Multiple sequence alignment - TraesCS7A01G423600

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 TraesCS7A01G423600 chr7A 100.000 3503 0 0 1 3503 616221619 616218117 0.000000e+00 6469.0
1 TraesCS7A01G423600 chr7A 96.970 33 1 0 169 201 616221411 616221379 4.880000e-04 56.5
2 TraesCS7A01G423600 chr7A 96.970 33 1 0 209 241 616221451 616221419 4.880000e-04 56.5
3 TraesCS7A01G423600 chr7B 92.732 2559 95 33 412 2916 579994620 579997141 0.000000e+00 3611.0
4 TraesCS7A01G423600 chr7B 88.961 462 37 6 2937 3398 579997296 579997743 3.050000e-155 558.0
5 TraesCS7A01G423600 chr7B 87.209 86 4 1 79 164 579994415 579994493 1.340000e-14 91.6
6 TraesCS7A01G423600 chr7B 82.500 120 4 8 245 364 579994516 579994618 4.820000e-14 89.8
7 TraesCS7A01G423600 chr7D 92.917 2372 91 37 559 2857 536764199 536766566 0.000000e+00 3378.0
8 TraesCS7A01G423600 chr7D 84.615 429 28 14 2990 3407 536767696 536768097 3.280000e-105 392.0
9 TraesCS7A01G423600 chr7D 79.710 345 21 17 222 565 536761019 536761315 1.650000e-48 204.0
10 TraesCS7A01G423600 chr7D 90.426 94 6 1 82 175 536760932 536761022 1.710000e-23 121.0
11 TraesCS7A01G423600 chr2D 81.677 1550 231 26 1136 2666 20359591 20361106 0.000000e+00 1240.0
12 TraesCS7A01G423600 chr4D 82.398 909 137 13 1764 2666 278346863 278345972 0.000000e+00 771.0
13 TraesCS7A01G423600 chr5A 79.426 209 39 2 1748 1954 638069168 638068962 1.010000e-30 145.0
14 TraesCS7A01G423600 chrUn 82.456 114 16 4 1740 1851 99864093 99864204 2.880000e-16 97.1
15 TraesCS7A01G423600 chr5B 94.286 35 2 0 1636 1670 641043188 641043222 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G423600 chr7A 616218117 616221619 3502 True 2194.00 6469 97.9800 1 3503 3 chr7A.!!$R1 3502
1 TraesCS7A01G423600 chr7B 579994415 579997743 3328 False 1087.60 3611 87.8505 79 3398 4 chr7B.!!$F1 3319
2 TraesCS7A01G423600 chr7D 536760932 536768097 7165 False 1023.75 3378 86.9170 82 3407 4 chr7D.!!$F1 3325
3 TraesCS7A01G423600 chr2D 20359591 20361106 1515 False 1240.00 1240 81.6770 1136 2666 1 chr2D.!!$F1 1530
4 TraesCS7A01G423600 chr4D 278345972 278346863 891 True 771.00 771 82.3980 1764 2666 1 chr4D.!!$R1 902


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
227 232 0.028902 AGCTTTGCCGTCGTTTGTTC 59.971 50.0 0.0 0.0 0.0 3.18 F
395 400 0.109342 CTCGGCCCAGCTCCATTATT 59.891 55.0 0.0 0.0 0.0 1.40 F
898 3840 0.325671 TCCTCATCCCACTCCACTCC 60.326 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 4511 1.448540 CGACTTGAGCCGCATCCTT 60.449 57.895 0.00 0.0 0.00 3.36 R
2343 5331 3.493830 GATGTCGGCCGGCGTGATA 62.494 63.158 32.38 19.2 0.00 2.15 R
2533 5521 1.866853 GCTGCAACAAGCCACCTACC 61.867 60.000 0.00 0.0 44.83 3.18 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
17 18 4.192000 CGACAAGCCGCTCAAGAT 57.808 55.556 0.00 0.00 0.00 2.40
18 19 1.712081 CGACAAGCCGCTCAAGATG 59.288 57.895 0.00 0.00 0.00 2.90
19 20 1.427020 GACAAGCCGCTCAAGATGC 59.573 57.895 0.00 0.00 0.00 3.91
20 21 1.300971 GACAAGCCGCTCAAGATGCA 61.301 55.000 0.00 0.00 0.00 3.96
21 22 1.303799 ACAAGCCGCTCAAGATGCAG 61.304 55.000 0.00 0.00 0.00 4.41
22 23 1.022982 CAAGCCGCTCAAGATGCAGA 61.023 55.000 0.00 0.00 0.00 4.26
23 24 1.023513 AAGCCGCTCAAGATGCAGAC 61.024 55.000 0.00 0.00 0.00 3.51
24 25 2.467826 GCCGCTCAAGATGCAGACC 61.468 63.158 0.00 0.00 0.00 3.85
25 26 1.078918 CCGCTCAAGATGCAGACCA 60.079 57.895 0.00 0.00 0.00 4.02
26 27 1.364626 CCGCTCAAGATGCAGACCAC 61.365 60.000 0.00 0.00 0.00 4.16
27 28 1.690283 CGCTCAAGATGCAGACCACG 61.690 60.000 0.00 0.00 0.00 4.94
28 29 0.390340 GCTCAAGATGCAGACCACGA 60.390 55.000 0.00 0.00 0.00 4.35
29 30 1.941209 GCTCAAGATGCAGACCACGAA 60.941 52.381 0.00 0.00 0.00 3.85
30 31 2.416747 CTCAAGATGCAGACCACGAAA 58.583 47.619 0.00 0.00 0.00 3.46
31 32 2.143122 TCAAGATGCAGACCACGAAAC 58.857 47.619 0.00 0.00 0.00 2.78
32 33 1.872952 CAAGATGCAGACCACGAAACA 59.127 47.619 0.00 0.00 0.00 2.83
33 34 2.479566 AGATGCAGACCACGAAACAT 57.520 45.000 0.00 0.00 0.00 2.71
34 35 2.783135 AGATGCAGACCACGAAACATT 58.217 42.857 0.00 0.00 0.00 2.71
35 36 2.485426 AGATGCAGACCACGAAACATTG 59.515 45.455 0.00 0.00 0.00 2.82
36 37 0.950836 TGCAGACCACGAAACATTGG 59.049 50.000 0.00 0.00 39.00 3.16
37 38 0.387239 GCAGACCACGAAACATTGGC 60.387 55.000 0.00 0.00 36.20 4.52
38 39 0.240945 CAGACCACGAAACATTGGCC 59.759 55.000 0.00 0.00 36.20 5.36
39 40 1.209127 GACCACGAAACATTGGCCG 59.791 57.895 0.00 0.00 36.20 6.13
40 41 2.126502 CCACGAAACATTGGCCGC 60.127 61.111 0.00 0.00 0.00 6.53
41 42 2.126502 CACGAAACATTGGCCGCC 60.127 61.111 1.04 1.04 0.00 6.13
42 43 2.596046 ACGAAACATTGGCCGCCA 60.596 55.556 8.43 8.43 0.00 5.69
43 44 2.126502 CGAAACATTGGCCGCCAC 60.127 61.111 13.00 0.00 30.78 5.01
44 45 2.126502 GAAACATTGGCCGCCACG 60.127 61.111 13.00 9.14 30.78 4.94
45 46 4.356442 AAACATTGGCCGCCACGC 62.356 61.111 13.00 0.00 30.78 5.34
