Multiple sequence alignment - TraesCS7B01G144700

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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 TraesCS7B01G144700 chr7B 100.000 3887 0 0 1 3887 186873109 186869223 0.000000e+00 7179.0
1 TraesCS7B01G144700 chr7B 87.500 80 7 3 1 80 710202772 710202696 5.350000e-14 89.8
2 TraesCS7B01G144700 chr7D 97.439 3202 62 7 703 3887 214328349 214331547 0.000000e+00 5441.0
3 TraesCS7B01G144700 chr7A 96.844 3264 78 7 635 3887 226713899 226717148 0.000000e+00 5433.0
4 TraesCS7B01G144700 chr2A 88.694 513 43 7 119 618 418797155 418796645 2.570000e-171 612.0
5 TraesCS7B01G144700 chr2A 86.364 88 9 3 1 85 67512263 67512350 4.140000e-15 93.5
6 TraesCS7B01G144700 chr5B 86.117 461 45 8 114 561 598760572 598760118 2.720000e-131 479.0
7 TraesCS7B01G144700 chr3B 82.268 485 57 19 110 590 786108894 786109353 3.640000e-105 392.0
8 TraesCS7B01G144700 chr3A 92.754 69 5 0 1 69 85441254 85441186 2.470000e-17 100.0
9 TraesCS7B01G144700 chr3A 89.333 75 6 2 1 75 434399268 434399340 4.140000e-15 93.5
10 TraesCS7B01G144700 chr6A 91.304 69 6 0 1 69 404288175 404288107 1.150000e-15 95.3
11 TraesCS7B01G144700 chr4A 86.905 84 9 2 1 82 567461827 567461910 4.140000e-15 93.5
12 TraesCS7B01G144700 chr4A 83.838 99 12 4 1 96 727098682 727098585 1.490000e-14 91.6
13 TraesCS7B01G144700 chr1D 86.905 84 10 1 1 84 190464611 190464529 4.140000e-15 93.5
14 TraesCS7B01G144700 chr6B 85.393 89 7 5 1 84 473174951 473175038 1.920000e-13 87.9
15 TraesCS7B01G144700 chr2B 100.000 29 0 0 449 477 704767921 704767893 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G144700 chr7B 186869223 186873109 3886 True 7179 7179 100.000 1 3887 1 chr7B.!!$R1 3886
1 TraesCS7B01G144700 chr7D 214328349 214331547 3198 False 5441 5441 97.439 703 3887 1 chr7D.!!$F1 3184
2 TraesCS7B01G144700 chr7A 226713899 226717148 3249 False 5433 5433 96.844 635 3887 1 chr7A.!!$F1 3252
3 TraesCS7B01G144700 chr2A 418796645 418797155 510 True 612 612 88.694 119 618 1 chr2A.!!$R1 499

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
283 284 0.107993 CATGAGACTGCCGATGTGGT 60.108 55.0 0.00 0.00 41.21 4.16 F
284 285 0.176680 ATGAGACTGCCGATGTGGTC 59.823 55.0 0.00 0.00 41.21 4.02 F
775 776 0.312416 CCTATCTCGGAAGCGAGTGG 59.688 60.0 0.00 0.00 37.30 4.00 F
