Multiple sequence alignment - TraesCS1D01G245400

Loading Multiple Alignment...

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 TraesCS1D01G245400 chr1D 100.000 7430 0 0 1 7430 336546338 336553767 0.000000e+00 13721.0
1 TraesCS1D01G245400 chr1D 98.551 69 1 0 326 394 336546582 336546650 1.010000e-23 122.0
2 TraesCS1D01G245400 chr1D 98.551 69 1 0 245 313 336546663 336546731 1.010000e-23 122.0
3 TraesCS1D01G245400 chr1D 75.263 190 35 10 3853 4035 480625475 480625659 6.180000e-11 80.5
4 TraesCS1D01G245400 chr1D 75.132 189 35 10 3854 4035 480623485 480623668 2.220000e-10 78.7
5 TraesCS1D01G245400 chr1D 74.211 190 36 11 3853 4035 480622822 480623005 4.810000e-07 67.6
6 TraesCS1D01G245400 chr1B 95.851 7062 214 31 419 7424 452310982 452318020 0.000000e+00 11345.0
7 TraesCS1D01G245400 chr1B 92.593 81 2 2 1 81 452310827 452310903 6.090000e-21 113.0
8 TraesCS1D01G245400 chr1B 90.278 72 6 1 321 392 452310910 452310980 7.940000e-15 93.5
9 TraesCS1D01G245400 chr1B 89.231 65 6 1 247 311 452310917 452310980 6.180000e-11 80.5
10 TraesCS1D01G245400 chr1A 96.547 3417 73 13 4036 7430 435060028 435063421 0.000000e+00 5614.0
11 TraesCS1D01G245400 chr1A 96.157 3227 90 15 649 3849 435056805 435060023 0.000000e+00 5241.0
12 TraesCS1D01G245400 chr1A 93.671 237 10 4 312 548 435056576 435056807 4.270000e-92 350.0
13 TraesCS1D01G245400 chr1A 94.074 135 8 0 83 217 566481169 566481035 9.770000e-49 206.0
14 TraesCS1D01G245400 chr1A 89.744 78 4 1 1 78 435056496 435056569 6.140000e-16 97.1
15 TraesCS1D01G245400 chr1A 91.045 67 4 2 247 313 435056592 435056656 1.030000e-13 89.8
16 TraesCS1D01G245400 chr3B 84.986 353 31 11 6163 6506 16225863 16225524 9.230000e-89 339.0
17 TraesCS1D01G245400 chr3B 88.679 53 6 0 3982 4034 751088626 751088678 1.730000e-06 65.8
18 TraesCS1D01G245400 chr7D 87.766 188 17 3 3853 4034 408739987 408740174 1.620000e-51 215.0
19 TraesCS1D01G245400 chr7D 100.000 30 0 0 5258 5287 29393067 29393038 1.000000e-03 56.5
20 TraesCS1D01G245400 chr4A 89.759 166 9 4 82 239 517406633 517406468 9.770000e-49 206.0
21 TraesCS1D01G245400 chr2D 92.308 143 11 0 75 217 81004926 81004784 3.510000e-48 204.0
22 TraesCS1D01G245400 chr2D 92.701 137 10 0 81 217 362930971 362930835 1.640000e-46 198.0
23 TraesCS1D01G245400 chr6B 92.857 140 9 1 78 217 132353412 132353550 1.260000e-47 202.0
24 TraesCS1D01G245400 chr2A 93.333 135 9 0 83 217 611314261 611314127 4.550000e-47 200.0
25 TraesCS1D01G245400 chr5D 90.000 150 13 2 71 220 272861643 272861496 7.610000e-45 193.0
26 TraesCS1D01G245400 chr5D 75.916 191 32 10 3853 4034 369379711 369379896 1.330000e-12 86.1
27 TraesCS1D01G245400 chr5D 82.979 94 14 2 3943 4036 336042754 336042845 4.780000e-12 84.2
28 TraesCS1D01G245400 chr5A 89.032 155 14 3 64 217 19681323 19681171 9.840000e-44 189.0
29 TraesCS1D01G245400 chr6A 89.404 151 13 3 68 218 42179127 42178980 3.540000e-43 187.0
30 TraesCS1D01G245400 chr3D 95.238 42 2 0 3854 3895 600094665 600094706 4.810000e-07 67.6
31 TraesCS1D01G245400 chr3D 88.679 53 6 0 3982 4034 563658328 563658380 1.730000e-06 65.8


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 TraesCS1D01G245400 chr1D 336546338 336553767 7429 False 13721.00 13721 100.00000 1 7430 1 chr1D.!!$F1 7429
1 TraesCS1D01G245400 chr1B 452310827 452318020 7193 False 2908.00 11345 91.98825 1 7424 4 chr1B.!!$F1 7423
2 TraesCS1D01G245400 chr1A 435056496 435063421 6925 False 2278.38 5614 93.43280 1 7430 5 chr1A.!!$F1 7429

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
301 302 0.042188 CATCCACGGCGAAATTAGCG 60.042 55.000 16.62 0.00 35.00 4.26 F
844 859 0.674269 GGCGTCGACATAAACCCCAA 60.674 55.000 17.16 0.00 0.00 4.12 F
1679 1723 1.227645 TGGTATCAGGCGATGCAGC 60.228 57.895 0.00 0.00 36.07 5.25 F
2358 2411 0.320771 GTGTTGCATGGAGGACTCGT 60.321 55.000 0.00 0.00 0.00 4.18 F
3105 3158 2.096248 AGCCGTTCAGGTTCAAAAACA 58.904 42.857 0.00 0.00 43.70 2.83 F
3417 3470 2.422479 CCTTGCAGATCCATGACTGTTG 59.578 50.000 13.11 6.53 36.62 3.33 F
3640 3701 2.746362 CAGTTTGAGGAACATGGAGCTC 59.254 50.000 4.71 4.71 40.84 4.09 F
3996 4064 3.808218 TTGCCCCCTCAACACTGCC 62.808 63.158 0.00 0.00 0.00 4.85 F
