAAGACA 58.990 39.130 0.00 0.00 0.00 3.41
296 297 6.112734 TCTAAGAAACAGCACACAAGAAAGA 58.887 36.000 0.00 0.00 0.00 2.52
297 298 6.363577 TCTAAGAAACAGCACACAAGAAAG 57.636 37.500 0.00 0.00 0.00 2.62
298 299 5.296780 CCTCTAAGAAACAGCACACAAGAAA 59.703 40.000 0.00 0.00 0.00 2.52
299 300 4.816385 CCTCTAAGAAACAGCACACAAGAA 59.184 41.667 0.00 0.00 0.00 2.52
300 301 4.100963 TCCTCTAAGAAACAGCACACAAGA 59.899 41.667 0.00 0.00 0.00 3.02
301 302 4.380531 TCCTCTAAGAAACAGCACACAAG 58.619 43.478 0.00 0.00 0.00 3.16
302 303 4.415881 TCCTCTAAGAAACAGCACACAA 57.584 40.909 0.00 0.00 0.00 3.33
303 304 4.284490 AGATCCTCTAAGAAACAGCACACA 59.716 41.667 0.00 0.00 0.00 3.72
304 305 4.629200 CAGATCCTCTAAGAAACAGCACAC 59.371 45.833 0.00 0.00 0.00 3.82
305 306 4.528206 TCAGATCCTCTAAGAAACAGCACA 59.472 41.667 0.00 0.00 0.00 4.57
308 309 7.470900 CAAAATCAGATCCTCTAAGAAACAGC 58.529 38.462 0.00 0.00 0.00 4.40
310 311 6.942005 TGCAAAATCAGATCCTCTAAGAAACA 59.058 34.615 0.00 0.00 0.00 2.83
311 312 7.094634 TGTGCAAAATCAGATCCTCTAAGAAAC 60.095 37.037 0.00 0.00 0.00 2.78
315 316 5.645067 TGTGTGCAAAATCAGATCCTCTAAG 59.355 40.000 0.00 0.00 0.00 2.18
316 317 5.412594 GTGTGTGCAAAATCAGATCCTCTAA 59.587 40.000 0.00 0.00 0.00 2.10
318 319 3.755378 GTGTGTGCAAAATCAGATCCTCT 59.245 43.478 0.00 0.00 0.00 3.69
319 320 3.503363 TGTGTGTGCAAAATCAGATCCTC 59.497 43.478 0.00 0.00 0.00 3.71
320 321 3.489355 TGTGTGTGCAAAATCAGATCCT 58.511 40.909 0.00 0.00 0.00 3.24
321 322 3.829948 CTGTGTGTGCAAAATCAGATCC 58.170 45.455 4.16 0.00 0.00 3.36
323 324 2.889045 AGCTGTGTGTGCAAAATCAGAT 59.111 40.909 12.11 4.56 0.00 2.90
324 325 2.033675 CAGCTGTGTGTGCAAAATCAGA 59.966 45.455 5.25 0.00 0.00 3.27
325 326 2.033675 TCAGCTGTGTGTGCAAAATCAG 59.966 45.455 14.67 0.00 0.00 2.90
326 327 2.022934 TCAGCTGTGTGTGCAAAATCA 58.977 42.857 14.67 0.00 0.00 2.57
327 328 2.780065 TCAGCTGTGTGTGCAAAATC 57.220 45.000 14.67 0.00 0.00 2.17
328 329 3.068448 TCATTCAGCTGTGTGTGCAAAAT 59.932 39.130 14.67 0.00 0.00 1.82
329 330 2.426381 TCATTCAGCTGTGTGTGCAAAA 59.574 40.909 14.67 0.00 0.00 2.44
330 331 2.022934 TCATTCAGCTGTGTGTGCAAA 58.977 42.857 14.67 0.00 0.00 3.68
331 332 1.677942 TCATTCAGCTGTGTGTGCAA 58.322 45.000 14.67 0.00 0.00 4.08