1491 1503 1.342074 TGTCAGTCTCCAGGTTCCTG 58.658 55.0 11.52 11.52 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1271 1283 1.531748 GAATCCGGGATCTTGGCCA 59.468 57.895 10.56 0.00 0.00 5.36 R
1515 1527 1.870016 GCTCTCGAAGAACGGCTCG 60.870 63.158 0.00 0.00 42.82 5.03 R
2088 2100 2.048023 CCATGGGCACTGCACGAAT 61.048 57.895 2.85 0.00 32.76 3.34 R
2961 2987 0.680921 GTAGCCCTGCATTGCAAGGA 60.681 55.000 26.87 6.99 42.28 3.36 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
48 49 9.561069 TTATTGTCTCTAAGGCATATTTCCTTC 57.439 33.333 8.83 0.00 42.57 3.46
49 50 6.560003 TGTCTCTAAGGCATATTTCCTTCA 57.440 37.500 8.83 0.42 42.57 3.02
50 51 6.586344 TGTCTCTAAGGCATATTTCCTTCAG 58.414 40.000 8.83 7.35 42.57 3.02
51 52 6.156949 TGTCTCTAAGGCATATTTCCTTCAGT 59.843 38.462 8.83 0.00 42.57 3.41
52 53 7.051000 GTCTCTAAGGCATATTTCCTTCAGTT 58.949 38.462 8.83 0.00 42.57 3.16
53 54 7.225734 GTCTCTAAGGCATATTTCCTTCAGTTC 59.774 40.741 8.83 3.74 42.57 3.01
54 55 7.126421 TCTCTAAGGCATATTTCCTTCAGTTCT 59.874 37.037 8.83 0.00 42.57 3.01
55 56 7.633789 TCTAAGGCATATTTCCTTCAGTTCTT 58.366 34.615 8.83 0.00 42.57 2.52
56 57 8.768397 TCTAAGGCATATTTCCTTCAGTTCTTA 58.232 33.333 8.83 0.00 42.57 2.10
57 58 7.872113 AAGGCATATTTCCTTCAGTTCTTAG 57.128 36.000 1.12 0.00 39.63 2.18
58 59 5.825151 AGGCATATTTCCTTCAGTTCTTAGC 59.175 40.000 0.00 0.00 0.00 3.09
59 60 5.590259 GGCATATTTCCTTCAGTTCTTAGCA 59.410 40.000 0.00 0.00 0.00 3.49
60 61 6.264067 GGCATATTTCCTTCAGTTCTTAGCAT 59.736 38.462 0.00 0.00 0.00 3.79
61 62 7.201857 GGCATATTTCCTTCAGTTCTTAGCATT 60.202 37.037 0.00 0.00 0.00 3.56
62 63 8.193438 GCATATTTCCTTCAGTTCTTAGCATTT 58.807 33.333 0.00 0.00 0.00 2.32
67 68 9.912634 TTTCCTTCAGTTCTTAGCATTTAAATG 57.087 29.630 21.54 21.54 39.40 2.32
68 69 8.862325 TCCTTCAGTTCTTAGCATTTAAATGA 57.138 30.769 28.33 8.73 38.70 2.57
69 70 9.466497 TCCTTCAGTTCTTAGCATTTAAATGAT 57.534 29.630 28.33 24.93 38.70 2.45
132 133 1.084289 AAATACTCCGCTTCAACCGC 58.916 50.000 0.00 0.00 0.00 5.68
144 145 2.744709 AACCGCCCGATTTCCACG 60.745 61.111 0.00 0.00 0.00 4.94
162 163 2.743718 CCATTATCCGCCGCCTCT 59.256 61.111 0.00 0.00 0.00 3.69
183 184 2.410060 ACGCGACGTGTGTCTTGA 59.590 55.556 15.93 0.00 43.21 3.02
218 219 2.173519 CACTACAACGGGAGGTTCCTA 58.826 52.381 0.00 0.00 36.49 2.94
235 236 8.201242 AGGTTCCTATTCCTCTTCAATATCTC 57.799 38.462 0.00 0.00 0.00 2.75
236 237 8.016054 AGGTTCCTATTCCTCTTCAATATCTCT 58.984 37.037 0.00 0.00 0.00 3.10