5538 5625 1.002544 CTTCGAACTCTTCCAGGGCTT 59.997 52.381 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2125 0.321564 TGCCTTAGCATCAGCGTTGT 60.322 50.000 0.00 0.0 46.52 3.32 R
2097 2144 2.683933 ACCGGATCCTGCGTTCCT 60.684 61.111 9.46 0.0 0.00 3.36 R
3147 3200 2.103094 TCCTCCATCTTTATCGCCACTG 59.897 50.000 0.00 0.0 0.00 3.66 R
3618 3679 2.373169 AGCTCCATGTTCCTCAAACTGA 59.627 45.455 0.00 0.0 38.76 3.41 R
3996 4064 3.054802 ACAGAGATTGTTGAAGGGGCTAG 60.055 47.826 0.00 0.0 36.31 3.42 R
5157 5244 1.419762 TCTAGCACAAGCAAACCAGGA 59.580 47.619 0.00 0.0 45.49 3.86 R
5538 5625 6.901081 TTCAGAACAATCACACTCTCTCTA 57.099 37.500 0.00 0.0 0.00 2.43 R
5718 5805 4.967036 ACCTTAATCTCTCAAGCATAGGC 58.033 43.478 0.00 0.0 41.61 3.93 R
6755 6842 0.392706 CGCAGTAGCATGGTATCCCA 59.607 55.000 8.06 0.0 42.27 4.37 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
24 25 1.670811 GGGCATGTAAATCACGGACTG 59.329 52.381 0.00 0.00 0.00 3.51
27 28 3.262420 GCATGTAAATCACGGACTGACT 58.738 45.455 0.00 0.00 0.00 3.41
28 29 4.430007 GCATGTAAATCACGGACTGACTA 58.570 43.478 0.00 0.00 0.00 2.59
29 30 4.868171 GCATGTAAATCACGGACTGACTAA 59.132 41.667 0.00 0.00 0.00 2.24
30 31 5.220416 GCATGTAAATCACGGACTGACTAAC 60.220 44.000 0.00 0.00 0.00 2.34
81 82 9.669353 CAATGCATGGACAATTATTCTAGTTAC 57.331 33.333 0.00 0.00 0.00 2.50
82 83 9.632638 AATGCATGGACAATTATTCTAGTTACT 57.367 29.630 0.00 0.00 0.00 2.24
84 85 9.542462 TGCATGGACAATTATTCTAGTTACTAC 57.458 33.333 0.00 0.00 0.00 2.73
85 86 9.765795 GCATGGACAATTATTCTAGTTACTACT 57.234 33.333 0.00 0.00 38.44 2.57
88 89 8.921205 TGGACAATTATTCTAGTTACTACTCCC 58.079 37.037 0.00 0.00 35.78 4.30
89 90 9.145442 GGACAATTATTCTAGTTACTACTCCCT 57.855 37.037 0.00 0.00 35.78 4.20
91 92 9.145442 ACAATTATTCTAGTTACTACTCCCTCC 57.855 37.037 0.00 0.00 35.78 4.30
92 93 7.999450 ATTATTCTAGTTACTACTCCCTCCG 57.001 40.000 0.00 0.00 35.78 4.63
93 94 4.851639 TTCTAGTTACTACTCCCTCCGT 57.148 45.455 0.00 0.00 35.78 4.69
94 95 4.851639 TCTAGTTACTACTCCCTCCGTT 57.148 45.455 0.00 0.00 35.78 4.44
95 96 4.775236 TCTAGTTACTACTCCCTCCGTTC 58.225 47.826 0.00 0.00 35.78 3.95
96 97 2.732763 AGTTACTACTCCCTCCGTTCC 58.267 52.381 0.00 0.00 0.00 3.62
97 98 2.311243 AGTTACTACTCCCTCCGTTCCT 59.689 50.000 0.00 0.00 0.00 3.36
98 99 3.525199 AGTTACTACTCCCTCCGTTCCTA 59.475 47.826 0.00 0.00 0.00 2.94
99 100 4.018050 AGTTACTACTCCCTCCGTTCCTAA 60.018 45.833 0.00 0.00 0.00 2.69
100 101 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
101 102 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
102 103 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
103 104 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
104 105 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
105 106 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
106 107 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
107 108 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
108 109 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
109 110 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
110 111 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
111 112 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
112 113 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
113 114 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
139 140 8.865420 AGAGATTCTACTCTAAACTACACACA 57.135 34.615 0.00 0.00 44.17 3.72
140 141 8.952278 AGAGATTCTACTCTAAACTACACACAG 58.048 37.037 0.00 0.00 44.17 3.66
141 142 8.865420 AGATTCTACTCTAAACTACACACAGA 57.135 34.615 0.00 0.00 0.00 3.41
142 143 9.469097 AGATTCTACTCTAAACTACACACAGAT 57.531 33.333 0.00 0.00 0.00 2.90
143 144 9.509855 GATTCTACTCTAAACTACACACAGATG 57.490 37.037 0.00 0.00 0.00 2.90
144 145 7.997773 TCTACTCTAAACTACACACAGATGT 57.002 36.000 0.00 0.00 40.80 3.06
145 146 9.511272 TTCTACTCTAAACTACACACAGATGTA 57.489 33.333 0.00 0.00 36.72 2.29
146 147 9.682465 TCTACTCTAAACTACACACAGATGTAT 57.318 33.333 0.00 0.00 36.72 2.29
187 188 9.400638 GAGTATAGATTCACTCATTTTACTCCG 57.599 37.037 0.00 0.00 40.74 4.63
188 189 8.915036 AGTATAGATTCACTCATTTTACTCCGT 58.085 33.333 0.00 0.00 0.00 4.69
191 192 9.698309 ATAGATTCACTCATTTTACTCCGTATG 57.302 33.333 0.00 0.00 0.00 2.39