332 333 1.900245 ATCATTCAGCTGTGTGTGCA 58.100 45.000 14.67 0.00 0.00 4.57
333 334 5.936686 ATATATCATTCAGCTGTGTGTGC 57.063 39.130 14.67 0.00 0.00 4.57
334 335 7.172019 TGCTTATATATCATTCAGCTGTGTGTG 59.828 37.037 14.67 8.61 0.00 3.82
335 336 7.219322 TGCTTATATATCATTCAGCTGTGTGT 58.781 34.615 14.67 7.33 0.00 3.72
336 337 7.662604 TGCTTATATATCATTCAGCTGTGTG 57.337 36.000 14.67 13.54 0.00 3.82
337 338 8.859236 ATTGCTTATATATCATTCAGCTGTGT 57.141 30.769 14.67 0.18 0.00 3.72
353 354 9.727859 TGTCAAAGTGTTACCTAATTGCTTATA 57.272 29.630 0.00 0.00 0.00 0.98
355 356 8.630054 ATGTCAAAGTGTTACCTAATTGCTTA 57.370 30.769 0.00 0.00 0.00 3.09
357 358 6.151144 GGATGTCAAAGTGTTACCTAATTGCT 59.849 38.462 0.00 0.00 0.00 3.91
358 359 6.072175 TGGATGTCAAAGTGTTACCTAATTGC 60.072 38.462 0.00 0.00 0.00 3.56
359 360 7.447374 TGGATGTCAAAGTGTTACCTAATTG 57.553 36.000 0.00 0.00 0.00 2.32
360 361 8.650143 ATTGGATGTCAAAGTGTTACCTAATT 57.350 30.769 0.00 0.00 39.05 1.40
361 362 9.396022 CTATTGGATGTCAAAGTGTTACCTAAT 57.604 33.333 0.00 0.00 39.05 1.73
362 363 8.598916 TCTATTGGATGTCAAAGTGTTACCTAA 58.401 33.333 0.00 0.00 39.05 2.69
364 365 7.016153 TCTATTGGATGTCAAAGTGTTACCT 57.984 36.000 0.00 0.00 39.05 3.08
365 366 7.697691 CATCTATTGGATGTCAAAGTGTTACC 58.302 38.462 2.03 0.00 44.88 2.85
380 381 7.526041 ACCCAAAATATAGTGCATCTATTGGA 58.474 34.615 18.24 4.86 37.29 3.53
381 382 7.667219 AGACCCAAAATATAGTGCATCTATTGG 59.333 37.037 12.15 13.05 39.70 3.16
383 384 9.950496 CTAGACCCAAAATATAGTGCATCTATT 57.050 33.333 12.15 4.09 39.70 1.73
384 385 8.543774 CCTAGACCCAAAATATAGTGCATCTAT 58.456 37.037 11.76 11.76 41.61 1.98
386 387 6.330250 ACCTAGACCCAAAATATAGTGCATCT 59.670 38.462 0.00 0.00 0.00 2.90
387 388 6.534634 ACCTAGACCCAAAATATAGTGCATC 58.465 40.000 0.00 0.00 0.00 3.91
388 389 6.330250 AGACCTAGACCCAAAATATAGTGCAT 59.670 38.462 0.00 0.00 0.00 3.96
389 390 5.665812 AGACCTAGACCCAAAATATAGTGCA 59.334 40.000 0.00 0.00 0.00 4.57
390 391 6.176014 AGACCTAGACCCAAAATATAGTGC 57.824 41.667 0.00 0.00 0.00 4.40
391 392 7.361457 TGAGACCTAGACCCAAAATATAGTG 57.639 40.000 0.00 0.00 0.00 2.74
392 393 8.568617 AATGAGACCTAGACCCAAAATATAGT 57.431 34.615 0.00 0.00 0.00 2.12
393 394 9.853177 AAAATGAGACCTAGACCCAAAATATAG 57.147 33.333 0.00 0.00 0.00 1.31
