Multiple sequence alignment - TraesCS7D01G184200

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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 TraesCS7D01G184200 chr7D 100.000 3149 0 0 1 3149 137791088 137787940 0.000000e+00 5816.0
1 TraesCS7D01G184200 chr7D 93.617 376 15 8 2 373 349949581 349949951 1.280000e-153 553.0
2 TraesCS7D01G184200 chr7D 91.645 383 24 7 2 380 499719266 499718888 1.000000e-144 523.0
3 TraesCS7D01G184200 chr7D 88.889 378 37 4 2616 2990 137716020 137715645 7.960000e-126 460.0
4 TraesCS7D01G184200 chr7D 88.654 379 37 4 2616 2990 137605560 137605184 1.030000e-124 457.0
5 TraesCS7D01G184200 chr7D 76.538 439 77 24 967 1391 137871943 137871517 1.900000e-52 217.0
6 TraesCS7D01G184200 chr7D 95.455 88 2 2 358 444 13070526 13070612 4.240000e-29 139.0
7 TraesCS7D01G184200 chr7A 95.529 2729 92 15 438 3149 137800808 137798093 0.000000e+00 4337.0
8 TraesCS7D01G184200 chr7A 75.172 435 84 19 976 1391 137827280 137826851 1.930000e-42 183.0
9 TraesCS7D01G184200 chr7B 95.721 2197 82 8 962 3149 103080111 103077918 0.000000e+00 3526.0
10 TraesCS7D01G184200 chr7B 87.139 381 39 5 2616 2990 102647243 102646867 1.040000e-114 424.0
11 TraesCS7D01G184200 chr7B 89.524 315 26 5 440 749 103080554 103080242 2.940000e-105 392.0
12 TraesCS7D01G184200 chr7B 87.004 277 30 5 2717 2990 102805708 102805435 1.100000e-79 307.0
13 TraesCS7D01G184200 chr7B 75.058 433 88 16 971 1391 103116923 103116499 1.930000e-42 183.0
14 TraesCS7D01G184200 chr7B 89.691 97 0 1 786 882 103080260 103080174 7.140000e-22 115.0
15 TraesCS7D01G184200 chr1D 94.490 363 15 5 2 361 320980450 320980090 3.550000e-154 555.0
16 TraesCS7D01G184200 chr1D 95.349 86 4 0 354 439 482916091 482916006 1.520000e-28 137.0
17 TraesCS7D01G184200 chr1D 93.478 92 5 1 354 444 62157445 62157536 5.480000e-28 135.0
18 TraesCS7D01G184200 chr3D 92.950 383 21 5 2 380 16130517 16130897 1.280000e-153 553.0
19 TraesCS7D01G184200 chr3D 92.950 383 22 4 2 380 556937173 556936792 1.280000e-153 553.0
20 TraesCS7D01G184200 chr3D 94.444 90 3 2 354 442 581988108 581988196 1.520000e-28 137.0
21 TraesCS7D01G184200 chr3D 78.571 140 20 7 492 624 516910568 516910704 2.010000e-12 84.2
22 TraesCS7D01G184200 chr5D 92.689 383 20 5 2 380 323861640 323861262 2.140000e-151 545.0
23 TraesCS7D01G184200 chr5D 86.000 150 14 6 300 444 418431502 418431355 1.510000e-33 154.0
24 TraesCS7D01G184200 chr2D 92.287 376 22 6 2 373 591579526 591579898 7.740000e-146 527.0
25 TraesCS7D01G184200 chr2D 94.382 89 3 2 358 445 633086348 633086435 5.480000e-28 135.0
26 TraesCS7D01G184200 chr6A 91.906 383 17 8 2 380 66418907 66419279 1.000000e-144 523.0
27 TraesCS7D01G184200 chr6A 91.957 373 24 5 5 373 519210600 519210230 4.660000e-143 518.0
28 TraesCS7D01G184200 chrUn 88.360 378 39 4 2616 2990 330791215 330791590 1.720000e-122 449.0
29 TraesCS7D01G184200 chrUn 93.407 91 5 1 354 443 83142268 83142178 1.970000e-27 134.0
30 TraesCS7D01G184200 chrUn 80.576 139 27 0 1241 1379 480092370 480092508 1.190000e-19 108.0
31 TraesCS7D01G184200 chr5A 91.753 97 7 1 354 449 601260376 601260472 1.970000e-27 134.0
32 TraesCS7D01G184200 chr1B 81.250 160 28 2 489 647 470550982 470551140 9.170000e-26 128.0
33 TraesCS7D01G184200 chr6D 92.308 91 4 3 354 442 428425069 428425158 3.300000e-25 126.0
34 TraesCS7D01G184200 chr5B 85.833 120 16 1 531 650 539258918 539259036 3.300000e-25 126.0


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 TraesCS7D01G184200 chr7D 137787940 137791088 3148 True 5816.000000 5816 100.000000 1 3149 1 chr7D.!!$R3 3148
1 TraesCS7D01G184200 chr7A 137798093 137800808 2715 True 4337.000000 4337 95.529000 438 3149 1 chr7A.!!$R1 2711
2 TraesCS7D01G184200 chr7B 103077918 103080554 2636 True 1344.333333 3526 91.645333 440 3149 3 chr7B.!!$R4 2709

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
239 240 0.163146 GTCGTGTTTAGCCGAACTGC 59.837 55.0 2.06 0.0 34.47 4.40 F
1450 1495 0.036875 CAACCTCCTGTTCTGGGTCC 59.963 60.0 0.00 0.0 34.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 1586 0.620556 TTCTTGGAGGATGGTCAGGC 59.379 55.0 0.0 0.0 0.00 4.85 R
