Multiple sequence alignment - TraesCS3D01G350100

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 TraesCS3D01G350100 chr3D 100.000 2609 0 0 1 2609 461314719 461312111 0.000000e+00 4819.0
1 TraesCS3D01G350100 chr3D 90.489 1146 71 17 452 1573 461373613 461372482 0.000000e+00 1478.0
2 TraesCS3D01G350100 chr3D 83.333 924 87 42 547 1429 461427268 461426371 0.000000e+00 791.0
3 TraesCS3D01G350100 chr3D 86.438 612 57 20 998 1584 461589540 461588930 0.000000e+00 647.0
4 TraesCS3D01G350100 chr3D 87.879 264 25 5 19 281 461381125 461380868 1.170000e-78 303.0
5 TraesCS3D01G350100 chr3D 90.566 106 10 0 1932 2037 461312731 461312626 9.730000e-30 141.0
6 TraesCS3D01G350100 chr3D 90.566 106 10 0 1989 2094 461312788 461312683 9.730000e-30 141.0
7 TraesCS3D01G350100 chr3D 91.860 86 6 1 183 267 461590166 461590081 4.560000e-23 119.0
8 TraesCS3D01G350100 chr3D 76.818 220 16 14 712 907 461589867 461589659 9.940000e-15 91.6
9 TraesCS3D01G350100 chr3B 91.357 1643 81 25 425 2037 612104904 612103293 0.000000e+00 2191.0
10 TraesCS3D01G350100 chr3B 87.092 612 53 16 998 1584 612360319 612359709 0.000000e+00 669.0
11 TraesCS3D01G350100 chr3B 85.783 626 53 14 1989 2609 612103398 612102804 4.740000e-177 630.0
12 TraesCS3D01G350100 chr3B 85.089 617 58 17 997 1589 612296049 612295443 1.340000e-167 599.0
13 TraesCS3D01G350100 chr3B 88.372 258 19 5 1 257 612105202 612104955 1.520000e-77 300.0
14 TraesCS3D01G350100 chr3B 81.955 133 12 5 678 799 612296345 612296214 4.590000e-18 102.0
15 TraesCS3D01G350100 chr3B 73.643 387 40 30 545 907 612360783 612360435 2.760000e-15 93.5
16 TraesCS3D01G350100 chr3A 91.672 1537 67 22 426 1934 603814662 603813159 0.000000e+00 2073.0
17 TraesCS3D01G350100 chr3A 92.765 622 36 5 1989 2609 603812813 603812200 0.000000e+00 891.0
18 TraesCS3D01G350100 chr3A 87.914 604 56 14 997 1584 603895863 603895261 0.000000e+00 695.0
19 TraesCS3D01G350100 chr3A 82.937 756 86 26 854 1584 603847479 603846742 2.190000e-180 641.0
20 TraesCS3D01G350100 chr3A 95.327 107 5 0 1931 2037 603812814 603812708 1.240000e-38 171.0
21 TraesCS3D01G350100 chr3A 75.926 216 20 16 715 907 603896177 603895971 5.980000e-12 82.4
22 TraesCS3D01G350100 chr7B 95.833 48 2 0 2558 2605 226609235 226609188 7.740000e-11 78.7
23 TraesCS3D01G350100 chr7B 88.889 54 5 1 2549 2602 226609134 226609186 6.030000e-07 65.8
24 TraesCS3D01G350100 chr4A 93.750 48 2 1 2558 2605 652870904 652870950 1.300000e-08 71.3
25 TraesCS3D01G350100 chr4A 91.837 49 4 0 2558 2606 705876970 705877018 4.660000e-08 69.4
26 TraesCS3D01G350100 chr4A 91.837 49 4 0 2558 2606 707390355 707390403 4.660000e-08 69.4
27 TraesCS3D01G350100 chr4A 88.889 54 5 1 2549 2602 652871004 652870952 6.030000e-07 65.8
28 TraesCS3D01G350100 chr1B 90.566 53 5 0 2557 2609 34323748 34323696 1.300000e-08 71.3


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 TraesCS3D01G350100 chr3D 461312111 461314719 2608 True 1700.333333 4819 93.710667 1 2609 3 chr3D.!!$R4 2608
1 TraesCS3D01G350100 chr3D 461372482 461373613 1131 True 1478.000000 1478 90.489000 452 1573 1 chr3D.!!$R1 1121
2 TraesCS3D01G350100 chr3D 461426371 461427268 897 True 791.000000 791 83.333000 547 1429 1 chr3D.!!$R3 882
3 TraesCS3D01G350100 chr3D 461588930 461590166 1236 True 285.866667 647 85.038667 183 1584 3 chr3D.!!$R5 1401
4 TraesCS3D01G350100 chr3B 612102804 612105202 2398 True 1040.333333 2191 88.504000 1 2609 3 chr3B.!!$R1 2608
5 TraesCS3D01G350100 chr3B 612359709 612360783 1074 True 381.250000 669 80.367500 545 1584 2 chr3B.!!$R3 1039
6 TraesCS3D01G350100 chr3B 612295443 612296345 902 True 350.500000 599 83.522000 678 1589 2 chr3B.!!$R2 911
7 TraesCS3D01G350100 chr3A 603812200 603814662 2462 True 1045.000000 2073 93.254667 426 2609 3 chr3A.!!$R2 2183
8 TraesCS3D01G350100 chr3A 603846742 603847479 737 True 641.000000 641 82.937000 854 1584 1 chr3A.!!$R1 730
9 TraesCS3D01G350100 chr3A 603895261 603896177 916 True 388.700000 695 81.920000 715 1584 2 chr3A.!!$R3 869

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
55 56 0.678048 GGCAACAAAGGGAGCTCGAT 60.678 55.0 7.83 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2012 1.338973 TCTGTTTCAGAACTACGCCGT 59.661 47.619 0.0 0.0 37.57 5.68 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
33 34 8.425577 AACAGTATGAATTTCTAGATTCCACG 57.574 34.615 0.00 0.00 39.69 4.94
44 45 1.202879 AGATTCCACGGAGGCAACAAA 60.203 47.619 0.00 0.00 41.41 2.83
47 48 2.268076 CCACGGAGGCAACAAAGGG 61.268 63.158 0.00 0.00 41.41 3.95
48 49 1.228124 CACGGAGGCAACAAAGGGA 60.228 57.895 0.00 0.00 41.41 4.20
49 50 1.073199 ACGGAGGCAACAAAGGGAG 59.927 57.895 0.00 0.00 41.41 4.30
50 51 2.335712 CGGAGGCAACAAAGGGAGC 61.336 63.158 0.00 0.00 41.41 4.70
51 52 1.075659 GGAGGCAACAAAGGGAGCT 59.924 57.895 0.00 0.00 41.41 4.09
52 53 0.962855 GGAGGCAACAAAGGGAGCTC 60.963 60.000 4.71 4.71 41.41 4.09