64 65 4.803426 CCCGGCGTCTCTGCTGTC 62.803 72.222 6.01 0.00 39.68 3.51
65 66 4.803426 CCGGCGTCTCTGCTGTCC 62.803 72.222 6.01 0.00 39.68 4.02
66 67 4.056125 CGGCGTCTCTGCTGTCCA 62.056 66.667 0.00 0.00 36.47 4.02
67 68 2.125753 GGCGTCTCTGCTGTCCAG 60.126 66.667 0.00 0.00 43.17 3.86
77 78 3.882025 CTGTCCAGCCGAAAGAGC 58.118 61.111 0.00 0.00 0.00 4.09
96 97 2.742372 GCCCGTCGCTGTTCATGT 60.742 61.111 0.00 0.00 0.00 3.21
97 98 2.740714 GCCCGTCGCTGTTCATGTC 61.741 63.158 0.00 0.00 0.00 3.06
121 126 4.137872 GCACGGCGGCACCTACTA 62.138 66.667 13.24 0.00 35.61 1.82
122 127 2.202703 CACGGCGGCACCTACTAC 60.203 66.667 13.24 0.00 35.61 2.73
123 128 3.455469 ACGGCGGCACCTACTACC 61.455 66.667 13.24 0.00 35.61 3.18
167 172 0.107459 GGACTCTCCAATCCACCAGC 60.107 60.000 0.00 0.00 36.28 4.85
171 176 1.203441 TCTCCAATCCACCAGCAGCT 61.203 55.000 0.00 0.00 0.00 4.24
172 177 0.323178 CTCCAATCCACCAGCAGCTT 60.323 55.000 0.00 0.00 0.00 3.74
173 178 0.112995 TCCAATCCACCAGCAGCTTT 59.887 50.000 0.00 0.00 0.00 3.51
174 179 0.245539 CCAATCCACCAGCAGCTTTG 59.754 55.000 0.00 0.00 0.00 2.77
175 180 0.389426 CAATCCACCAGCAGCTTTGC 60.389 55.000 0.00 0.00 0.00 3.68
176 181 1.538687 AATCCACCAGCAGCTTTGCC 61.539 55.000 0.00 0.00 34.90 4.52
177 182 4.047059 CCACCAGCAGCTTTGCCG 62.047 66.667 0.00 0.00 34.90 5.69
178 183 3.289834 CACCAGCAGCTTTGCCGT 61.290 61.111 0.00 0.00 34.90 5.68
179 184 2.980233 ACCAGCAGCTTTGCCGTC 60.980 61.111 0.00 0.00 34.90 4.79
180 185 4.093952 CCAGCAGCTTTGCCGTCG 62.094 66.667 0.00 0.00 34.90 5.12
202 207 0.320374 TGTTCACGGCCTCGAAAGAT 59.680 50.000 0.00 0.00 40.84 2.40
203 208 1.546923 TGTTCACGGCCTCGAAAGATA 59.453 47.619 0.00 0.00 40.84 1.98
204 209 2.194271 GTTCACGGCCTCGAAAGATAG 58.806 52.381 0.00 0.00 40.84 2.08
205 210 1.758936 TCACGGCCTCGAAAGATAGA 58.241 50.000 0.00 0.00 40.84 1.98
206 211 2.307768 TCACGGCCTCGAAAGATAGAT 58.692 47.619 0.00 0.00 40.84 1.98
207 212 2.693591 TCACGGCCTCGAAAGATAGATT 59.306 45.455 0.00 0.00 40.84 2.40
208 213 3.887110 TCACGGCCTCGAAAGATAGATTA 59.113 43.478 0.00 0.00 40.84 1.75
209 214 4.023107 TCACGGCCTCGAAAGATAGATTAG 60.023 45.833 0.00 0.00 40.84 1.73
210 215 3.246619 CGGCCTCGAAAGATAGATTAGC 58.753 50.000 0.00 0.00 40.84 3.09
211 216 3.057174 CGGCCTCGAAAGATAGATTAGCT 60.057 47.826 0.00 0.00 40.84 3.32
212 217 4.559704 CGGCCTCGAAAGATAGATTAGCTT 60.560 45.833 0.00 0.00 40.84 3.74
213 218 5.301555 GGCCTCGAAAGATAGATTAGCTTT 58.698 41.667 0.00 0.00 46.01 3.51
214 219 5.178438 GGCCTCGAAAGATAGATTAGCTTTG 59.822 44.000 4.28 0.00 43.67 2.77
215 220 5.333721 GCCTCGAAAGATAGATTAGCTTTGC 60.334 44.000 4.28 0.00 43.67 3.68
216 221 5.178438 CCTCGAAAGATAGATTAGCTTTGCC 59.822 44.000 4.28 0.00 43.67 4.52
217 222 4.745125 TCGAAAGATAGATTAGCTTTGCCG 59.255 41.667 4.28 3.64 43.67 5.69
218 223 4.508124 CGAAAGATAGATTAGCTTTGCCGT 59.492 41.667 4.28 0.00 43.67 5.68
219 224 5.332656 CGAAAGATAGATTAGCTTTGCCGTC 60.333 44.000 4.28 0.00 43.67 4.79
220 225 3.643763 AGATAGATTAGCTTTGCCGTCG 58.356 45.455 0.00 0.00 0.00 5.12
221 226 2.953466 TAGATTAGCTTTGCCGTCGT 57.047 45.000 0.00 0.00 0.00 4.34
222 227 2.094762 AGATTAGCTTTGCCGTCGTT 57.905 45.000 0.00 0.00 0.00 3.85
223 228 2.423577 AGATTAGCTTTGCCGTCGTTT 58.576 42.857 0.00 0.00 0.00 3.60
224 229 2.159627 AGATTAGCTTTGCCGTCGTTTG 59.840 45.455 0.00 0.00 0.00 2.93
225 230 1.301423 TTAGCTTTGCCGTCGTTTGT 58.699 45.000 0.00 0.00 0.00 2.83
226 231 1.301423 TAGCTTTGCCGTCGTTTGTT 58.699 45.000 0.00 0.00 0.00 2.83
227 232 0.028902 AGCTTTGCCGTCGTTTGTTC 59.971 50.000 0.00 0.00 0.00 3.18
228 233 0.248296 GCTTTGCCGTCGTTTGTTCA 60.248 50.000 0.00 0.00 0.00 3.18
229 234 1.462791 CTTTGCCGTCGTTTGTTCAC 58.537 50.000 0.00 0.00 0.00 3.18
230 235 0.247735 TTTGCCGTCGTTTGTTCACG 60.248 50.000 0.00 0.00 41.78 4.35
232 237 2.247267 CCGTCGTTTGTTCACGGC 59.753 61.111 0.00 0.00 46.08 5.68
233 238 2.247267 CGTCGTTTGTTCACGGCC 59.753 61.111 0.00 0.00 41.90 6.13
234 239 2.241880 CGTCGTTTGTTCACGGCCT 61.242 57.895 0.00 0.00 41.90 5.19
235 240 1.568025 GTCGTTTGTTCACGGCCTC 59.432 57.895 0.00 0.00 38.90 4.70
236 241 1.952133 TCGTTTGTTCACGGCCTCG 60.952 57.895 0.00 0.00 40.74 4.63
237 242 2.943653 GTTTGTTCACGGCCTCGG 59.056 61.111 0.00 0.00 41.39 4.63
238 243 1.595929 GTTTGTTCACGGCCTCGGA 60.596 57.895 0.00 0.00 41.39 4.55
239 244 1.146485 TTTGTTCACGGCCTCGGAA 59.854 52.632 0.00 0.00 41.39 4.30
240 245 0.882927 TTTGTTCACGGCCTCGGAAG 60.883 55.000 0.00 0.00 41.39 3.46
241 246 2.434359 GTTCACGGCCTCGGAAGG 60.434 66.667 0.00 0.00 46.44 3.46
242 247 2.602267 TTCACGGCCTCGGAAGGA 60.602 61.111 0.00 0.00 46.67 3.36
243 248 2.211410 TTCACGGCCTCGGAAGGAA 61.211 57.895 0.00 0.00 46.67 3.36
317 322 3.320541 CCACATCCACAAAGCAAAAGGTA 59.679 43.478 0.00 0.00 0.00 3.08
320 325 4.520492 ACATCCACAAAGCAAAAGGTAGAG 59.480 41.667 0.00 0.00 0.00 2.43
321 326 4.164843 TCCACAAAGCAAAAGGTAGAGT 57.835 40.909 0.00 0.00 0.00 3.24
