Multiple sequence alignment - TraesCS7B01G130200

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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 TraesCS7B01G130200 chr7B 100.000 5576 0 0 1 5576 156680169 156685744 0.000000e+00 10298.0
1 TraesCS7B01G130200 chr7B 93.878 49 2 1 4837 4885 86882303 86882256 7.750000e-09 73.1
2 TraesCS7B01G130200 chr7A 93.729 4098 162 36 846 4904 202736502 202740543 0.000000e+00 6056.0
3 TraesCS7B01G130200 chr7A 89.753 527 46 5 4907 5425 202740583 202741109 0.000000e+00 667.0
4 TraesCS7B01G130200 chr7A 90.000 160 14 1 5408 5567 202741835 202741992 7.320000e-49 206.0
5 TraesCS7B01G130200 chr7A 100.000 29 0 0 374 402 541435673 541435701 3.000000e-03 54.7
6 TraesCS7B01G130200 chr7D 90.169 3906 219 68 314 4147 193208160 193211972 0.000000e+00 4933.0
7 TraesCS7B01G130200 chr7D 90.569 668 53 8 4235 4897 193212386 193213048 0.000000e+00 876.0
8 TraesCS7B01G130200 chr7D 85.323 511 57 10 5038 5533 193213138 193213645 3.850000e-141 512.0
9 TraesCS7B01G130200 chr7D 79.255 188 23 10 80 267 193208011 193208182 3.530000e-22 117.0
10 TraesCS7B01G130200 chr7D 100.000 30 0 0 376 405 622360219 622360248 7.800000e-04 56.5
11 TraesCS7B01G130200 chr5B 76.792 293 60 7 5253 5539 679770438 679770148 2.080000e-34 158.0
12 TraesCS7B01G130200 chr4A 98.734 79 1 0 1 79 735868595 735868517 2.090000e-29 141.0
13 TraesCS7B01G130200 chr2A 98.718 78 1 0 1 78 183547374 183547297 7.530000e-29 139.0
14 TraesCS7B01G130200 chr2A 100.000 31 0 0 374 404 613473234 613473204 2.170000e-04 58.4
15 TraesCS7B01G130200 chr6B 97.468 79 1 1 1 79 686553296 686553219 3.500000e-27 134.0
16 TraesCS7B01G130200 chr6B 89.583 48 5 0 5240 5287 551258031 551258078 1.680000e-05 62.1
17 TraesCS7B01G130200 chr6B 89.796 49 4 1 5240 5287 551504086 551504134 1.680000e-05 62.1
18 TraesCS7B01G130200 chr4D 81.437 167 24 6 669 830 17968836 17968672 4.530000e-26 130.0
19 TraesCS7B01G130200 chr4D 93.333 45 3 0 5243 5287 228147791 228147835 3.610000e-07 67.6
20 TraesCS7B01G130200 chr1D 75.532 282 57 10 5251 5525 270211201 270210925 1.630000e-25 128.0
21 TraesCS7B01G130200 chr1D 91.667 48 2 2 4836 4883 204886029 204886074 1.300000e-06 65.8
22 TraesCS7B01G130200 chr1D 94.737 38 2 0 379 416 363615786 363615823 6.030000e-05 60.2
23 TraesCS7B01G130200 chr2B 93.443 61 3 1 5467 5526 106146804 106146744 7.690000e-14 89.8
24 TraesCS7B01G130200 chr6A 92.000 50 2 2 4836 4885 384043961 384043914 1.000000e-07 69.4
25 TraesCS7B01G130200 chr1A 92.000 50 3 1 34 82 394446617 394446568 1.000000e-07 69.4
26 TraesCS7B01G130200 chr4B 88.136 59 4 2 5243 5300 31281949 31281893 3.610000e-07 67.6
27 TraesCS7B01G130200 chr5A 87.931 58 4 3 4834 4890 311480797 311480852 1.300000e-06 65.8
28 TraesCS7B01G130200 chr5A 87.931 58 4 3 4834 4890 311496962 311497017 1.300000e-06 65.8
29 TraesCS7B01G130200 chr3B 87.931 58 3 3 4836 4891 136088892 136088837 1.300000e-06 65.8
30 TraesCS7B01G130200 chr3B 100.000 32 0 0 374 405 16807748 16807717 6.030000e-05 60.2
31 TraesCS7B01G130200 chr2D 89.091 55 3 3 4835 4887 569790409 569790356 1.300000e-06 65.8
32 TraesCS7B01G130200 chrUn 91.304 46 3 1 5242 5287 22883781 22883825 1.680000e-05 62.1
33 TraesCS7B01G130200 chrUn 100.000 31 0 0 374 404 53483713 53483743 2.170000e-04 58.4
34 TraesCS7B01G130200 chr6D 89.583 48 5 0 5243 5290 456385630 456385583 1.680000e-05 62.1
35 TraesCS7B01G130200 chr5D 100.000 29 0 0 377 405 11145138 11145166 3.000000e-03 54.7
36 TraesCS7B01G130200 chr5D 100.000 28 0 0 377 404 11145372 11145399 1.000000e-02 52.8
37 TraesCS7B01G130200 chr1B 100.000 28 0 0 379 406 486843252 486843279 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G130200 chr7B 156680169 156685744 5575 False 10298.000000 10298 100.000000 1 5576 1 chr7B.!!$F1 5575
1 TraesCS7B01G130200 chr7A 202736502 202741992 5490 False 2309.666667 6056 91.160667 846 5567 3 chr7A.!!$F2 4721
2 TraesCS7B01G130200 chr7D 193208011 193213645 5634 False 1609.500000 4933 86.329000 80 5533 4 chr7D.!!$F2 5453

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
66 67 0.257616 CCCGGGCCCTCAAAATCTTA 59.742 55.0 22.43 0.00 0.00 2.10 F
299 303 0.303493 TGTGTGCTTCTCGCGAAAAC 59.697 50.0 11.33 0.00 43.27 2.43 F
300 304 0.303493 GTGTGCTTCTCGCGAAAACA 59.697 50.0 11.33 7.55 43.27 2.83 F
857 872 0.555769 AAAAAGGTGGAGTGGGCTGA 59.444 50.0 0.00 0.00 0.00 4.26 F
2311 2349 0.164002 GGTCGACGCAGAGAAAAAGC 59.836 55.0 9.92 0.00 0.00 3.51 F
3062 3111 0.682532 TTGTGGGTGTCTGCTTGCAA 60.683 50.0 0.00 0.00 0.00 4.08 F
3233 3282 1.048601 AGTGTATATGGTGGAGCGGG 58.951 55.0 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1946 0.657840 CTACGCCATGTAAAGCAGCC 59.342 55.000 0.00 0.0 31.20 4.85 R
1960 1994 1.066002 GCAACAAGCAAAGCAGTCTCA 59.934 47.619 0.00 0.0 44.79 3.27 R
2126 2163 1.349627 GCGACATGCCGACATTCAG 59.650 57.895 5.30 0.0 37.76 3.02 R
2557 2605 0.886563 GCCTTGCTGCTCAAATGACT 59.113 50.000 0.00 0.0 33.65 3.41 R