53 54 1.301677 GAGGCAACAAAGGGAGCTCG 61.302 60.000 7.83 0.00 41.41 5.03
54 55 1.302511 GGCAACAAAGGGAGCTCGA 60.303 57.895 7.83 0.00 0.00 4.04
55 56 0.678048 GGCAACAAAGGGAGCTCGAT 60.678 55.000 7.83 0.00 0.00 3.59
56 57 0.729690 GCAACAAAGGGAGCTCGATC 59.270 55.000 7.83 0.00 0.00 3.69
96 97 1.600663 CGCCGCTCGTTCTAGATGATT 60.601 52.381 0.00 0.00 0.00 2.57
97 98 1.789464 GCCGCTCGTTCTAGATGATTG 59.211 52.381 0.00 0.00 0.00 2.67
99 100 2.034685 CCGCTCGTTCTAGATGATTGGA 59.965 50.000 0.00 0.00 0.00 3.53
101 102 4.112634 CGCTCGTTCTAGATGATTGGAAA 58.887 43.478 0.00 0.00 0.00 3.13
102 103 4.026475 CGCTCGTTCTAGATGATTGGAAAC 60.026 45.833 0.00 0.00 0.00 2.78
123 124 3.727518 CGAGCTATTCGTGTAGATCTCG 58.272 50.000 0.00 0.00 44.27 4.04
147 148 3.122850 CCGTTCGCCCGGTATAGT 58.877 61.111 0.00 0.00 43.07 2.12
156 157 4.562082 TCGCCCGGTATAGTCAATAAATG 58.438 43.478 0.00 0.00 0.00 2.32
157 158 4.039488 TCGCCCGGTATAGTCAATAAATGT 59.961 41.667 0.00 0.00 0.00 2.71
158 159 4.387862 CGCCCGGTATAGTCAATAAATGTC 59.612 45.833 0.00 0.00 0.00 3.06
228 230 2.032681 GAAACCCGTGCAGAGGCT 59.967 61.111 1.73 0.00 41.91 4.58
242 244 3.532155 GGCTGGGTCGAGATCGCT 61.532 66.667 0.00 0.00 39.60 4.93
246 248 3.838271 GGGTCGAGATCGCTGCCA 61.838 66.667 0.00 0.00 39.60 4.92
261 265 1.134694 GCCAGCGCGGAAGTAAAAG 59.865 57.895 20.06 0.00 36.56 2.27
263 267 0.721718 CCAGCGCGGAAGTAAAAGAG 59.278 55.000 9.80 0.00 36.56 2.85
267 271 1.153353 CGCGGAAGTAAAAGAGGCAA 58.847 50.000 0.00 0.00 0.00 4.52
268 272 1.737793 CGCGGAAGTAAAAGAGGCAAT 59.262 47.619 0.00 0.00 0.00 3.56
270 274 3.001330 CGCGGAAGTAAAAGAGGCAATAG 59.999 47.826 0.00 0.00 0.00 1.73
271 275 3.242772 GCGGAAGTAAAAGAGGCAATAGC 60.243 47.826 0.00 0.00 41.10 2.97
273 277 4.201822 CGGAAGTAAAAGAGGCAATAGCAC 60.202 45.833 0.00 0.00 44.61 4.40
274 278 4.700213 GGAAGTAAAAGAGGCAATAGCACA 59.300 41.667 0.00 0.00 44.61 4.57
275 279 5.392057 GGAAGTAAAAGAGGCAATAGCACAC 60.392 44.000 0.00 0.00 44.61 3.82
277 281 5.070001 AGTAAAAGAGGCAATAGCACACAA 58.930 37.500 0.00 0.00 44.61 3.33
279 283 2.867109 AGAGGCAATAGCACACAAGT 57.133 45.000 0.00 0.00 44.61 3.16
280 284 2.704572 AGAGGCAATAGCACACAAGTC 58.295 47.619 0.00 0.00 44.61 3.01
281 285 1.740025 GAGGCAATAGCACACAAGTCC 59.260 52.381 0.00 0.00 44.61 3.85
282 286 1.352352 AGGCAATAGCACACAAGTCCT 59.648 47.619 0.00 0.00 44.61 3.85
284 288 2.939103 GGCAATAGCACACAAGTCCTAG 59.061 50.000 0.00 0.00 44.61 3.02
285 289 3.369471 GGCAATAGCACACAAGTCCTAGA 60.369 47.826 0.00 0.00 44.61 2.43
286 290 4.253685 GCAATAGCACACAAGTCCTAGAA 58.746 43.478 0.00 0.00 41.58 2.10
287 291 4.093556 GCAATAGCACACAAGTCCTAGAAC 59.906 45.833 0.00 0.00 41.58 3.01
288 292 5.482908 CAATAGCACACAAGTCCTAGAACT 58.517 41.667 0.00 0.00 0.00 3.01
289 293 5.746990 ATAGCACACAAGTCCTAGAACTT 57.253 39.130 0.00 0.00 40.08 2.66
297 301 5.695851 CAAGTCCTAGAACTTGCACAATT 57.304 39.130 9.07 0.00 46.81 2.32
298 302 6.076981 CAAGTCCTAGAACTTGCACAATTT 57.923 37.500 9.07 0.00 46.81 1.82
299 303 7.202016 CAAGTCCTAGAACTTGCACAATTTA 57.798 36.000 9.07 0.00 46.81 1.40
300 304 7.301054 CAAGTCCTAGAACTTGCACAATTTAG 58.699 38.462 9.07 0.00 46.81 1.85
305 309 4.469657 AGAACTTGCACAATTTAGACCCA 58.530 39.130 0.00 0.00 0.00 4.51
306 310 4.892934 AGAACTTGCACAATTTAGACCCAA 59.107 37.500 0.00 0.00 0.00 4.12
307 311 5.362430 AGAACTTGCACAATTTAGACCCAAA 59.638 36.000 0.00 0.00 0.00 3.28
308 312 5.806654 ACTTGCACAATTTAGACCCAAAT 57.193 34.783 0.00 0.00 0.00 2.32
309 313 6.173427 ACTTGCACAATTTAGACCCAAATT 57.827 33.333 0.00 0.00 38.37 1.82
310 314 6.591001 ACTTGCACAATTTAGACCCAAATTT 58.409 32.000 0.00 0.00 36.26 1.82
311 315 6.705825 ACTTGCACAATTTAGACCCAAATTTC 59.294 34.615 0.00 0.00 36.26 2.17
312 316 6.166984 TGCACAATTTAGACCCAAATTTCA 57.833 33.333 0.00 0.00 36.26 2.69
313 317 6.586344 TGCACAATTTAGACCCAAATTTCAA 58.414 32.000 0.00 0.00 36.26 2.69
314 318 7.050377 TGCACAATTTAGACCCAAATTTCAAA 58.950 30.769 0.00 0.00 36.26 2.69
315 319 7.718753 TGCACAATTTAGACCCAAATTTCAAAT 59.281 29.630 0.00 0.00 36.26 2.32
316 320 8.567104 GCACAATTTAGACCCAAATTTCAAATT 58.433 29.630 0.00 0.00 36.26 1.82
317 321 9.881529 CACAATTTAGACCCAAATTTCAAATTG 57.118 29.630 12.75 12.75 42.93 2.32
318 322 9.625747 ACAATTTAGACCCAAATTTCAAATTGT 57.374 25.926 13.75 13.75 44.22 2.71
320 324 9.844257 AATTTAGACCCAAATTTCAAATTGTCA 57.156 25.926 12.12 0.17 35.12 3.58
321 325 8.655651 TTTAGACCCAAATTTCAAATTGTCAC 57.344 30.769 12.12 0.00 0.00 3.67
322 326 6.232581 AGACCCAAATTTCAAATTGTCACA 57.767 33.333 12.12 0.00 0.00 3.58
323 327 6.829849 AGACCCAAATTTCAAATTGTCACAT 58.170 32.000 12.12 0.00 0.00 3.21
324 328 6.707161 AGACCCAAATTTCAAATTGTCACATG 59.293 34.615 12.12 0.00 0.00 3.21
325 329 5.239087 ACCCAAATTTCAAATTGTCACATGC 59.761 36.000 0.00 0.00 0.00 4.06
326 330 5.238868 CCCAAATTTCAAATTGTCACATGCA 59.761 36.000 0.00 0.00 0.00 3.96
327 331 6.367421 CCAAATTTCAAATTGTCACATGCAG 58.633 36.000 0.00 0.00 0.00 4.41
328 332 6.017770 CCAAATTTCAAATTGTCACATGCAGT 60.018 34.615 0.00 0.00 0.00 4.40