2763 2818 0.249911 GGCAGGGATAAGTACTGGCG 60.250 60.0 0.0 0.0 45.66 5.69 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
68 69 4.821589 GCCCGCGTCAAGGAGGAG 62.822 72.222 4.92 0.00 0.00 3.69
69 70 3.068691 CCCGCGTCAAGGAGGAGA 61.069 66.667 4.92 0.00 0.00 3.71
70 71 2.646175 CCCGCGTCAAGGAGGAGAA 61.646 63.158 4.92 0.00 0.00 2.87
71 72 1.153745 CCGCGTCAAGGAGGAGAAG 60.154 63.158 4.92 0.00 0.00 2.85
72 73 1.153745 CGCGTCAAGGAGGAGAAGG 60.154 63.158 0.00 0.00 0.00 3.46
73 74 1.448717 GCGTCAAGGAGGAGAAGGC 60.449 63.158 0.00 0.00 0.00 4.35
74 75 1.219393 CGTCAAGGAGGAGAAGGCC 59.781 63.158 0.00 0.00 0.00 5.19
75 76 1.219393 GTCAAGGAGGAGAAGGCCG 59.781 63.158 0.00 0.00 0.00 6.13
76 77 1.078528 TCAAGGAGGAGAAGGCCGA 59.921 57.895 0.00 0.00 0.00 5.54
77 78 1.219393 CAAGGAGGAGAAGGCCGAC 59.781 63.158 0.00 0.00 0.00 4.79
78 79 2.352032 AAGGAGGAGAAGGCCGACG 61.352 63.158 0.00 0.00 0.00 5.12
79 80 2.754658 GGAGGAGAAGGCCGACGA 60.755 66.667 0.00 0.00 0.00 4.20
80 81 2.128507 GGAGGAGAAGGCCGACGAT 61.129 63.158 0.00 0.00 0.00 3.73
81 82 1.066587 GAGGAGAAGGCCGACGATG 59.933 63.158 0.00 0.00 0.00 3.84
82 83 1.379977 AGGAGAAGGCCGACGATGA 60.380 57.895 0.00 0.00 0.00 2.92
83 84 1.227002 GGAGAAGGCCGACGATGAC 60.227 63.158 0.00 0.00 0.00 3.06
84 85 1.586564 GAGAAGGCCGACGATGACG 60.587 63.158 0.00 0.00 45.75 4.35
85 86 1.989966 GAGAAGGCCGACGATGACGA 61.990 60.000 0.00 0.00 42.66 4.20
86 87 1.872679 GAAGGCCGACGATGACGAC 60.873 63.158 0.00 0.00 42.66 4.34
92 93 4.471726 GACGATGACGACGGCGGT 62.472 66.667 18.49 1.10 43.17 5.68
93 94 4.771356 ACGATGACGACGGCGGTG 62.771 66.667 18.49 5.32 43.17 4.94
94 95 4.470170 CGATGACGACGGCGGTGA 62.470 66.667 18.49 0.00 43.17 4.02
95 96 2.579787 GATGACGACGGCGGTGAG 60.580 66.667 18.49 1.36 43.17 3.51
96 97 4.129737 ATGACGACGGCGGTGAGG 62.130 66.667 18.49 0.00 43.17 3.86
98 99 3.823330 GACGACGGCGGTGAGGAT 61.823 66.667 18.49 0.00 43.17 3.24
99 100 4.129737 ACGACGGCGGTGAGGATG 62.130 66.667 18.49 0.00 43.17 3.51
100 101 4.873129 CGACGGCGGTGAGGATGG 62.873 72.222 13.24 0.00 0.00 3.51
120 121 4.157958 GCGACGACGGCGACTACT 62.158 66.667 30.26 0.00 41.64 2.57
121 122 2.021106 CGACGACGGCGACTACTC 59.979 66.667 22.49 1.83 41.64 2.59
122 123 2.021106 GACGACGGCGACTACTCG 59.979 66.667 22.49 15.07 43.28 4.18
123 124 3.431683 GACGACGGCGACTACTCGG 62.432 68.421 22.49 0.00 40.53 4.63
129 130 2.177531 GCGACTACTCGGCGTTCA 59.822 61.111 6.85 0.00 40.53 3.18
130 131 1.868251 GCGACTACTCGGCGTTCAG 60.868 63.158 6.85 4.80 40.53 3.02
142 143 2.492019 GCGTTCAGCCAGTTTCTTTT 57.508 45.000 0.00 0.00 40.81 2.27
143 144 2.809446 GCGTTCAGCCAGTTTCTTTTT 58.191 42.857 0.00 0.00 40.81 1.94
182 183 9.897744 ATATTTGCTATGTAATGAAAATCCACG 57.102 29.630 0.00 0.00 0.00 4.94
183 184 6.993786 TTGCTATGTAATGAAAATCCACGA 57.006 33.333 0.00 0.00 0.00 4.35
184 185 6.993786 TGCTATGTAATGAAAATCCACGAA 57.006 33.333 0.00 0.00 0.00 3.85
185 186 6.781138 TGCTATGTAATGAAAATCCACGAAC 58.219 36.000 0.00 0.00 0.00 3.95
186 187 6.372937 TGCTATGTAATGAAAATCCACGAACA 59.627 34.615 0.00 0.00 0.00 3.18
187 188 7.066887 TGCTATGTAATGAAAATCCACGAACAT 59.933 33.333 0.00 0.00 0.00 2.71
188 189 7.376866 GCTATGTAATGAAAATCCACGAACATG 59.623 37.037 0.00 0.00 0.00 3.21
189 190 6.567687 TGTAATGAAAATCCACGAACATGT 57.432 33.333 0.00 0.00 0.00 3.21
190 191 6.607689 TGTAATGAAAATCCACGAACATGTC 58.392 36.000 0.00 0.00 0.00 3.06
191 192 5.964958 AATGAAAATCCACGAACATGTCT 57.035 34.783 0.00 0.00 0.00 3.41
192 193 7.604545 TGTAATGAAAATCCACGAACATGTCTA 59.395 33.333 0.00 0.00 0.00 2.59
193 194 7.447374 AATGAAAATCCACGAACATGTCTAA 57.553 32.000 0.00 0.00 0.00 2.10
194 195 7.630242 ATGAAAATCCACGAACATGTCTAAT 57.370 32.000 0.00 0.00 0.00 1.73
195 196 8.731275 ATGAAAATCCACGAACATGTCTAATA 57.269 30.769 0.00 0.00 0.00 0.98
196 197 8.731275 TGAAAATCCACGAACATGTCTAATAT 57.269 30.769 0.00 0.00 0.00 1.28
197 198 9.825109 TGAAAATCCACGAACATGTCTAATATA 57.175 29.630 0.00 0.00 0.00 0.86
200 201 8.777865 AATCCACGAACATGTCTAATATATGG 57.222 34.615 0.00 0.00 31.27 2.74
201 202 6.163476 TCCACGAACATGTCTAATATATGGC 58.837 40.000 0.00 0.00 31.27 4.40
202 203 5.351465 CCACGAACATGTCTAATATATGGCC 59.649 44.000 0.00 0.00 31.27 5.36