242 243 5.946942 TCCTCTTCAATATCTCTGCAAGT 57.053 39.130 0.00 0.00 33.76 3.16
248 249 6.541278 TCTTCAATATCTCTGCAAGTGAATGG 59.459 38.462 0.00 0.00 40.20 3.16
249 250 5.748402 TCAATATCTCTGCAAGTGAATGGT 58.252 37.500 0.00 0.00 40.20 3.55
251 252 7.337938 TCAATATCTCTGCAAGTGAATGGTTA 58.662 34.615 0.00 0.00 40.20 2.85
280 281 1.520120 CGCATGAGACTGCCGATGT 60.520 57.895 0.00 0.00 39.00 3.06
282 283 1.434622 GCATGAGACTGCCGATGTGG 61.435 60.000 0.00 0.00 42.50 4.17
283 284 0.107993 CATGAGACTGCCGATGTGGT 60.108 55.000 0.00 0.00 41.21 4.16
284 285 0.176680 ATGAGACTGCCGATGTGGTC 59.823 55.000 0.00 0.00 41.21 4.02
285 286 0.900182 TGAGACTGCCGATGTGGTCT 60.900 55.000 0.00 0.00 41.05 3.85
286 287 0.459237 GAGACTGCCGATGTGGTCTG 60.459 60.000 0.00 0.00 38.87 3.51
287 288 1.448540 GACTGCCGATGTGGTCTGG 60.449 63.158 0.00 0.00 41.21 3.86
288 289 1.888436 GACTGCCGATGTGGTCTGGA 61.888 60.000 0.00 0.00 41.21 3.86
289 290 1.296392 CTGCCGATGTGGTCTGGAA 59.704 57.895 0.00 0.00 41.21 3.53
290 291 0.742281 CTGCCGATGTGGTCTGGAAG 60.742 60.000 0.00 0.00 41.21 3.46
291 292 2.109126 GCCGATGTGGTCTGGAAGC 61.109 63.158 0.00 0.00 41.21 3.86
292 293 1.811266 CCGATGTGGTCTGGAAGCG 60.811 63.158 0.00 0.00 0.00 4.68
293 294 1.811266 CGATGTGGTCTGGAAGCGG 60.811 63.158 0.00 0.00 0.00 5.52
294 295 1.450312 GATGTGGTCTGGAAGCGGG 60.450 63.158 0.00 0.00 0.00 6.13
295 296 3.628646 ATGTGGTCTGGAAGCGGGC 62.629 63.158 0.00 0.00 0.00 6.13
296 297 4.329545 GTGGTCTGGAAGCGGGCA 62.330 66.667 0.00 0.00 0.00 5.36
297 298 3.565214 TGGTCTGGAAGCGGGCAA 61.565 61.111 0.00 0.00 0.00 4.52
298 299 2.282180 GGTCTGGAAGCGGGCAAA 60.282 61.111 0.00 0.00 0.00 3.68
299 300 1.901464 GGTCTGGAAGCGGGCAAAA 60.901 57.895 0.00 0.00 0.00 2.44
300 301 1.250840 GGTCTGGAAGCGGGCAAAAT 61.251 55.000 0.00 0.00 0.00 1.82
301 302 0.603065 GTCTGGAAGCGGGCAAAATT 59.397 50.000 0.00 0.00 0.00 1.82
302 303 1.000843 GTCTGGAAGCGGGCAAAATTT 59.999 47.619 0.00 0.00 0.00 1.82
303 304 1.691434 TCTGGAAGCGGGCAAAATTTT 59.309 42.857 0.00 0.00 0.00 1.82
304 305 2.068519 CTGGAAGCGGGCAAAATTTTC 58.931 47.619 0.00 0.00 0.00 2.29
305 306 1.691434 TGGAAGCGGGCAAAATTTTCT 59.309 42.857 0.00 0.00 0.00 2.52
306 307 2.068519 GGAAGCGGGCAAAATTTTCTG 58.931 47.619 0.00 0.00 0.00 3.02
307 308 1.460743 GAAGCGGGCAAAATTTTCTGC 59.539 47.619 13.09 13.09 37.86 4.26