329 333 7.411274 CAAATTTCAAATTGTCACATGCAGTT 58.589 30.769 0.00 0.00 0.00 3.16
330 334 6.774354 ATTTCAAATTGTCACATGCAGTTC 57.226 33.333 0.00 0.00 0.00 3.01
331 335 4.915158 TCAAATTGTCACATGCAGTTCA 57.085 36.364 0.00 0.00 0.00 3.18
332 336 5.259832 TCAAATTGTCACATGCAGTTCAA 57.740 34.783 0.00 0.17 0.00 2.69
333 337 5.283294 TCAAATTGTCACATGCAGTTCAAG 58.717 37.500 0.00 0.00 0.00 3.02
334 338 4.924305 AATTGTCACATGCAGTTCAAGT 57.076 36.364 0.00 0.00 0.00 3.16
335 339 4.924305 ATTGTCACATGCAGTTCAAGTT 57.076 36.364 0.00 0.00 0.00 2.66
336 340 3.969117 TGTCACATGCAGTTCAAGTTC 57.031 42.857 0.00 0.00 0.00 3.01
337 341 3.544684 TGTCACATGCAGTTCAAGTTCT 58.455 40.909 0.00 0.00 0.00 3.01
338 342 4.702831 TGTCACATGCAGTTCAAGTTCTA 58.297 39.130 0.00 0.00 0.00 2.10
339 343 4.751600 TGTCACATGCAGTTCAAGTTCTAG 59.248 41.667 0.00 0.00 0.00 2.43
340 344 4.153117 GTCACATGCAGTTCAAGTTCTAGG 59.847 45.833 0.00 0.00 0.00 3.02
341 345 3.438087 CACATGCAGTTCAAGTTCTAGGG 59.562 47.826 0.00 0.00 0.00 3.53
342 346 2.859165 TGCAGTTCAAGTTCTAGGGG 57.141 50.000 0.00 0.00 0.00 4.79
343 347 2.054799 TGCAGTTCAAGTTCTAGGGGT 58.945 47.619 0.00 0.00 0.00 4.95
344 348 2.224523 TGCAGTTCAAGTTCTAGGGGTG 60.225 50.000 0.00 0.00 0.00 4.61
345 349 2.224548 GCAGTTCAAGTTCTAGGGGTGT 60.225 50.000 0.00 0.00 0.00 4.16
346 350 3.007614 GCAGTTCAAGTTCTAGGGGTGTA 59.992 47.826 0.00 0.00 0.00 2.90
347 351 4.822026 CAGTTCAAGTTCTAGGGGTGTAG 58.178 47.826 0.00 0.00 0.00 2.74
348 352 4.283722 CAGTTCAAGTTCTAGGGGTGTAGT 59.716 45.833 0.00 0.00 0.00 2.73
349 353 4.906060 AGTTCAAGTTCTAGGGGTGTAGTT 59.094 41.667 0.00 0.00 0.00 2.24
350 354 5.368816 AGTTCAAGTTCTAGGGGTGTAGTTT 59.631 40.000 0.00 0.00 0.00 2.66
351 355 5.899631 TCAAGTTCTAGGGGTGTAGTTTT 57.100 39.130 0.00 0.00 0.00 2.43
352 356 5.617252 TCAAGTTCTAGGGGTGTAGTTTTG 58.383 41.667 0.00 0.00 0.00 2.44
353 357 4.017177 AGTTCTAGGGGTGTAGTTTTGC 57.983 45.455 0.00 0.00 0.00 3.68
354 358 3.393278 AGTTCTAGGGGTGTAGTTTTGCA 59.607 43.478 0.00 0.00 0.00 4.08
355 359 3.412237 TCTAGGGGTGTAGTTTTGCAC 57.588 47.619 0.00 0.00 38.97 4.57
356 360 2.706723 TCTAGGGGTGTAGTTTTGCACA 59.293 45.455 0.00 0.00 41.15 4.57
357 361 1.687563 AGGGGTGTAGTTTTGCACAC 58.312 50.000 0.00 0.00 41.97 3.82
358 362 1.214424 AGGGGTGTAGTTTTGCACACT 59.786 47.619 3.29 3.29 42.29 3.55
359 363 2.028876 GGGGTGTAGTTTTGCACACTT 58.971 47.619 3.08 0.00 42.29 3.16
360 364 2.429250 GGGGTGTAGTTTTGCACACTTT 59.571 45.455 3.08 0.00 42.29 2.66
361 365 3.633065 GGGGTGTAGTTTTGCACACTTTA 59.367 43.478 3.08 0.00 42.29 1.85
362 366 4.098196 GGGGTGTAGTTTTGCACACTTTAA 59.902 41.667 3.08 0.00 42.29 1.52
363 367 5.394333 GGGGTGTAGTTTTGCACACTTTAAA 60.394 40.000 3.08 0.00 42.29 1.52
364 368 5.517411 GGGTGTAGTTTTGCACACTTTAAAC 59.483 40.000 3.08 2.48 43.64 2.01
365 369 6.327154 GGTGTAGTTTTGCACACTTTAAACT 58.673 36.000 14.48 14.48 43.64 2.66
366 370 7.415429 GGGTGTAGTTTTGCACACTTTAAACTA 60.415 37.037 12.83 12.83 43.64 2.24
367 371 7.969508 GGTGTAGTTTTGCACACTTTAAACTAA 59.030 33.333 16.72 8.16 41.83 2.24
368 372 9.344309 GTGTAGTTTTGCACACTTTAAACTAAA 57.656 29.630 16.72 11.30 41.83 1.85
369 373 9.909644 TGTAGTTTTGCACACTTTAAACTAAAA 57.090 25.926 16.72 8.82 41.83 1.52
371 375 8.819643 AGTTTTGCACACTTTAAACTAAAACA 57.180 26.923 9.62 0.00 38.62 2.83
372 376 9.430623 AGTTTTGCACACTTTAAACTAAAACAT 57.569 25.926 9.62 0.00 38.62 2.71
373 377 9.683651 GTTTTGCACACTTTAAACTAAAACATC 57.316 29.630 0.00 0.00 36.98 3.06
374 378 8.988064 TTTGCACACTTTAAACTAAAACATCA 57.012 26.923 0.00 0.00 0.00 3.07
375 379 7.979115 TGCACACTTTAAACTAAAACATCAC 57.021 32.000 0.00 0.00 0.00 3.06
376 380 7.539436 TGCACACTTTAAACTAAAACATCACA 58.461 30.769 0.00 0.00 0.00 3.58
377 381 8.194104 TGCACACTTTAAACTAAAACATCACAT 58.806 29.630 0.00 0.00 0.00 3.21
378 382 9.030301 GCACACTTTAAACTAAAACATCACATT 57.970 29.630 0.00 0.00 0.00 2.71
384 388 6.747659 AAACTAAAACATCACATTTCGTGC 57.252 33.333 0.00 0.00 45.92 5.34
385 389 5.431420 ACTAAAACATCACATTTCGTGCA 57.569 34.783 0.00 0.00 45.92 4.57
386 390 5.826586 ACTAAAACATCACATTTCGTGCAA 58.173 33.333 0.00 0.00 45.92 4.08
387 391 6.269315 ACTAAAACATCACATTTCGTGCAAA 58.731 32.000 0.00 0.00 45.92 3.68
388 392 6.922957 ACTAAAACATCACATTTCGTGCAAAT 59.077 30.769 0.00 0.00 45.92 2.32
389 393 6.601741 AAAACATCACATTTCGTGCAAATT 57.398 29.167 0.00 0.00 45.92 1.82
390 394 6.601741 AAACATCACATTTCGTGCAAATTT 57.398 29.167 0.00 0.00 45.92 1.82
391 395 6.601741 AACATCACATTTCGTGCAAATTTT 57.398 29.167 0.00 0.00 45.92 1.82
392 396 7.706281 AACATCACATTTCGTGCAAATTTTA 57.294 28.000 0.00 0.00 45.92 1.52
393 397 7.337150 ACATCACATTTCGTGCAAATTTTAG 57.663 32.000 0.00 0.00 45.92 1.85
394 398 6.365789 ACATCACATTTCGTGCAAATTTTAGG 59.634 34.615 0.00 0.00 45.92 2.69
395 399 6.078202 TCACATTTCGTGCAAATTTTAGGA 57.922 33.333 0.00 0.00 45.92 2.94
396 400 5.918011 TCACATTTCGTGCAAATTTTAGGAC 59.082 36.000 0.00 0.00 45.92 3.85