203 204 5.931724 CACGAACATGTCTAATATATGGCCA 59.068 40.000 8.56 8.56 31.27 5.36
204 205 6.426633 CACGAACATGTCTAATATATGGCCAA 59.573 38.462 10.96 0.00 31.27 4.52
205 206 6.650807 ACGAACATGTCTAATATATGGCCAAG 59.349 38.462 10.96 0.21 31.27 3.61
206 207 6.650807 CGAACATGTCTAATATATGGCCAAGT 59.349 38.462 10.96 3.52 31.27 3.16
207 208 7.173218 CGAACATGTCTAATATATGGCCAAGTT 59.827 37.037 10.96 4.95 31.27 2.66
208 209 8.766994 AACATGTCTAATATATGGCCAAGTTT 57.233 30.769 10.96 4.03 31.27 2.66
209 210 8.169977 ACATGTCTAATATATGGCCAAGTTTG 57.830 34.615 10.96 3.78 31.27 2.93
210 211 6.633500 TGTCTAATATATGGCCAAGTTTGC 57.367 37.500 10.96 0.00 0.00 3.68
217 218 3.605013 GGCCAAGTTTGCCGAAATT 57.395 47.368 1.61 0.00 39.48 1.82
218 219 1.877637 GGCCAAGTTTGCCGAAATTT 58.122 45.000 1.61 0.00 39.48 1.82
219 220 3.033368 GGCCAAGTTTGCCGAAATTTA 57.967 42.857 1.61 0.00 39.48 1.40
220 221 2.993220 GGCCAAGTTTGCCGAAATTTAG 59.007 45.455 1.61 0.00 39.48 1.85
221 222 3.554129 GGCCAAGTTTGCCGAAATTTAGT 60.554 43.478 1.61 0.00 39.48 2.24
222 223 3.673338 GCCAAGTTTGCCGAAATTTAGTC 59.327 43.478 0.00 0.00 0.00 2.59
223 224 3.911964 CCAAGTTTGCCGAAATTTAGTCG 59.088 43.478 0.00 0.00 38.24 4.18
224 225 4.533222 CAAGTTTGCCGAAATTTAGTCGT 58.467 39.130 0.00 0.00 36.77 4.34
225 226 4.141855 AGTTTGCCGAAATTTAGTCGTG 57.858 40.909 0.00 0.00 36.77 4.35
226 227 3.562557 AGTTTGCCGAAATTTAGTCGTGT 59.437 39.130 0.00 0.00 36.77 4.49
227 228 4.035909 AGTTTGCCGAAATTTAGTCGTGTT 59.964 37.500 0.00 0.00 36.77 3.32
228 229 4.555348 TTGCCGAAATTTAGTCGTGTTT 57.445 36.364 0.00 0.00 36.77 2.83
229 230 5.670149 TTGCCGAAATTTAGTCGTGTTTA 57.330 34.783 0.00 0.00 36.77 2.01
230 231 5.272167 TGCCGAAATTTAGTCGTGTTTAG 57.728 39.130 0.00 0.00 36.77 1.85
231 232 4.086574 GCCGAAATTTAGTCGTGTTTAGC 58.913 43.478 0.00 0.00 36.77 3.09
232 233 4.644954 CCGAAATTTAGTCGTGTTTAGCC 58.355 43.478 0.00 0.00 36.77 3.93
233 234 4.320491 CGAAATTTAGTCGTGTTTAGCCG 58.680 43.478 0.00 0.00 33.80 5.52
234 235 4.090354 CGAAATTTAGTCGTGTTTAGCCGA 59.910 41.667 0.00 0.00 33.80 5.54
235 236 5.388682 CGAAATTTAGTCGTGTTTAGCCGAA 60.389 40.000 0.00 0.00 34.47 4.30
236 237 4.916099 ATTTAGTCGTGTTTAGCCGAAC 57.084 40.909 0.00 0.00 34.47 3.95
237 238 3.648339 TTAGTCGTGTTTAGCCGAACT 57.352 42.857 2.06 0.00 34.47 3.01
238 239 1.779569 AGTCGTGTTTAGCCGAACTG 58.220 50.000 2.06 0.00 34.47 3.16
239 240 0.163146 GTCGTGTTTAGCCGAACTGC 59.837 55.000 2.06 0.00 34.47 4.40
240 241 1.129809 CGTGTTTAGCCGAACTGCG 59.870 57.895 2.06 3.28 40.47 5.18
241 242 1.154469 GTGTTTAGCCGAACTGCGC 60.154 57.895 0.00 0.00 39.11 6.09
242 243 2.322081 TGTTTAGCCGAACTGCGCC 61.322 57.895 4.18 0.00 39.11 6.53
243 244 3.115892 TTTAGCCGAACTGCGCCG 61.116 61.111 4.18 0.00 39.11 6.46
244 245 3.576932 TTTAGCCGAACTGCGCCGA 62.577 57.895 4.18 0.00 39.11 5.54
245 246 3.576932 TTAGCCGAACTGCGCCGAA 62.577 57.895 4.18 0.00 39.11 4.30
248 249 3.041940 CCGAACTGCGCCGAACTT 61.042 61.111 4.18 0.00 39.11 2.66
249 250 2.604174 CCGAACTGCGCCGAACTTT 61.604 57.895 4.18 0.00 39.11 2.66
250 251 1.438710 CGAACTGCGCCGAACTTTG 60.439 57.895 4.18 0.00 0.00 2.77
251 252 1.725973 GAACTGCGCCGAACTTTGC 60.726 57.895 4.18 0.00 0.00 3.68
252 253 3.194272 AACTGCGCCGAACTTTGCC 62.194 57.895 4.18 0.00 0.00 4.52
253 254 4.741781 CTGCGCCGAACTTTGCCG 62.742 66.667 4.18 0.00 0.00 5.69
261 262 1.059942 CGAACTTTGCCGGAATTTGC 58.940 50.000 5.05 0.00 0.00 3.68
262 263 1.335872 CGAACTTTGCCGGAATTTGCT 60.336 47.619 5.05 0.00 0.00 3.91
263 264 2.095466 CGAACTTTGCCGGAATTTGCTA 60.095 45.455 5.05 0.00 0.00 3.49
264 265 3.427503 CGAACTTTGCCGGAATTTGCTAT 60.428 43.478 5.05 0.00 0.00 2.97
265 266 4.201871 CGAACTTTGCCGGAATTTGCTATA 60.202 41.667 5.05 0.00 0.00 1.31
266 267 5.505654 CGAACTTTGCCGGAATTTGCTATAT 60.506 40.000 5.05 0.00 0.00 0.86
267 268 6.293190 CGAACTTTGCCGGAATTTGCTATATA 60.293 38.462 5.05 0.00 0.00 0.86
268 269 7.524717 AACTTTGCCGGAATTTGCTATATAT 57.475 32.000 5.05 0.00 0.00 0.86
269 270 7.524717 ACTTTGCCGGAATTTGCTATATATT 57.475 32.000 5.05 0.00 0.00 1.28
270 271 7.951591 ACTTTGCCGGAATTTGCTATATATTT 58.048 30.769 5.05 0.00 0.00 1.40
271 272 8.421002 ACTTTGCCGGAATTTGCTATATATTTT 58.579 29.630 5.05 0.00 0.00 1.82
