Multiple sequence alignment - TraesCS6A01G218200

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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 TraesCS6A01G218200 chr6A 100.000 6457 0 0 1 6457 403325984 403319528 0.000000e+00 11924.0
1 TraesCS6A01G218200 chr6A 96.962 2469 69 4 3993 6457 403137085 403134619 0.000000e+00 4139.0
2 TraesCS6A01G218200 chr6D 96.356 5489 123 29 401 5872 283556579 283551151 0.000000e+00 8957.0
3 TraesCS6A01G218200 chr6D 96.000 200 7 1 5873 6071 283550921 283550722 2.250000e-84 324.0
4 TraesCS6A01G218200 chr6D 91.837 98 4 1 4 101 283559422 283559329 4.060000e-27 134.0
5 TraesCS6A01G218200 chr6B 95.170 5487 180 30 401 5862 444543369 444537943 0.000000e+00 8586.0
6 TraesCS6A01G218200 chr6B 92.105 190 15 0 5882 6071 444537727 444537538 1.070000e-67 268.0
7 TraesCS6A01G218200 chr6B 88.189 127 5 3 4 120 444543542 444543416 6.750000e-30 143.0
8 TraesCS6A01G218200 chr2B 89.460 389 31 5 6072 6457 195962244 195962625 3.500000e-132 483.0
9 TraesCS6A01G218200 chr2B 91.322 242 20 1 121 361 643974035 643974276 4.830000e-86 329.0
10 TraesCS6A01G218200 chr2B 88.750 240 24 3 123 360 104078879 104079117 2.280000e-74 291.0
11 TraesCS6A01G218200 chr2B 81.789 313 46 10 3458 3764 319356666 319356973 1.070000e-62 252.0
12 TraesCS6A01G218200 chr7D 89.203 389 31 6 6072 6457 390456676 390457056 5.860000e-130 475.0
13 TraesCS6A01G218200 chr7D 88.432 389 32 8 6072 6457 351726786 351726408 2.120000e-124 457.0
14 TraesCS6A01G218200 chr7D 82.143 364 50 7 2674 3034 160663209 160662858 1.360000e-76 298.0
15 TraesCS6A01G218200 chr7D 82.514 366 36 9 2674 3032 64515771 64516115 4.900000e-76 296.0
16 TraesCS6A01G218200 chr7D 100.000 32 0 0 768 799 574787005 574786974 6.990000e-05 60.2
17 TraesCS6A01G218200 chr1B 89.147 387 32 5 6074 6457 295877299 295876920 2.110000e-129 473.0
18 TraesCS6A01G218200 chr1B 88.430 242 24 4 123 362 896164 895925 8.190000e-74 289.0
19 TraesCS6A01G218200 chr1B 82.237 304 47 7 3466 3764 24104939 24104638 8.310000e-64 255.0
20 TraesCS6A01G218200 chr1B 79.630 108 20 2 5955 6061 391135670 391135564 6.940000e-10 76.8
21 TraesCS6A01G218200 chr1D 88.550 393 31 5 6072 6457 241231976 241232361 1.270000e-126 464.0
22 TraesCS6A01G218200 chr1D 83.836 365 46 9 2679 3032 79314471 79314109 1.040000e-87 335.0
23 TraesCS6A01G218200 chr2D 88.432 389 34 8 6072 6457 596314603 596314983 5.900000e-125 459.0
24 TraesCS6A01G218200 chr2D 81.875 320 40 10 3458 3764 439661340 439661026 2.990000e-63 254.0
25 TraesCS6A01G218200 chr1A 88.010 392 33 10 6072 6457 248218586 248218203 9.870000e-123 451.0
26 TraesCS6A01G218200 chr1A 84.463 354 42 8 2691 3032 98227407 98227055 2.880000e-88 337.0
27 TraesCS6A01G218200 chr5D 87.918 389 36 6 6072 6457 464012088 464011708 1.280000e-121 448.0
28 TraesCS6A01G218200 chr3A 95.565 248 11 0 121 368 640687247 640687000 1.300000e-106 398.0
29 TraesCS6A01G218200 chr3A 95.161 248 12 0 121 368 640704007 640703760 6.070000e-105 392.0
30 TraesCS6A01G218200 chr3A 95.142 247 12 0 122 368 640634591 640634345 2.180000e-104 390.0
31 TraesCS6A01G218200 chr3A 87.137 241 26 5 123 360 695974869 695974631 1.070000e-67 268.0
32 TraesCS6A01G218200 chr3D 86.310 336 38 4 2675 3002 510649382 510649717 6.160000e-95 359.0
33 TraesCS6A01G218200 chr3D 81.690 142 23 3 5920 6061 499963150 499963288 1.470000e-21 115.0
34 TraesCS6A01G218200 chr3D 76.190 189 36 6 5875 6058 452980534 452980718 2.480000e-14 91.6
35 TraesCS6A01G218200 chrUn 84.973 366 34 9 2674 3032 94876677 94877028 1.030000e-92 351.0
36 TraesCS6A01G218200 chrUn 82.857 385 45 16 2657 3032 221375829 221376201 6.240000e-85 326.0
37 TraesCS6A01G218200 chr7A 82.632 380 57 7 2661 3032 692893544 692893166 1.740000e-85 327.0
38 TraesCS6A01G218200 chr7A 82.552 384 49 14 2657 3032 5793357 5793730 8.080000e-84 322.0
39 TraesCS6A01G218200 chr2A 88.382 241 25 3 123 361 770377483 770377722 2.950000e-73 287.0
40 TraesCS6A01G218200 chr4B 87.967 241 24 5 123 360 24332192 24332430 4.930000e-71 279.0
41 TraesCS6A01G218200 chr4A 83.193 119 18 2 5944 6061 556231385 556231502 2.460000e-19 108.0
42 TraesCS6A01G218200 chr7B 78.659 164 32 3 5899 6061 1355705 1355544 8.850000e-19 106.0
43 TraesCS6A01G218200 chr5B 75.936 187 39 4 5873 6058 352606556 352606737 2.480000e-14 91.6


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 TraesCS6A01G218200 chr6A 403319528 403325984 6456 True 11924.000000 11924 100.000000 1 6457 1 chr6A.!!$R2 6456
1 TraesCS6A01G218200 chr6A 403134619 403137085 2466 True 4139.000000 4139 96.962000 3993 6457 1 chr6A.!!$R1 2464
2 TraesCS6A01G218200 chr6D 283550722 283559422 8700 True 3138.333333 8957 94.731000 4 6071 3 chr6D.!!$R1 6067
3 TraesCS6A01G218200 chr6B 444537538 444543542 6004 True 2999.000000 8586 91.821333 4 6071 3 chr6B.!!$R1 6067

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
727 3459 0.031585 TTATTCCCTGTCGATCGGCG 59.968 55.000 15.94 9.76 42.69 6.46 F
1545 4278 0.532573 TCCGATCACAAGCACCTCTC 59.467 55.000 0.00 0.00 0.00 3.20 F
1604 4337 1.379916 CAGGGTCTGCCACATTGGA 59.620 57.895 0.00 0.00 40.96 3.53 F
2914 5674 1.796459 CCAAACTTTGCAAGCATCTGC 59.204 47.619 0.00 0.00 42.95 4.26 F
3614 6374 1.076332 AAGGTCGCGTGCAATCTTAC 58.924 50.000 5.77 0.00 0.00 2.34 F