397 401 5.920273 CACATTTCGTGCAAATTTTAGGACT 59.080 36.000 0.00 0.00 39.19 3.85
398 402 6.420604 CACATTTCGTGCAAATTTTAGGACTT 59.579 34.615 0.00 0.00 39.19 3.01
399 403 6.420604 ACATTTCGTGCAAATTTTAGGACTTG 59.579 34.615 0.00 0.00 31.79 3.16
400 404 5.508200 TTCGTGCAAATTTTAGGACTTGT 57.492 34.783 0.00 0.00 0.00 3.16
401 405 4.854399 TCGTGCAAATTTTAGGACTTGTG 58.146 39.130 0.00 0.00 0.00 3.33
402 406 3.980775 CGTGCAAATTTTAGGACTTGTGG 59.019 43.478 0.00 0.00 0.00 4.17
403 407 4.499019 CGTGCAAATTTTAGGACTTGTGGT 60.499 41.667 0.00 0.00 0.00 4.16
404 408 4.744631 GTGCAAATTTTAGGACTTGTGGTG 59.255 41.667 0.00 0.00 0.00 4.17
405 409 3.740832 GCAAATTTTAGGACTTGTGGTGC 59.259 43.478 0.00 0.00 36.48 5.01
407 411 5.278758 GCAAATTTTAGGACTTGTGGTGCTA 60.279 40.000 0.00 0.00 44.77 3.49
408 412 6.572314 GCAAATTTTAGGACTTGTGGTGCTAT 60.572 38.462 0.00 0.00 45.74 2.97
409 413 7.378181 CAAATTTTAGGACTTGTGGTGCTATT 58.622 34.615 0.00 0.00 45.74 1.73
410 414 8.519526 CAAATTTTAGGACTTGTGGTGCTATTA 58.480 33.333 0.00 0.00 45.74 0.98
411 415 7.625828 ATTTTAGGACTTGTGGTGCTATTAC 57.374 36.000 0.00 0.00 45.74 1.89
412 416 3.629142 AGGACTTGTGGTGCTATTACC 57.371 47.619 0.00 0.00 44.77 2.85
413 417 3.182152 AGGACTTGTGGTGCTATTACCT 58.818 45.455 0.00 0.00 44.77 3.08
414 418 3.587506 AGGACTTGTGGTGCTATTACCTT 59.412 43.478 0.00 0.00 44.77 3.50
415 419 3.939592 GGACTTGTGGTGCTATTACCTTC 59.060 47.826 0.00 0.00 41.43 3.46
416 420 4.564821 GGACTTGTGGTGCTATTACCTTCA 60.565 45.833 0.00 0.00 41.43 3.02
417 421 4.980573 ACTTGTGGTGCTATTACCTTCAA 58.019 39.130 0.00 0.00 41.43 2.69
418 422 5.003804 ACTTGTGGTGCTATTACCTTCAAG 58.996 41.667 20.25 20.25 46.12 3.02
419 423 4.901197 TGTGGTGCTATTACCTTCAAGA 57.099 40.909 0.00 0.00 41.43 3.02
420 424 5.235850 TGTGGTGCTATTACCTTCAAGAA 57.764 39.130 0.00 0.00 41.43 2.52
421 425 5.626142 TGTGGTGCTATTACCTTCAAGAAA 58.374 37.500 0.00 0.00 41.43 2.52
422 426 6.065374 TGTGGTGCTATTACCTTCAAGAAAA 58.935 36.000 0.00 0.00 41.43 2.29
423 427 6.547880 TGTGGTGCTATTACCTTCAAGAAAAA 59.452 34.615 0.00 0.00 41.43 1.94
434 438 1.732809 TCAAGAAAAACACGCACACGA 59.267 42.857 0.00 0.00 43.93 4.35
445 450 1.870901 GCACACGATACGGACGTCC 60.871 63.158 25.28 25.28 42.07 4.79
524 534 2.033602 GTGGTTGCTTAGCCGGGT 59.966 61.111 12.58 12.58 0.00 5.28
687 727 9.950680 GTACTGTAGACTGTAGTAGTAGACTAG 57.049 40.741 0.16 0.00 41.47 2.57
727 774 3.036084 CGCGCGGTCAAACAGTCT 61.036 61.111 24.84 0.00 0.00 3.24
839 919 1.463553 GCACCAAACCCCAACCTCAG 61.464 60.000 0.00 0.00 0.00 3.35
877 970 2.113139 GGCATCCACCATACGGGG 59.887 66.667 0.00 0.00 42.91 5.73
1645 1879 2.202932 CCCCTGATGTTCCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
1646 1880 2.892425 CCCTGATGTTCCTCGCGC 60.892 66.667 0.00 0.00 0.00 6.86
1774 2012 4.481368 AAATGTTCATAGGCTGGTACGA 57.519 40.909 0.00 0.00 0.00 3.43
1872 2110 3.443681 ACTTATGGTCGCCCTTTTGAATG 59.556 43.478 0.00 0.00 0.00 2.67
2033 2619 6.439375 TCTGTTCCTACTAATGAAGGCTAACA 59.561 38.462 0.00 0.00 32.04 2.41
2034 2620 7.125811 TCTGTTCCTACTAATGAAGGCTAACAT 59.874 37.037 0.00 0.00 32.36 2.71
2035 2621 7.630082 TGTTCCTACTAATGAAGGCTAACATT 58.370 34.615 18.73 18.73 39.53 2.71
2036 2622 8.107095 TGTTCCTACTAATGAAGGCTAACATTT 58.893 33.333 19.53 9.58 37.75 2.32
2037 2623 8.398665 GTTCCTACTAATGAAGGCTAACATTTG 58.601 37.037 19.53 19.06 37.75 2.32
2038 2624 7.630082 TCCTACTAATGAAGGCTAACATTTGT 58.370 34.615 24.27 24.27 41.89 2.83
2039 2625 8.107095 TCCTACTAATGAAGGCTAACATTTGTT 58.893 33.333 25.19 16.07 40.56 2.83
2040 2626 8.739972 CCTACTAATGAAGGCTAACATTTGTTT 58.260 33.333 25.19 13.40 40.56 2.83
2041 2627 9.774742 CTACTAATGAAGGCTAACATTTGTTTC 57.225 33.333 25.19 4.72 40.56 2.78
2042 2628 7.305474 ACTAATGAAGGCTAACATTTGTTTCG 58.695 34.615 19.53 8.66 38.50 3.46
2043 2629 4.497473 TGAAGGCTAACATTTGTTTCGG 57.503 40.909 0.63 0.00 39.31 4.30
2044 2630 3.242518 GAAGGCTAACATTTGTTTCGGC 58.757 45.455 0.63 6.15 39.31 5.54
2045 2631 2.235016 AGGCTAACATTTGTTTCGGCA 58.765 42.857 15.87 0.00 39.31 5.69
2046 2632 2.625790 AGGCTAACATTTGTTTCGGCAA 59.374 40.909 15.87 0.00 39.31 4.52
2047 2633 2.986479 GGCTAACATTTGTTTCGGCAAG 59.014 45.455 0.63 0.00 39.31 4.01
2048 2634 3.552068 GGCTAACATTTGTTTCGGCAAGT 60.552 43.478 0.63 0.00 39.31 3.16
2049 2635 3.668656 GCTAACATTTGTTTCGGCAAGTC 59.331 43.478 0.63 0.00 39.31 3.01
2050 2636 3.791973 AACATTTGTTTCGGCAAGTCA 57.208 38.095 0.00 0.00 33.93 3.41
2051 2637 3.791973 ACATTTGTTTCGGCAAGTCAA 57.208 38.095 0.00 0.00 0.00 3.18
2052 2638 4.320608 ACATTTGTTTCGGCAAGTCAAT 57.679 36.364 0.00 0.00 0.00 2.57
2053 2639 5.446143 ACATTTGTTTCGGCAAGTCAATA 57.554 34.783 0.00 0.00 0.00 1.90
2054 2640 6.024552 ACATTTGTTTCGGCAAGTCAATAT 57.975 33.333 0.00 0.00 0.00 1.28
2055 2641 6.454795 ACATTTGTTTCGGCAAGTCAATATT 58.545 32.000 0.00 0.00 0.00 1.28
2056 2642 6.586082 ACATTTGTTTCGGCAAGTCAATATTC 59.414 34.615 0.00 0.00 0.00 1.75
2057 2643 5.697473 TTGTTTCGGCAAGTCAATATTCA 57.303 34.783 0.00 0.00 0.00 2.57