192 193 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
193 194 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
194 195 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
195 196 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
196 197 7.833786 TCACTCATTTTACTCCGTATGTAGTT 58.166 34.615 0.00 0.00 0.00 2.24
197 198 8.308931 TCACTCATTTTACTCCGTATGTAGTTT 58.691 33.333 0.00 0.00 0.00 2.66
198 199 9.577110 CACTCATTTTACTCCGTATGTAGTTTA 57.423 33.333 0.00 0.00 0.00 2.01
205 206 8.978874 TTACTCCGTATGTAGTTTATAGTGGA 57.021 34.615 0.00 0.00 0.00 4.02
206 207 7.886629 ACTCCGTATGTAGTTTATAGTGGAA 57.113 36.000 0.00 0.00 0.00 3.53
207 208 8.474710 ACTCCGTATGTAGTTTATAGTGGAAT 57.525 34.615 0.00 0.00 0.00 3.01
208 209 8.574737 ACTCCGTATGTAGTTTATAGTGGAATC 58.425 37.037 0.00 0.00 0.00 2.52
209 210 8.701908 TCCGTATGTAGTTTATAGTGGAATCT 57.298 34.615 0.00 0.00 0.00 2.40
210 211 8.790718 TCCGTATGTAGTTTATAGTGGAATCTC 58.209 37.037 0.00 0.00 0.00 2.75
211 212 8.794553 CCGTATGTAGTTTATAGTGGAATCTCT 58.205 37.037 0.00 0.00 0.00 3.10
237 238 4.360951 AAAATTGAACGGAGGGAGTACA 57.639 40.909 0.00 0.00 0.00 2.90
238 239 4.569719 AAATTGAACGGAGGGAGTACAT 57.430 40.909 0.00 0.00 0.00 2.29
239 240 3.821421 ATTGAACGGAGGGAGTACATC 57.179 47.619 0.00 0.00 0.00 3.06
248 249 2.183300 GAGTACATCCACGGCGCA 59.817 61.111 10.83 0.00 0.00 6.09
249 250 1.878522 GAGTACATCCACGGCGCAG 60.879 63.158 10.83 8.25 0.00 5.18
250 251 2.125673 GTACATCCACGGCGCAGT 60.126 61.111 10.83 9.16 0.00 4.40
251 252 2.125713 TACATCCACGGCGCAGTG 60.126 61.111 30.27 30.27 41.53 3.66
257 258 2.353376 CACGGCGCAGTGGTTTTG 60.353 61.111 29.71 5.99 38.40 2.44
258 259 3.591835 ACGGCGCAGTGGTTTTGG 61.592 61.111 13.72 0.00 0.00 3.28
259 260 3.283684 CGGCGCAGTGGTTTTGGA 61.284 61.111 10.83 0.00 0.00 3.53
260 261 2.335011 GGCGCAGTGGTTTTGGAC 59.665 61.111 10.83 0.00 0.00 4.02
261 262 2.485795 GGCGCAGTGGTTTTGGACA 61.486 57.895 10.83 0.00 0.00 4.02
262 263 1.008538 GCGCAGTGGTTTTGGACAG 60.009 57.895 0.30 0.00 0.00 3.51
263 264 1.724582 GCGCAGTGGTTTTGGACAGT 61.725 55.000 0.30 0.00 0.00 3.55
264 265 0.738389 CGCAGTGGTTTTGGACAGTT 59.262 50.000 0.00 0.00 0.00 3.16
265 266 1.533756 CGCAGTGGTTTTGGACAGTTG 60.534 52.381 0.00 0.00 0.00 3.16
266 267 1.476488 GCAGTGGTTTTGGACAGTTGT 59.524 47.619 0.00 0.00 0.00 3.32
267 268 2.685897 GCAGTGGTTTTGGACAGTTGTA 59.314 45.455 0.00 0.00 0.00 2.41
268 269 3.129638 GCAGTGGTTTTGGACAGTTGTAA 59.870 43.478 0.00 0.00 0.00 2.41
269 270 4.668289 CAGTGGTTTTGGACAGTTGTAAC 58.332 43.478 0.00 0.00 0.00 2.50
270 271 3.697542 AGTGGTTTTGGACAGTTGTAACC 59.302 43.478 7.43 7.43 34.90 2.85
271 272 3.697542 GTGGTTTTGGACAGTTGTAACCT 59.302 43.478 13.11 0.00 35.20 3.50
272 273 4.883006 GTGGTTTTGGACAGTTGTAACCTA 59.117 41.667 13.11 1.79 35.20 3.08
273 274 5.357596 GTGGTTTTGGACAGTTGTAACCTAA 59.642 40.000 13.11 1.28 35.20 2.69
274 275 5.357596 TGGTTTTGGACAGTTGTAACCTAAC 59.642 40.000 13.11 7.56 35.20 2.34
275 276 5.591472 GGTTTTGGACAGTTGTAACCTAACT 59.409 40.000 7.20 0.00 38.84 2.24
276 277 6.095860 GGTTTTGGACAGTTGTAACCTAACTT 59.904 38.462 7.20 0.00 36.29 2.66
277 278 7.363181 GGTTTTGGACAGTTGTAACCTAACTTT 60.363 37.037 7.20 0.00 36.29 2.66
278 279 6.687081 TTGGACAGTTGTAACCTAACTTTG 57.313 37.500 0.00 0.00 36.29 2.77
279 280 4.577283 TGGACAGTTGTAACCTAACTTTGC 59.423 41.667 0.00 0.00 36.29 3.68
280 281 4.820173 GGACAGTTGTAACCTAACTTTGCT 59.180 41.667 0.00 0.00 36.29 3.91
281 282 5.049612 GGACAGTTGTAACCTAACTTTGCTC 60.050 44.000 0.00 0.00 36.29 4.26
282 283 4.820173 ACAGTTGTAACCTAACTTTGCTCC 59.180 41.667 0.00 0.00 36.29 4.70
283 284 4.819630 CAGTTGTAACCTAACTTTGCTCCA 59.180 41.667 0.00 0.00 36.29 3.86
284 285 5.473504 CAGTTGTAACCTAACTTTGCTCCAT 59.526 40.000 0.00 0.00 36.29 3.41
285 286 5.705905 AGTTGTAACCTAACTTTGCTCCATC 59.294 40.000 0.00 0.00 34.91 3.51
286 287 4.585879 TGTAACCTAACTTTGCTCCATCC 58.414 43.478 0.00 0.00 0.00 3.51
287 288 3.806949 AACCTAACTTTGCTCCATCCA 57.193 42.857 0.00 0.00 0.00 3.41
288 289 3.073274 ACCTAACTTTGCTCCATCCAC 57.927 47.619 0.00 0.00 0.00 4.02
289 290 2.009774 CCTAACTTTGCTCCATCCACG 58.990 52.381 0.00 0.00 0.00 4.94
290 291 2.009774 CTAACTTTGCTCCATCCACGG 58.990 52.381 0.00 0.00 0.00 4.94