308 309 0.392336 AGCGGGCAAAATTTTCTGCA 59.608 45.000 19.81 0.00 40.46 4.41
309 310 1.202627 AGCGGGCAAAATTTTCTGCAA 60.203 42.857 19.81 0.00 40.46 4.08
310 311 1.069973 GCGGGCAAAATTTTCTGCAAC 60.070 47.619 14.97 7.61 40.46 4.17
311 312 2.208431 CGGGCAAAATTTTCTGCAACA 58.792 42.857 14.97 0.00 40.46 3.33
312 313 2.807392 CGGGCAAAATTTTCTGCAACAT 59.193 40.909 14.97 0.00 40.46 2.71
313 314 3.250521 CGGGCAAAATTTTCTGCAACATT 59.749 39.130 14.97 0.00 40.46 2.71
314 315 4.450419 CGGGCAAAATTTTCTGCAACATTA 59.550 37.500 14.97 0.00 40.46 1.90
315 316 5.614449 CGGGCAAAATTTTCTGCAACATTAC 60.614 40.000 14.97 0.00 40.46 1.89
316 317 5.334802 GGGCAAAATTTTCTGCAACATTACC 60.335 40.000 14.97 3.61 40.46 2.85
317 318 5.469760 GGCAAAATTTTCTGCAACATTACCT 59.530 36.000 14.97 0.00 40.46 3.08
318 319 6.648725 GGCAAAATTTTCTGCAACATTACCTA 59.351 34.615 14.97 0.00 40.46 3.08
319 320 7.334171 GGCAAAATTTTCTGCAACATTACCTAT 59.666 33.333 14.97 0.00 40.46 2.57
320 321 9.364989 GCAAAATTTTCTGCAACATTACCTATA 57.635 29.630 9.48 0.00 38.48 1.31
329 330 9.764363 TCTGCAACATTACCTATATTGTAGAAG 57.236 33.333 0.00 0.00 38.51 2.85
330 331 9.547753 CTGCAACATTACCTATATTGTAGAAGT 57.452 33.333 0.00 0.00 35.70 3.01
331 332 9.899661 TGCAACATTACCTATATTGTAGAAGTT 57.100 29.630 0.00 0.00 0.00 2.66
351 352 2.859526 TTTTCGCAACATCACTTGCA 57.140 40.000 4.88 0.00 45.88 4.08
352 353 2.859526 TTTCGCAACATCACTTGCAA 57.140 40.000 0.00 0.00 45.88 4.08
353 354 2.859526 TTCGCAACATCACTTGCAAA 57.140 40.000 0.00 0.00 45.88 3.68
354 355 2.859526 TCGCAACATCACTTGCAAAA 57.140 40.000 0.00 0.00 45.88 2.44
355 356 3.156511 TCGCAACATCACTTGCAAAAA 57.843 38.095 0.00 0.00 45.88 1.94
434 435 7.853524 CATCACTTATGTTGCAAAAACAATGT 58.146 30.769 0.00 0.00 33.42 2.71
435 436 8.976471 CATCACTTATGTTGCAAAAACAATGTA 58.024 29.630 0.00 0.00 33.42 2.29
436 437 8.572828 TCACTTATGTTGCAAAAACAATGTAG 57.427 30.769 0.00 0.00 33.42 2.74
437 438 7.168972 TCACTTATGTTGCAAAAACAATGTAGC 59.831 33.333 0.00 0.00 33.42 3.58
438 439 7.169645 CACTTATGTTGCAAAAACAATGTAGCT 59.830 33.333 0.00 0.00 33.42 3.32
439 440 7.382218 ACTTATGTTGCAAAAACAATGTAGCTC 59.618 33.333 0.00 0.00 33.42 4.09
440 441 5.003692 TGTTGCAAAAACAATGTAGCTCA 57.996 34.783 0.00 0.00 0.00 4.26
441 442 5.414360 TGTTGCAAAAACAATGTAGCTCAA 58.586 33.333 0.00 0.00 0.00 3.02
442 443 5.871524 TGTTGCAAAAACAATGTAGCTCAAA 59.128 32.000 0.00 0.00 0.00 2.69
