Multiple sequence alignment - TraesCS7B01G362300

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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 TraesCS7B01G362300 chr7B 100.000 3723 0 0 1 3723 624150528 624146806 0.000000e+00 6876.0
1 TraesCS7B01G362300 chr7B 93.127 2386 96 36 653 2985 623977682 623975312 0.000000e+00 3435.0
2 TraesCS7B01G362300 chr7B 83.163 392 31 18 3237 3623 623975154 623974793 3.590000e-85 326.0
3 TraesCS7B01G362300 chr7B 91.489 94 8 0 3052 3145 623975295 623975202 3.020000e-26 130.0
4 TraesCS7B01G362300 chr7A 93.744 1087 53 10 1906 2980 657091030 657089947 0.000000e+00 1616.0
5 TraesCS7B01G362300 chr7A 91.527 956 50 15 981 1924 657091981 657091045 0.000000e+00 1288.0
6 TraesCS7B01G362300 chr7A 84.840 686 54 26 306 973 657092679 657092026 0.000000e+00 645.0
7 TraesCS7B01G362300 chr7A 81.292 449 48 25 3262 3694 657089756 657089328 7.710000e-87 331.0
8 TraesCS7B01G362300 chr7A 84.530 181 20 6 3055 3231 657089923 657089747 4.940000e-39 172.0
9 TraesCS7B01G362300 chr7A 91.667 108 9 0 77 184 657092910 657092803 2.320000e-32 150.0
10 TraesCS7B01G362300 chr7D 92.364 956 59 7 981 1922 568393671 568392716 0.000000e+00 1349.0
11 TraesCS7B01G362300 chr7D 93.387 499 32 1 2288 2786 568392363 568391866 0.000000e+00 737.0
12 TraesCS7B01G362300 chr7D 86.123 454 34 10 3295 3723 568388600 568388151 2.620000e-126 462.0
13 TraesCS7B01G362300 chr7D 92.000 325 18 6 1906 2226 568392702 568392382 2.040000e-122 449.0
14 TraesCS7B01G362300 chr7D 86.400 250 24 5 2780 3026 568389003 568388761 7.930000e-67 265.0
15 TraesCS7B01G362300 chr7D 94.521 146 7 1 828 973 568393860 568393716 1.350000e-54 224.0
16 TraesCS7B01G362300 chr7D 97.222 36 1 0 2216 2251 509699893 509699928 1.120000e-05 62.1
17 TraesCS7B01G362300 chr7D 97.143 35 1 0 2217 2251 509836008 509835974 4.020000e-05 60.2
18 TraesCS7B01G362300 chr1A 72.746 1420 263 79 1280 2633 541146507 541147868 7.600000e-97 364.0
19 TraesCS7B01G362300 chr1A 75.855 497 72 32 1359 1815 541399774 541399286 3.770000e-50 209.0
20 TraesCS7B01G362300 chr1B 73.267 1010 195 47 1673 2656 610970756 610969796 2.170000e-77 300.0
21 TraesCS7B01G362300 chr1D 74.443 763 144 41 1948 2694 445263517 445264244 7.870000e-72 281.0
22 TraesCS7B01G362300 chr2B 83.333 264 40 4 2395 2656 736409007 736408746 1.340000e-59 241.0
23 TraesCS7B01G362300 chr2D 80.347 173 18 7 815 977 161647282 161647116 2.350000e-22 117.0
24 TraesCS7B01G362300 chr4A 88.889 54 5 1 2215 2267 650312228 650312175 8.630000e-07 65.8
25 TraesCS7B01G362300 chr4A 100.000 29 0 0 1783 1811 63812091 63812119 2.000000e-03 54.7
26 TraesCS7B01G362300 chr3B 97.297 37 1 0 2215 2251 70312887 70312923 3.100000e-06 63.9
27 TraesCS7B01G362300 chr3A 97.297 37 1 0 2215 2251 56770939 56770975 3.100000e-06 63.9


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 TraesCS7B01G362300 chr7B 624146806 624150528 3722 True 6876.000000 6876 100.000000 1 3723 1 chr7B.!!$R1 3722
1 TraesCS7B01G362300 chr7B 623974793 623977682 2889 True 1297.000000 3435 89.259667 653 3623 3 chr7B.!!$R2 2970
2 TraesCS7B01G362300 chr7A 657089328 657092910 3582 True 700.333333 1616 87.933333 77 3694 6 chr7A.!!$R1 3617
3 TraesCS7B01G362300 chr7D 568388151 568393860 5709 True 581.000000 1349 90.799167 828 3723 6 chr7D.!!$R2 2895
4 TraesCS7B01G362300 chr1A 541146507 541147868 1361 False 364.000000 364 72.746000 1280 2633 1 chr1A.!!$F1 1353
5 TraesCS7B01G362300 chr1B 610969796 610970756 960 True 300.000000 300 73.267000 1673 2656 1 chr1B.!!$R1 983
6 TraesCS7B01G362300 chr1D 445263517 445264244 727 False 281.000000 281 74.443000 1948 2694 1 chr1D.!!$F1 746

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
46 47 0.239347 ACCACGTTCGGTTCGAGTAG 59.761 55.0 0.00 0.00 34.91 2.57 F
476 526 0.301687 GCAGATCCGTGCATGTTACG 59.698 55.0 14.92 14.92 43.41 3.18 F
2097 2312 0.250727 GCTACCACCCAAAGCTGTCA 60.251 55.0 0.00 0.00 33.40 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2312 0.179045 GCTCCGCCAGTCCATATTGT 60.179 55.0 0.0 0.0 0.00 2.71 R
2149 2368 1.125711 ATAGTACCCCATGTCCCGCC 61.126 60.0 0.0 0.0 0.00 6.13 R
3232 6388 0.101040 CGGCAAGGCATTGTGGTATG 59.899 55.0 13.3 0.0 38.76 2.39 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
18 19 3.467776 GAGGTTGGATCTCACTGGC 57.532 57.895 0.00 0.00 0.00 4.85
19 20 0.908198 GAGGTTGGATCTCACTGGCT 59.092 55.000 0.00 0.00 0.00 4.75
20 21 1.280421 GAGGTTGGATCTCACTGGCTT 59.720 52.381 0.00 0.00 0.00 4.35
21 22 1.280421 AGGTTGGATCTCACTGGCTTC 59.720 52.381 0.00 0.00 0.00 3.86
22 23 1.680249 GGTTGGATCTCACTGGCTTCC 60.680 57.143 0.00 0.00 0.00 3.46
23 24 1.280421 GTTGGATCTCACTGGCTTCCT 59.720 52.381 0.00 0.00 0.00 3.36
24 25 1.198713 TGGATCTCACTGGCTTCCTC 58.801 55.000 0.00 0.00 0.00 3.71
25 26 0.467804 GGATCTCACTGGCTTCCTCC 59.532 60.000 0.00 0.00 0.00 4.30
26 27 1.198713 GATCTCACTGGCTTCCTCCA 58.801 55.000 0.00 0.00 34.42 3.86
27 28 1.556911 GATCTCACTGGCTTCCTCCAA 59.443 52.381 0.00 0.00 35.36 3.53
28 29 0.687354 TCTCACTGGCTTCCTCCAAC 59.313 55.000 0.00 0.00 35.36 3.77
29 30 0.322008 CTCACTGGCTTCCTCCAACC 60.322 60.000 0.00 0.00 35.36 3.77