4161 6923 4.412207 GTTTCAGAAATATTGTGCGGGAC 58.588 43.478 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 4349 2.352127 CGCTATCTCCGAATGCATCAGA 60.352 50.000 0.00 0.00 0.00 3.27 R
2784 5543 1.135139 TGTACAGAGCTCCTCGAATGC 59.865 52.381 10.93 0.00 35.36 3.56 R
2983 5743 1.276421 GTGCACCCACTCTACACTCAT 59.724 52.381 5.22 0.00 38.93 2.90 R
4596 7358 1.332377 GCGTGCGATGCTTAGCTAAAG 60.332 52.381 7.74 3.37 38.32 1.85 R
4913 7678 1.619654 CTGGACAATGCAGGGAAACA 58.380 50.000 0.00 0.00 31.71 2.83 R
6060 9061 2.750350 CACTTTCGGGGAGGTGCT 59.250 61.111 0.00 0.00 0.00 4.40 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
72 87 9.012161 GGGAGTAGTACTATAATAACTCCACTG 57.988 40.741 28.92 0.00 42.97 3.66
109 124 5.126061 GCATCAAATGTGGACTAATGGACTT 59.874 40.000 0.00 0.00 0.00 3.01
110 125 6.558009 CATCAAATGTGGACTAATGGACTTG 58.442 40.000 0.00 0.00 0.00 3.16
111 126 4.458989 TCAAATGTGGACTAATGGACTTGC 59.541 41.667 0.00 0.00 0.00 4.01
112 127 3.719268 ATGTGGACTAATGGACTTGCA 57.281 42.857 0.00 0.00 0.00 4.08
113 128 3.719268 TGTGGACTAATGGACTTGCAT 57.281 42.857 0.00 0.00 0.00 3.96
114 129 3.609853 TGTGGACTAATGGACTTGCATC 58.390 45.455 0.00 0.00 0.00 3.91
115 130 2.945668 GTGGACTAATGGACTTGCATCC 59.054 50.000 0.00 0.00 39.45 3.51
121 136 3.942351 TGGACTTGCATCCAGTGAG 57.058 52.632 4.87 0.00 44.14 3.51
122 137 1.059098 TGGACTTGCATCCAGTGAGT 58.941 50.000 4.87 0.00 44.14 3.41
123 138 2.256306 TGGACTTGCATCCAGTGAGTA 58.744 47.619 4.87 0.00 44.14 2.59
124 139 2.840038 TGGACTTGCATCCAGTGAGTAT 59.160 45.455 4.87 0.00 44.14 2.12
125 140 3.118629 TGGACTTGCATCCAGTGAGTATC 60.119 47.826 4.87 0.00 44.14 2.24
126 141 3.118629 GGACTTGCATCCAGTGAGTATCA 60.119 47.826 1.24 0.00 40.15 2.15
127 142 4.977132 GGACTTGCATCCAGTGAGTATCAG 60.977 50.000 1.24 0.00 42.05 2.90
128 143 7.923973 GGACTTGCATCCAGTGAGTATCAGG 62.924 52.000 1.24 0.00 42.05 3.86
145 160 7.584122 GTATCAGGTGATACCAAGACTTAGA 57.416 40.000 16.32 0.00 46.87 2.10
146 161 8.184304 GTATCAGGTGATACCAAGACTTAGAT 57.816 38.462 16.32 0.00 46.87 1.98
147 162 6.471233 TCAGGTGATACCAAGACTTAGATG 57.529 41.667 0.28 0.00 41.95 2.90
148 163 5.053145 CAGGTGATACCAAGACTTAGATGC 58.947 45.833 0.28 0.00 41.95 3.91
149 164 4.965532 AGGTGATACCAAGACTTAGATGCT 59.034 41.667 0.28 0.00 41.95 3.79
150 165 5.069781 AGGTGATACCAAGACTTAGATGCTC 59.930 44.000 0.28 0.00 41.95 4.26
151 166 5.293560 GTGATACCAAGACTTAGATGCTCC 58.706 45.833 0.00 0.00 0.00 4.70
152 167 4.345257 TGATACCAAGACTTAGATGCTCCC 59.655 45.833 0.00 0.00 0.00 4.30
153 168 2.551270 ACCAAGACTTAGATGCTCCCA 58.449 47.619 0.00 0.00 0.00 4.37
154 169 3.118531 ACCAAGACTTAGATGCTCCCAT 58.881 45.455 0.00 0.00 0.00 4.00
155 170 3.118112 ACCAAGACTTAGATGCTCCCATG 60.118 47.826 0.00 0.00 0.00 3.66
156 171 3.135348 CCAAGACTTAGATGCTCCCATGA 59.865 47.826 0.00 0.00 0.00 3.07
157 172 4.202440 CCAAGACTTAGATGCTCCCATGAT 60.202 45.833 0.00 0.00 0.00 2.45
158 173 5.012458 CCAAGACTTAGATGCTCCCATGATA 59.988 44.000 0.00 0.00 0.00 2.15
159 174 5.736951 AGACTTAGATGCTCCCATGATAC 57.263 43.478 0.00 0.00 0.00 2.24
160 175 4.219507 AGACTTAGATGCTCCCATGATACG 59.780 45.833 0.00 0.00 0.00 3.06
161 176 4.152647 ACTTAGATGCTCCCATGATACGA 58.847 43.478 0.00 0.00 0.00 3.43
162 177 4.219507 ACTTAGATGCTCCCATGATACGAG 59.780 45.833 0.00 0.00 0.00 4.18
165 180 3.997672 GCTCCCATGATACGAGCTT 57.002 52.632 13.49 0.00 44.52 3.74
166 181 1.789506 GCTCCCATGATACGAGCTTC 58.210 55.000 13.49 0.00 44.52 3.86
167 182 1.342819 GCTCCCATGATACGAGCTTCT 59.657 52.381 13.49 0.00 44.52 2.85
168 183 2.224161 GCTCCCATGATACGAGCTTCTT 60.224 50.000 13.49 0.00 44.52 2.52
169 184 3.388308 CTCCCATGATACGAGCTTCTTG 58.612 50.000 0.00 0.00 0.00 3.02
170 185 2.766263 TCCCATGATACGAGCTTCTTGT 59.234 45.455 0.00 0.00 32.27 3.16
171 186 3.126831 CCCATGATACGAGCTTCTTGTC 58.873 50.000 0.00 0.00 29.93 3.18
172 187 3.430790 CCCATGATACGAGCTTCTTGTCA 60.431 47.826 0.00 0.00 29.93 3.58
173 188 3.801050 CCATGATACGAGCTTCTTGTCAG 59.199 47.826 0.00 0.00 29.93 3.51
174 189 4.428209 CATGATACGAGCTTCTTGTCAGT 58.572 43.478 0.00 0.00 29.93 3.41
175 190 4.521130 TGATACGAGCTTCTTGTCAGTT 57.479 40.909 0.00 0.00 29.93 3.16
176 191 4.237724 TGATACGAGCTTCTTGTCAGTTG 58.762 43.478 0.00 0.00 29.93 3.16
177 192 1.871080 ACGAGCTTCTTGTCAGTTGG 58.129 50.000 0.00 0.00 0.00 3.77
178 193 1.412710 ACGAGCTTCTTGTCAGTTGGA 59.587 47.619 0.00 0.00 0.00 3.53
179 194 2.037772 ACGAGCTTCTTGTCAGTTGGAT 59.962 45.455 0.00 0.00 0.00 3.41
180 195 2.670414 CGAGCTTCTTGTCAGTTGGATC 59.330 50.000 0.00 0.00 0.00 3.36
181 196 3.616076 CGAGCTTCTTGTCAGTTGGATCT 60.616 47.826 0.00 0.00 0.00 2.75
182 197 4.322567 GAGCTTCTTGTCAGTTGGATCTT 58.677 43.478 0.00 0.00 0.00 2.40
183 198 5.482908 GAGCTTCTTGTCAGTTGGATCTTA 58.517 41.667 0.00 0.00 0.00 2.10
184 199 5.486526 AGCTTCTTGTCAGTTGGATCTTAG 58.513 41.667 0.00 0.00 0.00 2.18
185 200 5.247110 AGCTTCTTGTCAGTTGGATCTTAGA 59.753 40.000 0.00 0.00 0.00 2.10
186 201 6.070309 AGCTTCTTGTCAGTTGGATCTTAGAT 60.070 38.462 0.00 0.00 0.00 1.98
187 202 6.257630 GCTTCTTGTCAGTTGGATCTTAGATC 59.742 42.308 13.44 13.44 0.00 2.75
188 203 6.227298 TCTTGTCAGTTGGATCTTAGATCC 57.773 41.667 29.06 29.06 38.66 3.36
189 204 5.721480 TCTTGTCAGTTGGATCTTAGATCCA 59.279 40.000 33.07 33.07 45.71 3.41