4299 4696 0.244721 CTCAGCGGTCATCAGTCACA 59.755 55.000 0.00 0.0 0.00 3.58 R
4392 4789 1.447317 CCACTTGTGCTGCGAAAGGT 61.447 55.000 15.69 0.0 0.00 3.50 R
4588 4988 1.561542 ACAGAAATTGATCCGAGGGCT 59.438 47.619 0.00 0.0 0.00 5.19 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
46 47 6.961359 ATAAGCCCAAAATTTTACTTTCGC 57.039 33.333 14.54 6.63 0.00 4.70
47 48 3.659786 AGCCCAAAATTTTACTTTCGCC 58.340 40.909 2.44 0.00 0.00 5.54
48 49 2.739913 GCCCAAAATTTTACTTTCGCCC 59.260 45.455 2.44 0.00 0.00 6.13
49 50 3.331150 CCCAAAATTTTACTTTCGCCCC 58.669 45.455 2.44 0.00 0.00 5.80
50 51 2.990514 CCAAAATTTTACTTTCGCCCCG 59.009 45.455 2.44 0.00 0.00 5.73
51 52 2.990514 CAAAATTTTACTTTCGCCCCGG 59.009 45.455 2.44 0.00 0.00 5.73
52 53 1.179152 AATTTTACTTTCGCCCCGGG 58.821 50.000 15.80 15.80 0.00 5.73
53 54 1.317431 ATTTTACTTTCGCCCCGGGC 61.317 55.000 19.64 19.64 46.75 6.13
62 63 4.777854 GCCCCGGGCCCTCAAAAT 62.778 66.667 22.43 0.00 44.06 1.82
63 64 2.442087 CCCCGGGCCCTCAAAATC 60.442 66.667 22.43 0.00 0.00 2.17
64 65 2.683475 CCCGGGCCCTCAAAATCT 59.317 61.111 22.43 0.00 0.00 2.40
65 66 1.000359 CCCGGGCCCTCAAAATCTT 60.000 57.895 22.43 0.00 0.00 2.40
66 67 0.257616 CCCGGGCCCTCAAAATCTTA 59.742 55.000 22.43 0.00 0.00 2.10
67 68 1.680338 CCGGGCCCTCAAAATCTTAG 58.320 55.000 22.43 0.00 0.00 2.18
68 69 1.680338 CGGGCCCTCAAAATCTTAGG 58.320 55.000 22.43 0.00 0.00 2.69
69 70 1.211949 CGGGCCCTCAAAATCTTAGGA 59.788 52.381 22.43 0.00 31.64 2.94
70 71 2.656002 GGGCCCTCAAAATCTTAGGAC 58.344 52.381 17.04 0.00 31.64 3.85
71 72 2.656002 GGCCCTCAAAATCTTAGGACC 58.344 52.381 0.00 0.00 31.64 4.46
72 73 2.289565 GCCCTCAAAATCTTAGGACCG 58.710 52.381 0.00 0.00 31.64 4.79
73 74 2.919228 CCCTCAAAATCTTAGGACCGG 58.081 52.381 0.00 0.00 31.64 5.28
74 75 2.289565 CCTCAAAATCTTAGGACCGGC 58.710 52.381 0.00 0.00 31.64 6.13
75 76 2.289565 CTCAAAATCTTAGGACCGGCC 58.710 52.381 0.00 3.58 0.00 6.13
76 77 1.064979 TCAAAATCTTAGGACCGGCCC 60.065 52.381 0.00 0.00 37.37 5.80
77 78 1.064685 CAAAATCTTAGGACCGGCCCT 60.065 52.381 15.88 15.88 40.29 5.19
78 79 0.546598 AAATCTTAGGACCGGCCCTG 59.453 55.000 21.23 3.27 37.10 4.45
97 98 4.770874 GCCGAACGCTGCCCCTTA 62.771 66.667 0.00 0.00 0.00 2.69
141 142 7.687941 ATGTATGTGTTTCTGGGTTTTAGAG 57.312 36.000 0.00 0.00 0.00 2.43
146 147 6.626302 TGTGTTTCTGGGTTTTAGAGTTTTG 58.374 36.000 0.00 0.00 0.00 2.44
148 149 7.094631 GTGTTTCTGGGTTTTAGAGTTTTGTT 58.905 34.615 0.00 0.00 0.00 2.83
150 151 5.845391 TCTGGGTTTTAGAGTTTTGTTGG 57.155 39.130 0.00 0.00 0.00 3.77
152 153 3.769844 TGGGTTTTAGAGTTTTGTTGGCA 59.230 39.130 0.00 0.00 0.00 4.92
157 158 7.186128 GGTTTTAGAGTTTTGTTGGCATTTTG 58.814 34.615 0.00 0.00 0.00 2.44
161 162 6.816134 AGAGTTTTGTTGGCATTTTGTTTT 57.184 29.167 0.00 0.00 0.00 2.43
199 203 9.744468 TTTCTAGGTTTTAAAGATTTCTTGTGC 57.256 29.630 0.00 0.00 36.12 4.57
200 204 7.581476 TCTAGGTTTTAAAGATTTCTTGTGCG 58.419 34.615 0.00 0.00 36.12 5.34
250 254 0.537143 TGCCGTGCTTCTTGTGGAAT 60.537 50.000 0.00 0.00 33.01 3.01
274 278 5.771469 CACATGTAGTGCTTTTGATGGAAA 58.229 37.500 0.00 0.00 42.15 3.13
275 279 6.215121 CACATGTAGTGCTTTTGATGGAAAA 58.785 36.000 0.00 0.00 42.15 2.29
286 290 7.109006 CTTTTGATGGAAAAGTTATGTGTGC 57.891 36.000 0.00 0.00 43.90 4.57
287 291 6.403866 TTTGATGGAAAAGTTATGTGTGCT 57.596 33.333 0.00 0.00 0.00 4.40
288 292 6.403866 TTGATGGAAAAGTTATGTGTGCTT 57.596 33.333 0.00 0.00 0.00 3.91
289 293 6.012658 TGATGGAAAAGTTATGTGTGCTTC 57.987 37.500 0.00 0.00 0.00 3.86
290 294 5.769662 TGATGGAAAAGTTATGTGTGCTTCT 59.230 36.000 0.00 0.00 0.00 2.85
291 295 5.689383 TGGAAAAGTTATGTGTGCTTCTC 57.311 39.130 0.00 0.00 0.00 2.87
292 296 4.213270 TGGAAAAGTTATGTGTGCTTCTCG 59.787 41.667 0.00 0.00 0.00 4.04
293 297 3.813529 AAAGTTATGTGTGCTTCTCGC 57.186 42.857 0.00 0.00 39.77 5.03
294 298 1.350193 AGTTATGTGTGCTTCTCGCG 58.650 50.000 0.00 0.00 43.27 5.87
295 299 1.067846 AGTTATGTGTGCTTCTCGCGA 60.068 47.619 9.26 9.26 43.27 5.87
296 300 1.724623 GTTATGTGTGCTTCTCGCGAA 59.275 47.619 11.33 0.00 43.27 4.70
297 301 2.073117 TATGTGTGCTTCTCGCGAAA 57.927 45.000 11.33 6.90 43.27 3.46
298 302 1.225855 ATGTGTGCTTCTCGCGAAAA 58.774 45.000 11.33 1.21 43.27 2.29
299 303 0.303493 TGTGTGCTTCTCGCGAAAAC 59.697 50.000 11.33 0.00 43.27 2.43
300 304 0.303493 GTGTGCTTCTCGCGAAAACA 59.697 50.000 11.33 7.55 43.27 2.83
301 305 1.010580 TGTGCTTCTCGCGAAAACAA 58.989 45.000 11.33 0.00 43.27 2.83
302 306 1.267832 TGTGCTTCTCGCGAAAACAAC 60.268 47.619 11.33 7.10 43.27 3.32
303 307 1.003866 GTGCTTCTCGCGAAAACAACT 60.004 47.619 11.33 0.00 43.27 3.16
304 308 1.668751 TGCTTCTCGCGAAAACAACTT 59.331 42.857 11.33 0.00 43.27 2.66
305 309 2.096819 TGCTTCTCGCGAAAACAACTTT 59.903 40.909 11.33 0.00 43.27 2.66
306 310 2.464016 GCTTCTCGCGAAAACAACTTTG 59.536 45.455 11.33 0.00 0.00 2.77
307 311 3.680789 CTTCTCGCGAAAACAACTTTGT 58.319 40.909 11.33 0.00 44.72 2.83