291 292 1.244019 AACTTTGCTCCATCCACGGC 61.244 55.000 0.00 0.00 0.00 5.68
292 293 2.745884 TTTGCTCCATCCACGGCG 60.746 61.111 4.80 4.80 0.00 6.46
293 294 3.247056 TTTGCTCCATCCACGGCGA 62.247 57.895 16.62 0.00 0.00 5.54
294 295 2.739849 TTTGCTCCATCCACGGCGAA 62.740 55.000 16.62 0.00 0.00 4.70
295 296 2.435938 GCTCCATCCACGGCGAAA 60.436 61.111 16.62 0.00 0.00 3.46
296 297 1.819632 GCTCCATCCACGGCGAAAT 60.820 57.895 16.62 0.00 0.00 2.17
297 298 1.376609 GCTCCATCCACGGCGAAATT 61.377 55.000 16.62 0.00 0.00 1.82
298 299 1.948104 CTCCATCCACGGCGAAATTA 58.052 50.000 16.62 0.00 0.00 1.40
299 300 1.867233 CTCCATCCACGGCGAAATTAG 59.133 52.381 16.62 0.00 0.00 1.73
300 301 0.307760 CCATCCACGGCGAAATTAGC 59.692 55.000 16.62 0.00 0.00 3.09
301 302 0.042188 CATCCACGGCGAAATTAGCG 60.042 55.000 16.62 0.00 35.00 4.26
307 308 2.351210 GCGAAATTAGCGCGCTGG 60.351 61.111 41.85 23.21 46.53 4.85
308 309 2.351210 CGAAATTAGCGCGCTGGC 60.351 61.111 41.85 23.63 0.00 4.85
309 310 2.024729 GAAATTAGCGCGCTGGCC 59.975 61.111 41.85 21.92 35.02 5.36
310 311 3.469754 GAAATTAGCGCGCTGGCCC 62.470 63.158 41.85 22.61 35.02 5.80
326 327 3.735591 TGGCCCGTAGTAGATAAAATGC 58.264 45.455 0.00 0.00 0.00 3.56
338 339 5.173774 AGATAAAATGCGCAGTGGTTATG 57.826 39.130 18.32 0.00 0.00 1.90
346 347 1.464608 CGCAGTGGTTATGGACAGTTG 59.535 52.381 0.00 0.00 0.00 3.16
357 358 6.938596 GGTTATGGACAGTTGTAACCTAACTT 59.061 38.462 12.23 0.00 41.67 2.66
427 429 2.257676 GACCCCGTCGTCAGTCAC 59.742 66.667 0.00 0.00 32.74 3.67
572 574 2.696409 TAACGGCTTTCACGCGTCCA 62.696 55.000 9.86 0.00 34.00 4.02
642 656 2.419198 CGGGATTCGCTCCAGAGG 59.581 66.667 6.25 0.00 46.98 3.69
777 792 1.450491 GCGGGCTTTTCTCTCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
843 858 1.078988 GGCGTCGACATAAACCCCA 60.079 57.895 17.16 0.00 0.00 4.96
844 859 0.674269 GGCGTCGACATAAACCCCAA 60.674 55.000 17.16 0.00 0.00 4.12
881 897 1.457831 GGGGAGCGTCAGGGAGTAT 60.458 63.158 0.00 0.00 0.00 2.12
884 901 1.249407 GGAGCGTCAGGGAGTATAGG 58.751 60.000 0.00 0.00 0.00 2.57
1368 1409 1.996755 GGAAACGAGACCGAATCGC 59.003 57.895 0.00 0.00 43.91 4.58
1679 1723 1.227645 TGGTATCAGGCGATGCAGC 60.228 57.895 0.00 0.00 36.07 5.25
1734 1778 2.890945 GCTAGGTGGTGGTTTTCATGTT 59.109 45.455 0.00 0.00 0.00 2.71
2078 2125 1.366111 GACGATGCTAAGGCGCCAAA 61.366 55.000 31.54 15.38 42.25 3.28
2250 2303 7.064016 GGGAGATCGCATATAGAAATTCTTGAC 59.936 40.741 0.00 0.00 0.00 3.18
2358 2411 0.320771 GTGTTGCATGGAGGACTCGT 60.321 55.000 0.00 0.00 0.00 4.18
2582 2635 3.140325 AGAGGCCGAAATGAGAAAACA 57.860 42.857 0.00 0.00 0.00 2.83
3105 3158 2.096248 AGCCGTTCAGGTTCAAAAACA 58.904 42.857 0.00 0.00 43.70 2.83
3147 3200 6.757237 TCTGAAGCTTCTGATGGATAAGATC 58.243 40.000 26.66 0.00 31.41 2.75
3417 3470 2.422479 CCTTGCAGATCCATGACTGTTG 59.578 50.000 13.11 6.53 36.62 3.33
3618 3679 8.964476 TTAACTTCAGAAAACTCAGACTTGAT 57.036 30.769 0.00 0.00 31.68 2.57
3640 3701 2.746362 CAGTTTGAGGAACATGGAGCTC 59.254 50.000 4.71 4.71 40.84 4.09
3996 4064 3.808218 TTGCCCCCTCAACACTGCC 62.808 63.158 0.00 0.00 0.00 4.85
4331 4418 8.517878 CGAGGGAAGCATGAATTTATTATTGAT 58.482 33.333 0.00 0.00 0.00 2.57
4611 4698 4.037684 GGGCAATCTCAAGATTTCCATCTG 59.962 45.833 18.87 3.38 45.58 2.90
4944 5031 7.639113 TGTTCCTTTCCATATAATGAACACC 57.361 36.000 0.00 0.00 0.00 4.16
5142 5229 5.008712 CACTGAAGGGAACAAAGTAAGAACC 59.991 44.000 0.00 0.00 0.00 3.62
5538 5625 1.002544 CTTCGAACTCTTCCAGGGCTT 59.997 52.381 0.00 0.00 0.00 4.35
5718 5805 8.729805 AAGAGGAAGCTTCACTTATTGATAAG 57.270 34.615 27.02 8.78 44.07 1.73
6075 6162 5.488919 TCTTCTAGATGTGGTTTGGAATCCT 59.511 40.000 0.00 0.00 0.00 3.24
6180 6267 3.470645 ACAGGTGAAGGTGACAAGTAC 57.529 47.619 0.00 0.00 0.00 2.73
6315 6402 9.661954 AAGTTGATATCTCAGGATAAGGTTCTA 57.338 33.333 3.98 0.00 37.87 2.10
6325 6412 5.480073 CAGGATAAGGTTCTAGAGGAGATGG 59.520 48.000 0.00 0.00 32.88 3.51
6483 6570 3.585862 ACAAGGTATGCTCTTACACGTG 58.414 45.455 15.48 15.48 0.00 4.49
6488 6575 2.315925 ATGCTCTTACACGTGGGATG 57.684 50.000 21.57 9.62 0.00 3.51
6491 6578 1.909376 CTCTTACACGTGGGATGTCG 58.091 55.000 21.57 0.90 0.00 4.35
6493 6580 1.614903 TCTTACACGTGGGATGTCGTT 59.385 47.619 21.57 0.00 38.23 3.85