396 397 9.681062 CTTAAAATGAGACCTAGACCCAAAATA 57.319 33.333 0.00 0.00 0.00 1.40
397 398 8.170730 ACTTAAAATGAGACCTAGACCCAAAAT 58.829 33.333 0.00 0.00 0.00 1.82
398 399 7.523415 ACTTAAAATGAGACCTAGACCCAAAA 58.477 34.615 0.00 0.00 0.00 2.44
399 400 7.086685 ACTTAAAATGAGACCTAGACCCAAA 57.913 36.000 0.00 0.00 0.00 3.28
400 401 6.697641 ACTTAAAATGAGACCTAGACCCAA 57.302 37.500 0.00 0.00 0.00 4.12
401 402 6.271391 TCAACTTAAAATGAGACCTAGACCCA 59.729 38.462 0.00 0.00 0.00 4.51
402 403 6.708285 TCAACTTAAAATGAGACCTAGACCC 58.292 40.000 0.00 0.00 0.00 4.46
405 406 9.621629 TTGTTTCAACTTAAAATGAGACCTAGA 57.378 29.630 0.00 0.00 31.59 2.43
408 409 8.406297 GTCTTGTTTCAACTTAAAATGAGACCT 58.594 33.333 7.80 0.00 31.59 3.85
410 411 9.567848 TTGTCTTGTTTCAACTTAAAATGAGAC 57.432 29.630 0.00 0.00 34.47 3.36
411 412 9.787532 CTTGTCTTGTTTCAACTTAAAATGAGA 57.212 29.630 0.00 0.00 0.00 3.27
412 413 9.573133 ACTTGTCTTGTTTCAACTTAAAATGAG 57.427 29.630 0.00 0.00 0.00 2.90
417 418 9.296400 GCATTACTTGTCTTGTTTCAACTTAAA 57.704 29.630 0.00 0.00 0.00 1.52
418 419 7.918562 GGCATTACTTGTCTTGTTTCAACTTAA 59.081 33.333 0.00 0.00 0.00 1.85
419 420 7.422399 GGCATTACTTGTCTTGTTTCAACTTA 58.578 34.615 0.00 0.00 0.00 2.24
436 3452 2.308570 TCATGTTCCTGTGGGCATTACT 59.691 45.455 0.00 0.00 0.00 2.24
437 3453 2.722094 TCATGTTCCTGTGGGCATTAC 58.278 47.619 0.00 0.00 0.00 1.89
438 3454 3.010027 TCTTCATGTTCCTGTGGGCATTA 59.990 43.478 0.00 0.00 0.00 1.90
439 3455 2.173519 CTTCATGTTCCTGTGGGCATT 58.826 47.619 0.00 0.00 0.00 3.56
442 3458 1.168714 GTCTTCATGTTCCTGTGGGC 58.831 55.000 0.00 0.00 0.00 5.36
443 3459 1.073763 TGGTCTTCATGTTCCTGTGGG 59.926 52.381 0.00 0.00 0.00 4.61
453 3469 2.165030 GCCATGTTTCCTGGTCTTCATG 59.835 50.000 12.80 12.80 36.10 3.07
459 3475 0.036388 TCGAGCCATGTTTCCTGGTC 60.036 55.000 0.00 0.00 36.10 4.02
476 3492 3.539592 GCGTCATGTGATTACTTCGTTCG 60.540 47.826 0.00 0.00 0.00 3.95
485 3501 2.091852 TGCAGTGCGTCATGTGATTA 57.908 45.000 11.20 0.00 0.00 1.75
492 3508 4.874534 GCATTTGCAGTGCGTCAT 57.125 50.000 11.20 0.00 41.59 3.06
526 3543 4.688879 TCGGTATTCAGTACAAGCAACTTG 59.311 41.667 5.80 5.80 45.85 3.16
527 3544 4.890088 TCGGTATTCAGTACAAGCAACTT 58.110 39.130 0.00 0.00 34.87 2.66