30 31 1.059584 TCACTGGCTTCCTCCAACCA 61.060 55.000 0.00 0.00 35.36 3.67
31 32 0.890996 CACTGGCTTCCTCCAACCAC 60.891 60.000 0.00 0.00 35.36 4.16
32 33 1.672356 CTGGCTTCCTCCAACCACG 60.672 63.158 0.00 0.00 35.36 4.94
33 34 2.397413 CTGGCTTCCTCCAACCACGT 62.397 60.000 0.00 0.00 35.36 4.49
34 35 1.228154 GGCTTCCTCCAACCACGTT 60.228 57.895 0.00 0.00 0.00 3.99
35 36 1.235281 GGCTTCCTCCAACCACGTTC 61.235 60.000 0.00 0.00 0.00 3.95
36 37 1.566018 GCTTCCTCCAACCACGTTCG 61.566 60.000 0.00 0.00 0.00 3.95
37 38 0.949105 CTTCCTCCAACCACGTTCGG 60.949 60.000 0.00 0.00 0.00 4.30
38 39 1.688269 TTCCTCCAACCACGTTCGGT 61.688 55.000 0.00 0.00 42.71 4.69
40 41 1.226030 CCTCCAACCACGTTCGGTTC 61.226 60.000 7.31 0.00 46.60 3.62
41 42 1.554042 CTCCAACCACGTTCGGTTCG 61.554 60.000 7.31 2.01 46.60 3.95
42 43 1.592131 CCAACCACGTTCGGTTCGA 60.592 57.895 7.31 0.00 46.60 3.71
43 44 1.554042 CCAACCACGTTCGGTTCGAG 61.554 60.000 7.31 0.00 46.60 4.04
44 45 0.872881 CAACCACGTTCGGTTCGAGT 60.873 55.000 7.31 0.00 46.60 4.18
45 46 0.667993 AACCACGTTCGGTTCGAGTA 59.332 50.000 4.53 0.00 46.60 2.59
46 47 0.239347 ACCACGTTCGGTTCGAGTAG 59.761 55.000 0.00 0.00 34.91 2.57
47 48 0.455633 CCACGTTCGGTTCGAGTAGG 60.456 60.000 0.00 0.00 37.14 3.18
48 49 1.069378 CACGTTCGGTTCGAGTAGGC 61.069 60.000 0.00 0.00 37.14 3.93
49 50 1.515736 CGTTCGGTTCGAGTAGGCC 60.516 63.158 0.00 0.00 37.14 5.19
50 51 1.515736 GTTCGGTTCGAGTAGGCCG 60.516 63.158 0.00 0.00 44.95 6.13
51 52 3.346631 TTCGGTTCGAGTAGGCCGC 62.347 63.158 0.00 0.00 43.45 6.53
52 53 4.867599 CGGTTCGAGTAGGCCGCC 62.868 72.222 0.00 0.00 37.69 6.13
53 54 4.525949 GGTTCGAGTAGGCCGCCC 62.526 72.222 5.55 0.00 0.00 6.13
54 55 4.525949 GTTCGAGTAGGCCGCCCC 62.526 72.222 5.55 0.00 0.00 5.80
69 70 3.738481 CCCCCGATCCAAGGCCAA 61.738 66.667 5.01 0.00 0.00 4.52
70 71 2.124151 CCCCGATCCAAGGCCAAG 60.124 66.667 5.01 0.00 0.00 3.61
71 72 2.830370 CCCGATCCAAGGCCAAGC 60.830 66.667 5.01 0.00 0.00 4.01
117 118 1.000359 CCCCAAAATTCCCCGCTCT 60.000 57.895 0.00 0.00 0.00 4.09
143 144 0.386478 CCTTTTCTTCAGCACGCTGC 60.386 55.000 14.25 0.00 45.46 5.25
150 151 1.300971 TTCAGCACGCTGCCTGAATC 61.301 55.000 14.25 0.00 46.52 2.52
153 154 3.869272 CACGCTGCCTGAATCCGC 61.869 66.667 0.00 0.00 0.00 5.54
162 163 0.820891 CCTGAATCCGCCCAATCCAG 60.821 60.000 0.00 0.00 0.00 3.86
171 172 0.460635 GCCCAATCCAGCGTACGTAA 60.461 55.000 17.90 0.23 0.00 3.18
174 175 2.339418 CCAATCCAGCGTACGTAACAA 58.661 47.619 17.90 0.00 0.00 2.83
175 176 2.933906 CCAATCCAGCGTACGTAACAAT 59.066 45.455 17.90 2.02 0.00 2.71
184 185 3.000122 GCGTACGTAACAATAAATCGGCA 60.000 43.478 17.90 0.00 0.00 5.69
185 186 4.498916 CGTACGTAACAATAAATCGGCAC 58.501 43.478 7.22 0.00 0.00 5.01
201 202 2.711885 GGCACGTAACAATAAATCGGC 58.288 47.619 0.00 0.00 0.00 5.54
202 203 2.353579 GGCACGTAACAATAAATCGGCT 59.646 45.455 0.00 0.00 0.00 5.52
203 204 3.181504 GGCACGTAACAATAAATCGGCTT 60.182 43.478 0.00 0.00 0.00 4.35
204 205 3.783943 GCACGTAACAATAAATCGGCTTG 59.216 43.478 0.00 0.00 0.00 4.01
205 206 4.339429 CACGTAACAATAAATCGGCTTGG 58.661 43.478 0.00 0.00 0.00 3.61
206 207 4.004982 ACGTAACAATAAATCGGCTTGGT 58.995 39.130 0.00 0.00 0.00 3.67
207 208 4.093850 ACGTAACAATAAATCGGCTTGGTC 59.906 41.667 0.00 0.00 0.00 4.02
208 209 4.331717 CGTAACAATAAATCGGCTTGGTCT 59.668 41.667 0.00 0.00 0.00 3.85
215 216 2.029838 ATCGGCTTGGTCTTGATGTC 57.970 50.000 0.00 0.00 0.00 3.06
218 219 2.565391 TCGGCTTGGTCTTGATGTCTTA 59.435 45.455 0.00 0.00 0.00 2.10
239 240 3.114616 CAAGACCTGAGCGTGGCG 61.115 66.667 0.00 0.00 0.00 5.69
252 300 1.438651 CGTGGCGGAGATCTGAAAAA 58.561 50.000 0.00 0.00 0.00 1.94
253 301 1.128692 CGTGGCGGAGATCTGAAAAAC 59.871 52.381 0.00 0.00 0.00 2.43
268 316 4.551671 TGAAAAACAAAGAGGGATTGGGA 58.448 39.130 0.00 0.00 32.02 4.37
269 317 5.154418 TGAAAAACAAAGAGGGATTGGGAT 58.846 37.500 0.00 0.00 32.02 3.85
271 319 4.402616 AAACAAAGAGGGATTGGGATGA 57.597 40.909 0.00 0.00 32.02 2.92
272 320 3.372440 ACAAAGAGGGATTGGGATGAC 57.628 47.619 0.00 0.00 32.02 3.06
273 321 2.649312 ACAAAGAGGGATTGGGATGACA 59.351 45.455 0.00 0.00 32.02 3.58
274 322 3.285484 CAAAGAGGGATTGGGATGACAG 58.715 50.000 0.00 0.00 0.00 3.51
275 323 1.516110 AGAGGGATTGGGATGACAGG 58.484 55.000 0.00 0.00 0.00 4.00
276 324 1.216990 GAGGGATTGGGATGACAGGT 58.783 55.000 0.00 0.00 0.00 4.00
277 325 2.022035 AGAGGGATTGGGATGACAGGTA 60.022 50.000 0.00 0.00 0.00 3.08
278 326 2.104963 GAGGGATTGGGATGACAGGTAC 59.895 54.545 0.00 0.00 0.00 3.34
279 327 2.127708 GGGATTGGGATGACAGGTACT 58.872 52.381 0.00 0.00 43.88 2.73
294 342 2.844348 AGGTACTGTAGGTGGGAAATGG 59.156 50.000 0.00 0.00 37.18 3.16
295 343 2.841881 GGTACTGTAGGTGGGAAATGGA 59.158 50.000 0.00 0.00 0.00 3.41
296 344 3.264964 GGTACTGTAGGTGGGAAATGGAA 59.735 47.826 0.00 0.00 0.00 3.53
297 345 3.434940 ACTGTAGGTGGGAAATGGAAC 57.565 47.619 0.00 0.00 0.00 3.62
298 346 2.986728 ACTGTAGGTGGGAAATGGAACT 59.013 45.455 0.00 0.00 0.00 3.01
299 347 3.244911 ACTGTAGGTGGGAAATGGAACTG 60.245 47.826 0.00 0.00 0.00 3.16
300 348 2.983192 TGTAGGTGGGAAATGGAACTGA 59.017 45.455 0.00 0.00 0.00 3.41
301 349 3.591527 TGTAGGTGGGAAATGGAACTGAT 59.408 43.478 0.00 0.00 0.00 2.90
302 350 3.091633 AGGTGGGAAATGGAACTGATG 57.908 47.619 0.00 0.00 0.00 3.07