6547 6634 6.079712 AGCCTTCCACCAGTTCTATAATTT 57.920 37.500 0.00 0.00 0.00 1.82
6640 6727 9.912634 AAATTTTGTATGGTTAGTTGATGTCTG 57.087 29.630 0.00 0.00 0.00 3.51
6641 6728 6.494893 TTTGTATGGTTAGTTGATGTCTGC 57.505 37.500 0.00 0.00 0.00 4.26
6744 6831 6.657117 TGTGTGCATATAAAAGAGCCAACTTA 59.343 34.615 0.00 0.00 0.00 2.24
6745 6832 7.175816 TGTGTGCATATAAAAGAGCCAACTTAA 59.824 33.333 0.00 0.00 0.00 1.85
6746 6833 8.026607 GTGTGCATATAAAAGAGCCAACTTAAA 58.973 33.333 0.00 0.00 0.00 1.52
6747 6834 8.243426 TGTGCATATAAAAGAGCCAACTTAAAG 58.757 33.333 0.00 0.00 0.00 1.85
6748 6835 7.220875 GTGCATATAAAAGAGCCAACTTAAAGC 59.779 37.037 0.00 0.00 0.00 3.51
6749 6836 7.093988 TGCATATAAAAGAGCCAACTTAAAGCA 60.094 33.333 0.00 0.00 0.00 3.91
6750 6837 7.759433 GCATATAAAAGAGCCAACTTAAAGCAA 59.241 33.333 0.00 0.00 0.00 3.91
6751 6838 9.076596 CATATAAAAGAGCCAACTTAAAGCAAC 57.923 33.333 0.00 0.00 0.00 4.17
6752 6839 5.337578 AAAAGAGCCAACTTAAAGCAACA 57.662 34.783 0.00 0.00 0.00 3.33
6753 6840 5.535753 AAAGAGCCAACTTAAAGCAACAT 57.464 34.783 0.00 0.00 0.00 2.71
6754 6841 5.535753 AAGAGCCAACTTAAAGCAACATT 57.464 34.783 0.00 0.00 0.00 2.71
6755 6842 5.535753 AGAGCCAACTTAAAGCAACATTT 57.464 34.783 0.00 0.00 0.00 2.32
6815 6902 3.620821 GCTCTGCATCTTACAAGAGGAAC 59.379 47.826 7.76 0.00 39.04 3.62
6821 6908 3.936372 TCTTACAAGAGGAACTGGACG 57.064 47.619 0.00 0.00 41.55 4.79
6822 6909 3.493334 TCTTACAAGAGGAACTGGACGA 58.507 45.455 0.00 0.00 41.55 4.20
6823 6910 3.255149 TCTTACAAGAGGAACTGGACGAC 59.745 47.826 0.00 0.00 41.55 4.34
6828 6915 2.379972 AGAGGAACTGGACGACCTATG 58.620 52.381 5.33 0.00 41.55 2.23
6912 7001 7.490657 TGATACCCTCAGTGTGTTTACTATT 57.509 36.000 0.00 0.00 0.00 1.73
6922 7011 8.151596 TCAGTGTGTTTACTATTTGATGTACCA 58.848 33.333 0.00 0.00 0.00 3.25
6955 7044 8.349983 TGTTGGTTAAAAGCTTCTTTATCACTC 58.650 33.333 0.00 0.00 0.00 3.51
7018 7107 5.660417 TGCCAGCAATAATGGAATAAAGGAA 59.340 36.000 0.00 0.00 40.51 3.36
7156 7245 4.378774 GAGATATCTGCAGCAGTCACATT 58.621 43.478 22.10 5.17 32.61 2.71
7166 7255 5.824097 TGCAGCAGTCACATTTATACATGAT 59.176 36.000 5.88 0.00 0.00 2.45
7193 7282 2.672996 TGGCTGGCCTTCGCTTTC 60.673 61.111 13.05 0.00 36.94 2.62
7194 7283 3.804193 GGCTGGCCTTCGCTTTCG 61.804 66.667 3.32 0.00 34.44 3.46
7248 7338 3.493699 GCAGATAATGCGTAAGTACCCCA 60.494 47.826 0.00 0.00 46.99 4.96
7330 7421 8.672823 AAACTTTTACTTCGTCCTATGTCTTT 57.327 30.769 0.00 0.00 0.00 2.52
7424 7515 5.429130 GGCTAATAAACCTGCTTCACTAGT 58.571 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 7.450944 ACTTATATTTAGGAACGGAGGGAGTAG 59.549 40.741 0.00 0.00 0.00 2.57
82 83 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
84 85 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
85 86 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
86 87 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
87 88 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
113 114 9.955102 TGTGTGTAGTTTAGAGTAGAATCTCTA 57.045 33.333 0.00 0.00 43.46 2.43
114 115 8.865420 TGTGTGTAGTTTAGAGTAGAATCTCT 57.135 34.615 0.00 1.94 45.33 3.10
115 116 8.948145 TCTGTGTGTAGTTTAGAGTAGAATCTC 58.052 37.037 0.00 0.00 34.96 2.75
116 117 8.865420 TCTGTGTGTAGTTTAGAGTAGAATCT 57.135 34.615 0.00 0.00 0.00 2.40
117 118 9.509855 CATCTGTGTGTAGTTTAGAGTAGAATC 57.490 37.037 0.00 0.00 0.00 2.52
118 119 9.026121 ACATCTGTGTGTAGTTTAGAGTAGAAT 57.974 33.333 0.00 0.00 37.14 2.40
119 120 8.405418 ACATCTGTGTGTAGTTTAGAGTAGAA 57.595 34.615 0.00 0.00 37.14 2.10
120 121 7.997773 ACATCTGTGTGTAGTTTAGAGTAGA 57.002 36.000 0.00 0.00 37.14 2.59
161 162 9.400638 CGGAGTAAAATGAGTGAATCTATACTC 57.599 37.037 0.00 0.00 42.77 2.59
162 163 8.915036 ACGGAGTAAAATGAGTGAATCTATACT 58.085 33.333 0.00 0.00 41.94 2.12
183 184 8.794553 AGATTCCACTATAAACTACATACGGAG 58.205 37.037 0.00 0.00 0.00 4.63
184 185 8.701908 AGATTCCACTATAAACTACATACGGA 57.298 34.615 0.00 0.00 0.00 4.69
185 186 8.794553 AGAGATTCCACTATAAACTACATACGG 58.205 37.037 0.00 0.00 0.00 4.02
215 216 4.721132 TGTACTCCCTCCGTTCAATTTTT 58.279 39.130 0.00 0.00 0.00 1.94
216 217 4.360951 TGTACTCCCTCCGTTCAATTTT 57.639 40.909 0.00 0.00 0.00 1.82