322 327 5.298989 TCCACAAAGCAAAAGGTAGAGTA 57.701 39.130 0.00 0.00 0.00 2.59
323 328 5.686753 TCCACAAAGCAAAAGGTAGAGTAA 58.313 37.500 0.00 0.00 0.00 2.24
324 329 5.763204 TCCACAAAGCAAAAGGTAGAGTAAG 59.237 40.000 0.00 0.00 0.00 2.34
325 330 5.452777 CACAAAGCAAAAGGTAGAGTAAGC 58.547 41.667 0.00 0.00 0.00 3.09
326 331 5.008613 CACAAAGCAAAAGGTAGAGTAAGCA 59.991 40.000 0.00 0.00 0.00 3.91
327 332 5.239525 ACAAAGCAAAAGGTAGAGTAAGCAG 59.760 40.000 0.00 0.00 0.00 4.24
368 373 0.643820 GCAACCGTCGTACTGTATGC 59.356 55.000 2.09 0.00 0.00 3.14
380 385 4.378563 CGTACTGTATGCTCTAATCCTCGG 60.379 50.000 0.00 0.00 0.00 4.63
389 394 2.105806 CTAATCCTCGGCCCAGCTCC 62.106 65.000 0.00 0.00 0.00 4.70
390 395 2.889521 TAATCCTCGGCCCAGCTCCA 62.890 60.000 0.00 0.00 0.00 3.86
391 396 4.804420 TCCTCGGCCCAGCTCCAT 62.804 66.667 0.00 0.00 0.00 3.41
392 397 3.801997 CCTCGGCCCAGCTCCATT 61.802 66.667 0.00 0.00 0.00 3.16
393 398 2.443394 CCTCGGCCCAGCTCCATTA 61.443 63.158 0.00 0.00 0.00 1.90
394 399 1.757306 CTCGGCCCAGCTCCATTAT 59.243 57.895 0.00 0.00 0.00 1.28
395 400 0.109342 CTCGGCCCAGCTCCATTATT 59.891 55.000 0.00 0.00 0.00 1.40
396 401 1.347707 CTCGGCCCAGCTCCATTATTA 59.652 52.381 0.00 0.00 0.00 0.98
397 402 1.985159 TCGGCCCAGCTCCATTATTAT 59.015 47.619 0.00 0.00 0.00 1.28
398 403 2.375174 TCGGCCCAGCTCCATTATTATT 59.625 45.455 0.00 0.00 0.00 1.40
399 404 3.585289 TCGGCCCAGCTCCATTATTATTA 59.415 43.478 0.00 0.00 0.00 0.98
400 405 4.227300 TCGGCCCAGCTCCATTATTATTAT 59.773 41.667 0.00 0.00 0.00 1.28
401 406 4.949856 CGGCCCAGCTCCATTATTATTATT 59.050 41.667 0.00 0.00 0.00 1.40
402 407 6.069905 TCGGCCCAGCTCCATTATTATTATTA 60.070 38.462 0.00 0.00 0.00 0.98
403 408 6.772716 CGGCCCAGCTCCATTATTATTATTAT 59.227 38.462 0.00 0.00 0.00 1.28
404 409 7.285401 CGGCCCAGCTCCATTATTATTATTATT 59.715 37.037 0.00 0.00 0.00 1.40
405 410 9.640952 GGCCCAGCTCCATTATTATTATTATTA 57.359 33.333 0.00 0.00 0.00 0.98
434 439 3.634397 ATTATCAGTGGACTGTGTGGG 57.366 47.619 6.68 0.00 44.12 4.61
481 486 1.310933 AAGATCGAGGCCACGTACGT 61.311 55.000 22.14 16.72 34.70 3.57
483 488 2.659017 GATCGAGGCCACGTACGTCC 62.659 65.000 19.94 17.80 34.70 4.79
484 489 4.487412 CGAGGCCACGTACGTCCC 62.487 72.222 19.94 20.75 0.00 4.46
485 490 4.487412 GAGGCCACGTACGTCCCG 62.487 72.222 19.94 10.05 0.00 5.14
488 493 4.783734 GCCACGTACGTCCCGGTC 62.784 72.222 19.94 9.53 0.00 4.79
503 508 2.357517 GTCGTGGTGGTGCTCCTG 60.358 66.667 6.34 0.00 34.23 3.86
510 515 4.994471 TGGTGCTCCTGCGTGCTG 62.994 66.667 6.34 0.00 43.34 4.41
513 518 2.666190 TGCTCCTGCGTGCTGAAC 60.666 61.111 0.00 0.00 43.34 3.18
514 519 3.426568 GCTCCTGCGTGCTGAACC 61.427 66.667 0.00 0.00 0.00 3.62
515 520 3.114616 CTCCTGCGTGCTGAACCG 61.115 66.667 0.00 0.00 0.00 4.44
516 521 3.865929 CTCCTGCGTGCTGAACCGT 62.866 63.158 0.00 0.00 0.00 4.83
517 522 2.048597 CCTGCGTGCTGAACCGTA 60.049 61.111 0.00 0.00 0.00 4.02
518 523 2.380410 CCTGCGTGCTGAACCGTAC 61.380 63.158 0.00 0.00 0.00 3.67
561 3455 1.000274 GTGGGTTGATCAAAGTGGTGC 60.000 52.381 10.35 0.00 0.00 5.01
581 3475 3.831883 GTGCATGCATGGACGGAT 58.168 55.556 31.53 0.00 39.29 4.18
857 3799 1.441732 CCCCGCGCCACCTATAAAAC 61.442 60.000 0.00 0.00 0.00 2.43
860 3802 0.745128 CGCGCCACCTATAAAACCCA 60.745 55.000 0.00 0.00 0.00 4.51
861 3803 0.736636 GCGCCACCTATAAAACCCAC 59.263 55.000 0.00 0.00 0.00 4.61
865 3807 1.641714 CCACCTATAAAACCCACCCCA 59.358 52.381 0.00 0.00 0.00 4.96
867 3809 1.642238 ACCTATAAAACCCACCCCACC 59.358 52.381 0.00 0.00 0.00 4.61
898 3840 0.325671 TCCTCATCCCACTCCACTCC 60.326 60.000 0.00 0.00 0.00 3.85
984 3938 1.358725 CGCGCACCAAAGCTAAGCTA 61.359 55.000 8.75 0.00 38.25 3.32
985 3939 0.802494 GCGCACCAAAGCTAAGCTAA 59.198 50.000 0.30 0.00 38.25 3.09
986 3940 1.199097 GCGCACCAAAGCTAAGCTAAA 59.801 47.619 0.30 0.00 38.25 1.85
987 3941 2.729156 GCGCACCAAAGCTAAGCTAAAG 60.729 50.000 0.30 0.00 38.25 1.85
988 3942 2.729156 CGCACCAAAGCTAAGCTAAAGC 60.729 50.000 12.03 12.03 38.25 3.51
1536 4511 1.141665 CATCATCGACGAGGCCACA 59.858 57.895 5.01 0.00 0.00 4.17
2007 4988 4.030452 GACAACACGCAGCTGGCC 62.030 66.667 17.12 0.00 40.31 5.36
2505 5493 2.584965 AGAGGAGAAGATGGAGTGAGGA 59.415 50.000 0.00 0.00 0.00 3.71
2512 5500 5.028802 AGAAGATGGAGTGAGGAAGATCAA 58.971 41.667 0.00 0.00 0.00 2.57
2533 5521 3.674528 AGACACAGAGATTGACCAGTG 57.325 47.619 0.00 0.00 0.00 3.66
2585 5573 6.976925 GGAGGATTGCAGATGAAATTAACTTG 59.023 38.462 0.00 0.00 0.00 3.16
2678 5666 1.242076 ACAAGTGGCTGCTTGATCAC 58.758 50.000 22.34 2.91 46.34 3.06
2711 5699 8.596380 CGATAGATCCTCTTGTAGTTTTTGTTC 58.404 37.037 0.00 0.00 39.76 3.18
2759 5760 6.992715 AGTTAAGCTCAGAAGAAAAAGCAGTA 59.007 34.615 0.00 0.00 37.22 2.74
2863 5933 5.116882 AGGTCAGGATAAAATACGAGCAAC 58.883 41.667 0.00 0.00 0.00 4.17
2908 5978 2.802415 CGAAGATGGAGTGAGGCAGATG 60.802 54.545 0.00 0.00 0.00 2.90
2936 6111 4.156190 ACTGAGATTGACCAGTACGTACAG 59.844 45.833 26.55 18.88 41.38 2.74