303 351 1.478105 GGTGGGAAATGGAACTGATGC 59.522 52.381 0.00 0.00 0.00 3.91
304 352 2.170166 GTGGGAAATGGAACTGATGCA 58.830 47.619 0.00 0.00 0.00 3.96
318 366 3.199508 ACTGATGCACTTGATTAGCTCCT 59.800 43.478 0.00 0.00 0.00 3.69
325 373 4.274459 GCACTTGATTAGCTCCTGGTTATG 59.726 45.833 0.00 0.00 0.00 1.90
338 386 6.183360 GCTCCTGGTTATGGTCTAAATTGTTC 60.183 42.308 0.00 0.00 0.00 3.18
342 390 8.244113 CCTGGTTATGGTCTAAATTGTTCTTTC 58.756 37.037 0.00 0.00 0.00 2.62
383 431 1.611977 TCTACACTGCTGCTTACACGT 59.388 47.619 0.00 0.00 0.00 4.49
386 436 1.301716 ACTGCTGCTTACACGTGGG 60.302 57.895 21.57 10.57 0.00 4.61
388 438 3.431725 GCTGCTTACACGTGGGGC 61.432 66.667 21.57 19.51 0.00 5.80
395 445 0.956410 TTACACGTGGGGCGATTTGG 60.956 55.000 21.57 0.00 44.77 3.28
410 460 3.871006 CGATTTGGGAAACAGATCATCGA 59.129 43.478 0.00 0.00 39.90 3.59
415 465 7.695480 TTTGGGAAACAGATCATCGATTTTA 57.305 32.000 0.00 0.00 0.00 1.52
420 470 8.286097 GGGAAACAGATCATCGATTTTAATCTC 58.714 37.037 0.00 0.00 33.24 2.75
445 495 6.093404 TCTGATGCTTCGTGTTAGTTCTTAG 58.907 40.000 0.00 0.00 0.00 2.18
446 496 5.168569 TGATGCTTCGTGTTAGTTCTTAGG 58.831 41.667 0.00 0.00 0.00 2.69
447 497 3.323243 TGCTTCGTGTTAGTTCTTAGGC 58.677 45.455 0.00 0.00 0.00 3.93
449 499 3.933332 GCTTCGTGTTAGTTCTTAGGCAT 59.067 43.478 0.00 0.00 0.00 4.40
450 500 4.392138 GCTTCGTGTTAGTTCTTAGGCATT 59.608 41.667 0.00 0.00 0.00 3.56
451 501 5.671329 GCTTCGTGTTAGTTCTTAGGCATTG 60.671 44.000 0.00 0.00 0.00 2.82
452 502 4.250464 TCGTGTTAGTTCTTAGGCATTGG 58.750 43.478 0.00 0.00 0.00 3.16
453 503 3.374058 CGTGTTAGTTCTTAGGCATTGGG 59.626 47.826 0.00 0.00 0.00 4.12
459 509 4.053871 TTAGGCATTGGGCGGGCA 62.054 61.111 3.27 0.00 46.16 5.36
476 526 0.301687 GCAGATCCGTGCATGTTACG 59.698 55.000 14.92 14.92 43.41 3.18
477 527 1.921243 CAGATCCGTGCATGTTACGA 58.079 50.000 21.00 10.84 43.82 3.43
478 528 2.267426 CAGATCCGTGCATGTTACGAA 58.733 47.619 21.00 6.19 43.82 3.85
479 529 2.029244 CAGATCCGTGCATGTTACGAAC 59.971 50.000 21.00 13.24 43.82 3.95
480 530 2.094182 AGATCCGTGCATGTTACGAACT 60.094 45.455 21.00 14.69 43.82 3.01
481 531 3.129813 AGATCCGTGCATGTTACGAACTA 59.870 43.478 21.00 8.13 43.82 2.24
508 558 9.445878 ACTCATGAACATATATGATTCATGACC 57.554 33.333 34.85 14.20 46.00 4.02
509 559 8.483307 TCATGAACATATATGATTCATGACCG 57.517 34.615 34.85 24.50 46.00 4.79
512 562 6.650390 TGAACATATATGATTCATGACCGGTG 59.350 38.462 14.63 0.00 0.00 4.94
515 565 4.687901 ATATGATTCATGACCGGTGACA 57.312 40.909 14.63 4.70 0.00 3.58
516 566 2.385013 TGATTCATGACCGGTGACAG 57.615 50.000 14.63 0.00 0.00 3.51
517 567 1.623311 TGATTCATGACCGGTGACAGT 59.377 47.619 14.63 0.00 0.00 3.55
519 569 3.450817 TGATTCATGACCGGTGACAGTAT 59.549 43.478 14.63 0.00 0.00 2.12
523 573 4.211920 TCATGACCGGTGACAGTATGATA 58.788 43.478 14.63 0.00 39.69 2.15
524 574 4.037565 TCATGACCGGTGACAGTATGATAC 59.962 45.833 14.63 0.00 39.69 2.24
525 575 3.358118 TGACCGGTGACAGTATGATACA 58.642 45.455 14.63 0.00 39.69 2.29
526 576 3.958147 TGACCGGTGACAGTATGATACAT 59.042 43.478 14.63 0.00 39.69 2.29
527 577 5.134661 TGACCGGTGACAGTATGATACATA 58.865 41.667 14.63 0.00 39.69 2.29
528 578 5.595133 TGACCGGTGACAGTATGATACATAA 59.405 40.000 14.63 0.00 39.69 1.90
573 627 3.004419 CGCTATCCACCTTATCTTCACGA 59.996 47.826 0.00 0.00 0.00 4.35
574 628 4.299978 GCTATCCACCTTATCTTCACGAC 58.700 47.826 0.00 0.00 0.00 4.34
575 629 3.821421 ATCCACCTTATCTTCACGACC 57.179 47.619 0.00 0.00 0.00 4.79
576 630 2.816411 TCCACCTTATCTTCACGACCT 58.184 47.619 0.00 0.00 0.00 3.85
602 656 4.769488 CCTTAGAGCATGCAGAGGTAGATA 59.231 45.833 21.98 0.00 0.00 1.98
609 663 4.313282 CATGCAGAGGTAGATACATGTGG 58.687 47.826 9.11 0.00 32.76 4.17
625 679 2.426522 TGTGGCATCTCTTGTAGTTGC 58.573 47.619 0.00 0.00 46.13 4.17
628 682 2.821307 GCATCTCTTGTAGTTGCAGC 57.179 50.000 0.00 0.00 46.13 5.25
717 785 8.946085 GTTGTTAATTCCTCATTCATCAGTGTA 58.054 33.333 0.00 0.00 0.00 2.90
730 816 6.912203 TCATCAGTGTAACAGAAAAACGAA 57.088 33.333 0.00 0.00 41.43 3.85
731 817 7.490962 TCATCAGTGTAACAGAAAAACGAAT 57.509 32.000 0.00 0.00 41.43 3.34
732 818 7.351981 TCATCAGTGTAACAGAAAAACGAATG 58.648 34.615 0.00 0.00 41.43 2.67
733 819 5.507077 TCAGTGTAACAGAAAAACGAATGC 58.493 37.500 0.00 0.00 41.43 3.56
734 820 5.065346 TCAGTGTAACAGAAAAACGAATGCA 59.935 36.000 0.00 0.00 41.43 3.96
735 821 5.396362 CAGTGTAACAGAAAAACGAATGCAG 59.604 40.000 0.00 0.00 41.43 4.41
736 822 5.065988 AGTGTAACAGAAAAACGAATGCAGT 59.934 36.000 0.00 0.00 41.43 4.40
737 823 5.395486 GTGTAACAGAAAAACGAATGCAGTC 59.605 40.000 3.54 3.54 36.32 3.51
738 824 3.253371 ACAGAAAAACGAATGCAGTCG 57.747 42.857 32.41 32.41 46.54 4.18
739 825 2.032030 ACAGAAAAACGAATGCAGTCGG 60.032 45.455 35.79 20.53 45.40 4.79
740 826 1.069227 AGAAAAACGAATGCAGTCGGC 60.069 47.619 35.79 20.46 45.40 5.54
755 841 2.164624 AGTCGGCAGAGACAGTTATCAC 59.835 50.000 8.54 0.00 43.24 3.06
758 844 2.159043 CGGCAGAGACAGTTATCACCAT 60.159 50.000 0.00 0.00 0.00 3.55
763 849 5.482006 CAGAGACAGTTATCACCATGTTCA 58.518 41.667 0.00 0.00 0.00 3.18
764 850 6.111382 CAGAGACAGTTATCACCATGTTCAT 58.889 40.000 0.00 0.00 0.00 2.57
768 854 8.862325 AGACAGTTATCACCATGTTCATAAAA 57.138 30.769 0.00 0.00 0.00 1.52