272 273 9.260002 CTTTGCCGGAATTTGCTATATATTTTT 57.740 29.630 5.05 0.00 0.00 1.94
273 274 8.810652 TTGCCGGAATTTGCTATATATTTTTC 57.189 30.769 5.05 0.00 0.00 2.29
274 275 8.177119 TGCCGGAATTTGCTATATATTTTTCT 57.823 30.769 5.05 0.00 0.00 2.52
275 276 8.637986 TGCCGGAATTTGCTATATATTTTTCTT 58.362 29.630 5.05 0.00 0.00 2.52
276 277 9.476202 GCCGGAATTTGCTATATATTTTTCTTT 57.524 29.630 5.05 0.00 0.00 2.52
292 293 2.725008 TTTTTGAACGCGCCTGGG 59.275 55.556 5.73 0.00 0.00 4.45
293 294 2.851071 TTTTTGAACGCGCCTGGGG 61.851 57.895 5.73 6.36 0.00 4.96
334 335 4.410400 GGACCAACTCGCCCCCAG 62.410 72.222 0.00 0.00 0.00 4.45
335 336 4.410400 GACCAACTCGCCCCCAGG 62.410 72.222 0.00 0.00 0.00 4.45
346 347 2.732289 CCCCCAGGCCGATATTTTG 58.268 57.895 0.00 0.00 0.00 2.44
347 348 1.463553 CCCCCAGGCCGATATTTTGC 61.464 60.000 0.00 0.00 0.00 3.68
348 349 1.654220 CCCAGGCCGATATTTTGCG 59.346 57.895 0.00 0.00 0.00 4.85
349 350 1.008538 CCAGGCCGATATTTTGCGC 60.009 57.895 0.00 0.00 0.00 6.09
350 351 1.008538 CAGGCCGATATTTTGCGCC 60.009 57.895 4.18 0.00 0.00 6.53
351 352 2.051345 GGCCGATATTTTGCGCCG 60.051 61.111 4.18 0.00 0.00 6.46
352 353 2.051345 GCCGATATTTTGCGCCGG 60.051 61.111 13.63 13.63 42.74 6.13
353 354 2.051345 CCGATATTTTGCGCCGGC 60.051 61.111 19.07 19.07 40.52 6.13
354 355 2.542907 CCGATATTTTGCGCCGGCT 61.543 57.895 26.68 6.90 40.82 5.52
355 356 1.082756 CGATATTTTGCGCCGGCTC 60.083 57.895 26.68 18.89 40.82 4.70
356 357 1.771073 CGATATTTTGCGCCGGCTCA 61.771 55.000 26.68 21.91 40.82 4.26
357 358 0.317020 GATATTTTGCGCCGGCTCAC 60.317 55.000 26.68 14.53 40.82 3.51
358 359 1.724582 ATATTTTGCGCCGGCTCACC 61.725 55.000 26.68 10.54 40.82 4.02
369 370 2.844839 GCTCACCCCTAGGCCGAT 60.845 66.667 2.05 0.00 36.11 4.18
370 371 2.444256 GCTCACCCCTAGGCCGATT 61.444 63.158 2.05 0.00 36.11 3.34
371 372 1.984288 GCTCACCCCTAGGCCGATTT 61.984 60.000 2.05 0.00 36.11 2.17
372 373 0.546598 CTCACCCCTAGGCCGATTTT 59.453 55.000 2.05 0.00 36.11 1.82
373 374 0.996583 TCACCCCTAGGCCGATTTTT 59.003 50.000 2.05 0.00 36.11 1.94
387 388 3.972276 TTTTTGCGCCGGCTCACC 61.972 61.111 26.68 10.54 40.82 4.02
402 403 4.360405 ACCCCAGGCGGCGATTTT 62.360 61.111 12.98 0.00 0.00 1.82
403 404 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
404 405 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
405 406 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
406 407 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
412 413 3.592814 GCGATTTTAGGCGCCCCC 61.593 66.667 26.15 5.00 46.93 5.40
473 474 2.564947 CCCAGAGATCAGGCCTGTATAC 59.435 54.545 31.58 20.39 0.00 1.47
560 561 8.987890 ACCAGTTTTCAAAATGCACATTTATAC 58.012 29.630 8.92 4.24 39.88 1.47
561 562 8.161610 CCAGTTTTCAAAATGCACATTTATACG 58.838 33.333 8.92 0.14 39.88 3.06
594 600 7.718272 AATTCTGAAAACAATTGTGGATGTG 57.282 32.000 12.82 1.94 0.00 3.21
688 700 9.813446 CAATCCCCAAAAATTTCAAATCAAAAA 57.187 25.926 0.00 0.00 0.00 1.94
730 742 4.927422 TCCACAAATGTTTTCGGAGTTTC 58.073 39.130 0.00 0.00 0.00 2.78
739 751 4.331717 TGTTTTCGGAGTTTCTGAACACTC 59.668 41.667 17.13 17.13 41.11 3.51
740 752 2.417339 TCGGAGTTTCTGAACACTCG 57.583 50.000 18.01 15.00 40.45 4.18
752 764 6.671614 TCTGAACACTCGTTACATGTTTTT 57.328 33.333 2.30 0.00 36.70 1.94
827 839 6.579666 GTGATTTTTGAAAATTTGGAGCATGC 59.420 34.615 10.51 10.51 38.64 4.06
887 899 2.123726 GGCCGGCCTTTGATCCAT 60.124 61.111 38.76 0.00 0.00 3.41
888 900 1.150536 GGCCGGCCTTTGATCCATA 59.849 57.895 38.76 0.00 0.00 2.74
1447 1492 1.303643 GGCAACCTCCTGTTCTGGG 60.304 63.158 0.00 0.00 34.00 4.45
1450 1495 0.036875 CAACCTCCTGTTCTGGGTCC 59.963 60.000 0.00 0.00 34.00 4.46
1512 1557 2.574955 AAACCGCGAGCTCCTCAGT 61.575 57.895 8.23 0.00 0.00 3.41
1541 1586 1.800655 CGAGAAGGTGATCAAGCCGAG 60.801 57.143 0.00 0.00 0.00 4.63
1550 1595 1.630126 ATCAAGCCGAGCCTGACCAT 61.630 55.000 0.16 0.00 31.54 3.55
1765 1810 7.543868 TCGCCAGGAAAATACAATTTTTACATG 59.456 33.333 0.00 0.00 32.76 3.21
1771 1816 7.148656 GGAAAATACAATTTTTACATGCGCTGT 60.149 33.333 9.73 13.16 42.13 4.40
1797 1842 5.710513 TTTCACAGGATGATTTGGTGAAG 57.289 39.130 0.00 0.00 45.73 3.02