528 3545 4.530710 TCGGTATTCAGTACAAGCAACT 57.469 40.909 0.00 0.00 34.87 3.16
529 3546 6.479001 ACATATCGGTATTCAGTACAAGCAAC 59.521 38.462 0.00 0.00 34.87 4.17
530 3547 6.578944 ACATATCGGTATTCAGTACAAGCAA 58.421 36.000 0.00 0.00 34.87 3.91
531 3548 6.156748 ACATATCGGTATTCAGTACAAGCA 57.843 37.500 0.00 0.00 34.87 3.91
532 3549 6.700081 TGAACATATCGGTATTCAGTACAAGC 59.300 38.462 0.00 0.00 34.87 4.01
533 3550 7.382488 CCTGAACATATCGGTATTCAGTACAAG 59.618 40.741 14.82 0.35 44.28 3.16
534 3551 7.207383 CCTGAACATATCGGTATTCAGTACAA 58.793 38.462 14.82 0.00 44.28 2.41
535 3552 6.737622 GCCTGAACATATCGGTATTCAGTACA 60.738 42.308 14.82 0.00 44.28 2.90
536 3553 5.634020 GCCTGAACATATCGGTATTCAGTAC 59.366 44.000 14.82 6.13 44.28 2.73
537 3554 5.279306 GGCCTGAACATATCGGTATTCAGTA 60.279 44.000 14.82 0.00 44.28 2.74
538 3555 4.503296 GGCCTGAACATATCGGTATTCAGT 60.503 45.833 14.82 0.00 44.28 3.41
539 3556 3.997021 GGCCTGAACATATCGGTATTCAG 59.003 47.826 10.77 10.77 45.00 3.02
540 3557 3.389656 TGGCCTGAACATATCGGTATTCA 59.610 43.478 3.32 0.00 32.01 2.57
550 3567 5.897250 TGTCTATACTTCTGGCCTGAACATA 59.103 40.000 20.15 17.34 0.00 2.29
567 3585 6.054941 CCATGGTTTATGTGCACTGTCTATA 58.945 40.000 19.41 3.99 34.87 1.31
572 3590 2.170166 CCCATGGTTTATGTGCACTGT 58.830 47.619 19.41 9.43 34.87 3.55
573 3591 1.135024 GCCCATGGTTTATGTGCACTG 60.135 52.381 19.41 4.90 39.59 3.66
574 3592 1.185315 GCCCATGGTTTATGTGCACT 58.815 50.000 19.41 6.22 39.59 4.40
577 3595 1.767759 AGAGCCCATGGTTTATGTGC 58.232 50.000 11.73 4.80 40.04 4.57
593 3611 3.773860 AGCGTGTGAAGACTGATAGAG 57.226 47.619 0.00 0.00 0.00 2.43
598 3616 2.201732 GTTGAAGCGTGTGAAGACTGA 58.798 47.619 0.00 0.00 0.00 3.41
607 3625 2.942376 TCTCAAATGTGTTGAAGCGTGT 59.058 40.909 0.00 0.00 0.00 4.49
614 3632 4.459330 TCACCATGTCTCAAATGTGTTGA 58.541 39.130 0.00 0.00 0.00 3.18
683 3701 0.675837 ACTCTAGTACTGGCACGCGA 60.676 55.000 15.93 0.00 0.00 5.87
699 3717 9.035607 CAATACTGGTTGAATGATAGTGTACTC 57.964 37.037 0.00 0.00 0.00 2.59
778 3796 2.095869 GTGCAATGCTGAAGAGACAGTG 60.096 50.000 6.82 0.00 39.73 3.66
814 3832 0.987294 AGGACCACATGAGACAAGGG 59.013 55.000 0.00 0.00 0.00 3.95
850 3868 1.907255 AGAAGGGTTAGGTGTGGCTAC 59.093 52.381 0.00 0.00 0.00 3.58