826 915 4.693283 TGTTCAATTGTTCAGAGTCTCGT 58.307 39.130 5.13 0.00 0.00 4.18
2097 2312 0.250727 GCTACCACCCAAAGCTGTCA 60.251 55.000 0.00 0.00 33.40 3.58
2134 2353 1.919956 GCATGACCAGCTGTCTGCAC 61.920 60.000 13.81 0.00 44.75 4.57
2135 2354 1.002868 ATGACCAGCTGTCTGCACC 60.003 57.895 13.81 0.00 44.75 5.01
2149 2368 2.586079 CACCGGCTGCTATCACCG 60.586 66.667 0.00 0.00 46.50 4.94
2384 2643 1.524355 CATGAACGATCCGAGTGATGC 59.476 52.381 0.00 0.00 32.41 3.91
2385 2644 0.817654 TGAACGATCCGAGTGATGCT 59.182 50.000 0.00 0.00 32.41 3.79
2400 2659 4.692625 AGTGATGCTGTGTACTGATGTTTC 59.307 41.667 0.00 0.00 0.00 2.78
2589 2852 2.992114 ACGGCTCTGTCTCGCCTT 60.992 61.111 0.00 0.00 44.11 4.35
2677 2943 2.854777 GTGTCGTGTCATCTAGATGTGC 59.145 50.000 27.80 21.87 39.72 4.57
2864 6015 5.130145 TGGATTTGGAAATTGTGTTGGTTCT 59.870 36.000 0.00 0.00 0.00 3.01
2882 6033 4.569015 GGTTCTAGAGGTGGAGAGAAGTCT 60.569 50.000 0.00 0.00 34.86 3.24
2897 6048 5.480073 AGAGAAGTCTAAGACATGAGCAAGT 59.520 40.000 0.00 0.00 34.60 3.16
2898 6049 5.477510 AGAAGTCTAAGACATGAGCAAGTG 58.522 41.667 0.00 0.00 34.60 3.16
2899 6050 4.881019 AGTCTAAGACATGAGCAAGTGT 57.119 40.909 0.00 0.00 34.60 3.55
2919 6070 3.118038 TGTCGGGATTAGGCAAATTAGCT 60.118 43.478 0.00 0.00 34.17 3.32
2920 6071 4.101898 TGTCGGGATTAGGCAAATTAGCTA 59.898 41.667 0.00 0.00 34.17 3.32
2932 6083 5.455392 GCAAATTAGCTAACGCATCATCAT 58.545 37.500 8.70 0.00 39.10 2.45
2933 6084 5.566774 GCAAATTAGCTAACGCATCATCATC 59.433 40.000 8.70 0.00 39.10 2.92
2934 6085 6.661669 CAAATTAGCTAACGCATCATCATCA 58.338 36.000 8.70 0.00 39.10 3.07
2945 6099 8.831715 AACGCATCATCATCAATATTACTACA 57.168 30.769 0.00 0.00 0.00 2.74
3016 6170 0.180406 ATAGACGGGGTGCACCATTC 59.820 55.000 35.78 26.14 42.91 2.67
3031 6185 4.458989 GCACCATTCAGTATCCTCAAAACA 59.541 41.667 0.00 0.00 0.00 2.83
3032 6186 5.048083 GCACCATTCAGTATCCTCAAAACAA 60.048 40.000 0.00 0.00 0.00 2.83
3033 6187 6.381801 CACCATTCAGTATCCTCAAAACAAC 58.618 40.000 0.00 0.00 0.00 3.32
3034 6188 5.476945 ACCATTCAGTATCCTCAAAACAACC 59.523 40.000 0.00 0.00 0.00 3.77
3035 6189 5.105756 CCATTCAGTATCCTCAAAACAACCC 60.106 44.000 0.00 0.00 0.00 4.11
3036 6190 4.028993 TCAGTATCCTCAAAACAACCCC 57.971 45.455 0.00 0.00 0.00 4.95
3037 6191 3.089284 CAGTATCCTCAAAACAACCCCC 58.911 50.000 0.00 0.00 0.00 5.40
3038 6192 2.089201 GTATCCTCAAAACAACCCCCG 58.911 52.381 0.00 0.00 0.00 5.73
3039 6193 0.898326 ATCCTCAAAACAACCCCCGC 60.898 55.000 0.00 0.00 0.00 6.13
3040 6194 1.830408 CCTCAAAACAACCCCCGCA 60.830 57.895 0.00 0.00 0.00 5.69
3041 6195 1.362355 CTCAAAACAACCCCCGCAC 59.638 57.895 0.00 0.00 0.00 5.34
3042 6196 1.379977 TCAAAACAACCCCCGCACA 60.380 52.632 0.00 0.00 0.00 4.57
3043 6197 0.970937 TCAAAACAACCCCCGCACAA 60.971 50.000 0.00 0.00 0.00 3.33
3044 6198 0.529555 CAAAACAACCCCCGCACAAG 60.530 55.000 0.00 0.00 0.00 3.16
3045 6199 0.684805 AAAACAACCCCCGCACAAGA 60.685 50.000 0.00 0.00 0.00 3.02
3046 6200 0.684805 AAACAACCCCCGCACAAGAA 60.685 50.000 0.00 0.00 0.00 2.52
3047 6201 0.684805 AACAACCCCCGCACAAGAAA 60.685 50.000 0.00 0.00 0.00 2.52
3048 6202 0.684805 ACAACCCCCGCACAAGAAAA 60.685 50.000 0.00 0.00 0.00 2.29
3049 6203 0.461961 CAACCCCCGCACAAGAAAAA 59.538 50.000 0.00 0.00 0.00 1.94
3135 6289 7.237982 TCTATTCAAGAAACAAATTCCTCCCA 58.762 34.615 0.00 0.00 38.94 4.37
3145 6299 5.497474 ACAAATTCCTCCCATGTACTGTAC 58.503 41.667 10.98 10.98 0.00 2.90
3146 6300 4.402056 AATTCCTCCCATGTACTGTACG 57.598 45.455 12.87 0.24 0.00 3.67
3157 6313 5.175126 CCATGTACTGTACGTTATAAGCAGC 59.825 44.000 9.88 0.00 0.00 5.25
3159 6315 2.805845 ACTGTACGTTATAAGCAGCGG 58.194 47.619 0.00 0.00 0.00 5.52
3185 6341 3.189287 GTGTCACAAATGGAGTCCATCAC 59.811 47.826 25.01 21.14 44.40 3.06
3203 6359 5.975344 CCATCACATCATGCTGAATGTTAAC 59.025 40.000 3.02 0.00 37.56 2.01
3204 6360 5.565592 TCACATCATGCTGAATGTTAACC 57.434 39.130 3.02 0.00 37.56 2.85
3206 6362 4.094739 CACATCATGCTGAATGTTAACCGA 59.905 41.667 3.02 0.00 37.56 4.69
3207 6363 4.333649 ACATCATGCTGAATGTTAACCGAG 59.666 41.667 3.02 0.00 37.56 4.63
3208 6364 4.200838 TCATGCTGAATGTTAACCGAGA 57.799 40.909 2.48 0.00 37.56 4.04
3209 6365 4.183865 TCATGCTGAATGTTAACCGAGAG 58.816 43.478 2.48 0.00 37.56 3.20
3212 6368 5.592104 TGCTGAATGTTAACCGAGAGATA 57.408 39.130 2.48 0.00 0.00 1.98
3213 6369 5.972935 TGCTGAATGTTAACCGAGAGATAA 58.027 37.500 2.48 0.00 0.00 1.75
3215 6371 6.312918 TGCTGAATGTTAACCGAGAGATAAAC 59.687 38.462 2.48 0.00 0.00 2.01
3216 6372 6.535508 GCTGAATGTTAACCGAGAGATAAACT 59.464 38.462 2.48 0.00 0.00 2.66
3217 6373 7.064728 GCTGAATGTTAACCGAGAGATAAACTT 59.935 37.037 2.48 0.00 0.00 2.66
3218 6374 8.251750 TGAATGTTAACCGAGAGATAAACTTG 57.748 34.615 2.48 0.00 0.00 3.16
3219 6375 8.092068 TGAATGTTAACCGAGAGATAAACTTGA 58.908 33.333 2.48 0.00 0.00 3.02
3221 6377 7.647907 TGTTAACCGAGAGATAAACTTGAAC 57.352 36.000 2.48 0.00 0.00 3.18
3222 6378 7.439381 TGTTAACCGAGAGATAAACTTGAACT 58.561 34.615 2.48 0.00 0.00 3.01
3223 6379 7.384115 TGTTAACCGAGAGATAAACTTGAACTG 59.616 37.037 2.48 0.00 0.00 3.16
3224 6380 5.723672 ACCGAGAGATAAACTTGAACTGA 57.276 39.130 0.00 0.00 0.00 3.41
3225 6381 5.715070 ACCGAGAGATAAACTTGAACTGAG 58.285 41.667 0.00 0.00 0.00 3.35