308 312 3.046285 TCTCGCGAAAACAACTTTGTG 57.954 42.857 11.33 0.00 41.31 3.33
309 313 1.512771 CTCGCGAAAACAACTTTGTGC 59.487 47.619 11.33 0.00 41.31 4.57
310 314 1.131504 TCGCGAAAACAACTTTGTGCT 59.868 42.857 6.20 0.00 41.31 4.40
311 315 2.352034 TCGCGAAAACAACTTTGTGCTA 59.648 40.909 6.20 0.00 41.31 3.49
312 316 3.102276 CGCGAAAACAACTTTGTGCTAA 58.898 40.909 0.00 0.00 41.31 3.09
313 317 3.177643 CGCGAAAACAACTTTGTGCTAAG 59.822 43.478 0.00 0.00 41.31 2.18
314 318 4.102649 GCGAAAACAACTTTGTGCTAAGT 58.897 39.130 0.00 0.00 41.31 2.24
315 319 4.027702 GCGAAAACAACTTTGTGCTAAGTG 60.028 41.667 0.00 0.00 41.31 3.16
316 320 5.092781 CGAAAACAACTTTGTGCTAAGTGT 58.907 37.500 0.00 0.00 41.31 3.55
317 321 6.252281 CGAAAACAACTTTGTGCTAAGTGTA 58.748 36.000 0.00 0.00 41.31 2.90
318 322 6.743627 CGAAAACAACTTTGTGCTAAGTGTAA 59.256 34.615 0.00 0.00 41.31 2.41
319 323 7.044966 CGAAAACAACTTTGTGCTAAGTGTAAG 60.045 37.037 0.00 0.00 41.31 2.34
320 324 5.169836 ACAACTTTGTGCTAAGTGTAAGC 57.830 39.130 0.00 0.00 40.49 3.09
338 342 2.945447 GCACATATTTGCTTCTGCCA 57.055 45.000 6.60 0.00 39.59 4.92
339 343 2.805845 GCACATATTTGCTTCTGCCAG 58.194 47.619 6.60 0.00 39.59 4.85
340 344 2.424601 GCACATATTTGCTTCTGCCAGA 59.575 45.455 6.60 0.00 39.59 3.86
341 345 3.119388 GCACATATTTGCTTCTGCCAGAA 60.119 43.478 7.00 7.00 39.59 3.02
378 382 3.727419 CCAAAGGCACTGCTTATGC 57.273 52.632 0.00 0.00 40.86 3.14
385 389 1.466360 GGCACTGCTTATGCTTTCACG 60.466 52.381 0.00 0.00 42.93 4.35
391 395 2.416547 TGCTTATGCTTTCACGAGAAGC 59.583 45.455 12.77 12.77 40.48 3.86
393 397 3.726190 GCTTATGCTTTCACGAGAAGCAC 60.726 47.826 20.64 9.49 39.18 4.40
395 399 1.882912 TGCTTTCACGAGAAGCACAT 58.117 45.000 16.57 0.00 34.92 3.21
410 414 3.056952 GCACATATTTGCTTCCACGAG 57.943 47.619 6.60 0.00 39.59 4.18
412 416 3.313526 GCACATATTTGCTTCCACGAGAT 59.686 43.478 6.60 0.00 39.59 2.75
420 424 1.599542 GCTTCCACGAGATGCATAACC 59.400 52.381 0.00 0.00 43.45 2.85
421 425 1.860950 CTTCCACGAGATGCATAACCG 59.139 52.381 0.00 6.24 0.00 4.44
423 427 0.930310 CCACGAGATGCATAACCGTG 59.070 55.000 27.13 27.13 46.83 4.94
427 431 1.258982 CGAGATGCATAACCGTGCTTC 59.741 52.381 0.00 6.65 45.27 3.86
493 498 6.817396 CACATCATGTGCTTTCAGAAAAATG 58.183 36.000 4.43 0.22 41.89 2.32
494 499 6.422701 CACATCATGTGCTTTCAGAAAAATGT 59.577 34.615 4.43 0.00 41.89 2.71
499 504 9.376075 TCATGTGCTTTCAGAAAAATGTAAAAA 57.624 25.926 0.00 0.00 0.00 1.94
501 506 7.969314 TGTGCTTTCAGAAAAATGTAAAAACC 58.031 30.769 0.00 0.00 0.00 3.27
502 507 7.116819 GTGCTTTCAGAAAAATGTAAAAACCG 58.883 34.615 0.00 0.00 0.00 4.44
518 527 7.762159 TGTAAAAACCGAAAGAAAGAAAAGCAT 59.238 29.630 0.00 0.00 0.00 3.79
520 529 4.918810 ACCGAAAGAAAGAAAAGCATGT 57.081 36.364 0.00 0.00 0.00 3.21
523 532 4.229876 CGAAAGAAAGAAAAGCATGTCCC 58.770 43.478 0.00 0.00 0.00 4.46
532 541 2.871096 AAGCATGTCCCGTCCTTTAA 57.129 45.000 0.00 0.00 0.00 1.52
553 568 1.460273 AAAACGCAACCATTCGGGCT 61.460 50.000 0.00 0.00 42.05 5.19
630 645 3.930229 TGTCAGATTTTCCGTGGTATTCG 59.070 43.478 0.00 0.00 0.00 3.34
706 721 8.693542 AAGTTCAGCAAAATCTATTAACATGC 57.306 30.769 0.00 0.00 0.00 4.06
725 740 6.219473 ACATGCGATCTAATTTCGAAGATCT 58.781 36.000 18.16 0.00 38.88 2.75
762 777 6.442952 TCAAATAATGAAAACAGTTCGGTGG 58.557 36.000 0.00 0.00 34.30 4.61
771 786 2.438411 ACAGTTCGGTGGTTTTTGACA 58.562 42.857 0.00 0.00 0.00 3.58
857 872 0.555769 AAAAAGGTGGAGTGGGCTGA 59.444 50.000 0.00 0.00 0.00 4.26
947 963 1.227089 CTTGGACCTCTCATCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
1323 1340 1.515954 CGCACCCGTCCTTCACTAT 59.484 57.895 0.00 0.00 0.00 2.12
1383 1417 2.634940 TGCTCACTCCTTGCTCTTACTT 59.365 45.455 0.00 0.00 0.00 2.24
1491 1525 8.084073 ACGGTATAATACGTAATGCAGTATTGT 58.916 33.333 15.62 12.56 41.80 2.71
1519 1553 4.767409 GGCTTACTCCATTATTCCATTCCC 59.233 45.833 0.00 0.00 0.00 3.97
1526 1560 7.947484 ACTCCATTATTCCATTCCCATATCAT 58.053 34.615 0.00 0.00 0.00 2.45
1590 1624 9.268282 CCTAATCCTACTTCCTTTATATGGCTA 57.732 37.037 0.00 0.00 0.00 3.93
1701 1735 4.519540 AAGAACAAACTGTGCTGTTGTT 57.480 36.364 11.86 9.85 34.45 2.83
1702 1736 3.836949 AGAACAAACTGTGCTGTTGTTG 58.163 40.909 11.76 0.00 34.21 3.33
1718 1752 6.416750 GCTGTTGTTGTCCTGTTTTTATACAC 59.583 38.462 0.00 0.00 0.00 2.90
1885 1919 1.217942 GGTTATCCCCCAATGAAGCCT 59.782 52.381 0.00 0.00 0.00 4.58
1912 1946 4.747810 AGCTCACAAAGGAAAACTTGTTG 58.252 39.130 0.00 0.00 39.96 3.33
1933 1967 1.327764 GCTGCTTTACATGGCGTAGAC 59.672 52.381 0.00 0.00 0.00 2.59
1960 1994 6.658816 TGGTGTATTTTGATGTTAGACTGCAT 59.341 34.615 0.00 0.00 0.00 3.96
1992 2026 3.544356 GCTTGTTGCAGAAGAGGTAAC 57.456 47.619 10.85 0.00 42.31 2.50
2004 2038 4.043435 AGAAGAGGTAACATTTTCCTGCCT 59.957 41.667 0.00 0.00 41.41 4.75
2126 2163 8.181573 TCAGAAACAAAAGTCTTGTGTTATGTC 58.818 33.333 19.36 13.92 34.46 3.06
2151 2188 0.317436 GTCGGCATGTCGCACAAAAA 60.317 50.000 16.44 0.00 45.17 1.94
2157 2194 2.155539 GCATGTCGCACAAAAATCAACC 59.844 45.455 0.00 0.00 41.79 3.77