2058 2644 5.895636 TGTTTCGGCAAGTCAATATTCAT 57.104 34.783 0.00 0.00 0.00 2.57
2059 2645 6.993786 TGTTTCGGCAAGTCAATATTCATA 57.006 33.333 0.00 0.00 0.00 2.15
2060 2646 7.384439 TGTTTCGGCAAGTCAATATTCATAA 57.616 32.000 0.00 0.00 0.00 1.90
2061 2647 7.821652 TGTTTCGGCAAGTCAATATTCATAAA 58.178 30.769 0.00 0.00 0.00 1.40
2062 2648 7.967854 TGTTTCGGCAAGTCAATATTCATAAAG 59.032 33.333 0.00 0.00 0.00 1.85
2063 2649 7.624360 TTCGGCAAGTCAATATTCATAAAGT 57.376 32.000 0.00 0.00 0.00 2.66
2064 2650 7.624360 TCGGCAAGTCAATATTCATAAAGTT 57.376 32.000 0.00 0.00 0.00 2.66
2065 2651 8.050778 TCGGCAAGTCAATATTCATAAAGTTT 57.949 30.769 0.00 0.00 0.00 2.66
2066 2652 8.181573 TCGGCAAGTCAATATTCATAAAGTTTC 58.818 33.333 0.00 0.00 0.00 2.78
2067 2653 8.184192 CGGCAAGTCAATATTCATAAAGTTTCT 58.816 33.333 0.00 0.00 0.00 2.52
2068 2654 9.294030 GGCAAGTCAATATTCATAAAGTTTCTG 57.706 33.333 0.00 0.00 0.00 3.02
2069 2655 9.846248 GCAAGTCAATATTCATAAAGTTTCTGT 57.154 29.630 0.00 0.00 0.00 3.41
2075 2661 9.294030 CAATATTCATAAAGTTTCTGTTCCTGC 57.706 33.333 0.00 0.00 0.00 4.85
2076 2662 5.705609 TTCATAAAGTTTCTGTTCCTGCC 57.294 39.130 0.00 0.00 0.00 4.85
2077 2663 4.724399 TCATAAAGTTTCTGTTCCTGCCA 58.276 39.130 0.00 0.00 0.00 4.92
2078 2664 5.136828 TCATAAAGTTTCTGTTCCTGCCAA 58.863 37.500 0.00 0.00 0.00 4.52
2079 2665 5.774690 TCATAAAGTTTCTGTTCCTGCCAAT 59.225 36.000 0.00 0.00 0.00 3.16
2080 2666 4.326504 AAAGTTTCTGTTCCTGCCAATG 57.673 40.909 0.00 0.00 0.00 2.82
2081 2667 3.228188 AGTTTCTGTTCCTGCCAATGA 57.772 42.857 0.00 0.00 0.00 2.57
2082 2668 3.565307 AGTTTCTGTTCCTGCCAATGAA 58.435 40.909 0.00 0.00 0.00 2.57
2083 2669 3.571401 AGTTTCTGTTCCTGCCAATGAAG 59.429 43.478 0.00 0.00 0.00 3.02
2084 2670 2.205022 TCTGTTCCTGCCAATGAAGG 57.795 50.000 0.00 0.00 34.65 3.46
2105 2691 4.699257 AGGCTAGCATTTTCTTCAGAACAG 59.301 41.667 18.24 0.00 33.13 3.16
2192 2778 6.023103 CGGTTACGTCAAATAAATAAACACGC 60.023 38.462 0.00 0.00 34.81 5.34
2292 2878 7.750229 TGCATTCTTAATAGATAAAGGCTGG 57.250 36.000 0.00 0.00 0.00 4.85
2301 2887 9.747898 TTAATAGATAAAGGCTGGAAACTGAAA 57.252 29.630 0.00 0.00 0.00 2.69
2308 2894 1.000171 GCTGGAAACTGAAAGCAAGGG 60.000 52.381 0.00 0.00 37.60 3.95
2367 2953 2.852449 TCACCGGCACATCTAAACAAA 58.148 42.857 0.00 0.00 0.00 2.83
2377 2963 9.646336 CGGCACATCTAAACAAATAGTATAAAC 57.354 33.333 0.00 0.00 0.00 2.01
2449 3035 5.739752 ACATAACATGTGTCCATCATTCG 57.260 39.130 0.00 0.00 43.01 3.34
2542 3128 6.187682 AACTAACAAAGTTGGCATAGCCTAT 58.812 36.000 9.71 0.00 46.90 2.57
2565 3151 2.732366 CAGTATGCATCGTACTCGCTT 58.268 47.619 0.19 0.00 34.39 4.68
2588 3174 8.870879 GCTTCGTCCCATAATATAAGATGTTAC 58.129 37.037 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.986817 CCGTGGAATCTAGAAATTCATACTGT 59.013 38.462 0.00 0.00 37.38 3.55
10 11 7.210174 TCCGTGGAATCTAGAAATTCATACTG 58.790 38.462 0.00 0.00 37.38 2.74
11 12 7.361457 TCCGTGGAATCTAGAAATTCATACT 57.639 36.000 0.00 0.00 37.38 2.12
33 34 0.962855 GAGCTCCCTTTGTTGCCTCC 60.963 60.000 0.87 0.00 0.00 4.30
44 45 0.895530 TCAAAACGATCGAGCTCCCT 59.104 50.000 24.34 0.00 0.00 4.20
47 48 2.092838 CCTGTTCAAAACGATCGAGCTC 59.907 50.000 24.34 2.73 0.00 4.09
48 49 2.069273 CCTGTTCAAAACGATCGAGCT 58.931 47.619 24.34 2.41 0.00 4.09
49 50 1.128692 CCCTGTTCAAAACGATCGAGC 59.871 52.381 24.34 0.89 0.00 5.03
50 51 2.412089 GTCCCTGTTCAAAACGATCGAG 59.588 50.000 24.34 5.62 0.00 4.04
51 52 2.409975 GTCCCTGTTCAAAACGATCGA 58.590 47.619 24.34 0.00 0.00 3.59
52 53 1.126113 CGTCCCTGTTCAAAACGATCG 59.874 52.381 14.88 14.88 35.45 3.69
53 54 2.140717 ACGTCCCTGTTCAAAACGATC 58.859 47.619 0.00 0.00 37.13 3.69
54 55 2.140717 GACGTCCCTGTTCAAAACGAT 58.859 47.619 3.51 0.00 37.13 3.73
55 56 1.574134 GACGTCCCTGTTCAAAACGA 58.426 50.000 3.51 0.00 37.13 3.85
56 57 0.231279 CGACGTCCCTGTTCAAAACG 59.769 55.000 10.58 0.00 39.16 3.60
143 144 4.506654 GCCGTCACGACATTTATTGACTAT 59.493 41.667 0.00 0.00 36.93 2.12
144 145 3.861113 GCCGTCACGACATTTATTGACTA 59.139 43.478 0.00 0.00 36.93 2.59
145 146 2.671396 GCCGTCACGACATTTATTGACT 59.329 45.455 0.00 0.00 36.93 3.41
146 147 2.413796 TGCCGTCACGACATTTATTGAC 59.586 45.455 0.00 0.00 35.93 3.18
147 148 2.670905 CTGCCGTCACGACATTTATTGA 59.329 45.455 0.00 0.00 0.00 2.57
156 157 2.042520 TTTGTTGCTGCCGTCACGAC 62.043 55.000 0.00 0.00 0.00 4.34
157 158 1.369839 TTTTGTTGCTGCCGTCACGA 61.370 50.000 0.00 0.00 0.00 4.35
158 159 1.063327 TTTTGTTGCTGCCGTCACG 59.937 52.632 0.00 0.00 0.00 4.35
228 230 3.838271 GGCAGCGATCTCGACCCA 61.838 66.667 3.33 0.00 43.02 4.51
242 244 1.573829 CTTTTACTTCCGCGCTGGCA 61.574 55.000 5.56 0.00 39.92 4.92
246 248 1.019805 GCCTCTTTTACTTCCGCGCT 61.020 55.000 5.56 0.00 0.00 5.92
261 265 1.740025 GGACTTGTGTGCTATTGCCTC 59.260 52.381 0.00 0.00 38.71 4.70
263 267 1.826385 AGGACTTGTGTGCTATTGCC 58.174 50.000 0.00 0.00 43.13 4.52
267 271 5.746990 AAGTTCTAGGACTTGTGTGCTAT 57.253 39.130 15.98 0.00 44.18 2.97
277 281 6.651225 GTCTAAATTGTGCAAGTTCTAGGACT 59.349 38.462 0.00 0.00 30.75 3.85