3226 6382 5.477291 ACCGAGAGATAAACTTGAACTGAGA 59.523 40.000 0.00 0.00 0.00 3.27
3227 6383 6.153680 ACCGAGAGATAAACTTGAACTGAGAT 59.846 38.462 0.00 0.00 0.00 2.75
3228 6384 7.038659 CCGAGAGATAAACTTGAACTGAGATT 58.961 38.462 0.00 0.00 0.00 2.40
3229 6385 8.191446 CCGAGAGATAAACTTGAACTGAGATTA 58.809 37.037 0.00 0.00 0.00 1.75
3230 6386 9.574458 CGAGAGATAAACTTGAACTGAGATTAA 57.426 33.333 0.00 0.00 0.00 1.40
3232 6388 9.660180 AGAGATAAACTTGAACTGAGATTAACC 57.340 33.333 0.00 0.00 0.00 2.85
3233 6389 9.436957 GAGATAAACTTGAACTGAGATTAACCA 57.563 33.333 0.00 0.00 0.00 3.67
3234 6390 9.965902 AGATAAACTTGAACTGAGATTAACCAT 57.034 29.630 0.00 0.00 0.00 3.55
3242 6398 7.402054 TGAACTGAGATTAACCATACCACAAT 58.598 34.615 0.00 0.00 0.00 2.71
3248 6404 5.360714 AGATTAACCATACCACAATGCCTTG 59.639 40.000 0.00 0.00 38.39 3.61
3251 6407 0.101040 CATACCACAATGCCTTGCCG 59.899 55.000 1.19 0.00 35.69 5.69
3284 6440 6.183360 CCGATGAATTGATTTTGGTGGGATTA 60.183 38.462 0.00 0.00 0.00 1.75
3286 6442 7.222611 CGATGAATTGATTTTGGTGGGATTAAC 59.777 37.037 0.00 0.00 0.00 2.01
3287 6443 6.706295 TGAATTGATTTTGGTGGGATTAACC 58.294 36.000 0.00 0.00 38.26 2.85
3322 6478 3.378112 TGAACTGAAAACAGAAGCACCAG 59.622 43.478 0.00 0.00 0.00 4.00
3381 6537 0.106967 GGATCAGCCAAGGGTCTTCC 60.107 60.000 0.00 0.00 36.34 3.46
3459 6628 1.265905 GCTACAACCGTTTCAACCAGG 59.734 52.381 0.00 0.00 0.00 4.45
3460 6629 2.567985 CTACAACCGTTTCAACCAGGT 58.432 47.619 0.00 0.00 38.88 4.00
3461 6630 1.842052 ACAACCGTTTCAACCAGGTT 58.158 45.000 0.00 0.00 46.76 3.50
3548 6721 4.641396 CTGGACAAGGAACACAAGTATGA 58.359 43.478 0.00 0.00 0.00 2.15
3566 6739 9.208022 CAAGTATGAAATTAGTCAGTGACAGAA 57.792 33.333 24.73 17.63 34.60 3.02
3571 6770 4.866508 ATTAGTCAGTGACAGAACCGAA 57.133 40.909 24.73 7.52 34.60 4.30
3578 6777 5.681543 GTCAGTGACAGAACCGAAAATTTTC 59.318 40.000 18.54 19.08 32.09 2.29
3585 6784 3.888930 AGAACCGAAAATTTTCAGCCAGA 59.111 39.130 26.20 0.00 37.01 3.86
3601 6802 3.118038 AGCCAGACTTACAACAACCTGAA 60.118 43.478 0.00 0.00 0.00 3.02
3604 6805 5.472137 GCCAGACTTACAACAACCTGAAATA 59.528 40.000 0.00 0.00 0.00 1.40
3605 6806 6.348540 GCCAGACTTACAACAACCTGAAATAG 60.349 42.308 0.00 0.00 0.00 1.73
3607 6808 7.118390 CCAGACTTACAACAACCTGAAATAGAG 59.882 40.741 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.908198 AGCCAGTGAGATCCAACCTC 59.092 55.000 0.00 0.00 0.00 3.85
1 2 1.280421 GAAGCCAGTGAGATCCAACCT 59.720 52.381 0.00 0.00 0.00 3.50
2 3 1.680249 GGAAGCCAGTGAGATCCAACC 60.680 57.143 0.00 0.00 0.00 3.77
3 4 1.280421 AGGAAGCCAGTGAGATCCAAC 59.720 52.381 9.70 0.00 32.47 3.77
4 5 1.556911 GAGGAAGCCAGTGAGATCCAA 59.443 52.381 9.70 0.00 32.47 3.53
5 6 1.198713 GAGGAAGCCAGTGAGATCCA 58.801 55.000 9.70 0.00 32.47 3.41
6 7 0.467804 GGAGGAAGCCAGTGAGATCC 59.532 60.000 0.00 0.00 0.00 3.36
7 8 1.198713 TGGAGGAAGCCAGTGAGATC 58.801 55.000 0.00 0.00 33.10 2.75
8 9 1.280421 GTTGGAGGAAGCCAGTGAGAT 59.720 52.381 0.00 0.00 39.52 2.75
9 10 0.687354 GTTGGAGGAAGCCAGTGAGA 59.313 55.000 0.00 0.00 39.52 3.27
10 11 0.322008 GGTTGGAGGAAGCCAGTGAG 60.322 60.000 0.00 0.00 39.52 3.51
11 12 1.059584 TGGTTGGAGGAAGCCAGTGA 61.060 55.000 0.00 0.00 39.52 3.41
12 13 0.890996 GTGGTTGGAGGAAGCCAGTG 60.891 60.000 0.00 0.00 39.52 3.66
13 14 1.456287 GTGGTTGGAGGAAGCCAGT 59.544 57.895 0.00 0.00 39.52 4.00
14 15 1.672356 CGTGGTTGGAGGAAGCCAG 60.672 63.158 0.00 0.00 39.52 4.85
15 16 1.990160 AACGTGGTTGGAGGAAGCCA 61.990 55.000 0.00 0.00 35.78 4.75
16 17 1.228154 AACGTGGTTGGAGGAAGCC 60.228 57.895 0.00 0.00 0.00 4.35
17 18 1.566018 CGAACGTGGTTGGAGGAAGC 61.566 60.000 0.00 0.00 0.00 3.86
18 19 0.949105 CCGAACGTGGTTGGAGGAAG 60.949 60.000 0.00 0.00 0.00 3.46
19 20 1.070105 CCGAACGTGGTTGGAGGAA 59.930 57.895 0.00 0.00 0.00 3.36
20 21 2.135581 ACCGAACGTGGTTGGAGGA 61.136 57.895 0.00 0.00 39.99 3.71
21 22 2.424302 ACCGAACGTGGTTGGAGG 59.576 61.111 0.00 0.00 39.99 4.30
27 28 0.239347 CTACTCGAACCGAACGTGGT 59.761 55.000 0.00 0.00 46.67 4.16
28 29 0.455633 CCTACTCGAACCGAACGTGG 60.456 60.000 0.00 0.00 34.74 4.94
29 30 1.069378 GCCTACTCGAACCGAACGTG 61.069 60.000 0.00 0.00 34.74 4.49
30 31 1.211190 GCCTACTCGAACCGAACGT 59.789 57.895 0.00 0.00 34.74 3.99
31 32 1.515736 GGCCTACTCGAACCGAACG 60.516 63.158 0.00 0.00 34.74 3.95
32 33 4.491101 GGCCTACTCGAACCGAAC 57.509 61.111 0.00 0.00 34.74 3.95
36 37 4.525949 GGGCGGCCTACTCGAACC 62.526 72.222 22.87 0.00 0.00 3.62
37 38 4.525949 GGGGCGGCCTACTCGAAC 62.526 72.222 28.80 4.21 0.00 3.95
52 53 3.721370 CTTGGCCTTGGATCGGGGG 62.721 68.421 3.32 0.00 0.00 5.40
53 54 2.124151 CTTGGCCTTGGATCGGGG 60.124 66.667 3.32 0.00 0.00 5.73
54 55 2.830370 GCTTGGCCTTGGATCGGG 60.830 66.667 3.32 0.00 0.00 5.14
55 56 2.830370 GGCTTGGCCTTGGATCGG 60.830 66.667 3.32 0.00 46.69 4.18
66 67 3.443045 GTGCGTGATGGGGCTTGG 61.443 66.667 0.00 0.00 0.00 3.61
67 68 3.803082 CGTGCGTGATGGGGCTTG 61.803 66.667 0.00 0.00 0.00 4.01
68 69 2.457743 TTACGTGCGTGATGGGGCTT 62.458 55.000 7.55 0.00 0.00 4.35
69 70 2.852495 CTTACGTGCGTGATGGGGCT 62.852 60.000 7.55 0.00 0.00 5.19
70 71 2.435234 TTACGTGCGTGATGGGGC 60.435 61.111 7.55 0.00 0.00 5.80
71 72 1.079405 ACTTACGTGCGTGATGGGG 60.079 57.895 7.55 0.00 0.00 4.96