855 3873 2.567615 AGCAGTAGAAGGGTTAGGTGTG 59.432 50.000 0.00 0.00 0.00 3.82
928 3949 9.212641 GTGATGCTTAGATTGCTATCTTATTCA 57.787 33.333 15.84 9.48 41.38 2.57
932 3953 6.931281 GGTGTGATGCTTAGATTGCTATCTTA 59.069 38.462 15.84 6.34 41.38 2.10
986 4007 5.008415 GGATGAATCATGATTCTGTGGTGTC 59.992 44.000 36.15 24.01 45.55 3.67
998 4019 4.643334 CCAGCTTCTTTGGATGAATCATGA 59.357 41.667 0.00 0.00 37.96 3.07
1276 11199 6.748333 AATCAAACACATCACATACTCCAG 57.252 37.500 0.00 0.00 0.00 3.86
1332 11255 2.971330 CCTCACTATGGAGCTCAGGAAT 59.029 50.000 17.19 5.90 33.47 3.01
1364 11287 0.662619 TGAAGGCAAACAACTCGCAG 59.337 50.000 0.00 0.00 0.00 5.18
1437 11361 7.819415 CCTGACAACTGACATATCTAACTGAAA 59.181 37.037 0.00 0.00 0.00 2.69
1482 11406 8.584157 TCTGCTAAGATGAGAAAATAGGATCTC 58.416 37.037 0.00 0.00 41.95 2.75
1690 11620 5.352569 AGCTTCAAATTCTCCGTTGACTATG 59.647 40.000 0.00 0.00 33.58 2.23
1773 11703 9.908152 TTGACACTATTATGTATAATCGAGGTG 57.092 33.333 0.63 8.47 34.91 4.00
1804 11734 3.445805 GGTTGGTTCCAGTTCAAGTTCAA 59.554 43.478 0.00 0.00 0.00 2.69
1836 11768 1.868109 GCAAACGGAACAAAAGGAGGC 60.868 52.381 0.00 0.00 0.00 4.70
1851 11791 3.944422 TCAGACGAAAGACAAGCAAAC 57.056 42.857 0.00 0.00 0.00 2.93
1941 11881 3.405831 TCAGTTGAGACTCAAGGCAATG 58.594 45.455 18.24 7.03 37.00 2.82
2107 12049 4.690748 TCCAGTACAAAATTGAGCTTCTCG 59.309 41.667 0.00 0.00 32.35 4.04
2110 12052 5.447818 CCGATCCAGTACAAAATTGAGCTTC 60.448 44.000 0.00 0.00 0.00 3.86
2161 12104 9.588432 AATATATCCCCTAATCTGGTAAATCCA 57.412 33.333 0.00 0.00 45.01 3.41
2169 12112 6.378280 GCCAAACAATATATCCCCTAATCTGG 59.622 42.308 0.00 0.00 0.00 3.86
2212 14851 5.859205 AATGGGCAGGATAAATGTTTCTC 57.141 39.130 0.00 0.00 0.00 2.87
2215 14854 6.172630 GTTCAAATGGGCAGGATAAATGTTT 58.827 36.000 0.00 0.00 0.00 2.83
2223 14862 1.923356 AACGTTCAAATGGGCAGGAT 58.077 45.000 0.00 0.00 0.00 3.24
2233 14872 9.813080 CCAAAAATTTACAAAGAAACGTTCAAA 57.187 25.926 0.00 0.00 0.00 2.69
2278 14918 5.100751 ACAAGTCAAAGAATTCTTCTGCG 57.899 39.130 20.71 10.14 40.59 5.18
2352 14992 3.159213 ACAAACATCATTCCTCCAGCA 57.841 42.857 0.00 0.00 0.00 4.41
2363 15003 7.095857 GCAATCGAAAAATGGTTACAAACATCA 60.096 33.333 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.