2937 6112 3.119602 TGAGATTGACCAGTACGTACAGC 60.120 47.826 26.55 13.01 0.00 4.40
2938 6113 2.823747 AGATTGACCAGTACGTACAGCA 59.176 45.455 26.55 15.23 0.00 4.41
2939 6114 2.717580 TTGACCAGTACGTACAGCAG 57.282 50.000 26.55 14.13 0.00 4.24
2940 6115 1.900245 TGACCAGTACGTACAGCAGA 58.100 50.000 26.55 5.65 0.00 4.26
2941 6116 2.232399 TGACCAGTACGTACAGCAGAA 58.768 47.619 26.55 5.79 0.00 3.02
2943 6118 1.544691 ACCAGTACGTACAGCAGAAGG 59.455 52.381 26.55 16.87 0.00 3.46
2944 6119 1.816835 CCAGTACGTACAGCAGAAGGA 59.183 52.381 26.55 0.00 0.00 3.36
2945 6120 2.230508 CCAGTACGTACAGCAGAAGGAA 59.769 50.000 26.55 0.00 0.00 3.36
2965 6166 9.886132 GAAGGAACTAATAACTTCAGTATTCCA 57.114 33.333 0.00 0.00 38.49 3.53
2967 6168 9.838339 AGGAACTAATAACTTCAGTATTCCATG 57.162 33.333 0.00 0.00 36.02 3.66
2968 6169 9.057089 GGAACTAATAACTTCAGTATTCCATGG 57.943 37.037 4.97 4.97 0.00 3.66
2976 6177 5.367937 ACTTCAGTATTCCATGGTATCTGCT 59.632 40.000 12.58 4.60 0.00 4.24
2994 7116 3.997681 CTGCTGCATCAGATTCAGATAGG 59.002 47.826 12.23 0.00 36.19 2.57
3011 7133 6.874664 TCAGATAGGTCGATATGTAGAGTGAC 59.125 42.308 0.00 0.00 0.00 3.67
3012 7134 6.651225 CAGATAGGTCGATATGTAGAGTGACA 59.349 42.308 0.00 0.00 0.00 3.58
3044 7173 1.131883 GTCATCATGTGGCTGCTTGAC 59.868 52.381 0.00 0.00 0.00 3.18
3074 7203 7.448748 AACTATTCTTCCTTTTGTTGCGTAT 57.551 32.000 0.00 0.00 0.00 3.06
3075 7204 8.556213 AACTATTCTTCCTTTTGTTGCGTATA 57.444 30.769 0.00 0.00 0.00 1.47
3095 7224 2.517959 AGTGGTACGCCTGTGTACTTA 58.482 47.619 17.63 7.41 43.36 2.24
3114 7243 8.150296 TGTACTTACATGATGGATGGATGTTAG 58.850 37.037 0.00 0.00 35.41 2.34
3224 7353 8.014517 CACTTCTTCTATTCTTGTTTGAGCTTC 58.985 37.037 0.00 0.00 0.00 3.86
3261 7390 7.775093 TGATGTCAAAATTTAGGTCAGGATAGG 59.225 37.037 0.00 0.00 0.00 2.57
3322 7451 0.869730 CCGAATTGAAAACGACGGGT 59.130 50.000 0.00 0.00 36.17 5.28
3327 7456 4.318974 CGAATTGAAAACGACGGGTAAAGT 60.319 41.667 0.00 0.00 0.00 2.66
3350 7479 0.390735 ATACGTCGTGCCTTTCCACC 60.391 55.000 8.47 0.00 32.10 4.61
3359 7488 3.181485 CGTGCCTTTCCACCTTGTTTTTA 60.181 43.478 0.00 0.00 32.10 1.52
3360 7489 4.678309 CGTGCCTTTCCACCTTGTTTTTAA 60.678 41.667 0.00 0.00 32.10 1.52
3363 7492 6.422701 GTGCCTTTCCACCTTGTTTTTAATAC 59.577 38.462 0.00 0.00 0.00 1.89
3367 7496 4.080687 TCCACCTTGTTTTTAATACGGGG 58.919 43.478 0.00 0.00 0.00 5.73
3407 7537 9.431887 CTTTATTACCAGTTTAGCAGAGTTACA 57.568 33.333 0.00 0.00 0.00 2.41
3408 7538 9.781633 TTTATTACCAGTTTAGCAGAGTTACAA 57.218 29.630 0.00 0.00 0.00 2.41
3409 7539 7.668525 ATTACCAGTTTAGCAGAGTTACAAC 57.331 36.000 0.00 0.00 0.00 3.32
3410 7540 5.031066 ACCAGTTTAGCAGAGTTACAACA 57.969 39.130 0.00 0.00 0.00 3.33
3411 7541 5.621193 ACCAGTTTAGCAGAGTTACAACAT 58.379 37.500 0.00 0.00 0.00 2.71
3412 7542 5.701290 ACCAGTTTAGCAGAGTTACAACATC 59.299 40.000 0.00 0.00 0.00 3.06
3413 7543 5.934625 CCAGTTTAGCAGAGTTACAACATCT 59.065 40.000 0.00 0.00 0.00 2.90
3414 7544 7.097192 CCAGTTTAGCAGAGTTACAACATCTA 58.903 38.462 0.00 0.00 0.00 1.98
3415 7545 7.063544 CCAGTTTAGCAGAGTTACAACATCTAC 59.936 40.741 0.00 0.00 0.00 2.59
3416 7546 7.598869 CAGTTTAGCAGAGTTACAACATCTACA 59.401 37.037 0.00 0.00 0.00 2.74
3417 7547 7.815068 AGTTTAGCAGAGTTACAACATCTACAG 59.185 37.037 0.00 0.00 0.00 2.74
3418 7548 5.730296 AGCAGAGTTACAACATCTACAGT 57.270 39.130 0.00 0.00 0.00 3.55
3419 7549 5.715070 AGCAGAGTTACAACATCTACAGTC 58.285 41.667 0.00 0.00 0.00 3.51
3420 7550 4.865365 GCAGAGTTACAACATCTACAGTCC 59.135 45.833 0.00 0.00 0.00 3.85
3421 7551 5.096169 CAGAGTTACAACATCTACAGTCCG 58.904 45.833 0.00 0.00 0.00 4.79
3422 7552 5.008331 AGAGTTACAACATCTACAGTCCGA 58.992 41.667 0.00 0.00 0.00 4.55
3423 7553 5.056894 AGTTACAACATCTACAGTCCGAC 57.943 43.478 0.00 0.00 0.00 4.79
3424 7554 2.631418 ACAACATCTACAGTCCGACG 57.369 50.000 0.00 0.00 0.00 5.12
3425 7555 1.884579 ACAACATCTACAGTCCGACGT 59.115 47.619 0.00 0.00 0.00 4.34
3426 7556 2.095364 ACAACATCTACAGTCCGACGTC 60.095 50.000 5.18 5.18 0.00 4.34
3427 7557 2.110901 ACATCTACAGTCCGACGTCT 57.889 50.000 14.70 0.00 0.00 4.18
3428 7558 2.008329 ACATCTACAGTCCGACGTCTC 58.992 52.381 14.70 4.16 0.00 3.36
3429 7559 2.007608 CATCTACAGTCCGACGTCTCA 58.992 52.381 14.70 0.00 0.00 3.27
3430 7560 2.174363 TCTACAGTCCGACGTCTCAA 57.826 50.000 14.70 0.00 0.00 3.02
3431 7561 2.497138 TCTACAGTCCGACGTCTCAAA 58.503 47.619 14.70 0.00 0.00 2.69
3432 7562 2.225019 TCTACAGTCCGACGTCTCAAAC 59.775 50.000 14.70 6.22 0.00 2.93
3433 7563 0.031721 ACAGTCCGACGTCTCAAACC 59.968 55.000 14.70 0.00 0.00 3.27
3434 7564 0.031585 CAGTCCGACGTCTCAAACCA 59.968 55.000 14.70 0.00 0.00 3.67
3435 7565 0.966920 AGTCCGACGTCTCAAACCAT 59.033 50.000 14.70 0.00 0.00 3.55
3436 7566 1.067776 AGTCCGACGTCTCAAACCATC 60.068 52.381 14.70 0.00 0.00 3.51
3437 7567 1.067776 GTCCGACGTCTCAAACCATCT 60.068 52.381 14.70 0.00 0.00 2.90
3438 7568 1.201647 TCCGACGTCTCAAACCATCTC 59.798 52.381 14.70 0.00 0.00 2.75