72 73 1.082117 GGACTTACGTGCGTGATGGG 61.082 60.000 7.55 0.00 0.00 4.00
73 74 1.082117 GGGACTTACGTGCGTGATGG 61.082 60.000 7.55 0.00 31.41 3.51
74 75 1.082117 GGGGACTTACGTGCGTGATG 61.082 60.000 7.55 0.42 31.41 3.07
75 76 1.217244 GGGGACTTACGTGCGTGAT 59.783 57.895 7.55 0.00 31.41 3.06
82 83 0.111061 GGGGTTTTGGGGACTTACGT 59.889 55.000 0.00 0.00 0.00 3.57
117 118 3.306088 CGTGCTGAAGAAAAGGGAGAGTA 60.306 47.826 0.00 0.00 0.00 2.59
143 144 0.820891 CTGGATTGGGCGGATTCAGG 60.821 60.000 0.36 0.00 0.00 3.86
153 154 1.283736 GTTACGTACGCTGGATTGGG 58.716 55.000 16.72 0.00 0.00 4.12
162 163 3.000122 TGCCGATTTATTGTTACGTACGC 60.000 43.478 16.72 0.00 0.00 4.42
171 172 5.554822 ATTGTTACGTGCCGATTTATTGT 57.445 34.783 0.00 0.00 0.00 2.71
174 175 7.067116 CGATTTATTGTTACGTGCCGATTTAT 58.933 34.615 0.00 0.00 0.00 1.40
175 176 6.412460 CGATTTATTGTTACGTGCCGATTTA 58.588 36.000 0.00 0.00 0.00 1.40
184 185 4.004982 ACCAAGCCGATTTATTGTTACGT 58.995 39.130 0.00 0.00 0.00 3.57
185 186 4.331717 AGACCAAGCCGATTTATTGTTACG 59.668 41.667 0.00 0.00 0.00 3.18
187 188 5.941058 TCAAGACCAAGCCGATTTATTGTTA 59.059 36.000 0.00 0.00 0.00 2.41
188 189 4.764823 TCAAGACCAAGCCGATTTATTGTT 59.235 37.500 0.00 0.00 0.00 2.83
189 190 4.331968 TCAAGACCAAGCCGATTTATTGT 58.668 39.130 0.00 0.00 0.00 2.71
190 191 4.963276 TCAAGACCAAGCCGATTTATTG 57.037 40.909 0.00 0.00 0.00 1.90
191 192 4.949856 ACATCAAGACCAAGCCGATTTATT 59.050 37.500 0.00 0.00 0.00 1.40
192 193 4.526970 ACATCAAGACCAAGCCGATTTAT 58.473 39.130 0.00 0.00 0.00 1.40
193 194 3.938963 GACATCAAGACCAAGCCGATTTA 59.061 43.478 0.00 0.00 0.00 1.40
194 195 2.749621 GACATCAAGACCAAGCCGATTT 59.250 45.455 0.00 0.00 0.00 2.17
195 196 2.026822 AGACATCAAGACCAAGCCGATT 60.027 45.455 0.00 0.00 0.00 3.34
196 197 1.556911 AGACATCAAGACCAAGCCGAT 59.443 47.619 0.00 0.00 0.00 4.18
197 198 0.976641 AGACATCAAGACCAAGCCGA 59.023 50.000 0.00 0.00 0.00 5.54
198 199 1.813513 AAGACATCAAGACCAAGCCG 58.186 50.000 0.00 0.00 0.00 5.52
199 200 4.393371 GTCTTAAGACATCAAGACCAAGCC 59.607 45.833 27.12 0.00 43.12 4.35
200 201 5.538067 GTCTTAAGACATCAAGACCAAGC 57.462 43.478 27.12 0.00 43.12 4.01
215 216 2.989840 CACGCTCAGGTCTTGTCTTAAG 59.010 50.000 0.00 0.00 0.00 1.85
218 219 0.034059 CCACGCTCAGGTCTTGTCTT 59.966 55.000 0.00 0.00 0.00 3.01
222 223 3.114616 CGCCACGCTCAGGTCTTG 61.115 66.667 0.00 0.00 0.00 3.02
223 224 4.379243 CCGCCACGCTCAGGTCTT 62.379 66.667 0.00 0.00 0.00 3.01
227 228 3.781770 GATCTCCGCCACGCTCAGG 62.782 68.421 0.00 0.00 0.00 3.86
239 240 5.316987 TCCCTCTTTGTTTTTCAGATCTCC 58.683 41.667 0.00 0.00 0.00 3.71
252 300 2.649312 TGTCATCCCAATCCCTCTTTGT 59.351 45.455 0.00 0.00 0.00 2.83
253 301 3.285484 CTGTCATCCCAATCCCTCTTTG 58.715 50.000 0.00 0.00 0.00 2.77
268 316 2.043939 TCCCACCTACAGTACCTGTCAT 59.956 50.000 0.00 0.00 41.21 3.06
269 317 1.430075 TCCCACCTACAGTACCTGTCA 59.570 52.381 0.00 0.00 41.21 3.58
272 320 3.370527 CCATTTCCCACCTACAGTACCTG 60.371 52.174 0.00 0.00 37.52 4.00
273 321 2.844348 CCATTTCCCACCTACAGTACCT 59.156 50.000 0.00 0.00 0.00 3.08
274 322 2.841881 TCCATTTCCCACCTACAGTACC 59.158 50.000 0.00 0.00 0.00 3.34
275 323 4.019591 AGTTCCATTTCCCACCTACAGTAC 60.020 45.833 0.00 0.00 0.00 2.73
276 324 4.019681 CAGTTCCATTTCCCACCTACAGTA 60.020 45.833 0.00 0.00 0.00 2.74
277 325 2.986728 AGTTCCATTTCCCACCTACAGT 59.013 45.455 0.00 0.00 0.00 3.55
278 326 3.009033 TCAGTTCCATTTCCCACCTACAG 59.991 47.826 0.00 0.00 0.00 2.74
279 327 2.983192 TCAGTTCCATTTCCCACCTACA 59.017 45.455 0.00 0.00 0.00 2.74
280 328 3.713826 TCAGTTCCATTTCCCACCTAC 57.286 47.619 0.00 0.00 0.00 3.18
281 329 3.624707 GCATCAGTTCCATTTCCCACCTA 60.625 47.826 0.00 0.00 0.00 3.08
282 330 2.885554 GCATCAGTTCCATTTCCCACCT 60.886 50.000 0.00 0.00 0.00 4.00
283 331 1.478105 GCATCAGTTCCATTTCCCACC 59.522 52.381 0.00 0.00 0.00 4.61
284 332 2.094545 GTGCATCAGTTCCATTTCCCAC 60.095 50.000 0.00 0.00 0.00 4.61
285 333 2.170166 GTGCATCAGTTCCATTTCCCA 58.830 47.619 0.00 0.00 0.00 4.37
286 334 2.450476 AGTGCATCAGTTCCATTTCCC 58.550 47.619 0.00 0.00 0.00 3.97
287 335 3.507233 TCAAGTGCATCAGTTCCATTTCC 59.493 43.478 0.00 0.00 0.00 3.13
288 336 4.771590 TCAAGTGCATCAGTTCCATTTC 57.228 40.909 0.00 0.00 0.00 2.17
289 337 5.733620 AATCAAGTGCATCAGTTCCATTT 57.266 34.783 0.00 0.00 0.00 2.32
290 338 5.163581 GCTAATCAAGTGCATCAGTTCCATT 60.164 40.000 0.00 0.00 0.00 3.16
291 339 4.337555 GCTAATCAAGTGCATCAGTTCCAT 59.662 41.667 0.00 0.00 0.00 3.41
292 340 3.691118 GCTAATCAAGTGCATCAGTTCCA 59.309 43.478 0.00 0.00 0.00 3.53
293 341 3.944015 AGCTAATCAAGTGCATCAGTTCC 59.056 43.478 0.00 0.00 0.00 3.62
294 342 4.034975 GGAGCTAATCAAGTGCATCAGTTC 59.965 45.833 0.00 0.00 0.00 3.01
295 343 3.944015 GGAGCTAATCAAGTGCATCAGTT 59.056 43.478 0.00 0.00 0.00 3.16
296 344 3.199508 AGGAGCTAATCAAGTGCATCAGT 59.800 43.478 0.00 0.00 0.00 3.41
297 345 3.560481 CAGGAGCTAATCAAGTGCATCAG 59.440 47.826 0.00 0.00 0.00 2.90
298 346 3.538591 CAGGAGCTAATCAAGTGCATCA 58.461 45.455 0.00 0.00 0.00 3.07
299 347 2.877168 CCAGGAGCTAATCAAGTGCATC 59.123 50.000 0.00 0.00 0.00 3.91
300 348 2.240667 ACCAGGAGCTAATCAAGTGCAT 59.759 45.455 0.00 0.00 0.00 3.96
301 349 1.630369 ACCAGGAGCTAATCAAGTGCA 59.370 47.619 0.00 0.00 0.00 4.57