443 444 6.369890 TGTTGCAAAAACAATGTAGCTCAAAA 59.630 30.769 0.00 0.00 0.00 2.44
444 445 6.974932 TGCAAAAACAATGTAGCTCAAAAA 57.025 29.167 0.00 0.00 0.00 1.94
445 446 6.770076 TGCAAAAACAATGTAGCTCAAAAAC 58.230 32.000 0.00 0.00 0.00 2.43
446 447 6.369890 TGCAAAAACAATGTAGCTCAAAAACA 59.630 30.769 0.00 0.00 0.00 2.83
447 448 7.065563 TGCAAAAACAATGTAGCTCAAAAACAT 59.934 29.630 0.00 0.00 35.40 2.71
448 449 7.909641 GCAAAAACAATGTAGCTCAAAAACATT 59.090 29.630 6.06 6.06 42.91 2.71
449 450 9.771915 CAAAAACAATGTAGCTCAAAAACATTT 57.228 25.926 8.72 0.50 40.83 2.32
450 451 9.986833 AAAAACAATGTAGCTCAAAAACATTTC 57.013 25.926 8.72 0.00 40.83 2.17
451 452 8.947055 AAACAATGTAGCTCAAAAACATTTCT 57.053 26.923 8.72 0.00 40.83 2.52
452 453 7.935338 ACAATGTAGCTCAAAAACATTTCTG 57.065 32.000 8.72 3.01 40.83 3.02
453 454 6.421801 ACAATGTAGCTCAAAAACATTTCTGC 59.578 34.615 8.72 0.00 40.83 4.26
454 455 5.512753 TGTAGCTCAAAAACATTTCTGCA 57.487 34.783 0.00 0.00 0.00 4.41
455 456 5.900425 TGTAGCTCAAAAACATTTCTGCAA 58.100 33.333 0.00 0.00 0.00 4.08
456 457 5.748152 TGTAGCTCAAAAACATTTCTGCAAC 59.252 36.000 0.00 0.00 0.00 4.17
457 458 4.757594 AGCTCAAAAACATTTCTGCAACA 58.242 34.783 0.00 0.00 0.00 3.33
458 459 5.362263 AGCTCAAAAACATTTCTGCAACAT 58.638 33.333 0.00 0.00 0.00 2.71
459 460 5.235616 AGCTCAAAAACATTTCTGCAACATG 59.764 36.000 0.00 0.00 0.00 3.21
460 461 5.234757 GCTCAAAAACATTTCTGCAACATGA 59.765 36.000 0.00 0.00 0.00 3.07
461 462 6.586868 TCAAAAACATTTCTGCAACATGAC 57.413 33.333 0.00 0.00 0.00 3.06
462 463 6.104665 TCAAAAACATTTCTGCAACATGACA 58.895 32.000 0.00 0.00 0.00 3.58
463 464 6.762187 TCAAAAACATTTCTGCAACATGACAT 59.238 30.769 0.00 0.00 0.00 3.06
464 465 7.924947 TCAAAAACATTTCTGCAACATGACATA 59.075 29.630 0.00 0.00 0.00 2.29
465 466 8.714179 CAAAAACATTTCTGCAACATGACATAT 58.286 29.630 0.00 0.00 0.00 1.78
466 467 7.821595 AAACATTTCTGCAACATGACATATG 57.178 32.000 0.00 0.00 0.00 1.78
467 468 6.519679 ACATTTCTGCAACATGACATATGT 57.480 33.333 8.43 8.43 0.00 2.29
468 469 6.927416 ACATTTCTGCAACATGACATATGTT 58.073 32.000 10.30 0.00 42.38 2.71
478 479 6.519679 ACATGACATATGTTGCAAATGTCT 57.480 33.333 29.33 18.69 46.22 3.41
479 480 6.927416 ACATGACATATGTTGCAAATGTCTT 58.073 32.000 29.33 23.98 46.22 3.01
480 481 7.380536 ACATGACATATGTTGCAAATGTCTTT 58.619 30.769 29.33 19.89 46.22 2.52