194 209 2.910688 TGGATCTTAGATCCAACGGC 57.089 50.000 34.17 12.88 44.54 5.68
195 210 2.398588 TGGATCTTAGATCCAACGGCT 58.601 47.619 34.17 0.00 44.54 5.52
196 211 2.365617 TGGATCTTAGATCCAACGGCTC 59.634 50.000 34.17 11.60 44.54 4.70
197 212 2.608261 GGATCTTAGATCCAACGGCTCG 60.608 54.545 30.30 0.00 38.09 5.03
198 213 1.471119 TCTTAGATCCAACGGCTCGT 58.529 50.000 0.00 0.00 43.97 4.18
199 214 2.646930 TCTTAGATCCAACGGCTCGTA 58.353 47.619 0.62 0.00 39.99 3.43
200 215 2.617308 TCTTAGATCCAACGGCTCGTAG 59.383 50.000 0.62 0.00 39.99 3.51
201 216 1.315690 TAGATCCAACGGCTCGTAGG 58.684 55.000 0.62 0.00 39.99 3.18
202 217 0.683504 AGATCCAACGGCTCGTAGGT 60.684 55.000 0.62 0.00 39.99 3.08
203 218 0.527817 GATCCAACGGCTCGTAGGTG 60.528 60.000 0.62 0.00 39.99 4.00
204 219 1.956629 ATCCAACGGCTCGTAGGTGG 61.957 60.000 9.38 9.38 39.99 4.61
205 220 2.654877 CAACGGCTCGTAGGTGGT 59.345 61.111 0.62 0.00 39.99 4.16
206 221 1.005394 CAACGGCTCGTAGGTGGTT 60.005 57.895 0.62 0.00 39.99 3.67
207 222 0.601841 CAACGGCTCGTAGGTGGTTT 60.602 55.000 0.62 0.00 39.99 3.27
208 223 0.107268 AACGGCTCGTAGGTGGTTTT 59.893 50.000 0.62 0.00 39.99 2.43
209 224 0.601841 ACGGCTCGTAGGTGGTTTTG 60.602 55.000 0.00 0.00 38.73 2.44
210 225 0.320073 CGGCTCGTAGGTGGTTTTGA 60.320 55.000 0.00 0.00 0.00 2.69
211 226 1.874739 CGGCTCGTAGGTGGTTTTGAA 60.875 52.381 0.00 0.00 0.00 2.69
212 227 1.804748 GGCTCGTAGGTGGTTTTGAAG 59.195 52.381 0.00 0.00 0.00 3.02
213 228 1.804748 GCTCGTAGGTGGTTTTGAAGG 59.195 52.381 0.00 0.00 0.00 3.46
214 229 1.804748 CTCGTAGGTGGTTTTGAAGGC 59.195 52.381 0.00 0.00 0.00 4.35
215 230 1.418637 TCGTAGGTGGTTTTGAAGGCT 59.581 47.619 0.00 0.00 0.00 4.58
216 231 1.535462 CGTAGGTGGTTTTGAAGGCTG 59.465 52.381 0.00 0.00 0.00 4.85
217 232 1.269723 GTAGGTGGTTTTGAAGGCTGC 59.730 52.381 0.00 0.00 0.00 5.25
218 233 0.396974 AGGTGGTTTTGAAGGCTGCA 60.397 50.000 0.50 0.00 0.00 4.41
219 234 0.463620 GGTGGTTTTGAAGGCTGCAA 59.536 50.000 3.04 3.04 0.00 4.08
220 235 1.070601 GGTGGTTTTGAAGGCTGCAAT 59.929 47.619 9.16 0.00 0.00 3.56
221 236 2.298729 GGTGGTTTTGAAGGCTGCAATA 59.701 45.455 9.16 0.71 0.00 1.90
222 237 3.317150 GTGGTTTTGAAGGCTGCAATAC 58.683 45.455 17.63 17.63 0.00 1.89
223 238 3.005791 GTGGTTTTGAAGGCTGCAATACT 59.994 43.478 22.83 0.00 30.98 2.12
224 239 3.640967 TGGTTTTGAAGGCTGCAATACTT 59.359 39.130 22.83 0.00 30.98 2.24
225 240 3.989817 GGTTTTGAAGGCTGCAATACTTG 59.010 43.478 22.83 0.00 30.98 3.16
226 241 4.501400 GGTTTTGAAGGCTGCAATACTTGT 60.501 41.667 22.83 0.00 30.98 3.16
227 242 4.935352 TTTGAAGGCTGCAATACTTGTT 57.065 36.364 9.16 0.00 0.00 2.83
228 243 4.503741 TTGAAGGCTGCAATACTTGTTC 57.496 40.909 3.04 0.00 0.00 3.18
229 244 2.483877 TGAAGGCTGCAATACTTGTTCG 59.516 45.455 0.50 0.00 0.00 3.95
230 245 0.804989 AGGCTGCAATACTTGTTCGC 59.195 50.000 0.50 0.00 0.00 4.70
231 246 0.521291 GGCTGCAATACTTGTTCGCA 59.479 50.000 0.50 0.00 0.00 5.10
232 247 1.068610 GGCTGCAATACTTGTTCGCAA 60.069 47.619 0.50 0.00 35.53 4.85
233 248 2.415893 GGCTGCAATACTTGTTCGCAAT 60.416 45.455 0.50 0.00 36.39 3.56
234 249 3.244976 GCTGCAATACTTGTTCGCAATT 58.755 40.909 0.00 0.00 36.39 2.32
235 250 3.674753 GCTGCAATACTTGTTCGCAATTT 59.325 39.130 0.00 0.00 36.39 1.82
236 251 4.150451 GCTGCAATACTTGTTCGCAATTTT 59.850 37.500 0.00 0.00 36.39 1.82
237 252 5.333263 GCTGCAATACTTGTTCGCAATTTTT 60.333 36.000 0.00 0.00 36.39 1.94
238 253 6.128956 GCTGCAATACTTGTTCGCAATTTTTA 60.129 34.615 0.00 0.00 36.39 1.52
239 254 7.332003 TGCAATACTTGTTCGCAATTTTTAG 57.668 32.000 0.00 0.00 36.39 1.85
240 255 7.142021 TGCAATACTTGTTCGCAATTTTTAGA 58.858 30.769 0.00 0.00 36.39 2.10
241 256 7.114247 TGCAATACTTGTTCGCAATTTTTAGAC 59.886 33.333 0.00 0.00 36.39 2.59
242 257 7.326063 GCAATACTTGTTCGCAATTTTTAGACT 59.674 33.333 0.00 0.00 36.39 3.24
243 258 9.180678 CAATACTTGTTCGCAATTTTTAGACTT 57.819 29.630 0.00 0.00 36.39 3.01
244 259 8.950403 ATACTTGTTCGCAATTTTTAGACTTC 57.050 30.769 0.00 0.00 36.39 3.01
245 260 6.791303 ACTTGTTCGCAATTTTTAGACTTCA 58.209 32.000 0.00 0.00 36.39 3.02
246 261 7.254852 ACTTGTTCGCAATTTTTAGACTTCAA 58.745 30.769 0.00 0.00 36.39 2.69
247 262 7.757624 ACTTGTTCGCAATTTTTAGACTTCAAA 59.242 29.630 0.00 0.00 36.39 2.69
248 263 8.467402 TTGTTCGCAATTTTTAGACTTCAAAA 57.533 26.923 0.00 0.00 31.15 2.44
249 264 8.114359 TGTTCGCAATTTTTAGACTTCAAAAG 57.886 30.769 0.00 0.00 0.00 2.27
250 265 7.971168 TGTTCGCAATTTTTAGACTTCAAAAGA 59.029 29.630 0.00 0.00 0.00 2.52
251 266 8.968242 GTTCGCAATTTTTAGACTTCAAAAGAT 58.032 29.630 0.00 0.00 0.00 2.40
252 267 8.728088 TCGCAATTTTTAGACTTCAAAAGATC 57.272 30.769 0.00 0.00 0.00 2.75
253 268 8.567948 TCGCAATTTTTAGACTTCAAAAGATCT 58.432 29.630 0.00 0.00 0.00 2.75
254 269 9.185192 CGCAATTTTTAGACTTCAAAAGATCTT 57.815 29.630 0.88 0.88 0.00 2.40
277 292 5.893897 TTTTGCAAAAATGTTCAAAGCCT 57.106 30.435 21.94 0.00 31.20 4.58
278 293 5.893897 TTTGCAAAAATGTTCAAAGCCTT 57.106 30.435 10.02 0.00 0.00 4.35
279 294 5.482686 TTGCAAAAATGTTCAAAGCCTTC 57.517 34.783 0.00 0.00 0.00 3.46
280 295 3.876320 TGCAAAAATGTTCAAAGCCTTCC 59.124 39.130 0.00 0.00 0.00 3.46
281 296 3.059665 GCAAAAATGTTCAAAGCCTTCCG 60.060 43.478 0.00 0.00 0.00 4.30
282 297 3.385193 AAAATGTTCAAAGCCTTCCGG 57.615 42.857 0.00 0.00 0.00 5.14
283 298 2.286365 AATGTTCAAAGCCTTCCGGA 57.714 45.000 0.00 0.00 0.00 5.14