217 218 4.514401 GATGTACTCCCTCCGTTCAATTT 58.486 43.478 0.00 0.00 0.00 1.82
218 219 3.118371 GGATGTACTCCCTCCGTTCAATT 60.118 47.826 0.00 0.00 38.19 2.32
219 220 2.434702 GGATGTACTCCCTCCGTTCAAT 59.565 50.000 0.00 0.00 38.19 2.57
220 221 1.829222 GGATGTACTCCCTCCGTTCAA 59.171 52.381 0.00 0.00 38.19 2.69
221 222 1.272816 TGGATGTACTCCCTCCGTTCA 60.273 52.381 8.36 0.00 44.23 3.18
222 223 1.136500 GTGGATGTACTCCCTCCGTTC 59.864 57.143 8.36 0.00 44.23 3.95
223 224 1.192428 GTGGATGTACTCCCTCCGTT 58.808 55.000 8.36 0.00 44.23 4.44
224 225 1.035932 CGTGGATGTACTCCCTCCGT 61.036 60.000 8.36 0.00 44.23 4.69
225 226 1.734137 CGTGGATGTACTCCCTCCG 59.266 63.158 8.36 5.92 44.23 4.63
226 227 2.029307 GCCGTGGATGTACTCCCTCC 62.029 65.000 8.36 3.94 44.23 4.30
227 228 1.442148 GCCGTGGATGTACTCCCTC 59.558 63.158 8.36 3.48 44.23 4.30
228 229 2.423898 CGCCGTGGATGTACTCCCT 61.424 63.158 8.36 0.00 44.23 4.20
229 230 2.106332 CGCCGTGGATGTACTCCC 59.894 66.667 8.36 3.66 44.23 4.30
230 231 2.585247 GCGCCGTGGATGTACTCC 60.585 66.667 0.00 0.00 45.19 3.85
231 232 1.878522 CTGCGCCGTGGATGTACTC 60.879 63.158 4.18 0.00 0.00 2.59
232 233 2.184322 CTGCGCCGTGGATGTACT 59.816 61.111 4.18 0.00 0.00 2.73
233 234 2.125673 ACTGCGCCGTGGATGTAC 60.126 61.111 4.18 0.00 0.00 2.90
234 235 2.125713 CACTGCGCCGTGGATGTA 60.126 61.111 22.60 0.00 0.00 2.29
240 241 2.353376 CAAAACCACTGCGCCGTG 60.353 61.111 23.26 23.26 34.71 4.94
241 242 3.591835 CCAAAACCACTGCGCCGT 61.592 61.111 4.18 0.00 0.00 5.68
242 243 3.283684 TCCAAAACCACTGCGCCG 61.284 61.111 4.18 0.00 0.00 6.46
243 244 2.335011 GTCCAAAACCACTGCGCC 59.665 61.111 4.18 0.00 0.00 6.53
244 245 1.008538 CTGTCCAAAACCACTGCGC 60.009 57.895 0.00 0.00 0.00 6.09
245 246 0.738389 AACTGTCCAAAACCACTGCG 59.262 50.000 0.00 0.00 0.00 5.18
246 247 1.476488 ACAACTGTCCAAAACCACTGC 59.524 47.619 0.00 0.00 0.00 4.40
247 248 4.439563 GGTTACAACTGTCCAAAACCACTG 60.440 45.833 7.19 0.00 34.62 3.66
248 249 3.697542 GGTTACAACTGTCCAAAACCACT 59.302 43.478 7.19 0.00 34.62 4.00
249 250 3.697542 AGGTTACAACTGTCCAAAACCAC 59.302 43.478 12.53 0.00 36.10 4.16
250 251 3.970842 AGGTTACAACTGTCCAAAACCA 58.029 40.909 12.53 0.00 36.10 3.67
251 252 5.591472 AGTTAGGTTACAACTGTCCAAAACC 59.409 40.000 4.69 4.69 34.96 3.27
252 253 6.688637 AGTTAGGTTACAACTGTCCAAAAC 57.311 37.500 0.00 0.00 34.96 2.43
253 254 7.540299 CAAAGTTAGGTTACAACTGTCCAAAA 58.460 34.615 0.00 0.00 36.38 2.44
254 255 6.404954 GCAAAGTTAGGTTACAACTGTCCAAA 60.405 38.462 0.00 0.00 36.38 3.28
255 256 5.066764 GCAAAGTTAGGTTACAACTGTCCAA 59.933 40.000 0.00 0.00 36.38 3.53
256 257 4.577283 GCAAAGTTAGGTTACAACTGTCCA 59.423 41.667 0.00 0.00 36.38 4.02
257 258 4.820173 AGCAAAGTTAGGTTACAACTGTCC 59.180 41.667 0.00 0.00 36.38 4.02
258 259 5.049612 GGAGCAAAGTTAGGTTACAACTGTC 60.050 44.000 0.00 0.00 36.38 3.51
259 260 4.820173 GGAGCAAAGTTAGGTTACAACTGT 59.180 41.667 0.00 0.00 36.38 3.55
260 261 4.819630 TGGAGCAAAGTTAGGTTACAACTG 59.180 41.667 0.00 0.00 36.38 3.16
261 262 5.043737 TGGAGCAAAGTTAGGTTACAACT 57.956 39.130 0.00 0.00 37.85 3.16
262 263 5.106277 GGATGGAGCAAAGTTAGGTTACAAC 60.106 44.000 0.00 0.00 0.00 3.32
263 264 5.007682 GGATGGAGCAAAGTTAGGTTACAA 58.992 41.667 0.00 0.00 0.00 2.41
264 265 4.042311 TGGATGGAGCAAAGTTAGGTTACA 59.958 41.667 0.00 0.00 0.00 2.41
265 266 4.395231 GTGGATGGAGCAAAGTTAGGTTAC 59.605 45.833 0.00 0.00 0.00 2.50
266 267 4.585879 GTGGATGGAGCAAAGTTAGGTTA 58.414 43.478 0.00 0.00 0.00 2.85
267 268 3.421844 GTGGATGGAGCAAAGTTAGGTT 58.578 45.455 0.00 0.00 0.00 3.50
268 269 2.615493 CGTGGATGGAGCAAAGTTAGGT 60.615 50.000 0.00 0.00 0.00 3.08
269 270 2.009774 CGTGGATGGAGCAAAGTTAGG 58.990 52.381 0.00 0.00 0.00 2.69
270 271 2.009774 CCGTGGATGGAGCAAAGTTAG 58.990 52.381 0.00 0.00 0.00 2.34
271 272 1.948611 GCCGTGGATGGAGCAAAGTTA 60.949 52.381 0.00 0.00 0.00 2.24
272 273 1.244019 GCCGTGGATGGAGCAAAGTT 61.244 55.000 0.00 0.00 0.00 2.66
273 274 1.675641 GCCGTGGATGGAGCAAAGT 60.676 57.895 0.00 0.00 0.00 2.66
274 275 2.753966 CGCCGTGGATGGAGCAAAG 61.754 63.158 0.00 0.00 0.00 2.77
275 276 2.739849 TTCGCCGTGGATGGAGCAAA 62.740 55.000 0.00 0.00 0.00 3.68
276 277 2.739849 TTTCGCCGTGGATGGAGCAA 62.740 55.000 0.00 0.00 0.00 3.91