481 482 7.543172 ACATGACATATGTTGCAAATGTCTTTC 59.457 33.333 29.33 14.29 46.22 2.62
482 483 6.085573 TGACATATGTTGCAAATGTCTTTCG 58.914 36.000 29.33 7.68 46.22 3.46
483 484 4.858692 ACATATGTTGCAAATGTCTTTCGC 59.141 37.500 9.03 0.00 0.00 4.70
484 485 2.859526 TGTTGCAAATGTCTTTCGCA 57.140 40.000 0.00 0.00 31.25 5.10
485 486 3.156511 TGTTGCAAATGTCTTTCGCAA 57.843 38.095 0.00 0.00 36.71 4.85
486 487 3.715495 TGTTGCAAATGTCTTTCGCAAT 58.285 36.364 0.00 0.00 38.91 3.56
487 488 4.864633 TGTTGCAAATGTCTTTCGCAATA 58.135 34.783 0.00 0.00 38.91 1.90
488 489 4.679197 TGTTGCAAATGTCTTTCGCAATAC 59.321 37.500 0.00 0.00 38.91 1.89
489 490 4.495911 TGCAAATGTCTTTCGCAATACA 57.504 36.364 0.00 0.00 30.65 2.29
490 491 4.225984 TGCAAATGTCTTTCGCAATACAC 58.774 39.130 0.00 0.00 30.65 2.90
491 492 3.608073 GCAAATGTCTTTCGCAATACACC 59.392 43.478 0.00 0.00 0.00 4.16
492 493 4.615912 GCAAATGTCTTTCGCAATACACCT 60.616 41.667 0.00 0.00 0.00 4.00
493 494 5.460646 CAAATGTCTTTCGCAATACACCTT 58.539 37.500 0.00 0.00 0.00 3.50
494 495 4.946784 ATGTCTTTCGCAATACACCTTC 57.053 40.909 0.00 0.00 0.00 3.46
495 496 4.002906 TGTCTTTCGCAATACACCTTCT 57.997 40.909 0.00 0.00 0.00 2.85
496 497 3.745975 TGTCTTTCGCAATACACCTTCTG 59.254 43.478 0.00 0.00 0.00 3.02
497 498 3.746492 GTCTTTCGCAATACACCTTCTGT 59.254 43.478 0.00 0.00 36.82 3.41
498 499 4.927425 GTCTTTCGCAATACACCTTCTGTA 59.073 41.667 0.00 0.00 39.78 2.74
499 500 4.927425 TCTTTCGCAATACACCTTCTGTAC 59.073 41.667 0.00 0.00 38.22 2.90
500 501 3.945981 TCGCAATACACCTTCTGTACA 57.054 42.857 0.00 0.00 38.22 2.90
501 502 4.260139 TCGCAATACACCTTCTGTACAA 57.740 40.909 0.00 0.00 38.22 2.41
502 503 4.633175 TCGCAATACACCTTCTGTACAAA 58.367 39.130 0.00 0.00 38.22 2.83
503 504 5.242434 TCGCAATACACCTTCTGTACAAAT 58.758 37.500 0.00 0.00 38.22 2.32
504 505 6.399743 TCGCAATACACCTTCTGTACAAATA 58.600 36.000 0.00 0.00 38.22 1.40
505 506 7.045416 TCGCAATACACCTTCTGTACAAATAT 58.955 34.615 0.00 0.00 38.22 1.28
506 507 7.551262 TCGCAATACACCTTCTGTACAAATATT 59.449 33.333 0.00 0.00 38.22 1.28
507 508 8.181573 CGCAATACACCTTCTGTACAAATATTT 58.818 33.333 0.00 0.00 38.22 1.40
508 509 9.503427 GCAATACACCTTCTGTACAAATATTTC 57.497 33.333 0.00 0.00 38.22 2.17
511 512 7.145932 ACACCTTCTGTACAAATATTTCTGC 57.854 36.000 0.00 0.00 0.00 4.26
512 513 6.714810 ACACCTTCTGTACAAATATTTCTGCA 59.285 34.615 0.00 0.00 0.00 4.41
513 514 7.230510 ACACCTTCTGTACAAATATTTCTGCAA 59.769 33.333 0.00 0.00 0.00 4.08