284 299 2.286365 ATGTTCAAAGCCTTCCGGAA 57.714 45.000 17.73 17.73 0.00 4.30
285 300 1.314730 TGTTCAAAGCCTTCCGGAAC 58.685 50.000 14.35 4.50 38.59 3.62
286 301 1.133915 TGTTCAAAGCCTTCCGGAACT 60.134 47.619 14.35 7.20 38.82 3.01
287 302 1.266989 GTTCAAAGCCTTCCGGAACTG 59.733 52.381 14.35 8.75 35.99 3.16
288 303 0.472471 TCAAAGCCTTCCGGAACTGT 59.528 50.000 14.35 1.66 0.00 3.55
289 304 1.133915 TCAAAGCCTTCCGGAACTGTT 60.134 47.619 14.35 2.38 0.00 3.16
290 305 1.001378 CAAAGCCTTCCGGAACTGTTG 60.001 52.381 14.35 11.24 0.00 3.33
291 306 0.537371 AAGCCTTCCGGAACTGTTGG 60.537 55.000 14.35 13.97 0.00 3.77
292 307 1.072505 GCCTTCCGGAACTGTTGGA 59.927 57.895 20.53 0.00 0.00 3.53
293 308 0.322546 GCCTTCCGGAACTGTTGGAT 60.323 55.000 20.53 0.00 0.00 3.41
294 309 1.886655 GCCTTCCGGAACTGTTGGATT 60.887 52.381 20.53 0.00 0.00 3.01
295 310 2.514803 CCTTCCGGAACTGTTGGATTT 58.485 47.619 14.35 0.00 0.00 2.17
296 311 2.228822 CCTTCCGGAACTGTTGGATTTG 59.771 50.000 14.35 0.00 0.00 2.32
297 312 2.940994 TCCGGAACTGTTGGATTTGA 57.059 45.000 0.00 0.00 0.00 2.69
298 313 2.778299 TCCGGAACTGTTGGATTTGAG 58.222 47.619 0.00 0.00 0.00 3.02
299 314 2.370519 TCCGGAACTGTTGGATTTGAGA 59.629 45.455 0.00 0.00 0.00 3.27
300 315 3.009033 TCCGGAACTGTTGGATTTGAGAT 59.991 43.478 0.00 0.00 0.00 2.75
301 316 3.375299 CCGGAACTGTTGGATTTGAGATC 59.625 47.826 0.00 0.00 0.00 2.75
302 317 3.375299 CGGAACTGTTGGATTTGAGATCC 59.625 47.826 0.00 0.00 38.66 3.36
303 318 4.335416 GGAACTGTTGGATTTGAGATCCA 58.665 43.478 0.00 0.00 45.71 3.41
309 324 3.433306 TGGATTTGAGATCCAACGGTT 57.567 42.857 1.68 0.00 44.54 4.44
310 325 3.343617 TGGATTTGAGATCCAACGGTTC 58.656 45.455 1.68 0.00 44.54 3.62
311 326 2.683362 GGATTTGAGATCCAACGGTTCC 59.317 50.000 0.00 0.00 38.09 3.62
312 327 3.610911 GATTTGAGATCCAACGGTTCCT 58.389 45.455 0.00 0.00 33.85 3.36
313 328 4.383770 GGATTTGAGATCCAACGGTTCCTA 60.384 45.833 0.00 0.00 38.09 2.94
314 329 3.887621 TTGAGATCCAACGGTTCCTAG 57.112 47.619 0.00 0.00 0.00 3.02
315 330 2.108168 TGAGATCCAACGGTTCCTAGG 58.892 52.381 0.82 0.82 0.00 3.02
316 331 2.291996 TGAGATCCAACGGTTCCTAGGA 60.292 50.000 7.62 7.62 0.00 2.94
317 332 2.362717 GAGATCCAACGGTTCCTAGGAG 59.637 54.545 12.26 3.05 0.00 3.69
318 333 0.831307 ATCCAACGGTTCCTAGGAGC 59.169 55.000 16.91 16.91 0.00 4.70
319 334 0.252103 TCCAACGGTTCCTAGGAGCT 60.252 55.000 23.20 3.62 0.00 4.09
320 335 0.175989 CCAACGGTTCCTAGGAGCTC 59.824 60.000 23.20 4.71 0.00 4.09
321 336 0.179134 CAACGGTTCCTAGGAGCTCG 60.179 60.000 23.20 23.93 0.00 5.03
322 337 0.611340 AACGGTTCCTAGGAGCTCGT 60.611 55.000 25.41 25.41 35.35 4.18
323 338 0.254178 ACGGTTCCTAGGAGCTCGTA 59.746 55.000 27.87 15.00 33.53 3.43
324 339 1.133853 ACGGTTCCTAGGAGCTCGTAT 60.134 52.381 27.87 13.59 33.53 3.06
325 340 1.536331 CGGTTCCTAGGAGCTCGTATC 59.464 57.143 23.20 6.43 0.00 2.24
326 341 2.584236 GGTTCCTAGGAGCTCGTATCA 58.416 52.381 23.20 3.81 0.00 2.15
327 342 3.158676 GGTTCCTAGGAGCTCGTATCAT 58.841 50.000 23.20 0.00 0.00 2.45
328 343 3.057174 GGTTCCTAGGAGCTCGTATCATG 60.057 52.174 23.20 5.20 0.00 3.07
329 344 2.796557 TCCTAGGAGCTCGTATCATGG 58.203 52.381 16.05 13.42 0.00 3.66
330 345 1.821753 CCTAGGAGCTCGTATCATGGG 59.178 57.143 16.05 9.89 0.00 4.00
331 346 2.555448 CCTAGGAGCTCGTATCATGGGA 60.555 54.545 16.05 0.00 31.45 4.37
332 347 1.626686 AGGAGCTCGTATCATGGGAG 58.373 55.000 7.25 0.00 0.00 4.30
339 354 4.790765 CTCGTATCATGGGAGCATCTAA 57.209 45.455 0.00 0.00 33.73 2.10
340 355 4.742417 CTCGTATCATGGGAGCATCTAAG 58.258 47.826 0.00 0.00 33.73 2.18
341 356 3.511540 TCGTATCATGGGAGCATCTAAGG 59.488 47.826 0.00 0.00 33.73 2.69
342 357 2.875094 ATCATGGGAGCATCTAAGGC 57.125 50.000 0.00 0.00 33.73 4.35
343 358 1.811778 TCATGGGAGCATCTAAGGCT 58.188 50.000 0.00 0.00 46.07 4.58
351 366 2.598565 AGCATCTAAGGCTCCGTATCA 58.401 47.619 0.00 0.00 36.81 2.15
352 367 2.297597 AGCATCTAAGGCTCCGTATCAC 59.702 50.000 0.00 0.00 36.81 3.06
353 368 2.610727 GCATCTAAGGCTCCGTATCACC 60.611 54.545 0.00 0.00 0.00 4.02
354 369 2.750141 TCTAAGGCTCCGTATCACCT 57.250 50.000 0.00 0.00 0.00 4.00
355 370 2.307768 TCTAAGGCTCCGTATCACCTG 58.692 52.381 0.00 0.00 31.32 4.00
356 371 2.092049 TCTAAGGCTCCGTATCACCTGA 60.092 50.000 0.00 0.00 31.32 3.86
357 372 1.794714 AAGGCTCCGTATCACCTGAT 58.205 50.000 0.00 0.00 38.51 2.90
358 373 2.677542 AGGCTCCGTATCACCTGATA 57.322 50.000 0.00 0.00 36.05 2.15
376 391 5.396772 CCTGATACTTTTCCTGCATCCAGTA 60.397 44.000 0.00 0.00 37.38 2.74
377 392 6.252599 TGATACTTTTCCTGCATCCAGTAT 57.747 37.500 0.00 0.00 37.38 2.12
450 3180 3.069443 GGAAAATCCAACTGGCAACAAGA 59.931 43.478 0.00 0.00 41.31 3.02
462 3192 1.600916 AACAAGACTTCGCAGCCCC 60.601 57.895 0.00 0.00 0.00 5.80
619 3350 1.145156 CGACACACTGACCCCACAA 59.855 57.895 0.00 0.00 0.00 3.33
622 3353 0.623723 ACACACTGACCCCACAACTT 59.376 50.000 0.00 0.00 0.00 2.66
656 3388 5.510861 GGCAGTCAGTGACTCTAACCTTTTA 60.511 44.000 23.08 0.00 41.37 1.52
727 3459 0.031585 TTATTCCCTGTCGATCGGCG 59.968 55.000 15.94 9.76 42.69 6.46
728 3460 1.105167 TATTCCCTGTCGATCGGCGT 61.105 55.000 15.94 0.00 41.80 5.68
766 3498 1.409064 TGCTTCCCACTACGCTGATAG 59.591 52.381 0.00 0.00 0.00 2.08
767 3499 1.409427 GCTTCCCACTACGCTGATAGT 59.591 52.381 0.00 0.00 35.72 2.12