1941 1986 1.385528 TGTATAGCGTTGAGAGGCGA 58.614 50.000 0.00 0.00 41.39 5.54
2040 2085 1.005340 CATCGCTGGCTGAGAAGAAC 58.995 55.000 1.51 0.00 0.00 3.01
2208 2253 5.186992 TGAGATTATCCGAGGAGTTTTGTCA 59.813 40.000 0.00 0.00 0.00 3.58
2211 2256 0.395312 TCCGAGGAGTTTTGTCACCC 59.605 55.000 0.00 0.00 0.00 4.61
2221 2266 3.117512 AGTTTTGTCACCCCAAGACTGAT 60.118 43.478 0.00 0.00 38.09 2.90
2287 2332 9.813080 GTGAATTGATAAAAAGTCTGTACAGTC 57.187 33.333 21.99 16.73 0.00 3.51
2342 2387 2.905415 TCATGAAAGGTCCTGCCAAT 57.095 45.000 0.00 0.00 40.61 3.16
2363 2408 6.623486 CAATAGATGGATTGTTGCAACTTCA 58.377 36.000 28.61 20.06 33.01 3.02
2364 2409 4.778534 AGATGGATTGTTGCAACTTCAG 57.221 40.909 28.61 0.00 0.00 3.02
2460 2508 4.520492 TCTGAGCTCGCTGATATGTATGAA 59.480 41.667 9.64 0.00 0.00 2.57
2645 2696 9.944376 TCTCAGCAATTTAACAACTAGTTATCT 57.056 29.630 8.04 0.00 42.03 1.98
2667 2722 8.697846 ATCTGATTGCTACAAAACAATTCATG 57.302 30.769 0.00 0.00 36.65 3.07
2763 2818 1.607628 CCTTATTGCTCATGCCTGCTC 59.392 52.381 6.70 0.00 38.71 4.26
2788 2843 1.479323 GTACTTATCCCTGCCACACGA 59.521 52.381 0.00 0.00 0.00 4.35
2845 2901 3.517901 AGATTGGTCACCGGAGTATTGAA 59.482 43.478 9.46 0.00 0.00 2.69
2870 2926 2.470983 AGCTGCCTCTTTTCTCTCAC 57.529 50.000 0.00 0.00 0.00 3.51
2896 2952 7.269084 CGTATCTGCTCATAGTGTTTTTGTTTG 59.731 37.037 0.00 0.00 0.00 2.93
2915 2971 5.298276 TGTTTGGACTGAAGTTTACATCACC 59.702 40.000 0.00 0.00 0.00 4.02
2916 2972 4.698201 TGGACTGAAGTTTACATCACCA 57.302 40.909 0.00 0.00 0.00 4.17
2942 2998 1.141657 TCACTGCTGCTTCTTTGAGGT 59.858 47.619 0.00 0.00 0.00 3.85
2958 3014 6.811170 TCTTTGAGGTGTTGTCATTTGTTTTC 59.189 34.615 0.00 0.00 0.00 2.29
2990 3046 2.622942 TCACTCCAATTCCAACTGTTGC 59.377 45.455 14.94 0.00 0.00 4.17
3074 3131 8.091449 AGTCACTACAGAGAAGGTTTTCTTATG 58.909 37.037 0.00 0.00 43.63 1.90
3118 3175 4.892934 TGGTGTTCTAAGGAGCAACAAAAT 59.107 37.500 0.00 0.00 45.01 1.82
3126 3183 4.341366 AGGAGCAACAAAATTTTCCTGG 57.659 40.909 0.00 0.00 33.95 4.45
3135 3192 5.983540 ACAAAATTTTCCTGGCTGTTTACA 58.016 33.333 0.00 0.00 0.00 2.41
3140 3197 4.647424 TTTCCTGGCTGTTTACAAACTG 57.353 40.909 6.41 6.83 39.59 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.821589 CTCCTCCTTGACGCGGGC 62.822 72.222 12.47 1.95 0.00 6.13
52 53 2.564553 CTTCTCCTCCTTGACGCGGG 62.565 65.000 12.47 0.89 0.00 6.13
53 54 1.153745 CTTCTCCTCCTTGACGCGG 60.154 63.158 12.47 0.00 0.00 6.46
54 55 1.153745 CCTTCTCCTCCTTGACGCG 60.154 63.158 3.53 3.53 0.00 6.01
55 56 1.448717 GCCTTCTCCTCCTTGACGC 60.449 63.158 0.00 0.00 0.00 5.19
56 57 1.219393 GGCCTTCTCCTCCTTGACG 59.781 63.158 0.00 0.00 0.00 4.35
57 58 1.219393 CGGCCTTCTCCTCCTTGAC 59.781 63.158 0.00 0.00 0.00 3.18
58 59 1.078528 TCGGCCTTCTCCTCCTTGA 59.921 57.895 0.00 0.00 0.00 3.02
59 60 1.219393 GTCGGCCTTCTCCTCCTTG 59.781 63.158 0.00 0.00 0.00 3.61
60 61 2.352032 CGTCGGCCTTCTCCTCCTT 61.352 63.158 0.00 0.00 0.00 3.36
61 62 2.575455 ATCGTCGGCCTTCTCCTCCT 62.575 60.000 0.00 0.00 0.00 3.69
62 63 2.128507 ATCGTCGGCCTTCTCCTCC 61.129 63.158 0.00 0.00 0.00 4.30
63 64 1.066587 CATCGTCGGCCTTCTCCTC 59.933 63.158 0.00 0.00 0.00 3.71
64 65 1.379977 TCATCGTCGGCCTTCTCCT 60.380 57.895 0.00 0.00 0.00 3.69
65 66 1.227002 GTCATCGTCGGCCTTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
66 67 1.586564 CGTCATCGTCGGCCTTCTC 60.587 63.158 0.00 0.00 0.00 2.87
67 68 2.044555 TCGTCATCGTCGGCCTTCT 61.045 57.895 0.00 0.00 38.33 2.85
68 69 1.872679 GTCGTCATCGTCGGCCTTC 60.873 63.158 0.00 0.00 38.33 3.46
69 70 2.181021 GTCGTCATCGTCGGCCTT 59.819 61.111 0.00 0.00 38.33 4.35
70 71 4.175489 CGTCGTCATCGTCGGCCT 62.175 66.667 0.00 0.00 42.57 5.19
75 76 4.471726 ACCGCCGTCGTCATCGTC 62.472 66.667 0.00 0.00 38.33 4.20
76 77 4.771356 CACCGCCGTCGTCATCGT 62.771 66.667 0.00 0.00 38.33 3.73
77 78 4.470170 TCACCGCCGTCGTCATCG 62.470 66.667 0.00 0.00 38.55 3.84
78 79 2.579787 CTCACCGCCGTCGTCATC 60.580 66.667 0.00 0.00 0.00 2.92
79 80 4.129737 CCTCACCGCCGTCGTCAT 62.130 66.667 0.00 0.00 0.00 3.06
81 82 3.823330 ATCCTCACCGCCGTCGTC 61.823 66.667 0.00 0.00 0.00 4.20
82 83 4.129737 CATCCTCACCGCCGTCGT 62.130 66.667 0.00 0.00 0.00 4.34