279 283 5.938125 GGTCTAAATTGTGCAAGTTCTAGGA 59.062 40.000 0.77 0.00 30.75 2.94
280 284 5.123979 GGGTCTAAATTGTGCAAGTTCTAGG 59.876 44.000 0.77 0.00 30.75 3.02
281 285 5.705441 TGGGTCTAAATTGTGCAAGTTCTAG 59.295 40.000 0.77 0.00 30.75 2.43
282 286 5.626142 TGGGTCTAAATTGTGCAAGTTCTA 58.374 37.500 0.77 0.00 30.75 2.10
284 288 4.846779 TGGGTCTAAATTGTGCAAGTTC 57.153 40.909 0.77 0.00 30.75 3.01
285 289 5.606348 TTTGGGTCTAAATTGTGCAAGTT 57.394 34.783 3.21 3.21 32.98 2.66
286 290 5.806654 ATTTGGGTCTAAATTGTGCAAGT 57.193 34.783 0.00 0.00 0.00 3.16
287 291 6.705381 TGAAATTTGGGTCTAAATTGTGCAAG 59.295 34.615 0.00 0.00 39.48 4.01
288 292 6.586344 TGAAATTTGGGTCTAAATTGTGCAA 58.414 32.000 0.00 0.00 39.48 4.08
289 293 6.166984 TGAAATTTGGGTCTAAATTGTGCA 57.833 33.333 0.00 0.00 39.48 4.57
291 295 9.881529 CAATTTGAAATTTGGGTCTAAATTGTG 57.118 29.630 0.00 0.00 39.48 3.33
292 296 9.625747 ACAATTTGAAATTTGGGTCTAAATTGT 57.374 25.926 15.39 15.39 45.12 2.71
294 298 9.844257 TGACAATTTGAAATTTGGGTCTAAATT 57.156 25.926 15.85 0.19 40.84 1.82
297 301 7.786030 TGTGACAATTTGAAATTTGGGTCTAA 58.214 30.769 15.85 6.18 0.00 2.10
298 302 7.353414 TGTGACAATTTGAAATTTGGGTCTA 57.647 32.000 15.85 6.92 0.00 2.59
299 303 6.232581 TGTGACAATTTGAAATTTGGGTCT 57.767 33.333 15.85 0.00 0.00 3.85
300 304 6.566376 GCATGTGACAATTTGAAATTTGGGTC 60.566 38.462 2.79 6.54 0.00 4.46
305 309 7.280428 TGAACTGCATGTGACAATTTGAAATTT 59.720 29.630 2.79 0.00 0.00 1.82
306 310 6.762187 TGAACTGCATGTGACAATTTGAAATT 59.238 30.769 2.79 0.00 0.00 1.82
307 311 6.282167 TGAACTGCATGTGACAATTTGAAAT 58.718 32.000 2.79 0.00 0.00 2.17
308 312 5.658468 TGAACTGCATGTGACAATTTGAAA 58.342 33.333 2.79 0.00 0.00 2.69
309 313 5.259832 TGAACTGCATGTGACAATTTGAA 57.740 34.783 2.79 0.00 0.00 2.69
310 314 4.915158 TGAACTGCATGTGACAATTTGA 57.085 36.364 2.79 0.00 0.00 2.69
311 315 5.045215 ACTTGAACTGCATGTGACAATTTG 58.955 37.500 0.00 0.00 34.00 2.32
312 316 5.266733 ACTTGAACTGCATGTGACAATTT 57.733 34.783 0.00 0.00 34.00 1.82
313 317 4.924305 ACTTGAACTGCATGTGACAATT 57.076 36.364 0.00 0.00 34.00 2.32
314 318 4.581824 AGAACTTGAACTGCATGTGACAAT 59.418 37.500 0.00 0.00 35.32 2.71
315 319 3.947196 AGAACTTGAACTGCATGTGACAA 59.053 39.130 0.00 0.00 35.32 3.18
316 320 3.544684 AGAACTTGAACTGCATGTGACA 58.455 40.909 0.00 0.00 35.32 3.58
317 321 4.153117 CCTAGAACTTGAACTGCATGTGAC 59.847 45.833 0.00 0.00 35.32 3.67
318 322 4.318332 CCTAGAACTTGAACTGCATGTGA 58.682 43.478 0.00 0.00 35.32 3.58
319 323 3.438087 CCCTAGAACTTGAACTGCATGTG 59.562 47.826 0.00 0.00 35.32 3.21
320 324 3.560025 CCCCTAGAACTTGAACTGCATGT 60.560 47.826 0.00 0.00 36.53 3.21
321 325 3.012518 CCCCTAGAACTTGAACTGCATG 58.987 50.000 0.00 0.00 0.00 4.06
322 326 2.644798 ACCCCTAGAACTTGAACTGCAT 59.355 45.455 0.00 0.00 0.00 3.96
323 327 2.054799 ACCCCTAGAACTTGAACTGCA 58.945 47.619 0.00 0.00 0.00 4.41
324 328 2.224548 ACACCCCTAGAACTTGAACTGC 60.225 50.000 0.00 0.00 0.00 4.40
325 329 3.771577 ACACCCCTAGAACTTGAACTG 57.228 47.619 0.00 0.00 0.00 3.16
326 330 4.490706 ACTACACCCCTAGAACTTGAACT 58.509 43.478 0.00 0.00 0.00 3.01
327 331 4.886496 ACTACACCCCTAGAACTTGAAC 57.114 45.455 0.00 0.00 0.00 3.18
328 332 5.899631 AAACTACACCCCTAGAACTTGAA 57.100 39.130 0.00 0.00 0.00 2.69
329 333 5.617252 CAAAACTACACCCCTAGAACTTGA 58.383 41.667 0.00 0.00 0.00 3.02
330 334 4.215613 GCAAAACTACACCCCTAGAACTTG 59.784 45.833 0.00 0.00 0.00 3.16
331 335 4.141344 TGCAAAACTACACCCCTAGAACTT 60.141 41.667 0.00 0.00 0.00 2.66
332 336 3.393278 TGCAAAACTACACCCCTAGAACT 59.607 43.478 0.00 0.00 0.00 3.01
333 337 3.501062 GTGCAAAACTACACCCCTAGAAC 59.499 47.826 0.00 0.00 0.00 3.01
334 338 3.136809 TGTGCAAAACTACACCCCTAGAA 59.863 43.478 0.00 0.00 35.90 2.10
335 339 2.706723 TGTGCAAAACTACACCCCTAGA 59.293 45.455 0.00 0.00 35.90 2.43
336 340 2.812011 GTGTGCAAAACTACACCCCTAG 59.188 50.000 0.00 0.00 40.90 3.02
337 341 2.440253 AGTGTGCAAAACTACACCCCTA 59.560 45.455 1.50 0.00 46.31 3.53
338 342 1.214424 AGTGTGCAAAACTACACCCCT 59.786 47.619 1.50 0.00 46.31 4.79
339 343 1.687563 AGTGTGCAAAACTACACCCC 58.312 50.000 1.50 0.00 46.31 4.95
340 344 3.793797 AAAGTGTGCAAAACTACACCC 57.206 42.857 3.85 0.00 46.31 4.61
341 345 6.327154 AGTTTAAAGTGTGCAAAACTACACC 58.673 36.000 9.62 0.00 46.31 4.16
342 346 8.898983 TTAGTTTAAAGTGTGCAAAACTACAC 57.101 30.769 15.38 6.70 41.59 2.90
343 347 9.909644 TTTTAGTTTAAAGTGTGCAAAACTACA 57.090 25.926 15.38 9.04 41.59 2.74
345 349 9.909644 TGTTTTAGTTTAAAGTGTGCAAAACTA 57.090 25.926 21.34 12.83 41.22 2.24
346 350 8.819643 TGTTTTAGTTTAAAGTGTGCAAAACT 57.180 26.923 21.34 14.48 42.91 2.66
347 351 9.683651 GATGTTTTAGTTTAAAGTGTGCAAAAC 57.316 29.630 17.42 17.42 35.97 2.43
348 352 9.424319 TGATGTTTTAGTTTAAAGTGTGCAAAA 57.576 25.926 5.77 2.21 0.00 2.44
349 353 8.865001 GTGATGTTTTAGTTTAAAGTGTGCAAA 58.135 29.630 5.77 0.00 0.00 3.68
350 354 8.029522 TGTGATGTTTTAGTTTAAAGTGTGCAA 58.970 29.630 5.77 0.00 0.00 4.08