768 3500 2.621998 GCTTCCCACTACGCTGATAGTA 59.378 50.000 0.00 0.00 33.50 1.82
814 3546 2.799126 AGTCACCATCTCGAGTCTCT 57.201 50.000 13.13 0.40 0.00 3.10
831 3563 5.990668 AGTCTCTGCCCGATTTTTATTACT 58.009 37.500 0.00 0.00 0.00 2.24
832 3564 7.120923 AGTCTCTGCCCGATTTTTATTACTA 57.879 36.000 0.00 0.00 0.00 1.82
833 3565 6.985059 AGTCTCTGCCCGATTTTTATTACTAC 59.015 38.462 0.00 0.00 0.00 2.73
835 3567 5.051816 TCTGCCCGATTTTTATTACTACGG 58.948 41.667 0.00 0.00 38.83 4.02
836 3568 5.021033 TGCCCGATTTTTATTACTACGGA 57.979 39.130 0.00 0.00 41.09 4.69
837 3569 5.051816 TGCCCGATTTTTATTACTACGGAG 58.948 41.667 0.00 0.00 41.09 4.63
838 3570 4.084171 GCCCGATTTTTATTACTACGGAGC 60.084 45.833 0.00 0.00 41.09 4.70
839 3571 5.051816 CCCGATTTTTATTACTACGGAGCA 58.948 41.667 0.00 0.00 41.09 4.26
840 3572 5.050567 CCCGATTTTTATTACTACGGAGCAC 60.051 44.000 0.00 0.00 41.09 4.40
843 3575 6.202188 CGATTTTTATTACTACGGAGCACCAT 59.798 38.462 0.00 0.00 35.59 3.55
865 3597 3.585990 GCCCACGCCCAATCATCG 61.586 66.667 0.00 0.00 0.00 3.84
874 3606 1.471676 GCCCAATCATCGTTCGTCTCT 60.472 52.381 0.00 0.00 0.00 3.10
1545 4278 0.532573 TCCGATCACAAGCACCTCTC 59.467 55.000 0.00 0.00 0.00 3.20
1567 4300 5.694816 TCGTCATTTCGTTTGTGCAATTAT 58.305 33.333 0.00 0.00 0.00 1.28
1572 4305 7.428183 GTCATTTCGTTTGTGCAATTATATCGT 59.572 33.333 0.00 0.00 0.00 3.73
1573 4306 8.604890 TCATTTCGTTTGTGCAATTATATCGTA 58.395 29.630 0.00 0.00 0.00 3.43
1574 4307 8.669801 CATTTCGTTTGTGCAATTATATCGTAC 58.330 33.333 0.00 0.00 0.00 3.67
1604 4337 1.379916 CAGGGTCTGCCACATTGGA 59.620 57.895 0.00 0.00 40.96 3.53
1631 4364 2.547211 GACCAATCTGATGCATTCGGAG 59.453 50.000 0.00 0.00 43.01 4.63
1681 4414 3.250280 TGCGACTACTTATCTAGCCGAAG 59.750 47.826 0.00 0.00 0.00 3.79
1870 4616 8.922931 TCTTGCTATTGCTATGATATGGAAAA 57.077 30.769 0.00 0.00 40.48 2.29
1871 4617 9.524496 TCTTGCTATTGCTATGATATGGAAAAT 57.476 29.630 0.00 0.00 40.48 1.82
1914 4660 4.891992 TCTCCTCTACCAGAAAACCAAG 57.108 45.455 0.00 0.00 0.00 3.61
1941 4687 4.202503 ACTCCAATGACTGTGTCAAATCCT 60.203 41.667 4.46 0.00 45.96 3.24
2081 4827 8.999431 GGTGTCTTTCTTCATGTATTTGAGTTA 58.001 33.333 0.00 0.00 0.00 2.24
2112 4860 6.463995 AAGAGTGCTAACAATTTTCCACAA 57.536 33.333 0.00 0.00 0.00 3.33
2464 5212 5.939296 TCTGATAATCATGAAGTTGCACACA 59.061 36.000 0.00 0.00 0.00 3.72
2512 5260 7.948357 ACAATTATCATGATGAATTGGGTCTG 58.052 34.615 29.53 18.15 42.34 3.51
2609 5357 2.996621 CGTCCTCTCTGTTCATTGAACC 59.003 50.000 23.22 8.96 41.35 3.62
2784 5543 2.871633 GCAAAGTTTGGTGGTCAAATGG 59.128 45.455 17.11 0.00 45.79 3.16
2785 5544 2.871633 CAAAGTTTGGTGGTCAAATGGC 59.128 45.455 7.78 0.00 45.79 4.40
2851 5611 6.255453 GTGCACTGTTTGAGCAAAATTTCTAA 59.745 34.615 10.32 0.00 43.40 2.10
2913 5673 2.798283 CACCAAACTTTGCAAGCATCTG 59.202 45.455 0.00 0.00 0.00 2.90
2914 5674 1.796459 CCAAACTTTGCAAGCATCTGC 59.204 47.619 0.00 0.00 42.95 4.26
2983 5743 7.516470 CGAAATGTTTTGCTATGTTTTCTTGCA 60.516 33.333 0.00 0.00 0.00 4.08
2993 5753 6.092670 GCTATGTTTTCTTGCATGAGTGTAGA 59.907 38.462 0.00 0.00 0.00 2.59
3397 6157 6.200854 ACTTTTGATCATTTCGGAAAAGCAAC 59.799 34.615 7.33 0.20 37.20 4.17
3472 6232 9.398170 CTTAACTCACCTGAACATTATTTTGTG 57.602 33.333 0.00 0.00 0.00 3.33
3614 6374 1.076332 AAGGTCGCGTGCAATCTTAC 58.924 50.000 5.77 0.00 0.00 2.34
4047 6809 4.973168 TGATCTGTCACCAAAGTAAGCTT 58.027 39.130 3.48 3.48 36.30 3.74
4161 6923 4.412207 GTTTCAGAAATATTGTGCGGGAC 58.588 43.478 0.00 0.00 0.00 4.46
4596 7358 8.765219 AGTACGTAATTCAAATGAGCACATATC 58.235 33.333 0.00 0.00 35.50 1.63
4913 7678 2.169352 AGCTCTGCTTTCACGTATCCAT 59.831 45.455 0.00 0.00 33.89 3.41
5187 7953 6.291377 TCTCACTGATCTAACTGCAAAAACT 58.709 36.000 0.00 0.00 0.00 2.66
5341 8107 6.752335 TTGAAATTGCTTCAGTTCATTTCG 57.248 33.333 0.00 0.00 44.84 3.46
5722 8494 8.673711 CCTCCGAAAGTCAATGACATATTTTTA 58.326 33.333 16.38 0.00 34.60 1.52
5863 8635 1.985473 TCATTTGCAGCAGGACAACT 58.015 45.000 0.00 0.00 0.00 3.16
5895 8896 1.952990 TGGTGACAAATGACGCATTGT 59.047 42.857 5.95 1.37 37.44 2.71
6228 9229 6.348950 GCAAGTATAACATGGCAGTAACACAA 60.349 38.462 0.00 0.00 0.00 3.33
6340 9341 7.727634 AGGATTGAGGAAATTGAGAAAGTCTTT 59.272 33.333 0.00 0.00 0.00 2.52
6364 9365 4.035208 AGCCAAAGTCTTCAAACAGTAACG 59.965 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.488645 ACGTTACCGATTTTTGTTGTTCT 57.511 34.783 0.00 0.00 37.88 3.01
1 2 5.967088 AGAACGTTACCGATTTTTGTTGTTC 59.033 36.000 0.00 0.00 37.88 3.18
10 11 7.662604 AGAAACATAAGAACGTTACCGATTT 57.337 32.000 0.00 0.00 37.88 2.17
72 87 6.639686 CCACATTTGATGCAGTAATTCATAGC 59.360 38.462 0.00 0.00 0.00 2.97
109 124 2.169144 CACCTGATACTCACTGGATGCA 59.831 50.000 0.00 0.00 0.00 3.96
110 125 2.432146 TCACCTGATACTCACTGGATGC 59.568 50.000 0.00 0.00 0.00 3.91
111 126 4.952071 ATCACCTGATACTCACTGGATG 57.048 45.455 0.00 0.00 32.01 3.51
122 137 7.255977 GCATCTAAGTCTTGGTATCACCTGATA 60.256 40.741 0.00 0.00 39.58 2.15
123 138 6.463614 GCATCTAAGTCTTGGTATCACCTGAT 60.464 42.308 0.00 0.00 39.58 2.90
124 139 5.163405 GCATCTAAGTCTTGGTATCACCTGA 60.163 44.000 0.00 0.00 39.58 3.86
125 140 5.053145 GCATCTAAGTCTTGGTATCACCTG 58.947 45.833 0.00 0.00 39.58 4.00
126 141 4.965532 AGCATCTAAGTCTTGGTATCACCT 59.034 41.667 0.00 0.00 39.58 4.00
127 142 5.283457 AGCATCTAAGTCTTGGTATCACC 57.717 43.478 0.00 0.00 39.22 4.02