302 350 2.409948 ACCAGGAGCTAATCAAGTGC 57.590 50.000 0.00 0.00 0.00 4.40
303 351 4.818546 CCATAACCAGGAGCTAATCAAGTG 59.181 45.833 0.00 0.00 0.00 3.16
304 352 4.475016 ACCATAACCAGGAGCTAATCAAGT 59.525 41.667 0.00 0.00 0.00 3.16
318 366 8.792633 CAGAAAGAACAATTTAGACCATAACCA 58.207 33.333 0.00 0.00 0.00 3.67
353 401 4.453819 AGCAGCAGTGTAGATTCTTGAAAC 59.546 41.667 0.00 0.00 0.00 2.78
368 416 1.301716 CCCACGTGTAAGCAGCAGT 60.302 57.895 15.65 0.00 0.00 4.40
383 431 0.897863 CTGTTTCCCAAATCGCCCCA 60.898 55.000 0.00 0.00 0.00 4.96
386 436 2.091541 TGATCTGTTTCCCAAATCGCC 58.908 47.619 0.00 0.00 0.00 5.54
388 438 3.871006 TCGATGATCTGTTTCCCAAATCG 59.129 43.478 0.00 0.00 37.58 3.34
395 445 9.050601 AGAGATTAAAATCGATGATCTGTTTCC 57.949 33.333 14.69 4.75 40.35 3.13
410 460 6.820656 ACACGAAGCATCAGAGAGATTAAAAT 59.179 34.615 0.00 0.00 33.72 1.82
415 465 3.883830 ACACGAAGCATCAGAGAGATT 57.116 42.857 0.00 0.00 33.72 2.40
420 470 4.489810 AGAACTAACACGAAGCATCAGAG 58.510 43.478 0.00 0.00 0.00 3.35
446 496 3.599704 GATCTGCCCGCCCAATGC 61.600 66.667 0.00 0.00 0.00 3.56
447 497 2.908940 GGATCTGCCCGCCCAATG 60.909 66.667 0.00 0.00 0.00 2.82
459 509 2.094182 AGTTCGTAACATGCACGGATCT 60.094 45.455 17.42 11.51 39.82 2.75
468 518 7.346208 TGTTCATGAGTTAGTTCGTAACATG 57.654 36.000 0.00 0.00 43.26 3.21
504 554 3.358118 TGTATCATACTGTCACCGGTCA 58.642 45.455 2.59 0.00 0.00 4.02
508 558 9.692749 ATAAACTTATGTATCATACTGTCACCG 57.307 33.333 0.00 0.00 0.00 4.94
526 576 9.781834 CGCCTCAAATAATCAACAATAAACTTA 57.218 29.630 0.00 0.00 0.00 2.24
527 577 7.275560 GCGCCTCAAATAATCAACAATAAACTT 59.724 33.333 0.00 0.00 0.00 2.66
528 578 6.751888 GCGCCTCAAATAATCAACAATAAACT 59.248 34.615 0.00 0.00 0.00 2.66
537 591 4.515191 GTGGATAGCGCCTCAAATAATCAA 59.485 41.667 2.29 0.00 0.00 2.57
548 602 2.016905 AGATAAGGTGGATAGCGCCT 57.983 50.000 2.29 0.00 0.00 5.52
551 605 3.004419 TCGTGAAGATAAGGTGGATAGCG 59.996 47.826 0.00 0.00 0.00 4.26
573 627 1.415659 CTGCATGCTCTAAGGCTAGGT 59.584 52.381 20.33 0.00 0.00 3.08
574 628 1.690893 TCTGCATGCTCTAAGGCTAGG 59.309 52.381 20.33 0.00 0.00 3.02
575 629 2.288948 CCTCTGCATGCTCTAAGGCTAG 60.289 54.545 20.33 4.32 0.00 3.42
576 630 1.690893 CCTCTGCATGCTCTAAGGCTA 59.309 52.381 20.33 0.00 0.00 3.93
602 656 3.988976 ACTACAAGAGATGCCACATGT 57.011 42.857 0.00 0.00 0.00 3.21
625 679 7.809806 TGAGACAATATAGATCAATACGTGCTG 59.190 37.037 0.00 0.00 0.00 4.41
628 682 7.542477 GGGTGAGACAATATAGATCAATACGTG 59.458 40.741 0.00 0.00 0.00 4.49
717 785 3.548014 CCGACTGCATTCGTTTTTCTGTT 60.548 43.478 22.72 0.00 37.29 3.16
732 818 0.243907 TAACTGTCTCTGCCGACTGC 59.756 55.000 0.00 0.00 36.63 4.40
733 819 2.164422 TGATAACTGTCTCTGCCGACTG 59.836 50.000 0.00 0.00 38.39 3.51
734 820 2.164624 GTGATAACTGTCTCTGCCGACT 59.835 50.000 0.00 0.00 35.00 4.18
735 821 2.531206 GTGATAACTGTCTCTGCCGAC 58.469 52.381 0.00 0.00 34.52 4.79
736 822 1.476891 GGTGATAACTGTCTCTGCCGA 59.523 52.381 0.00 0.00 0.00 5.54
737 823 1.204704 TGGTGATAACTGTCTCTGCCG 59.795 52.381 0.00 0.00 0.00 5.69
738 824 3.201290 CATGGTGATAACTGTCTCTGCC 58.799 50.000 0.00 0.00 0.00 4.85
739 825 3.866651 ACATGGTGATAACTGTCTCTGC 58.133 45.455 0.00 0.00 0.00 4.26
740 826 5.482006 TGAACATGGTGATAACTGTCTCTG 58.518 41.667 0.00 0.00 0.00 3.35
741 827 5.745312 TGAACATGGTGATAACTGTCTCT 57.255 39.130 0.00 0.00 0.00 3.10
742 828 8.492673 TTTATGAACATGGTGATAACTGTCTC 57.507 34.615 1.77 0.00 0.00 3.36
743 829 8.862325 TTTTATGAACATGGTGATAACTGTCT 57.138 30.769 1.77 0.00 0.00 3.41
794 880 9.599866 CTCTGAACAATTGAACATACATAGGTA 57.400 33.333 13.59 0.00 0.00 3.08
2097 2312 0.179045 GCTCCGCCAGTCCATATTGT 60.179 55.000 0.00 0.00 0.00 2.71
2149 2368 1.125711 ATAGTACCCCATGTCCCGCC 61.126 60.000 0.00 0.00 0.00 6.13
2384 2643 5.277974 CCCAACAAGAAACATCAGTACACAG 60.278 44.000 0.00 0.00 0.00 3.66
2385 2644 4.578516 CCCAACAAGAAACATCAGTACACA 59.421 41.667 0.00 0.00 0.00 3.72
2589 2852 1.134521 GGTGGATCAACATCGTAGGCA 60.135 52.381 1.86 0.00 0.00 4.75
2634 2897 6.652062 ACACCGTTTACCTCCTAAGTTAATTG 59.348 38.462 0.00 0.00 0.00 2.32
2677 2943 3.624410 TCAAGCAACTTGATCATGATCGG 59.376 43.478 26.52 22.97 44.27 4.18
2864 6015 5.251005 TGTCTTAGACTTCTCTCCACCTCTA 59.749 44.000 13.86 0.00 33.15 2.43
2882 6033 2.353704 CCCGACACTTGCTCATGTCTTA 60.354 50.000 11.34 0.00 42.56 2.10
2897 6048 3.118038 AGCTAATTTGCCTAATCCCGACA 60.118 43.478 8.30 0.00 0.00 4.35
2898 6049 3.477530 AGCTAATTTGCCTAATCCCGAC 58.522 45.455 8.30 0.00 0.00 4.79
2899 6050 3.857157 AGCTAATTTGCCTAATCCCGA 57.143 42.857 8.30 0.00 0.00 5.14
2901 6052 4.320275 GCGTTAGCTAATTTGCCTAATCCC 60.320 45.833 9.88 0.00 41.01 3.85
2919 6070 9.921637 TGTAGTAATATTGATGATGATGCGTTA 57.078 29.630 0.00 0.00 0.00 3.18
2920 6071 8.831715 TGTAGTAATATTGATGATGATGCGTT 57.168 30.769 0.00 0.00 0.00 4.84
2980 6134 8.619546 CCCCGTCTATGCTAGTTATACTTATAC 58.380 40.741 0.00 0.00 0.00 1.47
2984 6138 5.243283 CACCCCGTCTATGCTAGTTATACTT 59.757 44.000 0.00 0.00 0.00 2.24
2985 6139 4.765856 CACCCCGTCTATGCTAGTTATACT 59.234 45.833 0.00 0.00 0.00 2.12
2986 6140 4.617762 GCACCCCGTCTATGCTAGTTATAC 60.618 50.000 0.00 0.00 36.40 1.47
3031 6185 2.903404 TTTTTCTTGTGCGGGGGTT 58.097 47.368 0.00 0.00 0.00 4.11