83 84 4.873129 CCATCCTCACCGCCGTCG 62.873 72.222 0.00 0.00 0.00 5.12
103 104 4.157958 AGTAGTCGCCGTCGTCGC 62.158 66.667 0.00 0.00 36.96 5.19
104 105 2.021106 GAGTAGTCGCCGTCGTCG 59.979 66.667 0.00 0.00 36.96 5.12
105 106 2.021106 CGAGTAGTCGCCGTCGTC 59.979 66.667 7.09 0.00 39.88 4.20
106 107 3.494336 CCGAGTAGTCGCCGTCGT 61.494 66.667 14.65 0.00 45.41 4.34
107 108 4.883300 GCCGAGTAGTCGCCGTCG 62.883 72.222 14.65 1.76 45.41 5.12
108 109 4.883300 CGCCGAGTAGTCGCCGTC 62.883 72.222 14.62 3.09 41.83 4.79
111 112 2.578981 GAACGCCGAGTAGTCGCC 60.579 66.667 14.65 2.21 45.41 5.54
112 113 1.868251 CTGAACGCCGAGTAGTCGC 60.868 63.158 14.65 9.06 45.41 5.19
113 114 1.868251 GCTGAACGCCGAGTAGTCG 60.868 63.158 13.16 13.16 46.39 4.18
114 115 4.074454 GCTGAACGCCGAGTAGTC 57.926 61.111 0.00 0.00 0.00 2.59
123 124 2.492019 AAAAGAAACTGGCTGAACGC 57.508 45.000 0.00 0.00 38.13 4.84
156 157 9.897744 CGTGGATTTTCATTACATAGCAAATAT 57.102 29.630 0.00 0.00 0.00 1.28
157 158 9.114952 TCGTGGATTTTCATTACATAGCAAATA 57.885 29.630 0.00 0.00 0.00 1.40
158 159 7.995289 TCGTGGATTTTCATTACATAGCAAAT 58.005 30.769 0.00 0.00 0.00 2.32
159 160 7.384439 TCGTGGATTTTCATTACATAGCAAA 57.616 32.000 0.00 0.00 0.00 3.68
160 161 6.993786 TCGTGGATTTTCATTACATAGCAA 57.006 33.333 0.00 0.00 0.00 3.91
161 162 6.372937 TGTTCGTGGATTTTCATTACATAGCA 59.627 34.615 0.00 0.00 0.00 3.49
162 163 6.781138 TGTTCGTGGATTTTCATTACATAGC 58.219 36.000 0.00 0.00 0.00 2.97
163 164 8.397906 ACATGTTCGTGGATTTTCATTACATAG 58.602 33.333 0.00 0.00 0.00 2.23
164 165 8.275015 ACATGTTCGTGGATTTTCATTACATA 57.725 30.769 0.00 0.00 0.00 2.29
165 166 7.121168 AGACATGTTCGTGGATTTTCATTACAT 59.879 33.333 0.00 0.00 0.00 2.29
166 167 6.429692 AGACATGTTCGTGGATTTTCATTACA 59.570 34.615 0.00 0.00 0.00 2.41
167 168 6.842163 AGACATGTTCGTGGATTTTCATTAC 58.158 36.000 0.00 0.00 0.00 1.89
168 169 8.554835 TTAGACATGTTCGTGGATTTTCATTA 57.445 30.769 0.00 0.00 0.00 1.90
169 170 5.964958 AGACATGTTCGTGGATTTTCATT 57.035 34.783 0.00 0.00 0.00 2.57
170 171 7.630242 ATTAGACATGTTCGTGGATTTTCAT 57.370 32.000 0.00 0.00 0.00 2.57
171 172 8.731275 ATATTAGACATGTTCGTGGATTTTCA 57.269 30.769 0.00 0.00 0.00 2.69
174 175 9.219603 CCATATATTAGACATGTTCGTGGATTT 57.780 33.333 0.00 0.00 0.00 2.17
175 176 7.334421 GCCATATATTAGACATGTTCGTGGATT 59.666 37.037 0.00 0.00 0.00 3.01
176 177 6.818644 GCCATATATTAGACATGTTCGTGGAT 59.181 38.462 0.00 0.00 0.00 3.41
177 178 6.163476 GCCATATATTAGACATGTTCGTGGA 58.837 40.000 0.00 0.00 0.00 4.02
178 179 5.351465 GGCCATATATTAGACATGTTCGTGG 59.649 44.000 0.00 2.10 0.00 4.94
179 180 5.931724 TGGCCATATATTAGACATGTTCGTG 59.068 40.000 0.00 0.00 0.00 4.35
180 181 6.109156 TGGCCATATATTAGACATGTTCGT 57.891 37.500 0.00 0.00 0.00 3.85
181 182 6.650807 ACTTGGCCATATATTAGACATGTTCG 59.349 38.462 6.09 0.00 0.00 3.95
182 183 7.986085 ACTTGGCCATATATTAGACATGTTC 57.014 36.000 6.09 0.00 0.00 3.18
183 184 8.632679 CAAACTTGGCCATATATTAGACATGTT 58.367 33.333 6.09 11.28 0.00 2.71
184 185 7.255590 GCAAACTTGGCCATATATTAGACATGT 60.256 37.037 6.09 0.00 0.00 3.21
185 186 7.086376 GCAAACTTGGCCATATATTAGACATG 58.914 38.462 6.09 3.38 0.00 3.21
186 187 7.219484 GCAAACTTGGCCATATATTAGACAT 57.781 36.000 6.09 0.00 0.00 3.06
187 188 6.633500 GCAAACTTGGCCATATATTAGACA 57.367 37.500 6.09 0.00 0.00 3.41
201 202 3.911964 CGACTAAATTTCGGCAAACTTGG 59.088 43.478 0.00 0.00 32.66 3.61
202 203 4.378616 CACGACTAAATTTCGGCAAACTTG 59.621 41.667 0.00 0.00 40.92 3.16
203 204 4.035909 ACACGACTAAATTTCGGCAAACTT 59.964 37.500 0.00 0.00 40.92 2.66
204 205 3.562557 ACACGACTAAATTTCGGCAAACT 59.437 39.130 0.00 0.00 40.92 2.66
205 206 3.880610 ACACGACTAAATTTCGGCAAAC 58.119 40.909 0.00 0.00 40.92 2.93
206 207 4.555348 AACACGACTAAATTTCGGCAAA 57.445 36.364 0.00 0.00 40.92 3.68
207 208 4.555348 AAACACGACTAAATTTCGGCAA 57.445 36.364 0.00 0.00 40.92 4.52
208 209 4.377635 GCTAAACACGACTAAATTTCGGCA 60.378 41.667 0.00 0.00 40.92 5.69
209 210 4.086574 GCTAAACACGACTAAATTTCGGC 58.913 43.478 0.00 0.00 40.92 5.54
210 211 4.644954 GGCTAAACACGACTAAATTTCGG 58.355 43.478 0.00 0.00 40.92 4.30
211 212 4.090354 TCGGCTAAACACGACTAAATTTCG 59.910 41.667 0.00 0.00 42.36 3.46