128 143 5.293560 GGAGCATCTAAGTCTTGGTATCAC 58.706 45.833 0.00 0.00 33.73 3.06
129 144 4.345257 GGGAGCATCTAAGTCTTGGTATCA 59.655 45.833 0.00 0.00 33.73 2.15
130 145 4.345257 TGGGAGCATCTAAGTCTTGGTATC 59.655 45.833 0.00 0.00 33.73 2.24
131 146 4.298626 TGGGAGCATCTAAGTCTTGGTAT 58.701 43.478 0.00 0.00 33.73 2.73
132 147 3.719871 TGGGAGCATCTAAGTCTTGGTA 58.280 45.455 0.00 0.00 33.73 3.25
133 148 2.551270 TGGGAGCATCTAAGTCTTGGT 58.449 47.619 0.00 0.00 33.73 3.67
134 149 3.135348 TCATGGGAGCATCTAAGTCTTGG 59.865 47.826 0.00 0.00 33.73 3.61
135 150 4.412796 TCATGGGAGCATCTAAGTCTTG 57.587 45.455 0.00 0.00 33.73 3.02
136 151 5.279206 CGTATCATGGGAGCATCTAAGTCTT 60.279 44.000 0.00 0.00 33.73 3.01
137 152 4.219507 CGTATCATGGGAGCATCTAAGTCT 59.780 45.833 0.00 0.00 33.73 3.24
138 153 4.218635 TCGTATCATGGGAGCATCTAAGTC 59.781 45.833 0.00 0.00 33.73 3.01
139 154 4.152647 TCGTATCATGGGAGCATCTAAGT 58.847 43.478 0.00 0.00 33.73 2.24
140 155 4.742417 CTCGTATCATGGGAGCATCTAAG 58.258 47.826 0.00 0.00 33.73 2.18
141 156 4.790765 CTCGTATCATGGGAGCATCTAA 57.209 45.455 0.00 0.00 33.73 2.10
148 163 3.181471 ACAAGAAGCTCGTATCATGGGAG 60.181 47.826 0.00 0.00 0.00 4.30
149 164 2.766263 ACAAGAAGCTCGTATCATGGGA 59.234 45.455 0.00 0.00 0.00 4.37
150 165 3.126831 GACAAGAAGCTCGTATCATGGG 58.873 50.000 0.00 0.00 0.00 4.00
151 166 3.785486 TGACAAGAAGCTCGTATCATGG 58.215 45.455 0.00 0.00 0.00 3.66
152 167 4.428209 ACTGACAAGAAGCTCGTATCATG 58.572 43.478 0.00 0.00 0.00 3.07
153 168 4.727507 ACTGACAAGAAGCTCGTATCAT 57.272 40.909 0.00 0.00 0.00 2.45
154 169 4.237724 CAACTGACAAGAAGCTCGTATCA 58.762 43.478 0.00 0.00 0.00 2.15
155 170 3.614616 CCAACTGACAAGAAGCTCGTATC 59.385 47.826 0.00 0.00 0.00 2.24
156 171 3.258372 TCCAACTGACAAGAAGCTCGTAT 59.742 43.478 0.00 0.00 0.00 3.06
157 172 2.626266 TCCAACTGACAAGAAGCTCGTA 59.374 45.455 0.00 0.00 0.00 3.43
158 173 1.412710 TCCAACTGACAAGAAGCTCGT 59.587 47.619 0.00 0.00 0.00 4.18
159 174 2.154854 TCCAACTGACAAGAAGCTCG 57.845 50.000 0.00 0.00 0.00 5.03
160 175 3.936564 AGATCCAACTGACAAGAAGCTC 58.063 45.455 0.00 0.00 0.00 4.09
161 176 4.363991 AAGATCCAACTGACAAGAAGCT 57.636 40.909 0.00 0.00 0.00 3.74
162 177 5.482908 TCTAAGATCCAACTGACAAGAAGC 58.517 41.667 0.00 0.00 0.00 3.86
163 178 6.760770 GGATCTAAGATCCAACTGACAAGAAG 59.239 42.308 0.00 0.00 38.09 2.85
164 179 6.213397 TGGATCTAAGATCCAACTGACAAGAA 59.787 38.462 16.82 0.00 44.54 2.52
165 180 5.721480 TGGATCTAAGATCCAACTGACAAGA 59.279 40.000 16.82 0.00 44.54 3.02
166 181 5.982356 TGGATCTAAGATCCAACTGACAAG 58.018 41.667 16.82 0.00 44.54 3.16
175 190 2.365617 GAGCCGTTGGATCTAAGATCCA 59.634 50.000 15.76 15.76 45.71 3.41
176 191 2.608261 CGAGCCGTTGGATCTAAGATCC 60.608 54.545 0.00 0.00 35.75 3.36
177 192 2.034812 ACGAGCCGTTGGATCTAAGATC 59.965 50.000 0.00 0.00 36.35 2.75
178 193 2.032620 ACGAGCCGTTGGATCTAAGAT 58.967 47.619 0.00 0.00 36.35 2.40
179 194 1.471119 ACGAGCCGTTGGATCTAAGA 58.529 50.000 0.00 0.00 36.35 2.10
180 195 3.001395 CTACGAGCCGTTGGATCTAAG 57.999 52.381 5.57 0.00 41.54 2.18
188 203 0.601841 AAACCACCTACGAGCCGTTG 60.602 55.000 5.57 4.21 41.54 4.10
189 204 0.107268 AAAACCACCTACGAGCCGTT 59.893 50.000 5.57 0.00 41.54 4.44
190 205 0.601841 CAAAACCACCTACGAGCCGT 60.602 55.000 5.58 5.58 44.35 5.68
191 206 0.320073 TCAAAACCACCTACGAGCCG 60.320 55.000 0.00 0.00 0.00 5.52
192 207 1.804748 CTTCAAAACCACCTACGAGCC 59.195 52.381 0.00 0.00 0.00 4.70
193 208 1.804748 CCTTCAAAACCACCTACGAGC 59.195 52.381 0.00 0.00 0.00 5.03
194 209 1.804748 GCCTTCAAAACCACCTACGAG 59.195 52.381 0.00 0.00 0.00 4.18
195 210 1.418637 AGCCTTCAAAACCACCTACGA 59.581 47.619 0.00 0.00 0.00 3.43
196 211 1.535462 CAGCCTTCAAAACCACCTACG 59.465 52.381 0.00 0.00 0.00 3.51
197 212 1.269723 GCAGCCTTCAAAACCACCTAC 59.730 52.381 0.00 0.00 0.00 3.18
198 213 1.133637 TGCAGCCTTCAAAACCACCTA 60.134 47.619 0.00 0.00 0.00 3.08
199 214 0.396974 TGCAGCCTTCAAAACCACCT 60.397 50.000 0.00 0.00 0.00 4.00
200 215 0.463620 TTGCAGCCTTCAAAACCACC 59.536 50.000 0.00 0.00 0.00 4.61
201 216 2.531522 ATTGCAGCCTTCAAAACCAC 57.468 45.000 0.00 0.00 0.00 4.16
202 217 3.230134 AGTATTGCAGCCTTCAAAACCA 58.770 40.909 0.00 0.00 0.00 3.67
203 218 3.942130 AGTATTGCAGCCTTCAAAACC 57.058 42.857 0.00 0.00 0.00 3.27
218 233 9.394477 GAAGTCTAAAAATTGCGAACAAGTATT 57.606 29.630 0.00 0.00 39.69 1.89
219 234 8.564574 TGAAGTCTAAAAATTGCGAACAAGTAT 58.435 29.630 0.00 0.00 39.69 2.12
220 235 7.921787 TGAAGTCTAAAAATTGCGAACAAGTA 58.078 30.769 0.00 0.00 39.69 2.24
221 236 6.791303 TGAAGTCTAAAAATTGCGAACAAGT 58.209 32.000 0.00 0.00 39.69 3.16
222 237 7.678194 TTGAAGTCTAAAAATTGCGAACAAG 57.322 32.000 0.00 0.00 39.69 3.16
223 238 8.467402 TTTTGAAGTCTAAAAATTGCGAACAA 57.533 26.923 0.00 0.00 40.87 2.83
224 239 7.971168 TCTTTTGAAGTCTAAAAATTGCGAACA 59.029 29.630 0.00 0.00 0.00 3.18
225 240 8.335256 TCTTTTGAAGTCTAAAAATTGCGAAC 57.665 30.769 0.00 0.00 0.00 3.95
226 241 9.180678 GATCTTTTGAAGTCTAAAAATTGCGAA 57.819 29.630 0.00 0.00 0.00 4.70
227 242 8.567948 AGATCTTTTGAAGTCTAAAAATTGCGA 58.432 29.630 0.00 0.00 0.00 5.10
228 243 8.733857 AGATCTTTTGAAGTCTAAAAATTGCG 57.266 30.769 0.00 0.00 0.00 4.85
254 269 6.264841 AGGCTTTGAACATTTTTGCAAAAA 57.735 29.167 32.91 32.91 41.59 1.94