3439 7569 1.202582 CCGACGTCTCAAACCATCTCT 59.797 52.381 14.70 0.00 0.00 3.10
3440 7570 2.352814 CCGACGTCTCAAACCATCTCTT 60.353 50.000 14.70 0.00 0.00 2.85
3441 7571 3.119602 CCGACGTCTCAAACCATCTCTTA 60.120 47.826 14.70 0.00 0.00 2.10
3442 7572 4.440250 CCGACGTCTCAAACCATCTCTTAT 60.440 45.833 14.70 0.00 0.00 1.73
3443 7573 5.220989 CCGACGTCTCAAACCATCTCTTATA 60.221 44.000 14.70 0.00 0.00 0.98
3444 7574 5.681982 CGACGTCTCAAACCATCTCTTATAC 59.318 44.000 14.70 0.00 0.00 1.47
3445 7575 6.525578 ACGTCTCAAACCATCTCTTATACA 57.474 37.500 0.00 0.00 0.00 2.29
3446 7576 7.113658 ACGTCTCAAACCATCTCTTATACAT 57.886 36.000 0.00 0.00 0.00 2.29
3447 7577 7.556844 ACGTCTCAAACCATCTCTTATACATT 58.443 34.615 0.00 0.00 0.00 2.71
3448 7578 7.707035 ACGTCTCAAACCATCTCTTATACATTC 59.293 37.037 0.00 0.00 0.00 2.67
3449 7579 7.706607 CGTCTCAAACCATCTCTTATACATTCA 59.293 37.037 0.00 0.00 0.00 2.57
3450 7580 8.821894 GTCTCAAACCATCTCTTATACATTCAC 58.178 37.037 0.00 0.00 0.00 3.18
3451 7581 7.706607 TCTCAAACCATCTCTTATACATTCACG 59.293 37.037 0.00 0.00 0.00 4.35
3452 7582 6.761242 TCAAACCATCTCTTATACATTCACGG 59.239 38.462 0.00 0.00 0.00 4.94
3453 7583 6.479972 AACCATCTCTTATACATTCACGGA 57.520 37.500 0.00 0.00 0.00 4.69
3454 7584 6.672266 ACCATCTCTTATACATTCACGGAT 57.328 37.500 0.00 0.00 0.00 4.18
3455 7585 6.459066 ACCATCTCTTATACATTCACGGATG 58.541 40.000 0.00 0.00 0.00 3.51
3456 7586 5.349817 CCATCTCTTATACATTCACGGATGC 59.650 44.000 0.00 0.00 0.00 3.91
3457 7587 4.546570 TCTCTTATACATTCACGGATGCG 58.453 43.478 4.58 4.58 0.00 4.73
3458 7588 4.037565 TCTCTTATACATTCACGGATGCGT 59.962 41.667 6.39 6.39 0.00 5.24
3459 7589 4.295870 TCTTATACATTCACGGATGCGTC 58.704 43.478 10.14 0.00 0.00 5.19
3460 7590 1.865865 ATACATTCACGGATGCGTCC 58.134 50.000 15.54 15.54 41.40 4.79
3468 7598 3.409856 GGATGCGTCCGGTCAATG 58.590 61.111 9.75 0.00 34.13 2.82
3469 7599 1.153449 GGATGCGTCCGGTCAATGA 60.153 57.895 9.75 0.00 34.13 2.57
3470 7600 1.429148 GGATGCGTCCGGTCAATGAC 61.429 60.000 9.75 4.51 34.13 3.06
3485 7615 6.214191 GTCAATGACCAGACAATAGAGAGA 57.786 41.667 1.10 0.00 34.93 3.10
3486 7616 6.634805 GTCAATGACCAGACAATAGAGAGAA 58.365 40.000 1.10 0.00 34.93 2.87
3487 7617 7.099764 GTCAATGACCAGACAATAGAGAGAAA 58.900 38.462 1.10 0.00 34.93 2.52
3488 7618 7.604164 GTCAATGACCAGACAATAGAGAGAAAA 59.396 37.037 1.10 0.00 34.93 2.29
3489 7619 8.156820 TCAATGACCAGACAATAGAGAGAAAAA 58.843 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.712081 CATCTTGAGCGGCTTGTCG 59.288 57.895 2.97 0.00 0.00 4.35
1 2 1.300971 TGCATCTTGAGCGGCTTGTC 61.301 55.000 2.97 0.00 33.85 3.18
2 3 1.302752 TGCATCTTGAGCGGCTTGT 60.303 52.632 2.97 0.00 33.85 3.16
3 4 1.022982 TCTGCATCTTGAGCGGCTTG 61.023 55.000 2.97 0.00 38.26 4.01
4 5 1.023513 GTCTGCATCTTGAGCGGCTT 61.024 55.000 2.97 0.00 38.26 4.35
5 6 1.449246 GTCTGCATCTTGAGCGGCT 60.449 57.895 0.00 0.00 38.26 5.52
6 7 2.467826 GGTCTGCATCTTGAGCGGC 61.468 63.158 0.00 0.00 38.26 6.53
7 8 1.078918 TGGTCTGCATCTTGAGCGG 60.079 57.895 0.00 0.00 39.72 5.52
8 9 1.690283 CGTGGTCTGCATCTTGAGCG 61.690 60.000 0.00 0.00 33.88 5.03
9 10 0.390340 TCGTGGTCTGCATCTTGAGC 60.390 55.000 0.00 0.00 0.00 4.26
10 11 2.084610 TTCGTGGTCTGCATCTTGAG 57.915 50.000 0.00 0.00 0.00 3.02
11 12 2.143122 GTTTCGTGGTCTGCATCTTGA 58.857 47.619 0.00 0.00 0.00 3.02
12 13 1.872952 TGTTTCGTGGTCTGCATCTTG 59.127 47.619 0.00 0.00 0.00 3.02
13 14 2.254546 TGTTTCGTGGTCTGCATCTT 57.745 45.000 0.00 0.00 0.00 2.40
14 15 2.479566 ATGTTTCGTGGTCTGCATCT 57.520 45.000 0.00 0.00 0.00 2.90
15 16 2.414559 CCAATGTTTCGTGGTCTGCATC 60.415 50.000 0.00 0.00 0.00 3.91
16 17 1.541147 CCAATGTTTCGTGGTCTGCAT 59.459 47.619 0.00 0.00 0.00 3.96
17 18 0.950836 CCAATGTTTCGTGGTCTGCA 59.049 50.000 0.00 0.00 0.00 4.41
18 19 0.387239 GCCAATGTTTCGTGGTCTGC 60.387 55.000 0.00 0.00 37.23 4.26
19 20 0.240945 GGCCAATGTTTCGTGGTCTG 59.759 55.000 0.00 0.00 36.54 3.51
20 21 1.234615 CGGCCAATGTTTCGTGGTCT 61.235 55.000 2.24 0.00 37.37 3.85
21 22 1.209127 CGGCCAATGTTTCGTGGTC 59.791 57.895 2.24 0.00 37.23 4.02
22 23 2.914908 GCGGCCAATGTTTCGTGGT 61.915 57.895 2.24 0.00 37.23 4.16
23 24 2.126502 GCGGCCAATGTTTCGTGG 60.127 61.111 2.24 0.00 38.00 4.94
24 25 2.126502 GGCGGCCAATGTTTCGTG 60.127 61.111 15.62 0.00 0.00 4.35
25 26 2.596046 TGGCGGCCAATGTTTCGT 60.596 55.556 21.55 0.00 0.00 3.85
26 27 2.126502 GTGGCGGCCAATGTTTCG 60.127 61.111 25.70 0.00 34.18 3.46
27 28 2.126502 CGTGGCGGCCAATGTTTC 60.127 61.111 25.70 9.25 34.18 2.78
28 29 4.356442 GCGTGGCGGCCAATGTTT 62.356 61.111 25.70 0.00 34.18 2.83
47 48 4.803426 GACAGCAGAGACGCCGGG 62.803 72.222 2.18 0.00 0.00 5.73
48 49 4.803426 GGACAGCAGAGACGCCGG 62.803 72.222 0.00 0.00 0.00 6.13
49 50 3.978723 CTGGACAGCAGAGACGCCG 62.979 68.421 0.00 0.00 0.00 6.46
50 51 2.125753 CTGGACAGCAGAGACGCC 60.126 66.667 0.00 0.00 0.00 5.68