277 278 2.535485 ATTTCGCCGTGGATGGAGCA 62.535 55.000 0.00 0.00 0.00 4.26
278 279 1.376609 AATTTCGCCGTGGATGGAGC 61.377 55.000 0.00 0.00 0.00 4.70
279 280 1.867233 CTAATTTCGCCGTGGATGGAG 59.133 52.381 0.00 0.00 0.00 3.86
280 281 1.948104 CTAATTTCGCCGTGGATGGA 58.052 50.000 0.00 0.00 0.00 3.41
281 282 0.307760 GCTAATTTCGCCGTGGATGG 59.692 55.000 0.00 0.00 0.00 3.51
282 283 0.042188 CGCTAATTTCGCCGTGGATG 60.042 55.000 0.00 0.00 0.00 3.51
283 284 1.772063 GCGCTAATTTCGCCGTGGAT 61.772 55.000 0.00 0.00 46.18 3.41
284 285 2.457778 GCGCTAATTTCGCCGTGGA 61.458 57.895 0.00 0.00 46.18 4.02
285 286 2.022762 GCGCTAATTTCGCCGTGG 59.977 61.111 0.00 0.00 46.18 4.94
291 292 2.351210 GCCAGCGCGCTAATTTCG 60.351 61.111 36.02 20.28 0.00 3.46
292 293 2.024729 GGCCAGCGCGCTAATTTC 59.975 61.111 36.02 19.47 35.02 2.17
293 294 3.518068 GGGCCAGCGCGCTAATTT 61.518 61.111 36.02 9.11 44.27 1.82
301 302 1.521450 TATCTACTACGGGCCAGCGC 61.521 60.000 4.39 0.00 0.00 5.92
302 303 0.956633 TTATCTACTACGGGCCAGCG 59.043 55.000 4.39 1.48 0.00 5.18
303 304 3.464111 TTTTATCTACTACGGGCCAGC 57.536 47.619 4.39 0.00 0.00 4.85
304 305 3.746492 GCATTTTATCTACTACGGGCCAG 59.254 47.826 4.39 1.85 0.00 4.85
305 306 3.735591 GCATTTTATCTACTACGGGCCA 58.264 45.455 4.39 0.00 0.00 5.36
306 307 2.735134 CGCATTTTATCTACTACGGGCC 59.265 50.000 0.00 0.00 0.00 5.80
307 308 2.157085 GCGCATTTTATCTACTACGGGC 59.843 50.000 0.30 0.00 0.00 6.13
308 309 3.386486 TGCGCATTTTATCTACTACGGG 58.614 45.455 5.66 0.00 0.00 5.28
309 310 4.049186 ACTGCGCATTTTATCTACTACGG 58.951 43.478 12.24 0.00 0.00 4.02
310 311 4.085055 CCACTGCGCATTTTATCTACTACG 60.085 45.833 12.24 0.00 0.00 3.51
313 314 3.873910 ACCACTGCGCATTTTATCTACT 58.126 40.909 12.24 0.00 0.00 2.57
326 327 1.464608 CAACTGTCCATAACCACTGCG 59.535 52.381 0.00 0.00 0.00 5.18
338 339 4.820173 AGCAAAGTTAGGTTACAACTGTCC 59.180 41.667 0.00 0.00 36.38 4.02
346 347 4.395231 GTGGATGGAGCAAAGTTAGGTTAC 59.605 45.833 0.00 0.00 0.00 2.50
357 358 2.739849 TTTCGCCGTGGATGGAGCAA 62.740 55.000 0.00 0.00 0.00 3.91
411 412 2.203451 AGTGACTGACGACGGGGT 60.203 61.111 0.00 0.00 0.00 4.95
427 429 5.369187 CGCGCATTGATTAAATCTACTGAG 58.631 41.667 8.75 0.00 0.00 3.35
659 673 2.737376 GTGTCCTTGTCGTCGCCC 60.737 66.667 0.00 0.00 0.00 6.13
843 858 4.710167 GTTAGCGGGCGTGGGGTT 62.710 66.667 0.00 0.00 0.00 4.11
863 879 0.178970 TATACTCCCTGACGCTCCCC 60.179 60.000 0.00 0.00 0.00 4.81
865 881 1.202903 TCCTATACTCCCTGACGCTCC 60.203 57.143 0.00 0.00 0.00 4.70
881 897 6.397304 AGGTATGGTACTACTCCTACTCCTA 58.603 44.000 2.90 0.00 0.00 2.94
884 901 6.232692 CAGAGGTATGGTACTACTCCTACTC 58.767 48.000 4.47 0.00 0.00 2.59
1270 1311 0.985490 CCCTTCCTCCTCCTCTTGGG 60.985 65.000 0.00 0.00 0.00 4.12
1335 1376 2.445614 TCCGACTTGGAGGAGCCT 59.554 61.111 0.00 0.00 43.74 4.58
1392 1433 1.004560 TGCCTCCTTGCTCTTCACG 60.005 57.895 0.00 0.00 0.00 4.35
1462 1503 1.142185 CTGTCGTCACAGCCATAGCG 61.142 60.000 0.00 0.00 43.77 4.26
1563 1604 1.434622 CGGCACTGTGATGCTCATCC 61.435 60.000 12.86 0.00 45.38 3.51
1679 1723 2.742372 CACGACCTTTCAGCCCCG 60.742 66.667 0.00 0.00 0.00 5.73
1707 1751 3.728373 CCACCACCTAGCCCACCC 61.728 72.222 0.00 0.00 0.00 4.61
1734 1778 3.918294 TCATTCATGTGCTCCTCATCA 57.082 42.857 0.00 0.00 0.00 3.07
1777 1824 3.386237 AGTCGGCAGCTCCCTGTC 61.386 66.667 0.00 0.00 41.26 3.51
2078 2125 0.321564 TGCCTTAGCATCAGCGTTGT 60.322 50.000 0.00 0.00 46.52 3.32
2097 2144 2.683933 ACCGGATCCTGCGTTCCT 60.684 61.111 9.46 0.00 0.00 3.36
2250 2303 3.675698 GCACTTTTACTTCCTCGTCAGAG 59.324 47.826 0.00 0.00 43.98 3.35
2294 2347 3.015516 GGCAACGGTTTCCTCTTCA 57.984 52.632 2.10 0.00 0.00 3.02
2358 2411 3.678965 TGCTTAAGCCCCCATAATGAA 57.321 42.857 24.30 0.00 41.18 2.57
2550 2603 3.771577 TCGGCCTCTTCTTCTTCTTTT 57.228 42.857 0.00 0.00 0.00 2.27
2556 2609 2.834549 TCTCATTTCGGCCTCTTCTTCT 59.165 45.455 0.00 0.00 0.00 2.85
2582 2635 6.569226 CGAAGATGAGGCAATTTCTTTCTTGT 60.569 38.462 0.00 0.00 0.00 3.16
3025 3078 3.384467 TGCTTCTTTTCCTTCCCAGTTTG 59.616 43.478 0.00 0.00 0.00 2.93
3105 3158 3.318275 TCAGAAGTGACTGTCGCTTTAGT 59.682 43.478 30.54 18.75 46.13 2.24
3147 3200 2.103094 TCCTCCATCTTTATCGCCACTG 59.897 50.000 0.00 0.00 0.00 3.66