2167 2204 5.408299 GCACAAAAATCAACCCATAACTTCC 59.592 40.000 0.00 0.00 0.00 3.46
2190 2227 7.725251 TCCTCTGTCTTAATGTTGCAATTTTT 58.275 30.769 0.59 0.00 0.00 1.94
2224 2262 6.994496 TCTTGTTTTCTCTCTCATCACATTGT 59.006 34.615 0.00 0.00 0.00 2.71
2235 2273 7.446319 TCTCTCATCACATTGTTGTTGAGATTT 59.554 33.333 17.08 0.00 43.60 2.17
2311 2349 0.164002 GGTCGACGCAGAGAAAAAGC 59.836 55.000 9.92 0.00 0.00 3.51
2445 2492 8.879759 ACATTATGTTGTATGCTGTAACTGTAC 58.120 33.333 0.00 0.00 0.00 2.90
2452 2499 1.887854 TGCTGTAACTGTACCTACGCA 59.112 47.619 0.00 2.25 0.00 5.24
2502 2550 6.382869 AGTCAAGGAGTTTGATGTTTTGAG 57.617 37.500 0.00 0.00 46.85 3.02
2580 2628 2.489329 TCATTTGAGCAGCAAGGCTTAC 59.511 45.455 0.00 0.00 45.99 2.34
3062 3111 0.682532 TTGTGGGTGTCTGCTTGCAA 60.683 50.000 0.00 0.00 0.00 4.08
3136 3185 2.595124 AACCTTGCAAAAAGGGTTCG 57.405 45.000 13.53 0.00 41.71 3.95
3233 3282 1.048601 AGTGTATATGGTGGAGCGGG 58.951 55.000 0.00 0.00 0.00 6.13
3362 3411 7.866729 TGTACATTTTCAGTTTTCGCTCATTA 58.133 30.769 0.00 0.00 0.00 1.90
3437 3486 7.246311 AGTAGCTCGTCATTTGAATTTGATTG 58.754 34.615 0.00 0.00 0.00 2.67
3580 3632 1.679153 ACAAAAGAATTGTTCCGCGGT 59.321 42.857 27.15 3.60 0.00 5.68
3622 3674 8.436046 TGACGTACCTTATTTGTTTGTAGTTT 57.564 30.769 0.00 0.00 0.00 2.66
3640 3692 5.959618 AGTTTTCAGGGTGTATTTGCTAC 57.040 39.130 0.00 0.00 0.00 3.58
3680 3732 4.233123 TGGACGCTAACTTATGATACCG 57.767 45.455 0.00 0.00 0.00 4.02
3781 3849 4.970662 TTTGAGAATAAGTGCAGATGGC 57.029 40.909 0.00 0.00 45.13 4.40
3809 3877 2.301870 TCGATGAGTGGCAGGTTACTTT 59.698 45.455 0.00 0.00 0.00 2.66
3883 3951 1.068127 GGTGATGCATTCATTGGAGCC 59.932 52.381 0.00 0.00 36.54 4.70
3986 4054 2.632512 GTGAGGCCCCTTTGATTGAAAA 59.367 45.455 0.00 0.00 0.00 2.29
3987 4055 3.261643 GTGAGGCCCCTTTGATTGAAAAT 59.738 43.478 0.00 0.00 0.00 1.82
4034 4104 6.148948 GCTAAACAACAGCAATATGTGTTCA 58.851 36.000 0.00 0.00 38.93 3.18
4044 4115 8.255206 ACAGCAATATGTGTTCATTTTCATCAT 58.745 29.630 0.00 0.00 35.70 2.45
4071 4142 6.040209 TGTTAGCGGGTCTTGTAATCTTTA 57.960 37.500 0.00 0.00 0.00 1.85
4072 4143 6.465948 TGTTAGCGGGTCTTGTAATCTTTAA 58.534 36.000 0.00 0.00 0.00 1.52
4073 4144 6.369615 TGTTAGCGGGTCTTGTAATCTTTAAC 59.630 38.462 0.00 0.00 0.00 2.01
4075 4146 3.063045 GCGGGTCTTGTAATCTTTAACCG 59.937 47.826 0.00 0.00 40.44 4.44
4083 4154 8.548721 GTCTTGTAATCTTTAACCGGACATATG 58.451 37.037 9.46 0.00 0.00 1.78
4157 4228 3.380004 TGTACTGCCAAAAGTGTTGAAGG 59.620 43.478 0.00 0.00 0.00 3.46
4175 4246 6.550938 TGAAGGTCTGATCATACTTGATGT 57.449 37.500 10.68 0.00 42.73 3.06
4199 4270 7.125811 TGTGGCAAAGAGTAAGGAATAGTAGAT 59.874 37.037 0.00 0.00 0.00 1.98
4204 4285 5.906254 AGAGTAAGGAATAGTAGATCCCCC 58.094 45.833 0.00 0.00 36.31 5.40
4231 4312 1.139989 CGCATACCTCGGTGCTATTG 58.860 55.000 0.00 0.00 39.16 1.90
4248 4645 9.289782 GGTGCTATTGTATCTGATTTCCTTATT 57.710 33.333 0.00 0.00 0.00 1.40
4349 4746 2.799017 TGAGCTGATTCATTGTGCCTT 58.201 42.857 0.00 0.00 0.00 4.35
4392 4789 3.538591 CATGCCAGTTGAGAAGATGCTA 58.461 45.455 0.00 0.00 0.00 3.49
4446 4845 7.306866 GCTGCATTTGACTACTACTAGTATTGC 60.307 40.741 2.33 1.03 32.96 3.56
4588 4988 4.279420 TGTCTCTCTAGTATCCGCGTACTA 59.721 45.833 13.90 13.90 36.39 1.82
4614 5015 4.702131 CCTCGGATCAATTTCTGTTTCCTT 59.298 41.667 0.00 0.00 0.00 3.36
4636 5037 2.118732 TCTGTGGCCGTGGACCTA 59.881 61.111 0.00 0.00 0.00 3.08
4644 5045 2.775384 TGGCCGTGGACCTAAATAATCT 59.225 45.455 0.00 0.00 0.00 2.40
4655 5056 6.205658 GGACCTAAATAATCTGATTCTGGTGC 59.794 42.308 6.10 10.06 31.05 5.01
4667 5068 2.584835 TCTGGTGCAGTAATGCCTTT 57.415 45.000 13.34 0.00 32.61 3.11
4678 5079 4.026052 AGTAATGCCTTTGGAAATCCTGG 58.974 43.478 0.44 2.27 36.82 4.45
4713 5114 3.914364 GTGAAAATTGTGGCAATCGAGAC 59.086 43.478 0.00 0.00 0.00 3.36
4779 5180 6.163135 ACTCATAGTGGCTTCCATAACTAC 57.837 41.667 0.00 0.00 35.28 2.73
4799 5200 3.041946 ACCTCCTGGTATGATGAAGTCC 58.958 50.000 0.00 0.00 46.43 3.85
4864 5265 2.671396 CCCAGAAACGGTAGAACAATCG 59.329 50.000 0.00 0.00 0.00 3.34
4917 5355 4.332428 ACTACCTCAGTTGCTAAAACGT 57.668 40.909 0.00 0.00 31.59 3.99
4921 5359 3.746492 ACCTCAGTTGCTAAAACGTCATC 59.254 43.478 0.00 0.00 0.00 2.92
4929 5367 8.817100 CAGTTGCTAAAACGTCATCTATTATGA 58.183 33.333 0.00 0.00 0.00 2.15
4939 5377 8.815565 ACGTCATCTATTATGATATGGAGAGT 57.184 34.615 0.00 0.00 0.00 3.24
4940 5378 9.907229 ACGTCATCTATTATGATATGGAGAGTA 57.093 33.333 0.00 0.00 0.00 2.59
4956 5403 5.125417 TGGAGAGTATATGCAAAAGCCAAAC 59.875 40.000 0.00 0.00 0.00 2.93
4964 5411 3.589988 TGCAAAAGCCAAACGAAAGAAA 58.410 36.364 0.00 0.00 0.00 2.52
5024 5486 2.037901 TCCAATGCCAGTTCTTGCAAA 58.962 42.857 0.00 0.00 41.50 3.68
5025 5487 2.137523 CCAATGCCAGTTCTTGCAAAC 58.862 47.619 0.00 0.00 41.50 2.93
5026 5488 2.483363 CCAATGCCAGTTCTTGCAAACA 60.483 45.455 0.00 0.00 41.50 2.83
5027 5489 2.514205 ATGCCAGTTCTTGCAAACAC 57.486 45.000 0.00 0.00 41.50 3.32