351 355 7.539436 TGTGATGTTTTAGTTTAAAGTGTGCA 58.461 30.769 5.77 0.00 0.00 4.57
352 356 7.979115 TGTGATGTTTTAGTTTAAAGTGTGC 57.021 32.000 5.77 0.00 0.00 4.57
374 378 6.084326 AGTCCTAAAATTTGCACGAAATGT 57.916 33.333 0.00 0.00 34.30 2.71
375 379 6.420604 ACAAGTCCTAAAATTTGCACGAAATG 59.579 34.615 0.00 0.00 34.30 2.32
376 380 6.420604 CACAAGTCCTAAAATTTGCACGAAAT 59.579 34.615 0.00 0.00 35.65 2.17
377 381 5.746245 CACAAGTCCTAAAATTTGCACGAAA 59.254 36.000 0.00 0.00 0.00 3.46
378 382 5.277825 CACAAGTCCTAAAATTTGCACGAA 58.722 37.500 0.00 0.00 0.00 3.85
379 383 4.261405 CCACAAGTCCTAAAATTTGCACGA 60.261 41.667 0.00 0.00 0.00 4.35
380 384 3.980775 CCACAAGTCCTAAAATTTGCACG 59.019 43.478 0.00 0.00 0.00 5.34
381 385 4.744631 CACCACAAGTCCTAAAATTTGCAC 59.255 41.667 0.00 0.00 0.00 4.57
382 386 4.739137 GCACCACAAGTCCTAAAATTTGCA 60.739 41.667 0.00 0.00 0.00 4.08
383 387 3.740832 GCACCACAAGTCCTAAAATTTGC 59.259 43.478 0.00 0.00 0.00 3.68
384 388 5.200368 AGCACCACAAGTCCTAAAATTTG 57.800 39.130 0.00 0.00 0.00 2.32
385 389 7.539034 AATAGCACCACAAGTCCTAAAATTT 57.461 32.000 0.00 0.00 0.00 1.82
386 390 7.122204 GGTAATAGCACCACAAGTCCTAAAATT 59.878 37.037 0.00 0.00 38.55 1.82
387 391 6.602009 GGTAATAGCACCACAAGTCCTAAAAT 59.398 38.462 0.00 0.00 38.55 1.82
388 392 5.941647 GGTAATAGCACCACAAGTCCTAAAA 59.058 40.000 0.00 0.00 38.55 1.52
389 393 5.249852 AGGTAATAGCACCACAAGTCCTAAA 59.750 40.000 0.00 0.00 41.40 1.85
390 394 4.781087 AGGTAATAGCACCACAAGTCCTAA 59.219 41.667 0.00 0.00 41.40 2.69
391 395 4.359105 AGGTAATAGCACCACAAGTCCTA 58.641 43.478 0.00 0.00 41.40 2.94
392 396 3.182152 AGGTAATAGCACCACAAGTCCT 58.818 45.455 0.00 0.00 41.40 3.85
393 397 3.629142 AGGTAATAGCACCACAAGTCC 57.371 47.619 0.00 0.00 41.40 3.85
394 398 4.575885 TGAAGGTAATAGCACCACAAGTC 58.424 43.478 0.00 0.00 41.40 3.01
395 399 4.634012 TGAAGGTAATAGCACCACAAGT 57.366 40.909 0.00 0.00 41.40 3.16
396 400 5.245531 TCTTGAAGGTAATAGCACCACAAG 58.754 41.667 17.82 17.82 45.65 3.16
397 401 5.235850 TCTTGAAGGTAATAGCACCACAA 57.764 39.130 0.00 0.00 41.40 3.33
398 402 4.901197 TCTTGAAGGTAATAGCACCACA 57.099 40.909 0.00 0.00 41.40 4.17
399 403 6.569179 TTTTCTTGAAGGTAATAGCACCAC 57.431 37.500 0.00 0.00 41.40 4.16
400 404 6.547880 TGTTTTTCTTGAAGGTAATAGCACCA 59.452 34.615 0.00 0.00 41.40 4.17
401 405 6.861572 GTGTTTTTCTTGAAGGTAATAGCACC 59.138 38.462 0.00 0.00 39.02 5.01
402 406 6.577427 CGTGTTTTTCTTGAAGGTAATAGCAC 59.423 38.462 0.00 0.00 0.00 4.40
403 407 6.664515 CGTGTTTTTCTTGAAGGTAATAGCA 58.335 36.000 0.00 0.00 0.00 3.49
404 408 5.567915 GCGTGTTTTTCTTGAAGGTAATAGC 59.432 40.000 0.00 0.00 0.00 2.97
405 409 6.577427 GTGCGTGTTTTTCTTGAAGGTAATAG 59.423 38.462 0.00 0.00 0.00 1.73
406 410 6.038382 TGTGCGTGTTTTTCTTGAAGGTAATA 59.962 34.615 0.00 0.00 0.00 0.98
407 411 5.163602 TGTGCGTGTTTTTCTTGAAGGTAAT 60.164 36.000 0.00 0.00 0.00 1.89
408 412 4.156190 TGTGCGTGTTTTTCTTGAAGGTAA 59.844 37.500 0.00 0.00 0.00 2.85
409 413 3.690139 TGTGCGTGTTTTTCTTGAAGGTA 59.310 39.130 0.00 0.00 0.00 3.08
410 414 2.490115 TGTGCGTGTTTTTCTTGAAGGT 59.510 40.909 0.00 0.00 0.00 3.50
411 415 2.851824 GTGTGCGTGTTTTTCTTGAAGG 59.148 45.455 0.00 0.00 0.00 3.46
412 416 2.525891 CGTGTGCGTGTTTTTCTTGAAG 59.474 45.455 0.00 0.00 0.00 3.02
413 417 2.159824 TCGTGTGCGTGTTTTTCTTGAA 59.840 40.909 0.00 0.00 39.49 2.69
414 418 1.732809 TCGTGTGCGTGTTTTTCTTGA 59.267 42.857 0.00 0.00 39.49 3.02
415 419 2.166741 TCGTGTGCGTGTTTTTCTTG 57.833 45.000 0.00 0.00 39.49 3.02
416 420 3.602946 CGTATCGTGTGCGTGTTTTTCTT 60.603 43.478 0.00 0.00 39.49 2.52
417 421 2.097104 CGTATCGTGTGCGTGTTTTTCT 60.097 45.455 0.00 0.00 39.49 2.52
418 422 2.219355 CGTATCGTGTGCGTGTTTTTC 58.781 47.619 0.00 0.00 39.49 2.29
419 423 1.070443 CCGTATCGTGTGCGTGTTTTT 60.070 47.619 0.00 0.00 39.49 1.94
420 424 0.509499 CCGTATCGTGTGCGTGTTTT 59.491 50.000 0.00 0.00 39.49 2.43
421 425 0.318869 TCCGTATCGTGTGCGTGTTT 60.319 50.000 0.00 0.00 39.49 2.83
422 426 1.005294 GTCCGTATCGTGTGCGTGTT 61.005 55.000 0.00 0.00 39.49 3.32
423 427 1.443194 GTCCGTATCGTGTGCGTGT 60.443 57.895 0.00 0.00 39.49 4.49
500 509 2.436417 GGCTAAGCAACCACAGAATCA 58.564 47.619 0.00 0.00 0.00 2.57
597 611 7.006865 AGGTAGATCGCAGTATCTAGTCTAA 57.993 40.000 1.69 0.00 38.76 2.10
598 612 6.608539 AGGTAGATCGCAGTATCTAGTCTA 57.391 41.667 1.69 0.00 38.76 2.59
687 727 4.870991 GCTGTGGGAGAGATTTGTTACTAC 59.129 45.833 0.00 0.00 0.00 2.73
695 735 1.448540 CGCGCTGTGGGAGAGATTT 60.449 57.895 5.56 0.00 0.00 2.17
727 774 3.462982 ACGTGTCTGCATGTACTTTTCA 58.537 40.909 0.00 0.00 42.54 2.69
839 919 3.741344 CCTCTTATATAGTGTGCGCAACC 59.259 47.826 14.00 5.36 0.00 3.77
877 970 2.880268 TGTAATGCATATGTGGCTCTGC 59.120 45.455 0.00 0.00 35.21 4.26
1056 1216 3.079478 AGGAGCATGAGCAGGCGA 61.079 61.111 0.00 0.00 43.74 5.54
1488 1714 1.816863 GCGTCAGGTTCAGGTCCAGA 61.817 60.000 0.00 0.00 0.00 3.86
1774 2012 1.338973 TCTGTTTCAGAACTACGCCGT 59.661 47.619 0.00 0.00 37.57 5.68