3289 3342 3.091545 AGTCACCCCACAGCATATTTTG 58.908 45.455 0.00 0.00 0.00 2.44
3417 3470 7.981102 ACACCACTAAGGAAAATAGAAGAAC 57.019 36.000 0.00 0.00 41.22 3.01
3618 3679 2.373169 AGCTCCATGTTCCTCAAACTGA 59.627 45.455 0.00 0.00 38.76 3.41
3640 3701 4.934075 TTCTTGATCAGCGTGAATCTTG 57.066 40.909 0.00 0.00 0.00 3.02
3695 3757 4.649674 AGAATACAGGGATGAAGCTACGAA 59.350 41.667 0.00 0.00 0.00 3.85
3926 3989 9.227777 GACTAATATTTGATATTTAAGCCGGGT 57.772 33.333 0.00 0.00 36.82 5.28
3927 3990 9.226606 TGACTAATATTTGATATTTAAGCCGGG 57.773 33.333 2.18 0.00 36.82 5.73
3996 4064 3.054802 ACAGAGATTGTTGAAGGGGCTAG 60.055 47.826 0.00 0.00 36.31 3.42
4331 4418 5.114764 TGCATCTGATTCCTATTTGGTCA 57.885 39.130 0.00 0.00 37.07 4.02
4611 4698 5.808366 TGAGATCCCATACTGTTCCATAC 57.192 43.478 0.00 0.00 0.00 2.39
4944 5031 6.039717 TGTCTTCTTTCCCTGAAAAATCTGTG 59.960 38.462 0.00 0.00 30.84 3.66
5157 5244 1.419762 TCTAGCACAAGCAAACCAGGA 59.580 47.619 0.00 0.00 45.49 3.86
5538 5625 6.901081 TTCAGAACAATCACACTCTCTCTA 57.099 37.500 0.00 0.00 0.00 2.43
5718 5805 4.967036 ACCTTAATCTCTCAAGCATAGGC 58.033 43.478 0.00 0.00 41.61 3.93
6075 6162 1.778017 TAGCTTGCCTTCCCACAGCA 61.778 55.000 0.00 0.00 33.97 4.41
6180 6267 2.352960 GTCCTTTTCTGCTTGCCTATCG 59.647 50.000 0.00 0.00 0.00 2.92
6210 6297 4.039730 TCCTCTTGAGAGAAGACCAACTTG 59.960 45.833 9.55 0.00 44.74 3.16
6325 6412 0.255890 TTTAGCTGGTCATGGGAGGC 59.744 55.000 0.00 0.00 0.00 4.70
6478 6565 2.004583 ACATAACGACATCCCACGTG 57.995 50.000 9.08 9.08 42.43 4.49
6533 6620 7.338800 AGCATCCACAAAATTATAGAACTGG 57.661 36.000 0.00 0.00 0.00 4.00
6547 6634 5.421693 ACCAAAATAATGCTAGCATCCACAA 59.578 36.000 29.67 13.62 35.31 3.33
6640 6727 5.409520 TGACAATACAGTCAAACTCAGATGC 59.590 40.000 0.00 0.00 44.92 3.91
6744 6831 4.623647 GCATGGTATCCCAAATGTTGCTTT 60.624 41.667 0.00 0.00 46.04 3.51
6745 6832 3.118665 GCATGGTATCCCAAATGTTGCTT 60.119 43.478 0.00 0.00 46.04 3.91
6746 6833 2.431782 GCATGGTATCCCAAATGTTGCT 59.568 45.455 0.00 0.00 46.04 3.91
6747 6834 2.431782 AGCATGGTATCCCAAATGTTGC 59.568 45.455 0.00 0.00 46.04 4.17
6748 6835 4.889409 AGTAGCATGGTATCCCAAATGTTG 59.111 41.667 8.06 0.00 46.04 3.33
6749 6836 4.889409 CAGTAGCATGGTATCCCAAATGTT 59.111 41.667 8.06 0.00 46.04 2.71
6750 6837 4.464008 CAGTAGCATGGTATCCCAAATGT 58.536 43.478 8.06 0.00 46.04 2.71
6751 6838 3.254166 GCAGTAGCATGGTATCCCAAATG 59.746 47.826 8.06 0.00 46.04 2.32
6752 6839 3.490348 GCAGTAGCATGGTATCCCAAAT 58.510 45.455 8.06 0.00 46.04 2.32
6753 6840 2.744823 CGCAGTAGCATGGTATCCCAAA 60.745 50.000 8.06 0.00 42.27 3.28
6754 6841 1.202639 CGCAGTAGCATGGTATCCCAA 60.203 52.381 8.06 0.00 42.27 4.12
6755 6842 0.392706 CGCAGTAGCATGGTATCCCA 59.607 55.000 8.06 0.00 42.27 4.37
6815 6902 4.152402 CACAAAAACTCATAGGTCGTCCAG 59.848 45.833 0.51 0.00 35.89 3.86
6821 6908 4.622740 GCATTGCACAAAAACTCATAGGTC 59.377 41.667 3.15 0.00 0.00 3.85
6822 6909 4.281688 AGCATTGCACAAAAACTCATAGGT 59.718 37.500 11.91 0.00 0.00 3.08
6823 6910 4.813027 AGCATTGCACAAAAACTCATAGG 58.187 39.130 11.91 0.00 0.00 2.57
6828 6915 5.289434 GGCTTATAGCATTGCACAAAAACTC 59.711 40.000 11.91 0.00 44.75 3.01
6863 6952 8.843262 CAGACAATGAAATGAAGGCTGAATATA 58.157 33.333 0.00 0.00 0.00 0.86
6864 6953 7.558807 TCAGACAATGAAATGAAGGCTGAATAT 59.441 33.333 0.00 0.00 34.02 1.28
6865 6954 6.885918 TCAGACAATGAAATGAAGGCTGAATA 59.114 34.615 0.00 0.00 34.02 1.75
6939 7028 6.998802 AGTACTGTGAGTGATAAAGAAGCTT 58.001 36.000 0.00 0.00 0.00 3.74
6955 7044 4.737279 CGATGAGCAGACATAAGTACTGTG 59.263 45.833 0.00 1.19 34.60 3.66
7018 7107 4.079253 GACCATGAAAACATGTGGTAGGT 58.921 43.478 0.00 3.27 44.56 3.08
7156 7245 6.992123 CAGCCACTAAAGGACATCATGTATAA 59.008 38.462 0.00 0.00 0.00 0.98
7166 7255 1.133809 AGGCCAGCCACTAAAGGACA 61.134 55.000 12.03 0.00 38.92 4.02
7193 7282 2.002586 CTGCCACCATACTTGAGTTCG 58.997 52.381 0.00 0.00 0.00 3.95
7194 7283 1.740025 GCTGCCACCATACTTGAGTTC 59.260 52.381 0.00 0.00 0.00 3.01
7232 7322 2.745152 GCTGATGGGGTACTTACGCATT 60.745 50.000 5.88 0.00 40.93 3.56
7330 7421 4.501071 GACCAACAAAGCTCGGTCTATAA 58.499 43.478 10.37 0.00 43.79 0.98
7397 7488 4.402474 GTGAAGCAGGTTTATTAGCCCATT 59.598 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.