255 270 5.893897 AGGCTTTGAACATTTTTGCAAAA 57.106 30.435 20.46 20.46 30.78 2.44
256 271 5.163673 GGAAGGCTTTGAACATTTTTGCAAA 60.164 36.000 8.05 8.05 0.00 3.68
257 272 4.335037 GGAAGGCTTTGAACATTTTTGCAA 59.665 37.500 0.00 0.00 0.00 4.08
258 273 3.876320 GGAAGGCTTTGAACATTTTTGCA 59.124 39.130 0.00 0.00 0.00 4.08
259 274 3.059665 CGGAAGGCTTTGAACATTTTTGC 60.060 43.478 0.00 0.00 0.00 3.68
260 275 4.713854 CGGAAGGCTTTGAACATTTTTG 57.286 40.909 0.00 0.00 0.00 2.44
276 291 3.146066 TCAAATCCAACAGTTCCGGAAG 58.854 45.455 19.50 9.76 31.18 3.46
277 292 3.146066 CTCAAATCCAACAGTTCCGGAA 58.854 45.455 14.35 14.35 31.18 4.30
278 293 2.370519 TCTCAAATCCAACAGTTCCGGA 59.629 45.455 0.00 0.00 0.00 5.14
279 294 2.778299 TCTCAAATCCAACAGTTCCGG 58.222 47.619 0.00 0.00 0.00 5.14
280 295 3.375299 GGATCTCAAATCCAACAGTTCCG 59.625 47.826 0.00 0.00 38.09 4.30
281 296 4.335416 TGGATCTCAAATCCAACAGTTCC 58.665 43.478 4.30 0.00 44.54 3.62
289 304 3.343617 GAACCGTTGGATCTCAAATCCA 58.656 45.455 2.63 2.63 45.71 3.41
290 305 2.683362 GGAACCGTTGGATCTCAAATCC 59.317 50.000 0.00 0.00 37.08 3.01
291 306 3.610911 AGGAACCGTTGGATCTCAAATC 58.389 45.455 0.00 0.00 37.08 2.17
292 307 3.721087 AGGAACCGTTGGATCTCAAAT 57.279 42.857 0.00 0.00 37.08 2.32
293 308 3.055385 CCTAGGAACCGTTGGATCTCAAA 60.055 47.826 1.05 0.00 37.08 2.69
294 309 2.500098 CCTAGGAACCGTTGGATCTCAA 59.500 50.000 1.05 0.00 0.00 3.02
295 310 2.108168 CCTAGGAACCGTTGGATCTCA 58.892 52.381 1.05 0.00 0.00 3.27
296 311 2.362717 CTCCTAGGAACCGTTGGATCTC 59.637 54.545 13.77 0.00 0.00 2.75
297 312 2.389715 CTCCTAGGAACCGTTGGATCT 58.610 52.381 13.77 0.00 0.00 2.75
298 313 1.202545 GCTCCTAGGAACCGTTGGATC 60.203 57.143 13.77 0.00 0.00 3.36
299 314 0.831307 GCTCCTAGGAACCGTTGGAT 59.169 55.000 13.77 0.00 0.00 3.41
300 315 0.252103 AGCTCCTAGGAACCGTTGGA 60.252 55.000 13.77 0.00 0.00 3.53
301 316 0.175989 GAGCTCCTAGGAACCGTTGG 59.824 60.000 13.77 0.00 0.00 3.77
302 317 0.179134 CGAGCTCCTAGGAACCGTTG 60.179 60.000 13.77 0.61 0.00 4.10
303 318 0.611340 ACGAGCTCCTAGGAACCGTT 60.611 55.000 20.45 6.31 0.00 4.44
304 319 0.254178 TACGAGCTCCTAGGAACCGT 59.746 55.000 25.77 25.77 0.00 4.83
305 320 1.536331 GATACGAGCTCCTAGGAACCG 59.464 57.143 13.77 17.32 0.00 4.44
306 321 2.584236 TGATACGAGCTCCTAGGAACC 58.416 52.381 13.77 6.96 0.00 3.62
307 322 3.057174 CCATGATACGAGCTCCTAGGAAC 60.057 52.174 13.77 8.72 0.00 3.62
308 323 3.157881 CCATGATACGAGCTCCTAGGAA 58.842 50.000 13.77 0.00 0.00 3.36
309 324 2.555448 CCCATGATACGAGCTCCTAGGA 60.555 54.545 11.98 11.98 0.00 2.94
310 325 1.821753 CCCATGATACGAGCTCCTAGG 59.178 57.143 8.47 0.82 0.00 3.02
311 326 2.752354 CTCCCATGATACGAGCTCCTAG 59.248 54.545 8.47 0.00 0.00 3.02
312 327 2.796557 CTCCCATGATACGAGCTCCTA 58.203 52.381 8.47 0.89 0.00 2.94
313 328 1.626686 CTCCCATGATACGAGCTCCT 58.373 55.000 8.47 0.00 0.00 3.69
314 329 0.037790 GCTCCCATGATACGAGCTCC 60.038 60.000 8.47 0.00 44.52 4.70
315 330 3.505808 GCTCCCATGATACGAGCTC 57.494 57.895 2.73 2.73 44.52 4.09
318 333 4.381398 CCTTAGATGCTCCCATGATACGAG 60.381 50.000 0.00 0.00 0.00 4.18
319 334 3.511540 CCTTAGATGCTCCCATGATACGA 59.488 47.826 0.00 0.00 0.00 3.43
320 335 3.854666 CCTTAGATGCTCCCATGATACG 58.145 50.000 0.00 0.00 0.00 3.06
321 336 3.262915 AGCCTTAGATGCTCCCATGATAC 59.737 47.826 0.00 0.00 32.41 2.24
322 337 3.524826 AGCCTTAGATGCTCCCATGATA 58.475 45.455 0.00 0.00 32.41 2.15
323 338 2.346529 AGCCTTAGATGCTCCCATGAT 58.653 47.619 0.00 0.00 32.41 2.45
324 339 1.811778 AGCCTTAGATGCTCCCATGA 58.188 50.000 0.00 0.00 32.41 3.07
331 346 2.297597 GTGATACGGAGCCTTAGATGCT 59.702 50.000 0.00 0.00 43.03 3.79
332 347 2.610727 GGTGATACGGAGCCTTAGATGC 60.611 54.545 0.00 0.00 0.00 3.91
333 348 2.894126 AGGTGATACGGAGCCTTAGATG 59.106 50.000 0.00 0.00 0.00 2.90
334 349 2.894126 CAGGTGATACGGAGCCTTAGAT 59.106 50.000 0.00 0.00 0.00 1.98
335 350 2.092049 TCAGGTGATACGGAGCCTTAGA 60.092 50.000 0.00 0.00 0.00 2.10
336 351 2.307768 TCAGGTGATACGGAGCCTTAG 58.692 52.381 0.00 0.00 0.00 2.18
337 352 2.447408 TCAGGTGATACGGAGCCTTA 57.553 50.000 0.00 0.00 0.00 2.69
338 353 1.794714 ATCAGGTGATACGGAGCCTT 58.205 50.000 0.00 0.00 32.01 4.35
339 354 2.240279 GTATCAGGTGATACGGAGCCT 58.760 52.381 13.08 0.00 44.88 4.58
340 355 2.726832 GTATCAGGTGATACGGAGCC 57.273 55.000 13.08 0.00 44.88 4.70
347 362 5.692115 TGCAGGAAAAGTATCAGGTGATA 57.308 39.130 0.00 0.00 36.05 2.15
348 363 4.574674 TGCAGGAAAAGTATCAGGTGAT 57.425 40.909 0.00 0.00 38.51 3.06
349 364 4.517285 GATGCAGGAAAAGTATCAGGTGA 58.483 43.478 0.00 0.00 0.00 4.02
350 365 3.629398 GGATGCAGGAAAAGTATCAGGTG 59.371 47.826 0.00 0.00 30.84 4.00
351 366 3.266772 TGGATGCAGGAAAAGTATCAGGT 59.733 43.478 0.00 0.00 30.84 4.00
352 367 3.881688 CTGGATGCAGGAAAAGTATCAGG 59.118 47.826 6.28 0.00 30.84 3.86
353 368 4.521146 ACTGGATGCAGGAAAAGTATCAG 58.479 43.478 19.22 0.00 30.84 2.90
354 369 4.574674 ACTGGATGCAGGAAAAGTATCA 57.425 40.909 19.22 0.00 30.84 2.15
355 370 5.703130 GGATACTGGATGCAGGAAAAGTATC 59.297 44.000 19.22 19.46 42.71 2.24
356 371 5.456763 GGGATACTGGATGCAGGAAAAGTAT 60.457 44.000 19.22 6.71 34.42 2.12
357 372 4.141482 GGGATACTGGATGCAGGAAAAGTA 60.141 45.833 19.22 1.70 0.00 2.24
358 373 3.372025 GGGATACTGGATGCAGGAAAAGT 60.372 47.826 19.22 0.00 0.00 2.66
359 374 3.217626 GGGATACTGGATGCAGGAAAAG 58.782 50.000 19.22 0.00 0.00 2.27