212 213 5.520022 TCGGCTAAACACGACTAAATTTC 57.480 39.130 0.00 0.00 33.69 2.17
213 214 5.467735 AGTTCGGCTAAACACGACTAAATTT 59.532 36.000 0.00 0.00 39.04 1.82
214 215 4.992951 AGTTCGGCTAAACACGACTAAATT 59.007 37.500 0.00 0.00 39.04 1.82
215 216 4.387862 CAGTTCGGCTAAACACGACTAAAT 59.612 41.667 0.00 0.00 39.04 1.40
216 217 3.737266 CAGTTCGGCTAAACACGACTAAA 59.263 43.478 0.00 0.00 39.04 1.85
217 218 3.311106 CAGTTCGGCTAAACACGACTAA 58.689 45.455 0.00 0.00 39.04 2.24
218 219 2.923605 GCAGTTCGGCTAAACACGACTA 60.924 50.000 0.00 0.00 39.04 2.59
219 220 1.779569 CAGTTCGGCTAAACACGACT 58.220 50.000 0.00 0.00 39.04 4.18
220 221 0.163146 GCAGTTCGGCTAAACACGAC 59.837 55.000 0.00 0.00 39.04 4.34
221 222 1.279527 CGCAGTTCGGCTAAACACGA 61.280 55.000 0.00 0.00 34.71 4.35
222 223 1.129809 CGCAGTTCGGCTAAACACG 59.870 57.895 4.90 4.43 33.78 4.49
223 224 1.154469 GCGCAGTTCGGCTAAACAC 60.154 57.895 0.30 0.00 38.94 3.32
224 225 3.249999 GCGCAGTTCGGCTAAACA 58.750 55.556 0.30 0.00 38.94 2.83
231 232 2.604174 AAAGTTCGGCGCAGTTCGG 61.604 57.895 10.83 0.00 38.94 4.30
232 233 1.438710 CAAAGTTCGGCGCAGTTCG 60.439 57.895 10.83 2.99 42.12 3.95
233 234 1.725973 GCAAAGTTCGGCGCAGTTC 60.726 57.895 10.83 3.06 0.00 3.01
234 235 2.331451 GCAAAGTTCGGCGCAGTT 59.669 55.556 10.83 0.00 0.00 3.16
235 236 3.660111 GGCAAAGTTCGGCGCAGT 61.660 61.111 10.83 0.00 0.00 4.40
236 237 4.741781 CGGCAAAGTTCGGCGCAG 62.742 66.667 10.83 5.07 45.66 5.18
240 241 0.038618 AAATTCCGGCAAAGTTCGGC 60.039 50.000 0.00 0.00 45.31 5.54
241 242 1.696988 CAAATTCCGGCAAAGTTCGG 58.303 50.000 0.00 0.00 46.89 4.30
242 243 1.059942 GCAAATTCCGGCAAAGTTCG 58.940 50.000 0.00 0.00 0.00 3.95
243 244 2.438868 AGCAAATTCCGGCAAAGTTC 57.561 45.000 0.00 0.00 0.00 3.01
244 245 5.852282 ATATAGCAAATTCCGGCAAAGTT 57.148 34.783 0.00 0.00 0.00 2.66
245 246 7.524717 AATATATAGCAAATTCCGGCAAAGT 57.475 32.000 0.00 0.00 0.00 2.66
246 247 8.816640 AAAATATATAGCAAATTCCGGCAAAG 57.183 30.769 0.00 0.00 0.00 2.77
247 248 9.255304 GAAAAATATATAGCAAATTCCGGCAAA 57.745 29.630 0.00 0.00 0.00 3.68
248 249 8.637986 AGAAAAATATATAGCAAATTCCGGCAA 58.362 29.630 0.00 0.00 0.00 4.52
249 250 8.177119 AGAAAAATATATAGCAAATTCCGGCA 57.823 30.769 0.00 0.00 0.00 5.69
250 251 9.476202 AAAGAAAAATATATAGCAAATTCCGGC 57.524 29.630 0.00 0.00 0.00 6.13
275 276 2.725008 CCCAGGCGCGTTCAAAAA 59.275 55.556 8.43 0.00 0.00 1.94
276 277 3.291383 CCCCAGGCGCGTTCAAAA 61.291 61.111 8.43 0.00 0.00 2.44
310 311 4.760047 CGAGTTGGTCCCCAGCCG 62.760 72.222 0.00 0.00 35.27 5.52
313 314 4.410400 GGGCGAGTTGGTCCCCAG 62.410 72.222 0.00 0.00 36.26 4.45
317 318 4.410400 CTGGGGGCGAGTTGGTCC 62.410 72.222 0.00 0.00 0.00 4.46
318 319 4.410400 CCTGGGGGCGAGTTGGTC 62.410 72.222 0.00 0.00 0.00 4.02
328 329 1.463553 GCAAAATATCGGCCTGGGGG 61.464 60.000 0.00 0.00 0.00 5.40
329 330 1.795170 CGCAAAATATCGGCCTGGGG 61.795 60.000 0.00 0.00 0.00 4.96
330 331 1.654220 CGCAAAATATCGGCCTGGG 59.346 57.895 0.00 0.00 0.00 4.45
331 332 1.008538 GCGCAAAATATCGGCCTGG 60.009 57.895 0.30 0.00 0.00 4.45
332 333 1.008538 GGCGCAAAATATCGGCCTG 60.009 57.895 10.83 0.00 44.06 4.85
333 334 2.542907 CGGCGCAAAATATCGGCCT 61.543 57.895 10.83 0.00 46.53 5.19
334 335 2.051345 CGGCGCAAAATATCGGCC 60.051 61.111 10.83 0.00 46.53 6.13
335 336 2.051345 CCGGCGCAAAATATCGGC 60.051 61.111 10.83 0.00 45.92 5.54
336 337 2.051345 GCCGGCGCAAAATATCGG 60.051 61.111 12.58 12.53 43.13 4.18
337 338 1.082756 GAGCCGGCGCAAAATATCG 60.083 57.895 26.33 0.43 37.52 2.92
338 339 0.317020 GTGAGCCGGCGCAAAATATC 60.317 55.000 34.87 17.27 37.52 1.63
339 340 1.724582 GGTGAGCCGGCGCAAAATAT 61.725 55.000 34.87 7.50 37.52 1.28
340 341 2.403378 GGTGAGCCGGCGCAAAATA 61.403 57.895 34.87 9.02 37.52 1.40
341 342 3.747976 GGTGAGCCGGCGCAAAAT 61.748 61.111 34.87 9.34 37.52 1.82
352 353 1.984288 AAATCGGCCTAGGGGTGAGC 61.984 60.000 11.72 0.00 34.45 4.26
353 354 0.546598 AAAATCGGCCTAGGGGTGAG 59.453 55.000 11.72 0.00 34.45 3.51
354 355 0.996583 AAAAATCGGCCTAGGGGTGA 59.003 50.000 11.72 0.00 34.45 4.02
355 356 3.588742 AAAAATCGGCCTAGGGGTG 57.411 52.632 11.72 0.00 34.45 4.61
370 371 3.972276 GGTGAGCCGGCGCAAAAA 61.972 61.111 34.87 9.47 37.52 1.94