60 61 1.743252 GGCTCTTTCGGCTGGACAG 60.743 63.158 0.00 0.00 0.00 3.51
61 62 2.347490 GGCTCTTTCGGCTGGACA 59.653 61.111 0.00 0.00 0.00 4.02
62 63 2.815647 CGGCTCTTTCGGCTGGAC 60.816 66.667 0.00 0.00 32.91 4.02
63 64 4.760047 GCGGCTCTTTCGGCTGGA 62.760 66.667 0.00 0.00 36.65 3.86
117 122 4.229123 AGCAACTGAGGTAGGTAGGTAGTA 59.771 45.833 0.00 0.00 0.00 1.82
118 123 3.011482 AGCAACTGAGGTAGGTAGGTAGT 59.989 47.826 0.00 0.00 0.00 2.73
119 124 3.633065 GAGCAACTGAGGTAGGTAGGTAG 59.367 52.174 0.00 0.00 0.00 3.18
120 125 3.268856 AGAGCAACTGAGGTAGGTAGGTA 59.731 47.826 0.00 0.00 0.00 3.08
121 126 2.043252 AGAGCAACTGAGGTAGGTAGGT 59.957 50.000 0.00 0.00 0.00 3.08
122 127 2.691011 GAGAGCAACTGAGGTAGGTAGG 59.309 54.545 0.00 0.00 0.00 3.18
123 128 2.356382 CGAGAGCAACTGAGGTAGGTAG 59.644 54.545 0.00 0.00 0.00 3.18
158 163 3.690745 GCAAAGCTGCTGGTGGAT 58.309 55.556 1.35 0.00 45.74 3.41
167 172 0.248458 AACAAACGACGGCAAAGCTG 60.248 50.000 0.00 0.00 41.29 4.24
171 176 0.247735 CGTGAACAAACGACGGCAAA 60.248 50.000 0.00 0.00 46.49 3.68
172 177 1.348938 CGTGAACAAACGACGGCAA 59.651 52.632 0.00 0.00 46.49 4.52
173 178 2.526993 CCGTGAACAAACGACGGCA 61.527 57.895 0.00 0.00 45.55 5.69
174 179 2.247267 CCGTGAACAAACGACGGC 59.753 61.111 0.00 0.00 45.55 5.68
176 181 2.154427 GAGGCCGTGAACAAACGACG 62.154 60.000 0.00 0.00 46.49 5.12
177 182 1.568025 GAGGCCGTGAACAAACGAC 59.432 57.895 0.00 0.00 46.49 4.34
178 183 1.952133 CGAGGCCGTGAACAAACGA 60.952 57.895 0.00 0.00 46.49 3.85
179 184 1.492319 TTCGAGGCCGTGAACAAACG 61.492 55.000 8.43 0.00 43.20 3.60
180 185 0.658897 TTTCGAGGCCGTGAACAAAC 59.341 50.000 11.64 0.00 37.05 2.93
202 207 2.953466 ACGACGGCAAAGCTAATCTA 57.047 45.000 0.00 0.00 0.00 1.98
203 208 2.094762 AACGACGGCAAAGCTAATCT 57.905 45.000 0.00 0.00 0.00 2.40
204 209 2.095919 ACAAACGACGGCAAAGCTAATC 60.096 45.455 0.00 0.00 0.00 1.75
205 210 1.877443 ACAAACGACGGCAAAGCTAAT 59.123 42.857 0.00 0.00 0.00 1.73
206 211 1.301423 ACAAACGACGGCAAAGCTAA 58.699 45.000 0.00 0.00 0.00 3.09
207 212 1.262151 GAACAAACGACGGCAAAGCTA 59.738 47.619 0.00 0.00 0.00 3.32
208 213 0.028902 GAACAAACGACGGCAAAGCT 59.971 50.000 0.00 0.00 0.00 3.74
209 214 0.248296 TGAACAAACGACGGCAAAGC 60.248 50.000 0.00 0.00 0.00 3.51
210 215 1.462791 GTGAACAAACGACGGCAAAG 58.537 50.000 0.00 0.00 0.00 2.77
211 216 0.247735 CGTGAACAAACGACGGCAAA 60.248 50.000 0.00 0.00 46.49 3.68
212 217 1.348938 CGTGAACAAACGACGGCAA 59.651 52.632 0.00 0.00 46.49 4.52
213 218 2.526993 CCGTGAACAAACGACGGCA 61.527 57.895 0.00 0.00 45.55 5.69
214 219 2.247267 CCGTGAACAAACGACGGC 59.753 61.111 0.00 0.00 45.55 5.68
216 221 2.154427 GAGGCCGTGAACAAACGACG 62.154 60.000 0.00 0.00 46.49 5.12
217 222 1.568025 GAGGCCGTGAACAAACGAC 59.432 57.895 0.00 0.00 46.49 4.34
218 223 1.952133 CGAGGCCGTGAACAAACGA 60.952 57.895 0.00 0.00 46.49 3.85
219 224 2.549282 CGAGGCCGTGAACAAACG 59.451 61.111 0.00 0.00 43.20 3.60
220 225 1.161563 TTCCGAGGCCGTGAACAAAC 61.162 55.000 0.00 0.00 0.00 2.93
221 226 0.882927 CTTCCGAGGCCGTGAACAAA 60.883 55.000 0.00 0.00 0.00 2.83
222 227 1.301401 CTTCCGAGGCCGTGAACAA 60.301 57.895 0.00 0.00 0.00 2.83
223 228 2.342279 CTTCCGAGGCCGTGAACA 59.658 61.111 0.00 0.00 0.00 3.18
224 229 2.434359 CCTTCCGAGGCCGTGAAC 60.434 66.667 0.00 0.00 35.94 3.18
225 230 2.167398 CTTCCTTCCGAGGCCGTGAA 62.167 60.000 0.00 0.31 43.21 3.18
226 231 2.602267 TTCCTTCCGAGGCCGTGA 60.602 61.111 0.00 0.00 43.21 4.35
227 232 2.125512 CTTCCTTCCGAGGCCGTG 60.126 66.667 0.00 0.00 43.21 4.94
228 233 1.477685 TTTCTTCCTTCCGAGGCCGT 61.478 55.000 0.00 0.00 43.21 5.68
229 234 0.741221 CTTTCTTCCTTCCGAGGCCG 60.741 60.000 0.00 0.00 43.21 6.13
230 235 0.613777 TCTTTCTTCCTTCCGAGGCC 59.386 55.000 0.00 0.00 43.21 5.19
231 236 2.474410 TTCTTTCTTCCTTCCGAGGC 57.526 50.000 0.00 0.00 43.21 4.70
232 237 4.479786 AGATTCTTTCTTCCTTCCGAGG 57.520 45.455 0.00 0.00 45.02 4.63
233 238 6.091986 CAGAAAGATTCTTTCTTCCTTCCGAG 59.908 42.308 30.28 16.71 44.09 4.63
234 239 5.934625 CAGAAAGATTCTTTCTTCCTTCCGA 59.065 40.000 30.28 0.00 44.09 4.55
235 240 5.703130 ACAGAAAGATTCTTTCTTCCTTCCG 59.297 40.000 30.28 21.60 44.09 4.30
236 241 8.622948 TTACAGAAAGATTCTTTCTTCCTTCC 57.377 34.615 30.28 9.69 44.09 3.46
237 242 9.885934 GTTTACAGAAAGATTCTTTCTTCCTTC 57.114 33.333 30.28 19.60 44.09 3.46
238 243 8.851145 GGTTTACAGAAAGATTCTTTCTTCCTT 58.149 33.333 30.28 19.80 44.09 3.36
239 244 7.998964 TGGTTTACAGAAAGATTCTTTCTTCCT 59.001 33.333 30.28 20.39 44.09 3.36
240 245 8.166422 TGGTTTACAGAAAGATTCTTTCTTCC 57.834 34.615 30.28 24.99 44.09 3.46
283 288 3.149196 GTGGATGTGGAGAAAGCTTCAA 58.851 45.455 0.00 0.00 29.44 2.69
288 293 2.352127 GCTTTGTGGATGTGGAGAAAGC 60.352 50.000 0.00 0.00 40.10 3.51
293 298 3.553508 CCTTTTGCTTTGTGGATGTGGAG 60.554 47.826 0.00 0.00 0.00 3.86
294 299 2.364970 CCTTTTGCTTTGTGGATGTGGA 59.635 45.455 0.00 0.00 0.00 4.02
295 300 2.102925 ACCTTTTGCTTTGTGGATGTGG 59.897 45.455 0.00 0.00 0.00 4.17