360 375 2.580322 TGGGATACTGGATGCAGGAAAA 59.420 45.455 19.22 1.37 0.00 2.29
361 376 2.204463 TGGGATACTGGATGCAGGAAA 58.796 47.619 19.22 3.95 0.00 3.13
362 377 1.891933 TGGGATACTGGATGCAGGAA 58.108 50.000 19.22 6.59 0.00 3.36
363 378 1.891933 TTGGGATACTGGATGCAGGA 58.108 50.000 19.22 10.98 0.00 3.86
364 379 2.092212 ACTTTGGGATACTGGATGCAGG 60.092 50.000 19.22 0.68 0.00 4.85
365 380 3.287867 ACTTTGGGATACTGGATGCAG 57.712 47.619 13.34 13.34 0.00 4.41
435 3165 1.002468 CGAAGTCTTGTTGCCAGTTGG 60.002 52.381 0.00 0.00 38.53 3.77
462 3192 0.249489 AGCTGAATAACTAGCGGGCG 60.249 55.000 0.00 0.00 44.43 6.13
472 3202 2.686405 TCGCCTTCGTCTAGCTGAATAA 59.314 45.455 0.00 0.00 36.96 1.40
727 3459 2.285743 AGCAAGGGAGGGGAGGAC 60.286 66.667 0.00 0.00 0.00 3.85
728 3460 2.041265 GAGCAAGGGAGGGGAGGA 59.959 66.667 0.00 0.00 0.00 3.71
766 3498 0.672711 GGAGCGGGAGTTGTTGGTAC 60.673 60.000 0.00 0.00 0.00 3.34
767 3499 1.675219 GGAGCGGGAGTTGTTGGTA 59.325 57.895 0.00 0.00 0.00 3.25
768 3500 2.430367 GGAGCGGGAGTTGTTGGT 59.570 61.111 0.00 0.00 0.00 3.67
795 3527 2.364632 CAGAGACTCGAGATGGTGACT 58.635 52.381 21.68 6.22 0.00 3.41
814 3546 5.021033 TCCGTAGTAATAAAAATCGGGCA 57.979 39.130 0.00 0.00 37.54 5.36
831 3563 1.067416 GCGATGATGGTGCTCCGTA 59.933 57.895 0.00 0.00 36.30 4.02
832 3564 2.202932 GCGATGATGGTGCTCCGT 60.203 61.111 0.00 0.00 36.30 4.69
833 3565 2.969238 GGCGATGATGGTGCTCCG 60.969 66.667 0.00 0.00 36.30 4.63
835 3567 2.182842 GTGGGCGATGATGGTGCTC 61.183 63.158 0.00 0.00 0.00 4.26
836 3568 2.124570 GTGGGCGATGATGGTGCT 60.125 61.111 0.00 0.00 0.00 4.40
837 3569 3.576356 CGTGGGCGATGATGGTGC 61.576 66.667 0.00 0.00 41.33 5.01
838 3570 3.576356 GCGTGGGCGATGATGGTG 61.576 66.667 0.00 0.00 41.33 4.17
839 3571 4.856801 GGCGTGGGCGATGATGGT 62.857 66.667 0.00 0.00 41.24 3.55
843 3575 4.108299 ATTGGGCGTGGGCGATGA 62.108 61.111 0.00 0.00 41.24 2.92
865 3597 3.738590 GCTTCTGGGGATTAGAGACGAAC 60.739 52.174 0.00 0.00 0.00 3.95
874 3606 0.623723 GTGGGTGCTTCTGGGGATTA 59.376 55.000 0.00 0.00 0.00 1.75
978 3711 3.678717 CTCCCACAGCCGACGTACG 62.679 68.421 15.01 15.01 42.18 3.67
979 3712 2.181021 CTCCCACAGCCGACGTAC 59.819 66.667 0.00 0.00 0.00 3.67
980 3713 3.066190 CCTCCCACAGCCGACGTA 61.066 66.667 0.00 0.00 0.00 3.57
986 3719 4.864334 CCATCGCCTCCCACAGCC 62.864 72.222 0.00 0.00 0.00 4.85
1461 4194 0.036306 GGGGTGGCGAGAGAAGAAAA 59.964 55.000 0.00 0.00 0.00 2.29
1545 4278 5.990745 ATAATTGCACAAACGAAATGACG 57.009 34.783 0.00 0.00 39.31 4.35
1572 4305 5.435291 GCAGACCCTGTACTCTTAGTAGTA 58.565 45.833 0.00 0.00 30.12 1.82
1573 4306 4.271661 GCAGACCCTGTACTCTTAGTAGT 58.728 47.826 0.00 0.00 30.12 2.73
1574 4307 3.633065 GGCAGACCCTGTACTCTTAGTAG 59.367 52.174 0.00 0.00 30.12 2.57
1604 4337 2.730382 TGCATCAGATTGGTCATTGCT 58.270 42.857 0.00 0.00 31.26 3.91
1616 4349 2.352127 CGCTATCTCCGAATGCATCAGA 60.352 50.000 0.00 0.00 0.00 3.27
1631 4364 4.623167 CCATGCGCCTATATTATCGCTATC 59.377 45.833 4.18 0.00 46.73 2.08
1688 4421 4.037089 TGCATGCATAGAAATACAAGCTGG 59.963 41.667 18.46 0.00 0.00 4.85
1880 4626 9.213777 TCTGGTAGAGGAGAATAACAAATGTAT 57.786 33.333 0.00 0.00 0.00 2.29
1881 4627 8.603898 TCTGGTAGAGGAGAATAACAAATGTA 57.396 34.615 0.00 0.00 0.00 2.29
1882 4628 7.496346 TCTGGTAGAGGAGAATAACAAATGT 57.504 36.000 0.00 0.00 0.00 2.71
1883 4629 8.792830 TTTCTGGTAGAGGAGAATAACAAATG 57.207 34.615 0.00 0.00 0.00 2.32
1914 4660 3.995199 TGACACAGTCATTGGAGTCTTC 58.005 45.455 0.00 0.00 37.67 2.87
2081 4827 8.409358 AAAATTGTTAGCACTCTTATCCAAGT 57.591 30.769 0.00 0.00 33.20 3.16
2127 4875 9.078753 CACGTTTTCAACCTTAACACTTTTAAT 57.921 29.630 0.00 0.00 0.00 1.40
2784 5543 1.135139 TGTACAGAGCTCCTCGAATGC 59.865 52.381 10.93 0.00 35.36 3.56
2785 5544 3.510388 TTGTACAGAGCTCCTCGAATG 57.490 47.619 10.93 3.23 35.36 2.67
2913 5673 9.532697 GTGAAAATGATTATGAACAAATGTTGC 57.467 29.630 3.05 0.00 38.56 4.17
2983 5743 1.276421 GTGCACCCACTCTACACTCAT 59.724 52.381 5.22 0.00 38.93 2.90
2993 5753 4.320456 CAGCTCGGTGCACCCACT 62.320 66.667 29.95 20.69 45.94 4.00
3451 6211 7.202526 ACAACACAAAATAATGTTCAGGTGAG 58.797 34.615 0.00 0.00 36.92 3.51
3614 6374 0.109132 GGGCAAACCTGATCGCTTTG 60.109 55.000 5.57 5.57 35.85 2.77
3674 6434 5.763204 AGATACAGCTTTGAAGGAAAACGAA 59.237 36.000 0.00 0.00 0.00 3.85
3676 6436 5.613358 AGATACAGCTTTGAAGGAAAACG 57.387 39.130 0.00 0.00 0.00 3.60
4161 6923 4.379499 GCCACCTTAAGTTTTCCTTCATCG 60.379 45.833 0.97 0.00 34.46 3.84
4596 7358 1.332377 GCGTGCGATGCTTAGCTAAAG 60.332 52.381 7.74 3.37 38.32 1.85
4913 7678 1.619654 CTGGACAATGCAGGGAAACA 58.380 50.000 0.00 0.00 31.71 2.83
5341 8107 3.075148 GCTCAAGTTTCCCAGAGTTACC 58.925 50.000 0.00 0.00 0.00 2.85
5731 8503 4.817464 ACAGTCGCTACATTTTGGTGTTTA 59.183 37.500 0.00 0.00 33.62 2.01
5863 8635 4.991153 TTTGTCACCACAATAAGCACAA 57.009 36.364 0.00 0.00 42.28 3.33
6060 9061 2.750350 CACTTTCGGGGAGGTGCT 59.250 61.111 0.00 0.00 0.00 4.40
6340 9341 5.235616 CGTTACTGTTTGAAGACTTTGGCTA 59.764 40.000 0.00 0.00 0.00 3.93
6364 9365 9.806203 TTCATTCATATGTTGATGAAATTGACC 57.194 29.630 19.70 0.00 46.22 4.02
6398 9399 4.354087 ACTGGTTCTATTTCCTCAACCCTT 59.646 41.667 0.00 0.00 38.02 3.95


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

AutoCloner maintained by Alex Coulton.