1888 2126 6.565247 GCGTAGTAAGCAAACATTGTTACACT 60.565 38.462 1.76 4.94 33.53 3.55
1895 2133 4.404507 ACAGCGTAGTAAGCAAACATTG 57.595 40.909 10.76 1.54 37.01 2.82
1952 2538 6.640518 TGTTAGCCTTCATTAGTAGGAACAG 58.359 40.000 0.00 0.00 34.44 3.16
2006 2592 5.983540 AGCCTTCATTAGTAGGAACAGAAG 58.016 41.667 0.00 0.00 34.44 2.85
2033 2619 6.686630 TGAATATTGACTTGCCGAAACAAAT 58.313 32.000 0.00 0.00 0.00 2.32
2034 2620 6.078202 TGAATATTGACTTGCCGAAACAAA 57.922 33.333 0.00 0.00 0.00 2.83
2035 2621 5.697473 TGAATATTGACTTGCCGAAACAA 57.303 34.783 0.00 0.00 0.00 2.83
2036 2622 5.895636 ATGAATATTGACTTGCCGAAACA 57.104 34.783 0.00 0.00 0.00 2.83
2037 2623 7.968405 ACTTTATGAATATTGACTTGCCGAAAC 59.032 33.333 0.00 0.00 0.00 2.78
2038 2624 8.050778 ACTTTATGAATATTGACTTGCCGAAA 57.949 30.769 0.00 0.00 0.00 3.46
2039 2625 7.624360 ACTTTATGAATATTGACTTGCCGAA 57.376 32.000 0.00 0.00 0.00 4.30
2040 2626 7.624360 AACTTTATGAATATTGACTTGCCGA 57.376 32.000 0.00 0.00 0.00 5.54
2041 2627 8.184192 AGAAACTTTATGAATATTGACTTGCCG 58.816 33.333 0.00 0.00 0.00 5.69
2042 2628 9.294030 CAGAAACTTTATGAATATTGACTTGCC 57.706 33.333 0.00 0.00 0.00 4.52
2043 2629 9.846248 ACAGAAACTTTATGAATATTGACTTGC 57.154 29.630 3.14 0.00 0.00 4.01
2049 2635 9.294030 GCAGGAACAGAAACTTTATGAATATTG 57.706 33.333 3.14 0.00 0.00 1.90
2050 2636 8.470002 GGCAGGAACAGAAACTTTATGAATATT 58.530 33.333 3.14 0.00 0.00 1.28
2051 2637 7.615365 TGGCAGGAACAGAAACTTTATGAATAT 59.385 33.333 3.14 0.00 0.00 1.28
2052 2638 6.945435 TGGCAGGAACAGAAACTTTATGAATA 59.055 34.615 3.14 0.00 0.00 1.75
2053 2639 5.774690 TGGCAGGAACAGAAACTTTATGAAT 59.225 36.000 3.14 0.00 0.00 2.57
2054 2640 5.136828 TGGCAGGAACAGAAACTTTATGAA 58.863 37.500 3.14 0.00 0.00 2.57
2055 2641 4.724399 TGGCAGGAACAGAAACTTTATGA 58.276 39.130 3.14 0.00 0.00 2.15
2056 2642 5.452078 TTGGCAGGAACAGAAACTTTATG 57.548 39.130 0.00 0.00 0.00 1.90
2057 2643 5.774690 TCATTGGCAGGAACAGAAACTTTAT 59.225 36.000 0.00 0.00 0.00 1.40
2058 2644 5.136828 TCATTGGCAGGAACAGAAACTTTA 58.863 37.500 0.00 0.00 0.00 1.85
2059 2645 3.960102 TCATTGGCAGGAACAGAAACTTT 59.040 39.130 0.00 0.00 0.00 2.66
2060 2646 3.565307 TCATTGGCAGGAACAGAAACTT 58.435 40.909 0.00 0.00 0.00 2.66
2061 2647 3.228188 TCATTGGCAGGAACAGAAACT 57.772 42.857 0.00 0.00 0.00 2.66
2062 2648 3.305608 CCTTCATTGGCAGGAACAGAAAC 60.306 47.826 0.20 0.00 30.81 2.78
2063 2649 2.892852 CCTTCATTGGCAGGAACAGAAA 59.107 45.455 0.20 0.00 30.81 2.52
2064 2650 2.517959 CCTTCATTGGCAGGAACAGAA 58.482 47.619 0.20 0.00 30.81 3.02
2065 2651 2.205022 CCTTCATTGGCAGGAACAGA 57.795 50.000 0.20 0.00 30.81 3.41
2075 2661 4.996788 AGAAAATGCTAGCCTTCATTGG 57.003 40.909 13.29 0.00 33.61 3.16
2076 2662 5.957798 TGAAGAAAATGCTAGCCTTCATTG 58.042 37.500 21.99 0.00 38.49 2.82
2077 2663 5.948162 TCTGAAGAAAATGCTAGCCTTCATT 59.052 36.000 24.44 11.64 41.31 2.57
2078 2664 5.503927 TCTGAAGAAAATGCTAGCCTTCAT 58.496 37.500 24.44 13.56 41.31 2.57
2079 2665 4.910195 TCTGAAGAAAATGCTAGCCTTCA 58.090 39.130 23.40 23.40 40.33 3.02
2080 2666 5.182001 TGTTCTGAAGAAAATGCTAGCCTTC 59.818 40.000 18.41 18.41 35.58 3.46
2081 2667 5.072741 TGTTCTGAAGAAAATGCTAGCCTT 58.927 37.500 13.29 5.73 35.58 4.35
2082 2668 4.655963 TGTTCTGAAGAAAATGCTAGCCT 58.344 39.130 13.29 0.00 35.58 4.58
2083 2669 4.697352 TCTGTTCTGAAGAAAATGCTAGCC 59.303 41.667 13.29 0.00 35.58 3.93
2084 2670 5.869753 TCTGTTCTGAAGAAAATGCTAGC 57.130 39.130 8.10 8.10 35.58 3.42
2085 2671 7.869800 ACTTTCTGTTCTGAAGAAAATGCTAG 58.130 34.615 6.13 0.00 41.74 3.42
2086 2672 7.498900 TGACTTTCTGTTCTGAAGAAAATGCTA 59.501 33.333 6.13 0.00 41.74 3.49
2087 2673 6.319658 TGACTTTCTGTTCTGAAGAAAATGCT 59.680 34.615 6.13 0.00 41.74 3.79
2088 2674 6.498304 TGACTTTCTGTTCTGAAGAAAATGC 58.502 36.000 6.13 1.13 41.74 3.56
2089 2675 8.915871 TTTGACTTTCTGTTCTGAAGAAAATG 57.084 30.769 6.13 0.00 41.74 2.32
2287 2873 1.000171 CCTTGCTTTCAGTTTCCAGCC 60.000 52.381 0.00 0.00 0.00 4.85
2288 2874 1.000171 CCCTTGCTTTCAGTTTCCAGC 60.000 52.381 0.00 0.00 0.00 4.85
2289 2875 2.586425 TCCCTTGCTTTCAGTTTCCAG 58.414 47.619 0.00 0.00 0.00 3.86
2292 2878 4.385358 TTGTTCCCTTGCTTTCAGTTTC 57.615 40.909 0.00 0.00 0.00 2.78
2301 2887 3.450457 TGTTGAATGTTTGTTCCCTTGCT 59.550 39.130 0.00 0.00 0.00 3.91
2308 2894 7.461416 CGTCTTTGAACTGTTGAATGTTTGTTC 60.461 37.037 0.00 0.00 35.68 3.18
2377 2963 8.391106 GCTGTAGACCTTGTTTTGTTCTATATG 58.609 37.037 0.00 0.00 0.00 1.78
2440 3026 2.620115 CACCTGAAATCCCGAATGATGG 59.380 50.000 0.00 0.00 0.00 3.51
2449 3035 4.890158 AAAAATGACCACCTGAAATCCC 57.110 40.909 0.00 0.00 0.00 3.85
2476 3062 4.095483 GGGTAGAGTTTGTCTTCGATCGTA 59.905 45.833 15.94 4.34 36.64 3.43
2483 3069 3.764237 TGGTGGGTAGAGTTTGTCTTC 57.236 47.619 0.00 0.00 36.64 2.87
2542 3128 1.333791 CGAGTACGATGCATACTGCGA 60.334 52.381 11.94 0.00 43.98 5.10
2555 3141 0.659427 TATGGGACGAAGCGAGTACG 59.341 55.000 0.00 0.00 42.93 3.67


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

AutoCloner maintained by Alex Coulton.