5028 5490 0.459489 TGCCAGTTCTTGCAAACACC 59.541 50.000 0.00 0.00 33.87 4.16
5029 5491 0.459489 GCCAGTTCTTGCAAACACCA 59.541 50.000 0.00 0.00 0.00 4.17
5030 5492 1.069049 GCCAGTTCTTGCAAACACCAT 59.931 47.619 0.00 0.00 0.00 3.55
5031 5493 2.746269 CCAGTTCTTGCAAACACCATG 58.254 47.619 0.00 0.00 0.00 3.66
5032 5494 2.361757 CCAGTTCTTGCAAACACCATGA 59.638 45.455 0.00 0.00 0.00 3.07
5033 5495 3.006110 CCAGTTCTTGCAAACACCATGAT 59.994 43.478 0.00 0.00 0.00 2.45
5034 5496 4.501915 CCAGTTCTTGCAAACACCATGATT 60.502 41.667 0.00 0.00 0.00 2.57
5035 5497 5.278907 CCAGTTCTTGCAAACACCATGATTA 60.279 40.000 0.00 0.00 0.00 1.75
5036 5498 6.215121 CAGTTCTTGCAAACACCATGATTAA 58.785 36.000 0.00 0.00 0.00 1.40
5037 5499 6.700960 CAGTTCTTGCAAACACCATGATTAAA 59.299 34.615 0.00 0.00 0.00 1.52
5038 5500 7.224362 CAGTTCTTGCAAACACCATGATTAAAA 59.776 33.333 0.00 0.00 0.00 1.52
5083 5545 5.710099 TGGGCTGTAATCCACTCTTTAAAAG 59.290 40.000 0.00 0.00 0.00 2.27
5139 5601 8.617809 GTGAGAAGTAGTAGATCTTGTCTAAGG 58.382 40.741 0.00 0.00 41.00 2.69
5241 5705 8.709272 TCCCATGATGATGATTATTAAAGCAA 57.291 30.769 0.00 0.00 34.09 3.91
5312 5776 7.576861 AGAAGTTAGAGTGAGTATAAGAGGC 57.423 40.000 0.00 0.00 0.00 4.70
5319 5783 3.631227 AGTGAGTATAAGAGGCGGTACAC 59.369 47.826 0.00 0.00 0.00 2.90
5333 5797 2.014128 GGTACACCACATGGCACATAC 58.986 52.381 0.00 0.00 38.71 2.39
5348 5844 2.615447 CACATACGCAAGAGGCATGAAT 59.385 45.455 0.00 0.00 45.17 2.57
5394 5890 3.149196 GAGATGCTCAACCCAAACAGAA 58.851 45.455 0.00 0.00 0.00 3.02
5401 5897 4.620567 GCTCAACCCAAACAGAACAAAACT 60.621 41.667 0.00 0.00 0.00 2.66
5402 5898 5.393678 GCTCAACCCAAACAGAACAAAACTA 60.394 40.000 0.00 0.00 0.00 2.24
5421 5917 6.655078 AACTAAACTAAACTCACCGTCCTA 57.345 37.500 0.00 0.00 0.00 2.94
5443 6681 2.771372 AGAAGCAACCCAAACCAACAAT 59.229 40.909 0.00 0.00 0.00 2.71
5460 6698 7.159372 ACCAACAATTAGACGACTAACATCTT 58.841 34.615 9.49 0.00 40.71 2.40
5467 6705 9.877178 AATTAGACGACTAACATCTTCAAATCT 57.123 29.630 9.49 0.00 40.71 2.40
5492 6730 1.302511 AAGGACGCCACGAGCAAAT 60.303 52.632 0.00 0.00 44.04 2.32
5494 6732 0.036765 AGGACGCCACGAGCAAATAA 60.037 50.000 0.00 0.00 44.04 1.40
5547 6785 2.158871 TGAAGGCGTTGTCCTGTTTAGT 60.159 45.455 0.00 0.00 36.38 2.24
5549 6787 2.927028 AGGCGTTGTCCTGTTTAGTTT 58.073 42.857 0.00 0.00 34.56 2.66
5567 6805 3.811497 AGTTTAACACAGGTAAACTCGCC 59.189 43.478 12.96 0.00 39.08 5.54
5568 6806 3.472283 TTAACACAGGTAAACTCGCCA 57.528 42.857 0.00 0.00 0.00 5.69
5569 6807 2.561478 AACACAGGTAAACTCGCCAT 57.439 45.000 0.00 0.00 0.00 4.40
5570 6808 3.688694 AACACAGGTAAACTCGCCATA 57.311 42.857 0.00 0.00 0.00 2.74
5571 6809 3.688694 ACACAGGTAAACTCGCCATAA 57.311 42.857 0.00 0.00 0.00 1.90
5572 6810 4.216411 ACACAGGTAAACTCGCCATAAT 57.784 40.909 0.00 0.00 0.00 1.28
5573 6811 4.585879 ACACAGGTAAACTCGCCATAATT 58.414 39.130 0.00 0.00 0.00 1.40
5574 6812 4.394920 ACACAGGTAAACTCGCCATAATTG 59.605 41.667 0.00 0.00 0.00 2.32
5575 6813 4.634004 CACAGGTAAACTCGCCATAATTGA 59.366 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.927721 GCGAAAGTAAAATTTTGGGCTTATTAA 58.072 29.630 13.76 0.00 0.00 1.40
21 22 7.546316 GGCGAAAGTAAAATTTTGGGCTTATTA 59.454 33.333 13.76 0.00 36.40 0.98
22 23 6.370442 GGCGAAAGTAAAATTTTGGGCTTATT 59.630 34.615 13.76 2.21 36.40 1.40
23 24 5.872617 GGCGAAAGTAAAATTTTGGGCTTAT 59.127 36.000 13.76 6.46 36.40 1.73
24 25 5.231702 GGCGAAAGTAAAATTTTGGGCTTA 58.768 37.500 13.76 0.00 36.40 3.09
25 26 4.062293 GGCGAAAGTAAAATTTTGGGCTT 58.938 39.130 13.76 11.35 36.40 4.35
26 27 3.556213 GGGCGAAAGTAAAATTTTGGGCT 60.556 43.478 13.76 6.23 38.34 5.19
27 28 2.739913 GGGCGAAAGTAAAATTTTGGGC 59.260 45.455 13.76 7.25 37.83 5.36
28 29 3.331150 GGGGCGAAAGTAAAATTTTGGG 58.669 45.455 13.76 0.00 0.00 4.12
29 30 2.990514 CGGGGCGAAAGTAAAATTTTGG 59.009 45.455 13.76 0.00 0.00 3.28
30 31 2.990514 CCGGGGCGAAAGTAAAATTTTG 59.009 45.455 13.76 0.00 0.00 2.44
31 32 2.028839 CCCGGGGCGAAAGTAAAATTTT 60.029 45.455 14.71 8.75 0.00 1.82
32 33 1.546923 CCCGGGGCGAAAGTAAAATTT 59.453 47.619 14.71 0.00 0.00 1.82
33 34 1.179152 CCCGGGGCGAAAGTAAAATT 58.821 50.000 14.71 0.00 0.00 1.82
34 35 1.317431 GCCCGGGGCGAAAGTAAAAT 61.317 55.000 24.63 0.00 39.62 1.82
35 36 1.972752 GCCCGGGGCGAAAGTAAAA 60.973 57.895 24.63 0.00 39.62 1.52
36 37 2.360225 GCCCGGGGCGAAAGTAAA 60.360 61.111 24.63 0.00 39.62 2.01
46 47 2.442087 GATTTTGAGGGCCCGGGG 60.442 66.667 25.28 9.31 0.00 5.73
47 48 0.257616 TAAGATTTTGAGGGCCCGGG 59.742 55.000 19.09 19.09 0.00 5.73
48 49 1.680338 CTAAGATTTTGAGGGCCCGG 58.320 55.000 18.44 0.00 0.00 5.73
49 50 1.211949 TCCTAAGATTTTGAGGGCCCG 59.788 52.381 18.44 0.00 0.00 6.13
50 51 2.656002 GTCCTAAGATTTTGAGGGCCC 58.344 52.381 16.46 16.46 0.00 5.80
52 53 2.289565 CGGTCCTAAGATTTTGAGGGC 58.710 52.381 0.00 0.00 34.00 5.19
53 54 2.919228 CCGGTCCTAAGATTTTGAGGG 58.081 52.381 0.00 0.00 0.00 4.30
54 55 2.289565 GCCGGTCCTAAGATTTTGAGG 58.710 52.381 1.90 0.00 0.00 3.86