3032 6186 4.688770 TTTTTCTTGTGCGGGGGT 57.311 50.000 0.00 0.00 0.00 4.95
3055 6209 8.859090 TCACTTGATATTGTTTGTTTTGAGGAT 58.141 29.630 0.00 0.00 0.00 3.24
3056 6210 8.231692 TCACTTGATATTGTTTGTTTTGAGGA 57.768 30.769 0.00 0.00 0.00 3.71
3057 6211 8.870160 TTCACTTGATATTGTTTGTTTTGAGG 57.130 30.769 0.00 0.00 0.00 3.86
3105 6259 9.231297 AGGAATTTGTTTCTTGAATAGAATCGA 57.769 29.630 0.00 0.00 42.32 3.59
3111 6265 7.466746 TGGGAGGAATTTGTTTCTTGAATAG 57.533 36.000 0.00 0.00 34.56 1.73
3123 6277 4.570772 CGTACAGTACATGGGAGGAATTTG 59.429 45.833 11.37 0.00 0.00 2.32
3135 6289 4.974275 CGCTGCTTATAACGTACAGTACAT 59.026 41.667 11.37 1.76 0.00 2.29
3145 6299 3.184541 ACACTTACCGCTGCTTATAACG 58.815 45.455 0.00 0.00 0.00 3.18
3146 6300 4.032558 GTGACACTTACCGCTGCTTATAAC 59.967 45.833 0.00 0.00 0.00 1.89
3157 6313 3.399330 ACTCCATTTGTGACACTTACCG 58.601 45.455 7.20 0.00 0.00 4.02
3159 6315 4.385825 TGGACTCCATTTGTGACACTTAC 58.614 43.478 7.20 0.00 0.00 2.34
3203 6359 5.955488 TCTCAGTTCAAGTTTATCTCTCGG 58.045 41.667 0.00 0.00 0.00 4.63
3204 6360 9.574458 TTAATCTCAGTTCAAGTTTATCTCTCG 57.426 33.333 0.00 0.00 0.00 4.04
3206 6362 9.660180 GGTTAATCTCAGTTCAAGTTTATCTCT 57.340 33.333 0.00 0.00 0.00 3.10
3207 6363 9.436957 TGGTTAATCTCAGTTCAAGTTTATCTC 57.563 33.333 0.00 0.00 0.00 2.75
3208 6364 9.965902 ATGGTTAATCTCAGTTCAAGTTTATCT 57.034 29.630 0.00 0.00 0.00 1.98
3212 6368 7.942341 TGGTATGGTTAATCTCAGTTCAAGTTT 59.058 33.333 0.00 0.00 0.00 2.66
3213 6369 7.390718 GTGGTATGGTTAATCTCAGTTCAAGTT 59.609 37.037 0.00 0.00 0.00 2.66
3215 6371 6.878923 TGTGGTATGGTTAATCTCAGTTCAAG 59.121 38.462 0.00 0.00 0.00 3.02
3216 6372 6.774673 TGTGGTATGGTTAATCTCAGTTCAA 58.225 36.000 0.00 0.00 0.00 2.69
3217 6373 6.367374 TGTGGTATGGTTAATCTCAGTTCA 57.633 37.500 0.00 0.00 0.00 3.18
3218 6374 7.679638 GCATTGTGGTATGGTTAATCTCAGTTC 60.680 40.741 0.00 0.00 0.00 3.01
3219 6375 6.095440 GCATTGTGGTATGGTTAATCTCAGTT 59.905 38.462 0.00 0.00 0.00 3.16
3221 6377 5.009010 GGCATTGTGGTATGGTTAATCTCAG 59.991 44.000 0.00 0.00 0.00 3.35
3222 6378 4.887071 GGCATTGTGGTATGGTTAATCTCA 59.113 41.667 0.00 0.00 0.00 3.27
3223 6379 5.133221 AGGCATTGTGGTATGGTTAATCTC 58.867 41.667 0.00 0.00 0.00 2.75
3224 6380 5.129368 AGGCATTGTGGTATGGTTAATCT 57.871 39.130 0.00 0.00 0.00 2.40
3225 6381 5.591099 CAAGGCATTGTGGTATGGTTAATC 58.409 41.667 2.19 0.00 0.00 1.75
3226 6382 4.141959 GCAAGGCATTGTGGTATGGTTAAT 60.142 41.667 13.30 0.00 38.76 1.40
3227 6383 3.194542 GCAAGGCATTGTGGTATGGTTAA 59.805 43.478 13.30 0.00 38.76 2.01
3228 6384 2.757868 GCAAGGCATTGTGGTATGGTTA 59.242 45.455 13.30 0.00 38.76 2.85
3229 6385 1.550072 GCAAGGCATTGTGGTATGGTT 59.450 47.619 13.30 0.00 38.76 3.67
3230 6386 1.185315 GCAAGGCATTGTGGTATGGT 58.815 50.000 13.30 0.00 38.76 3.55
3231 6387 0.461135 GGCAAGGCATTGTGGTATGG 59.539 55.000 13.30 0.00 38.76 2.74
3232 6388 0.101040 CGGCAAGGCATTGTGGTATG 59.899 55.000 13.30 0.00 38.76 2.39
3233 6389 0.323360 ACGGCAAGGCATTGTGGTAT 60.323 50.000 13.30 0.00 38.76 2.73
3234 6390 0.538516 AACGGCAAGGCATTGTGGTA 60.539 50.000 13.30 0.00 38.76 3.25
3235 6391 1.398958 AAACGGCAAGGCATTGTGGT 61.399 50.000 13.30 8.07 38.76 4.16
3242 6398 1.896660 GGTCAGAAACGGCAAGGCA 60.897 57.895 0.00 0.00 0.00 4.75
3248 6404 1.369625 ATTCATCGGTCAGAAACGGC 58.630 50.000 0.00 0.00 0.00 5.68
3251 6407 6.308766 CCAAAATCAATTCATCGGTCAGAAAC 59.691 38.462 0.00 0.00 0.00 2.78
3284 6440 6.097915 TCAGTTCAAGTTTATCTCTCGGTT 57.902 37.500 0.00 0.00 0.00 4.44
3286 6442 7.042051 TGTTTTCAGTTCAAGTTTATCTCTCGG 60.042 37.037 0.00 0.00 0.00 4.63
3287 6443 7.851508 TGTTTTCAGTTCAAGTTTATCTCTCG 58.148 34.615 0.00 0.00 0.00 4.04
3322 6478 2.008329 CTGCTCATGCCTTTCTCTGTC 58.992 52.381 0.00 0.00 38.71 3.51
3395 6551 6.857437 AATGGAAATAGAGGAAACCCTTTG 57.143 37.500 0.00 0.00 33.25 2.77
3437 6593 2.356382 CTGGTTGAAACGGTTGTAGCAA 59.644 45.455 0.00 0.00 0.00 3.91
3459 6628 8.018520 CCTTTTGGTTTGTTTGTTTCCTTTAAC 58.981 33.333 0.00 0.00 34.07 2.01
3460 6629 7.308649 GCCTTTTGGTTTGTTTGTTTCCTTTAA 60.309 33.333 0.00 0.00 42.99 1.52
3461 6630 6.149640 GCCTTTTGGTTTGTTTGTTTCCTTTA 59.850 34.615 0.00 0.00 42.99 1.85
3544 6717 6.811665 CGGTTCTGTCACTGACTAATTTCATA 59.188 38.462 10.54 0.00 33.15 2.15
3545 6718 5.639506 CGGTTCTGTCACTGACTAATTTCAT 59.360 40.000 10.54 0.00 33.15 2.57
3546 6719 4.988540 CGGTTCTGTCACTGACTAATTTCA 59.011 41.667 10.54 0.00 33.15 2.69
3548 6721 5.209818 TCGGTTCTGTCACTGACTAATTT 57.790 39.130 10.54 0.00 33.15 1.82
3566 6739 3.222603 AGTCTGGCTGAAAATTTTCGGT 58.777 40.909 30.85 14.51 43.74 4.69
3571 6770 6.463995 TGTTGTAAGTCTGGCTGAAAATTT 57.536 33.333 0.00 0.00 0.00 1.82
3578 6777 2.549754 CAGGTTGTTGTAAGTCTGGCTG 59.450 50.000 0.00 0.00 0.00 4.85
3585 6784 7.074653 TCCTCTATTTCAGGTTGTTGTAAGT 57.925 36.000 0.00 0.00 32.20 2.24
3601 6802 2.776665 TGGGGCTTAGCTTCCTCTATT 58.223 47.619 3.59 0.00 0.00 1.73
3604 6805 0.621082 GTTGGGGCTTAGCTTCCTCT 59.379 55.000 3.59 0.00 0.00 3.69
3605 6806 0.394488 GGTTGGGGCTTAGCTTCCTC 60.394 60.000 3.59 0.00 0.00 3.71
3607 6808 0.681243 CAGGTTGGGGCTTAGCTTCC 60.681 60.000 3.59 7.16 0.00 3.46


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

AutoCloner maintained by Alex Coulton.