387 388 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
388 389 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
389 390 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
390 391 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
391 392 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
421 422 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
432 433 1.872313 GCTGCATGTCCTAAGAGCATC 59.128 52.381 0.00 0.00 34.35 3.91
433 434 1.476471 GGCTGCATGTCCTAAGAGCAT 60.476 52.381 0.50 0.00 34.35 3.79
434 435 0.107508 GGCTGCATGTCCTAAGAGCA 60.108 55.000 0.50 0.00 0.00 4.26
435 436 0.817229 GGGCTGCATGTCCTAAGAGC 60.817 60.000 0.50 0.00 37.49 4.09
436 437 0.543277 TGGGCTGCATGTCCTAAGAG 59.457 55.000 0.50 0.00 42.07 2.85
473 474 8.780616 ATTCTCCCATCTATACTGGATCTATG 57.219 38.462 0.00 0.00 35.70 2.23
575 580 4.118410 GTGCACATCCACAATTGTTTTCA 58.882 39.130 13.17 0.00 35.80 2.69
594 600 4.952262 ATTGTACACTCATGTGATGTGC 57.048 40.909 0.00 6.68 46.55 4.57
730 742 7.069569 CCTAAAAACATGTAACGAGTGTTCAG 58.930 38.462 0.00 0.00 39.54 3.02
739 751 8.596271 AAAAATTCCCCTAAAAACATGTAACG 57.404 30.769 0.00 0.00 0.00 3.18
1302 1347 3.834799 GCGTACAGGAGGGACGGG 61.835 72.222 0.91 0.00 37.08 5.28
1447 1492 1.603326 GTAGGAGTCGAAGATCCGGAC 59.397 57.143 6.12 0.11 40.67 4.79
1450 1495 0.953003 GGGTAGGAGTCGAAGATCCG 59.047 60.000 6.87 0.00 40.67 4.18
1541 1586 0.620556 TTCTTGGAGGATGGTCAGGC 59.379 55.000 0.00 0.00 0.00 4.85
1550 1595 4.080356 CACTTATCCCACATTCTTGGAGGA 60.080 45.833 0.00 0.00 39.24 3.71
1681 1726 1.451927 GGCGGAACATCCATGAGCA 60.452 57.895 0.00 0.00 35.91 4.26
1771 1816 4.039004 CACCAAATCATCCTGTGAAAACCA 59.961 41.667 0.00 0.00 40.97 3.67
1941 1986 1.301954 GGAGTACCGGGGCAACAAT 59.698 57.895 6.32 0.00 39.74 2.71
2040 2085 4.687483 GGATCCACAAAATTCTGCACAAAG 59.313 41.667 6.95 0.00 0.00 2.77
2140 2185 4.202419 ACCACAGTTTCAGTGTTATAGCCA 60.202 41.667 0.00 0.00 35.24 4.75
2342 2387 5.316167 ACTGAAGTTGCAACAATCCATCTA 58.684 37.500 30.11 11.13 0.00 1.98
2356 2401 9.683069 AGCAATTAATGAGTAAAACTGAAGTTG 57.317 29.630 0.00 0.00 38.44 3.16
2358 2403 8.230486 CGAGCAATTAATGAGTAAAACTGAAGT 58.770 33.333 0.00 0.00 0.00 3.01
2359 2404 8.230486 ACGAGCAATTAATGAGTAAAACTGAAG 58.770 33.333 0.00 0.00 0.00 3.02
2360 2405 8.094798 ACGAGCAATTAATGAGTAAAACTGAA 57.905 30.769 0.00 0.00 0.00 3.02
2361 2406 7.667043 ACGAGCAATTAATGAGTAAAACTGA 57.333 32.000 0.00 0.00 0.00 3.41
2362 2407 8.230486 AGAACGAGCAATTAATGAGTAAAACTG 58.770 33.333 0.00 0.00 0.00 3.16
2363 2408 8.230486 CAGAACGAGCAATTAATGAGTAAAACT 58.770 33.333 0.00 0.00 0.00 2.66
2364 2409 8.227791 TCAGAACGAGCAATTAATGAGTAAAAC 58.772 33.333 0.00 0.00 0.00 2.43
2564 2612 5.846714 AGTAACTAATGGGTAGGATCTGCAT 59.153 40.000 0.00 0.00 33.68 3.96
2675 2730 9.473007 TTGAACATGGATTGTAATTGATTCCTA 57.527 29.630 0.00 0.00 37.68 2.94
2683 2738 9.790344 TCCAAAATTTGAACATGGATTGTAATT 57.210 25.926 7.37 0.00 37.68 1.40
2763 2818 0.249911 GGCAGGGATAAGTACTGGCG 60.250 60.000 0.00 0.00 45.66 5.69
2788 2843 5.876357 TCCAACTAAAGCATAACCTTGAGT 58.124 37.500 0.00 0.00 38.00 3.41
2845 2901 5.046014 TGAGAGAAAAGAGGCAGCTAATCTT 60.046 40.000 0.00 0.00 34.81 2.40
2870 2926 6.408858 ACAAAAACACTATGAGCAGATACG 57.591 37.500 0.00 0.00 0.00 3.06
2896 2952 5.063880 AGTTGGTGATGTAAACTTCAGTCC 58.936 41.667 0.00 0.32 29.98 3.85
2915 2971 3.037431 AGAAGCAGCAGTGACTAGTTG 57.963 47.619 0.00 0.00 0.00 3.16
2916 2972 3.760580 AAGAAGCAGCAGTGACTAGTT 57.239 42.857 0.00 0.00 0.00 2.24
2942 2998 6.700960 CCATTAGCTGAAAACAAATGACAACA 59.299 34.615 0.00 0.00 30.77 3.33
2958 3014 4.518211 GGAATTGGAGTGATCCATTAGCTG 59.482 45.833 0.00 0.00 39.86 4.24
2976 3032 6.294731 GGACAGATAAAGCAACAGTTGGAATT 60.295 38.462 15.28 0.00 0.00 2.17
2990 3046 8.840321 CCTTAATGGTGTAATGGACAGATAAAG 58.160 37.037 0.00 0.00 39.29 1.85
3074 3131 8.082242 ACACCAATGTTATTCTAAAAGTGCTTC 58.918 33.333 0.00 0.00 34.46 3.86
3118 3175 4.707448 TCAGTTTGTAAACAGCCAGGAAAA 59.293 37.500 9.85 0.00 41.30 2.29
3126 3183 5.888412 CACCAAATCAGTTTGTAAACAGC 57.112 39.130 9.85 0.00 42.50 4.40


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

AutoCloner maintained by Alex Coulton.