55 56 2.289565 GGCCGGTCCTAAGATTTTGAG 58.710 52.381 1.90 0.00 0.00 3.02
56 57 1.064979 GGGCCGGTCCTAAGATTTTGA 60.065 52.381 20.78 0.00 34.39 2.69
57 58 1.064685 AGGGCCGGTCCTAAGATTTTG 60.065 52.381 30.70 0.00 34.92 2.44
58 59 1.064685 CAGGGCCGGTCCTAAGATTTT 60.065 52.381 31.20 0.00 34.92 1.82
59 60 0.546598 CAGGGCCGGTCCTAAGATTT 59.453 55.000 31.20 0.00 34.92 2.17
60 61 0.620700 ACAGGGCCGGTCCTAAGATT 60.621 55.000 31.20 6.93 34.92 2.40
61 62 1.003051 ACAGGGCCGGTCCTAAGAT 59.997 57.895 31.20 11.24 34.92 2.40
62 63 1.987855 CACAGGGCCGGTCCTAAGA 60.988 63.158 31.20 0.00 34.92 2.10
63 64 2.584608 CACAGGGCCGGTCCTAAG 59.415 66.667 31.20 20.02 34.92 2.18
64 65 3.712907 GCACAGGGCCGGTCCTAA 61.713 66.667 31.20 0.00 34.92 2.69
84 85 4.278310 AGATAAAATTAAGGGGCAGCGTT 58.722 39.130 0.00 0.00 0.00 4.84
87 88 9.613428 AATAAAAAGATAAAATTAAGGGGCAGC 57.387 29.630 0.00 0.00 0.00 5.25
117 118 7.231467 ACTCTAAAACCCAGAAACACATACAT 58.769 34.615 0.00 0.00 0.00 2.29
120 121 8.410141 CAAAACTCTAAAACCCAGAAACACATA 58.590 33.333 0.00 0.00 0.00 2.29
123 124 6.627243 ACAAAACTCTAAAACCCAGAAACAC 58.373 36.000 0.00 0.00 0.00 3.32
125 126 6.533723 CCAACAAAACTCTAAAACCCAGAAAC 59.466 38.462 0.00 0.00 0.00 2.78
126 127 6.635755 CCAACAAAACTCTAAAACCCAGAAA 58.364 36.000 0.00 0.00 0.00 2.52
127 128 5.394773 GCCAACAAAACTCTAAAACCCAGAA 60.395 40.000 0.00 0.00 0.00 3.02
128 129 4.098807 GCCAACAAAACTCTAAAACCCAGA 59.901 41.667 0.00 0.00 0.00 3.86
129 130 4.142049 TGCCAACAAAACTCTAAAACCCAG 60.142 41.667 0.00 0.00 0.00 4.45
130 131 3.769844 TGCCAACAAAACTCTAAAACCCA 59.230 39.130 0.00 0.00 0.00 4.51
185 189 3.988379 TGCTTCGCACAAGAAATCTTT 57.012 38.095 0.00 0.00 30.70 2.52
233 237 1.522668 TGATTCCACAAGAAGCACGG 58.477 50.000 0.00 0.00 45.68 4.94
250 254 7.735215 CTTTTCCATCAAAAGCACTACATGTGA 60.735 37.037 9.11 0.00 43.88 3.58
267 271 6.259550 AGAAGCACACATAACTTTTCCATC 57.740 37.500 0.00 0.00 0.00 3.51
268 272 5.106555 CGAGAAGCACACATAACTTTTCCAT 60.107 40.000 0.00 0.00 0.00 3.41
269 273 4.213270 CGAGAAGCACACATAACTTTTCCA 59.787 41.667 0.00 0.00 0.00 3.53
270 274 4.712763 CGAGAAGCACACATAACTTTTCC 58.287 43.478 0.00 0.00 0.00 3.13
272 276 6.981210 TTCGCGAGAAGCACACATAACTTTT 61.981 40.000 9.59 0.00 46.92 2.27
274 278 4.105367 TTCGCGAGAAGCACACATAACTT 61.105 43.478 9.59 0.00 46.92 2.66
275 279 2.609491 TTCGCGAGAAGCACACATAACT 60.609 45.455 9.59 0.00 46.92 2.24
276 280 1.724623 TTCGCGAGAAGCACACATAAC 59.275 47.619 9.59 0.00 46.92 1.89
278 282 3.804601 TTCGCGAGAAGCACACATA 57.195 47.368 9.59 0.00 46.92 2.29
279 283 4.673403 TTCGCGAGAAGCACACAT 57.327 50.000 9.59 0.00 46.92 3.21
284 288 6.436671 ACAAAGTTGTTTTCGCGAGAAGCA 62.437 41.667 12.89 13.21 41.36 3.91
285 289 4.029547 ACAAAGTTGTTTTCGCGAGAAGC 61.030 43.478 12.89 10.90 41.36 3.86
286 290 3.478516 CACAAAGTTGTTTTCGCGAGAAG 59.521 43.478 12.89 1.79 45.26 2.85
287 291 3.421741 CACAAAGTTGTTTTCGCGAGAA 58.578 40.909 9.59 8.82 43.87 2.87
288 292 2.789779 GCACAAAGTTGTTTTCGCGAGA 60.790 45.455 9.59 0.43 39.91 4.04
289 293 1.512771 GCACAAAGTTGTTTTCGCGAG 59.487 47.619 9.59 0.00 39.91 5.03
290 294 1.131504 AGCACAAAGTTGTTTTCGCGA 59.868 42.857 3.71 3.71 39.91 5.87
291 295 1.544686 AGCACAAAGTTGTTTTCGCG 58.455 45.000 0.00 0.00 39.91 5.87
292 296 4.027702 CACTTAGCACAAAGTTGTTTTCGC 60.028 41.667 0.00 0.00 39.91 4.70
293 297 5.092781 ACACTTAGCACAAAGTTGTTTTCG 58.907 37.500 0.00 0.00 39.91 3.46
294 298 7.253651 GCTTACACTTAGCACAAAGTTGTTTTC 60.254 37.037 0.00 0.00 39.91 2.29
295 299 6.530181 GCTTACACTTAGCACAAAGTTGTTTT 59.470 34.615 0.00 0.00 39.91 2.43
296 300 6.033966 GCTTACACTTAGCACAAAGTTGTTT 58.966 36.000 0.00 0.00 39.91 2.83
297 301 5.124776 TGCTTACACTTAGCACAAAGTTGTT 59.875 36.000 0.00 0.00 43.30 2.83
298 302 4.638421 TGCTTACACTTAGCACAAAGTTGT 59.362 37.500 0.00 0.00 43.30 3.32
299 303 5.168526 TGCTTACACTTAGCACAAAGTTG 57.831 39.130 0.00 0.00 43.30 3.16
319 323 2.424601 TCTGGCAGAAGCAAATATGTGC 59.575 45.455 16.28 10.09 44.61 4.57
320 324 4.669318 CTTCTGGCAGAAGCAAATATGTG 58.331 43.478 36.36 15.93 44.35 3.21
321 325 4.978083 CTTCTGGCAGAAGCAAATATGT 57.022 40.909 36.36 0.00 44.35 2.29
358 362 3.751627 GCATAAGCAGTGCCTTTGGCC 62.752 57.143 12.58 0.00 44.38 5.36
360 364 1.180029 AGCATAAGCAGTGCCTTTGG 58.820 50.000 12.58 0.00 45.49 3.28
361 365 3.248266 GAAAGCATAAGCAGTGCCTTTG 58.752 45.455 17.51 9.79 45.49 2.77
371 375 2.416547 TGCTTCTCGTGAAAGCATAAGC 59.583 45.455 14.66 7.64 38.61 3.09
372 376 3.433274 TGTGCTTCTCGTGAAAGCATAAG 59.567 43.478 19.25 1.59 38.02 1.73
378 382 4.790140 GCAAATATGTGCTTCTCGTGAAAG 59.210 41.667 10.84 0.00 41.51 2.62
391 395 4.787563 GCATCTCGTGGAAGCAAATATGTG 60.788 45.833 0.00 0.00 38.39 3.21
393 397 3.313249 TGCATCTCGTGGAAGCAAATATG 59.687 43.478 8.12 0.00 44.19 1.78
395 399 2.984562 TGCATCTCGTGGAAGCAAATA 58.015 42.857 8.12 0.00 44.19 1.40
473 478 8.939201 TTTTACATTTTTCTGAAAGCACATGA 57.061 26.923 0.00 0.00 0.00 3.07
492 497 7.091443 TGCTTTTCTTTCTTTCGGTTTTTACA 58.909 30.769 0.00 0.00 0.00 2.41