296 301 3.457610 ACCTTTTGCTTTGTGGATGTG 57.542 42.857 0.00 0.00 0.00 3.21
297 302 4.469657 TCTACCTTTTGCTTTGTGGATGT 58.530 39.130 0.00 0.00 0.00 3.06
298 303 4.520492 ACTCTACCTTTTGCTTTGTGGATG 59.480 41.667 0.00 0.00 0.00 3.51
299 304 4.729868 ACTCTACCTTTTGCTTTGTGGAT 58.270 39.130 0.00 0.00 0.00 3.41
317 322 1.893786 CCTCGGTGCTGCTTACTCT 59.106 57.895 0.00 0.00 0.00 3.24
320 325 2.047274 TGCCTCGGTGCTGCTTAC 60.047 61.111 0.00 0.00 0.00 2.34
321 326 2.047274 GTGCCTCGGTGCTGCTTA 60.047 61.111 0.00 0.00 0.00 3.09
368 373 1.118356 AGCTGGGCCGAGGATTAGAG 61.118 60.000 17.33 0.00 0.00 2.43
448 453 3.665675 ATCTTGGCCGACGGTGAGC 62.666 63.158 16.73 0.00 0.00 4.26
460 465 0.527817 GTACGTGGCCTCGATCTTGG 60.528 60.000 32.11 3.14 34.70 3.61
485 490 3.626924 AGGAGCACCACCACGACC 61.627 66.667 2.07 0.00 38.94 4.79
503 508 3.116531 GGGTACGGTTCAGCACGC 61.117 66.667 0.00 0.00 0.00 5.34
513 518 1.812507 GGCTAAGCAACGGGTACGG 60.813 63.158 0.00 0.00 46.48 4.02
515 520 2.458610 GCGGCTAAGCAACGGGTAC 61.459 63.158 0.00 0.00 37.05 3.34
516 521 2.125431 GCGGCTAAGCAACGGGTA 60.125 61.111 0.00 0.00 37.05 3.69
543 548 0.240945 CGCACCACTTTGATCAACCC 59.759 55.000 7.89 0.00 0.00 4.11
544 549 0.951558 ACGCACCACTTTGATCAACC 59.048 50.000 7.89 0.00 0.00 3.77
545 550 1.333619 ACACGCACCACTTTGATCAAC 59.666 47.619 7.89 0.00 0.00 3.18
546 551 1.333308 CACACGCACCACTTTGATCAA 59.667 47.619 3.38 3.38 0.00 2.57
561 3455 2.098871 CGTCCATGCATGCACACG 59.901 61.111 25.37 25.40 0.00 4.49
571 3465 2.173669 GTCGTGCCATCCGTCCATG 61.174 63.158 0.00 0.00 0.00 3.66
572 3466 2.186903 GTCGTGCCATCCGTCCAT 59.813 61.111 0.00 0.00 0.00 3.41
573 3467 4.077184 GGTCGTGCCATCCGTCCA 62.077 66.667 0.00 0.00 37.17 4.02
574 3468 4.832608 GGGTCGTGCCATCCGTCC 62.833 72.222 1.70 0.00 39.65 4.79
654 3563 0.238553 GAGGTGGCGAAAAAGTGCTC 59.761 55.000 0.00 0.00 0.00 4.26
655 3564 1.507141 CGAGGTGGCGAAAAAGTGCT 61.507 55.000 0.00 0.00 0.00 4.40
656 3565 1.082104 CGAGGTGGCGAAAAAGTGC 60.082 57.895 0.00 0.00 0.00 4.40
659 3568 2.561373 GGCGAGGTGGCGAAAAAG 59.439 61.111 0.00 0.00 0.00 2.27
708 3621 4.460873 CTTTCGCCGCGCCTTTCC 62.461 66.667 8.21 0.00 0.00 3.13
772 3706 4.927782 TGAGGTGGTGGTGCGTGC 62.928 66.667 0.00 0.00 0.00 5.34
773 3707 2.972505 GTGAGGTGGTGGTGCGTG 60.973 66.667 0.00 0.00 0.00 5.34
841 3780 0.745128 TGGGTTTTATAGGTGGCGCG 60.745 55.000 0.00 0.00 0.00 6.86
860 3802 4.677151 GAGGAGGTGGGGTGGGGT 62.677 72.222 0.00 0.00 0.00 4.95
865 3807 2.876858 AGGAGGAGGAGGTGGGGT 60.877 66.667 0.00 0.00 0.00 4.95
867 3809 0.762461 GATGAGGAGGAGGAGGTGGG 60.762 65.000 0.00 0.00 0.00 4.61
898 3840 3.792047 CGCGCTGTGTGGTGATGG 61.792 66.667 5.56 0.00 0.00 3.51
918 3860 2.111669 TGTGTGCTGGACTGCTGG 59.888 61.111 0.00 0.00 0.00 4.85
919 3861 1.227764 AGTGTGTGCTGGACTGCTG 60.228 57.895 0.00 0.00 0.00 4.41
920 3862 1.227764 CAGTGTGTGCTGGACTGCT 60.228 57.895 0.00 0.00 31.31 4.24
921 3863 3.337619 CAGTGTGTGCTGGACTGC 58.662 61.111 0.00 0.00 31.31 4.40
999 3968 1.415659 CAGTCCAGGACCATCTCCATC 59.584 57.143 16.72 0.00 42.46 3.51
1536 4511 1.448540 CGACTTGAGCCGCATCCTT 60.449 57.895 0.00 0.00 0.00 3.36
2046 5027 4.147449 CTGATGGACTCGCGCCCA 62.147 66.667 15.06 15.06 36.79 5.36
2343 5331 3.493830 GATGTCGGCCGGCGTGATA 62.494 63.158 32.38 19.20 0.00 2.15
2409 5397 4.116328 TCGCCGACGAGCCTCTTG 62.116 66.667 0.00 0.00 45.12 3.02
2479 5467 3.705579 CACTCCATCTTCTCCTCTGTCAT 59.294 47.826 0.00 0.00 0.00 3.06
2505 5493 5.936956 GGTCAATCTCTGTGTCTTTGATCTT 59.063 40.000 0.00 0.00 0.00 2.40
2512 5500 3.244353 CCACTGGTCAATCTCTGTGTCTT 60.244 47.826 0.00 0.00 33.07 3.01
2533 5521 1.866853 GCTGCAACAAGCCACCTACC 61.867 60.000 0.00 0.00 44.83 3.18
2559 5547 6.189859 AGTTAATTTCATCTGCAATCCTCCA 58.810 36.000 0.00 0.00 0.00 3.86
2585 5573 6.240894 TGGTGCTGATATCAAGGGATTATTC 58.759 40.000 6.90 0.00 34.89 1.75
2592 5580 3.672808 GATCTGGTGCTGATATCAAGGG 58.327 50.000 6.90 0.00 0.00 3.95
2759 5760 8.166422 ACAAAAGACGGAAGAAACTTTATGAT 57.834 30.769 0.00 0.00 34.49 2.45
2863 5933 3.482923 CGATCAACATTTTGTACCGACCG 60.483 47.826 0.00 0.00 34.02 4.79
2908 5978 5.163642 ACGTACTGGTCAATCTCAGTATCAC 60.164 44.000 6.49 0.00 44.86 3.06
2936 6111 8.950208 ATACTGAAGTTATTAGTTCCTTCTGC 57.050 34.615 0.00 0.00 36.76 4.26
2939 6114 9.886132 TGGAATACTGAAGTTATTAGTTCCTTC 57.114 33.333 0.00 0.00 33.55 3.46
2941 6116 9.838339 CATGGAATACTGAAGTTATTAGTTCCT 57.162 33.333 0.00 0.00 33.55 3.36
2943 6118 9.614792 ACCATGGAATACTGAAGTTATTAGTTC 57.385 33.333 21.47 0.00 34.82 3.01
2964 6165 3.121738 TCTGATGCAGCAGATACCATG 57.878 47.619 29.83 3.75 39.84 3.66
2976 6177 3.891366 TCGACCTATCTGAATCTGATGCA 59.109 43.478 12.09 0.00 0.00 3.96
2994 7116 7.585867 ACACATATGTCACTCTACATATCGAC 58.414 38.462 5.07 0.00 45.61 4.20
3011 7133 5.495502 CACATGATGACACGAACACATATG 58.504 41.667 0.00 0.00 0.00 1.78