493 498 7.514573 TGCTTTTCTTTCTTTCGGTTTTTAC 57.485 32.000 0.00 0.00 0.00 2.01
494 499 7.762159 ACATGCTTTTCTTTCTTTCGGTTTTTA 59.238 29.630 0.00 0.00 0.00 1.52
499 504 4.261614 GGACATGCTTTTCTTTCTTTCGGT 60.262 41.667 0.00 0.00 0.00 4.69
501 506 4.229876 GGGACATGCTTTTCTTTCTTTCG 58.770 43.478 0.00 0.00 0.00 3.46
502 507 4.229876 CGGGACATGCTTTTCTTTCTTTC 58.770 43.478 0.00 0.00 0.00 2.62
538 547 1.656818 ATTCAGCCCGAATGGTTGCG 61.657 55.000 0.00 0.00 44.54 4.85
539 548 0.532115 AATTCAGCCCGAATGGTTGC 59.468 50.000 0.01 0.00 43.83 4.17
609 624 3.930848 ACGAATACCACGGAAAATCTGAC 59.069 43.478 0.00 0.00 34.93 3.51
610 625 4.196626 ACGAATACCACGGAAAATCTGA 57.803 40.909 0.00 0.00 34.93 3.27
611 626 4.939509 AACGAATACCACGGAAAATCTG 57.060 40.909 0.00 0.00 34.93 2.90
694 709 9.471084 TTCGAAATTAGATCGCATGTTAATAGA 57.529 29.630 0.00 0.00 40.04 1.98
725 740 6.415798 TCATTATTTGATTTCTCGCGTTGA 57.584 33.333 5.77 2.87 0.00 3.18
740 755 6.399639 ACCACCGAACTGTTTTCATTATTT 57.600 33.333 0.00 0.00 0.00 1.40
743 758 5.838531 AAACCACCGAACTGTTTTCATTA 57.161 34.783 0.00 0.00 0.00 1.90
820 835 2.680974 TTTGGCGCTGAAGCTGGAGT 62.681 55.000 7.64 0.00 39.32 3.85
857 872 0.918983 ATCACATGGATTCACCGGGT 59.081 50.000 6.32 0.00 42.61 5.28
985 1002 6.525355 GCGTCAGCATTATTTTTCTTTTTCC 58.475 36.000 0.00 0.00 44.35 3.13
1323 1340 3.438183 GAAGGAACTAGGTAGGTGGTGA 58.562 50.000 0.00 0.00 38.49 4.02
1383 1417 0.824109 CATTGGACGCCTACTCCAGA 59.176 55.000 0.00 0.00 39.06 3.86
1418 1452 2.039480 TCTTGCAGCTCCTTGAGAATGT 59.961 45.455 0.00 0.00 0.00 2.71
1478 1512 8.746052 AGTAAGCCAATTACAATACTGCATTA 57.254 30.769 0.00 0.00 45.34 1.90
1491 1525 9.077885 GAATGGAATAATGGAGTAAGCCAATTA 57.922 33.333 0.00 0.00 42.16 1.40
1497 1531 5.385198 TGGGAATGGAATAATGGAGTAAGC 58.615 41.667 0.00 0.00 0.00 3.09
1526 1560 5.125417 GCTGCTATGATAAAACAAAGGACCA 59.875 40.000 0.00 0.00 0.00 4.02
1533 1567 5.840243 ATGCTGCTGCTATGATAAAACAA 57.160 34.783 17.00 0.00 40.48 2.83
1590 1624 9.244292 TGCTATCTGGAGTACGAAGATATATTT 57.756 33.333 12.62 0.00 33.57 1.40
1591 1625 8.809468 TGCTATCTGGAGTACGAAGATATATT 57.191 34.615 12.62 0.00 33.57 1.28
1592 1626 8.268605 TCTGCTATCTGGAGTACGAAGATATAT 58.731 37.037 12.62 0.00 33.57 0.86
1593 1627 7.621796 TCTGCTATCTGGAGTACGAAGATATA 58.378 38.462 12.62 7.18 33.57 0.86
1602 1636 2.564947 CCCCATCTGCTATCTGGAGTAC 59.435 54.545 0.00 0.00 35.48 2.73
1634 1668 8.239314 TGGTTATCGACGATTATATAGGTGAAC 58.761 37.037 16.73 9.58 0.00 3.18
1678 1712 4.236935 ACAACAGCACAGTTTGTTCTTTG 58.763 39.130 0.00 0.00 35.46 2.77
1701 1735 6.460781 AGATCACGTGTATAAAAACAGGACA 58.539 36.000 16.51 0.00 38.35 4.02
1702 1736 6.963049 AGATCACGTGTATAAAAACAGGAC 57.037 37.500 16.51 0.00 38.35 3.85
1718 1752 5.524284 AGGAATACGAGAATGAAGATCACG 58.476 41.667 0.00 0.00 37.01 4.35
1885 1919 3.117888 AGTTTTCCTTTGTGAGCTCCTCA 60.118 43.478 12.15 7.94 38.25 3.86
1912 1946 0.657840 CTACGCCATGTAAAGCAGCC 59.342 55.000 0.00 0.00 31.20 4.85
1933 1967 6.968904 GCAGTCTAACATCAAAATACACCATG 59.031 38.462 0.00 0.00 0.00 3.66
1960 1994 1.066002 GCAACAAGCAAAGCAGTCTCA 59.934 47.619 0.00 0.00 44.79 3.27
1992 2026 5.389859 TGTTATGTTGAGGCAGGAAAATG 57.610 39.130 0.00 0.00 0.00 2.32
2126 2163 1.349627 GCGACATGCCGACATTCAG 59.650 57.895 5.30 0.00 37.76 3.02
2151 2188 4.785376 AGACAGAGGAAGTTATGGGTTGAT 59.215 41.667 0.00 0.00 0.00 2.57
2157 2194 7.414540 GCAACATTAAGACAGAGGAAGTTATGG 60.415 40.741 0.00 0.00 0.00 2.74
2190 2227 8.335532 TGAGAGAGAAAACAAGAACAGAAAAA 57.664 30.769 0.00 0.00 0.00 1.94
2204 2241 7.282901 TCAACAACAATGTGATGAGAGAGAAAA 59.717 33.333 0.00 0.00 40.46 2.29
2224 2262 8.673711 CCCATAAACGAAGATAAATCTCAACAA 58.326 33.333 0.00 0.00 35.76 2.83
2235 2273 7.073457 TGGATTGATCCCATAAACGAAGATA 57.927 36.000 7.53 0.00 46.59 1.98
2311 2349 1.056700 AGGTCATCCAATCCCTCCCG 61.057 60.000 0.00 0.00 35.89 5.14
2389 2427 4.552184 GCTTACTCTGTTGTCGTTGGAAAC 60.552 45.833 0.00 0.00 45.31 2.78
2502 2550 6.749923 ACAAAAGATATCCACAGAAGCTTC 57.250 37.500 19.11 19.11 0.00 3.86
2538 2586 9.643693 AAATGACTTTAATCAATTGTGCTAAGG 57.356 29.630 5.13 5.23 30.82 2.69
2557 2605 0.886563 GCCTTGCTGCTCAAATGACT 59.113 50.000 0.00 0.00 33.65 3.41
2580 2628 4.334759 CAGATGCTGAACAAGGTGATTAGG 59.665 45.833 0.00 0.00 32.44 2.69
2594 2642 3.609256 ACTAGGGATCTCAGATGCTGA 57.391 47.619 6.09 0.00 38.25 4.26
2638 2686 4.397417 CAGGCCTGCATATTAAGATTAGGC 59.603 45.833 22.33 19.71 46.37 3.93
3233 3282 2.237392 ACTGTCTTTGATAGTCCAGGCC 59.763 50.000 0.00 0.00 27.99 5.19
3362 3411 4.128925 TCGTGCAATCAGATAAGCTTCT 57.871 40.909 0.00 0.00 0.00 2.85
3622 3674 4.650972 AAGGTAGCAAATACACCCTGAA 57.349 40.909 0.00 0.00 35.96 3.02
3680 3732 6.856895 AGCTGGATTTATAAAAGAAGCACAC 58.143 36.000 21.62 2.77 31.85 3.82
3729 3781 5.964758 ACAGAAGCAGACAAATGAAAAACA 58.035 33.333 0.00 0.00 0.00 2.83
3781 3849 2.456119 GCCACTCATCGAGCCAACG 61.456 63.158 0.00 0.00 32.04 4.10
3832 3900 7.140705 CAGTTGTATCTATGAGCTCTTCAGAG 58.859 42.308 16.19 2.31 44.69 3.35
3920 3988 5.596763 ACTACCCTTACCATCCAGAAGTTA 58.403 41.667 0.00 0.00 0.00 2.24
3921 3989 4.436079 ACTACCCTTACCATCCAGAAGTT 58.564 43.478 0.00 0.00 0.00 2.66
4011 4081 8.746922 AATGAACACATATTGCTGTTGTTTAG 57.253 30.769 0.00 0.00 30.59 1.85
4020 4090 9.661563 AAATGATGAAAATGAACACATATTGCT 57.338 25.926 0.00 0.00 0.00 3.91
4034 4104 7.285401 AGACCCGCTAACATAAATGATGAAAAT 59.715 33.333 0.00 0.00 39.06 1.82
4044 4115 6.646267 AGATTACAAGACCCGCTAACATAAA 58.354 36.000 0.00 0.00 0.00 1.40
4047 4118 4.755266 AGATTACAAGACCCGCTAACAT 57.245 40.909 0.00 0.00 0.00 2.71
4054 4125 3.619929 CCGGTTAAAGATTACAAGACCCG 59.380 47.826 0.00 0.00 0.00 5.28
4071 4142 2.775351 CCGCAACATATGTCCGGTT 58.225 52.632 27.14 5.64 34.56 4.44
4072 4143 1.600107 ACCGCAACATATGTCCGGT 59.400 52.632 31.68 31.68 46.37 5.28
4073 4144 1.942677 TTACCGCAACATATGTCCGG 58.057 50.000 30.73 30.73 44.19 5.14
4075 4146 2.931325 TCGTTTACCGCAACATATGTCC 59.069 45.455 9.23 2.68 36.19 4.02
4083 4154 3.479933 GCGTATCGTTTACCGCAAC 57.520 52.632 0.00 0.00 45.12 4.17
4095 4166 3.338249 ACATGGCATATGGAAGCGTATC 58.662 45.455 0.00 0.00 0.00 2.24
4157 4228 4.445453 TGCCACATCAAGTATGATCAGAC 58.555 43.478 12.62 12.62 44.53 3.51
4175 4246 7.202011 GGATCTACTATTCCTTACTCTTTGCCA 60.202 40.741 0.00 0.00 0.00 4.92
4248 4645 8.733458 CCAGTTCAAAATCTCAAAGACATATGA 58.267 33.333 10.38 0.00 0.00 2.15
4299 4696 0.244721 CTCAGCGGTCATCAGTCACA 59.755 55.000 0.00 0.00 0.00 3.58
4349 4746 3.129638 GCCGGTGCATAAACCTAATCAAA 59.870 43.478 1.90 0.00 38.14 2.69
4392 4789 1.447317 CCACTTGTGCTGCGAAAGGT 61.447 55.000 15.69 0.00 0.00 3.50
4446 4845 3.796178 CCATTTCATTTTCGCCCGTAATG 59.204 43.478 10.00 10.00 0.00 1.90
4588 4988 1.561542 ACAGAAATTGATCCGAGGGCT 59.438 47.619 0.00 0.00 0.00 5.19
4614 5015 4.624364 CCACGGCCACAGACAGCA 62.624 66.667 2.24 0.00 0.00 4.41
4636 5037 8.627403 CATTACTGCACCAGAATCAGATTATTT 58.373 33.333 0.00 0.00 35.18 1.40
4655 5056 4.142093 CCAGGATTTCCAAAGGCATTACTG 60.142 45.833 0.00 0.00 38.89 2.74
4667 5068 2.014010 AAAGCAAGCCAGGATTTCCA 57.986 45.000 0.00 0.00 38.89 3.53
4678 5079 6.852345 CCACAATTTTCACAATAAAAGCAAGC 59.148 34.615 0.00 0.00 32.20 4.01
4713 5114 8.802267 TGAAGAAAAATGTATCCCCTTGTAAAG 58.198 33.333 0.00 0.00 45.69 1.85
4779 5180 2.370189 GGGACTTCATCATACCAGGAGG 59.630 54.545 0.00 0.00 42.21 4.30
4944 5382 4.591998 TTTTCTTTCGTTTGGCTTTTGC 57.408 36.364 0.00 0.00 46.64 3.68
4998 5445 1.565759 AGAACTGGCATTGGATAGGCA 59.434 47.619 0.00 0.00 38.67 4.75
5024 5486 6.777580 AGACCAAGTCTTTTTAATCATGGTGT 59.222 34.615 0.00 0.00 40.28 4.16
5025 5487 7.040478 TGAGACCAAGTCTTTTTAATCATGGTG 60.040 37.037 0.00 0.00 43.53 4.17
5026 5488 7.004086 TGAGACCAAGTCTTTTTAATCATGGT 58.996 34.615 0.00 0.00 43.53 3.55
5027 5489 7.452880 TGAGACCAAGTCTTTTTAATCATGG 57.547 36.000 0.00 0.00 43.53 3.66
5028 5490 8.571336 AGTTGAGACCAAGTCTTTTTAATCATG 58.429 33.333 0.00 0.00 43.53 3.07
5029 5491 8.697507 AGTTGAGACCAAGTCTTTTTAATCAT 57.302 30.769 0.00 0.00 43.53 2.45
5030 5492 9.621629 TTAGTTGAGACCAAGTCTTTTTAATCA 57.378 29.630 0.00 0.00 43.53 2.57
5035 5497 9.014297 CCATATTAGTTGAGACCAAGTCTTTTT 57.986 33.333 0.00 0.00 43.53 1.94
5036 5498 7.611855 CCCATATTAGTTGAGACCAAGTCTTTT 59.388 37.037 0.00 0.00 43.53 2.27
5037 5499 7.112779 CCCATATTAGTTGAGACCAAGTCTTT 58.887 38.462 0.00 0.00 43.53 2.52
5038 5500 6.653989 CCCATATTAGTTGAGACCAAGTCTT 58.346 40.000 0.00 0.00 43.53 3.01
5083 5545 2.749280 AAGCCTAAATTTGCAGGTGC 57.251 45.000 8.48 0.00 42.50 5.01
5139 5601 2.550830 TGAACTCTTGGTGCTTCTCC 57.449 50.000 0.00 0.00 0.00 3.71
5184 5646 3.385314 TTGGATGCAAGGAATGGATGA 57.615 42.857 0.00 0.00 40.61 2.92
5312 5776 0.676466 ATGTGCCATGTGGTGTACCG 60.676 55.000 0.35 0.00 39.43 4.02
5319 5783 0.099259 CTTGCGTATGTGCCATGTGG 59.901 55.000 0.00 0.00 38.53 4.17
5333 5797 3.669824 GCATCATATTCATGCCTCTTGCG 60.670 47.826 5.40 0.00 45.60 4.85
5356 5852 4.735985 CATCTCATATCTCTCTGCTTCGG 58.264 47.826 0.00 0.00 0.00 4.30
5370 5866 4.019411 TCTGTTTGGGTTGAGCATCTCATA 60.019 41.667 0.00 0.00 40.39 2.15
5394 5890 6.037500 GGACGGTGAGTTTAGTTTAGTTTTGT 59.962 38.462 0.00 0.00 0.00 2.83
5401 5897 6.899393 TCTTAGGACGGTGAGTTTAGTTTA 57.101 37.500 0.00 0.00 0.00 2.01
5402 5898 5.796424 TCTTAGGACGGTGAGTTTAGTTT 57.204 39.130 0.00 0.00 0.00 2.66
5413 5909 0.323957 GGGTTGCTTCTTAGGACGGT 59.676 55.000 0.00 0.00 0.00 4.83
5421 5917 2.183679 TGTTGGTTTGGGTTGCTTCTT 58.816 42.857 0.00 0.00 0.00 2.52
5460 6698 3.596214 GCGTCCTTGGTTCTAGATTTGA 58.404 45.455 0.00 0.00 0.00 2.69
5467 6705 1.180456 TCGTGGCGTCCTTGGTTCTA 61.180 55.000 0.00 0.00 0.00 2.10
5539 6777 8.060090 CGAGTTTACCTGTGTTAAACTAAACAG 58.940 37.037 7.33 0.00 42.14 3.16
5547 6785 3.806380 TGGCGAGTTTACCTGTGTTAAA 58.194 40.909 0.00 0.00 0.00 1.52
5549 6787 3.688694 ATGGCGAGTTTACCTGTGTTA 57.311 42.857 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.