3012 7134 4.571984 CCACATGATGACACGAACACATAT 59.428 41.667 0.00 0.00 0.00 1.78
3015 7137 2.142319 CCACATGATGACACGAACACA 58.858 47.619 0.00 0.00 0.00 3.72
3044 7173 6.743575 ACAAAAGGAAGAATAGTTCGATGG 57.256 37.500 0.00 0.00 34.02 3.51
3074 7203 2.205022 AGTACACAGGCGTACCACTA 57.795 50.000 0.00 0.00 42.29 2.74
3075 7204 1.335145 AAGTACACAGGCGTACCACT 58.665 50.000 0.00 0.00 42.29 4.00
3087 7216 6.291377 ACATCCATCCATCATGTAAGTACAC 58.709 40.000 0.00 0.00 39.30 2.90
3095 7224 8.316946 CACTATACTAACATCCATCCATCATGT 58.683 37.037 0.00 0.00 31.90 3.21
3114 7243 7.214381 TGTCATGCCTGGTTAATACACTATAC 58.786 38.462 0.00 0.00 0.00 1.47
3148 7277 4.815533 ACTAGTGCTGACTGTCATCATT 57.184 40.909 16.32 14.56 33.21 2.57
3149 7278 5.196695 TCTACTAGTGCTGACTGTCATCAT 58.803 41.667 16.32 8.96 33.21 2.45
3150 7279 4.589908 TCTACTAGTGCTGACTGTCATCA 58.410 43.478 11.45 10.70 33.21 3.07
3151 7280 5.568685 TTCTACTAGTGCTGACTGTCATC 57.431 43.478 11.45 7.87 33.21 2.92
3152 7281 5.478679 ACTTTCTACTAGTGCTGACTGTCAT 59.521 40.000 11.45 0.00 33.21 3.06
3158 7287 6.366604 GGAAGAAACTTTCTACTAGTGCTGAC 59.633 42.308 5.39 0.00 39.61 3.51
3224 7353 7.703298 AAATTTTGACATCAATGATATGCGG 57.297 32.000 0.00 0.00 35.55 5.69
3261 7390 1.027357 ATCGCCATGCCTGAACAATC 58.973 50.000 0.00 0.00 0.00 2.67
3322 7451 5.818136 AAGGCACGACGTATACTACTTTA 57.182 39.130 0.00 0.00 0.00 1.85
3327 7456 3.016031 TGGAAAGGCACGACGTATACTA 58.984 45.455 0.00 0.00 0.00 1.82
3350 7479 4.218852 TGGCTTCCCCGTATTAAAAACAAG 59.781 41.667 0.00 0.00 35.87 3.16
3359 7488 0.034477 CCAAGTGGCTTCCCCGTATT 60.034 55.000 0.00 0.00 35.87 1.89
3360 7489 1.607612 CCAAGTGGCTTCCCCGTAT 59.392 57.895 0.00 0.00 35.87 3.06
3388 7518 5.031066 TGTTGTAACTCTGCTAAACTGGT 57.969 39.130 0.00 0.00 0.00 4.00
3390 7520 7.598869 TGTAGATGTTGTAACTCTGCTAAACTG 59.401 37.037 10.76 0.00 0.00 3.16
3407 7537 2.419324 GAGACGTCGGACTGTAGATGTT 59.581 50.000 10.46 0.00 36.81 2.71
3408 7538 2.008329 GAGACGTCGGACTGTAGATGT 58.992 52.381 10.46 9.46 39.10 3.06
3409 7539 2.007608 TGAGACGTCGGACTGTAGATG 58.992 52.381 10.46 4.15 0.00 2.90
3410 7540 2.398252 TGAGACGTCGGACTGTAGAT 57.602 50.000 10.46 0.00 0.00 1.98
3411 7541 2.174363 TTGAGACGTCGGACTGTAGA 57.826 50.000 10.46 0.00 0.00 2.59
3412 7542 2.582687 GTTTGAGACGTCGGACTGTAG 58.417 52.381 10.46 0.00 0.00 2.74
3413 7543 1.267806 GGTTTGAGACGTCGGACTGTA 59.732 52.381 10.46 0.00 0.00 2.74
3414 7544 0.031721 GGTTTGAGACGTCGGACTGT 59.968 55.000 10.46 5.99 0.00 3.55
3415 7545 0.031585 TGGTTTGAGACGTCGGACTG 59.968 55.000 10.46 2.73 0.00 3.51
3416 7546 0.966920 ATGGTTTGAGACGTCGGACT 59.033 50.000 10.46 0.00 0.00 3.85
3417 7547 1.067776 AGATGGTTTGAGACGTCGGAC 60.068 52.381 10.46 7.43 0.00 4.79
3418 7548 1.201647 GAGATGGTTTGAGACGTCGGA 59.798 52.381 10.46 0.00 0.00 4.55
3419 7549 1.202582 AGAGATGGTTTGAGACGTCGG 59.797 52.381 10.46 0.00 0.00 4.79
3420 7550 2.638556 AGAGATGGTTTGAGACGTCG 57.361 50.000 10.46 0.00 0.00 5.12
3421 7551 6.561614 TGTATAAGAGATGGTTTGAGACGTC 58.438 40.000 7.70 7.70 0.00 4.34
3422 7552 6.525578 TGTATAAGAGATGGTTTGAGACGT 57.474 37.500 0.00 0.00 0.00 4.34
3423 7553 7.706607 TGAATGTATAAGAGATGGTTTGAGACG 59.293 37.037 0.00 0.00 0.00 4.18
3424 7554 8.821894 GTGAATGTATAAGAGATGGTTTGAGAC 58.178 37.037 0.00 0.00 0.00 3.36
3425 7555 7.706607 CGTGAATGTATAAGAGATGGTTTGAGA 59.293 37.037 0.00 0.00 0.00 3.27
3426 7556 7.042456 CCGTGAATGTATAAGAGATGGTTTGAG 60.042 40.741 0.00 0.00 0.00 3.02
3427 7557 6.761242 CCGTGAATGTATAAGAGATGGTTTGA 59.239 38.462 0.00 0.00 0.00 2.69
3428 7558 6.761242 TCCGTGAATGTATAAGAGATGGTTTG 59.239 38.462 0.00 0.00 0.00 2.93
3429 7559 6.884832 TCCGTGAATGTATAAGAGATGGTTT 58.115 36.000 0.00 0.00 0.00 3.27
3430 7560 6.479972 TCCGTGAATGTATAAGAGATGGTT 57.520 37.500 0.00 0.00 0.00 3.67
3431 7561 6.459066 CATCCGTGAATGTATAAGAGATGGT 58.541 40.000 0.00 0.00 0.00 3.55
3432 7562 5.349817 GCATCCGTGAATGTATAAGAGATGG 59.650 44.000 0.00 0.00 31.46 3.51
3433 7563 5.061435 CGCATCCGTGAATGTATAAGAGATG 59.939 44.000 0.00 0.00 33.42 2.90
3434 7564 5.164233 CGCATCCGTGAATGTATAAGAGAT 58.836 41.667 0.00 0.00 0.00 2.75
3435 7565 4.546570 CGCATCCGTGAATGTATAAGAGA 58.453 43.478 0.00 0.00 0.00 3.10
3436 7566 4.893036 CGCATCCGTGAATGTATAAGAG 57.107 45.455 0.00 0.00 0.00 2.85
3451 7581 1.153449 TCATTGACCGGACGCATCC 60.153 57.895 9.46 0.00 42.28 3.51
3452 7582 1.429148 GGTCATTGACCGGACGCATC 61.429 60.000 19.65 0.00 43.14 3.91
3453 7583 1.449601 GGTCATTGACCGGACGCAT 60.450 57.895 19.65 0.00 43.14 4.73
3454 7584 2.047655 GGTCATTGACCGGACGCA 60.048 61.111 19.65 0.00 43.14 5.24
3462 7592 6.214191 TCTCTCTATTGTCTGGTCATTGAC 57.786 41.667 8.34 8.34 0.00 3.18
3463 7593 6.857437 TTCTCTCTATTGTCTGGTCATTGA 57.143 37.500 0.00 0.00 0.00 2.57
3464 7594 7.912056 TTTTCTCTCTATTGTCTGGTCATTG 57.088 36.000 0.00 0.00 0.00 2.82



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

AutoCloner maintained by Alex Coulton.