514 515 7.538678 CACCTTCTGTACAAATATTTCTGCAAC 59.461 37.037 0.00 0.00 0.00 4.17
515 516 7.230510 ACCTTCTGTACAAATATTTCTGCAACA 59.769 33.333 0.00 0.00 0.00 3.33
516 517 8.081633 CCTTCTGTACAAATATTTCTGCAACAA 58.918 33.333 0.00 0.00 0.00 2.83
517 518 9.121517 CTTCTGTACAAATATTTCTGCAACAAG 57.878 33.333 0.00 0.00 0.00 3.16
518 519 8.389779 TCTGTACAAATATTTCTGCAACAAGA 57.610 30.769 0.00 0.00 0.00 3.02
519 520 9.013229 TCTGTACAAATATTTCTGCAACAAGAT 57.987 29.630 0.00 0.00 0.00 2.40
520 521 8.969121 TGTACAAATATTTCTGCAACAAGATG 57.031 30.769 0.00 0.00 0.00 2.90
521 522 8.575589 TGTACAAATATTTCTGCAACAAGATGT 58.424 29.630 0.00 0.00 0.00 3.06
522 523 9.065871 GTACAAATATTTCTGCAACAAGATGTC 57.934 33.333 0.00 0.00 0.00 3.06
523 524 7.889469 ACAAATATTTCTGCAACAAGATGTCT 58.111 30.769 0.00 0.00 0.00 3.41
524 525 7.811236 ACAAATATTTCTGCAACAAGATGTCTG 59.189 33.333 0.00 0.00 0.00 3.51
525 526 7.458409 AATATTTCTGCAACAAGATGTCTGT 57.542 32.000 0.00 0.00 0.00 3.41
526 527 5.779529 ATTTCTGCAACAAGATGTCTGTT 57.220 34.783 0.00 0.00 0.00 3.16
527 528 4.556942 TTCTGCAACAAGATGTCTGTTG 57.443 40.909 10.57 10.57 43.90 3.33
533 534 5.570262 CAACAAGATGTCTGTTGCAAATG 57.430 39.130 0.00 0.00 36.86 2.32
534 535 5.283294 CAACAAGATGTCTGTTGCAAATGA 58.717 37.500 0.00 0.00 36.86 2.57
535 536 5.117355 ACAAGATGTCTGTTGCAAATGAG 57.883 39.130 0.00 0.00 0.00 2.90
536 537 4.581824 ACAAGATGTCTGTTGCAAATGAGT 59.418 37.500 0.00 0.00 0.00 3.41
537 538 5.068198 ACAAGATGTCTGTTGCAAATGAGTT 59.932 36.000 0.00 0.00 0.00 3.01
538 539 5.368256 AGATGTCTGTTGCAAATGAGTTC 57.632 39.130 0.00 2.83 0.00 3.01
539 540 5.068636 AGATGTCTGTTGCAAATGAGTTCT 58.931 37.500 0.00 4.98 0.00 3.01
540 541 4.556942 TGTCTGTTGCAAATGAGTTCTG 57.443 40.909 0.00 0.00 0.00 3.02
541 542 3.243168 TGTCTGTTGCAAATGAGTTCTGC 60.243 43.478 0.00 0.00 36.60 4.26
542 543 2.950975 TCTGTTGCAAATGAGTTCTGCA 59.049 40.909 0.00 0.00 44.04 4.41
547 548 3.708890 TGCAAATGAGTTCTGCAACTTG 58.291 40.909 0.00 0.00 43.37 3.16
548 549 3.380954 TGCAAATGAGTTCTGCAACTTGA 59.619 39.130 0.00 0.00 43.37 3.02
549 550 3.732721 GCAAATGAGTTCTGCAACTTGAC 59.267 43.478 0.00 0.00 43.37 3.18
550 551 4.498682 GCAAATGAGTTCTGCAACTTGACT 60.499 41.667 0.00 0.00 43.37 3.41
551 552 5.585390 CAAATGAGTTCTGCAACTTGACTT 58.415 37.500 0.00 0.00 43.37 3.01
552 553 5.841957 AATGAGTTCTGCAACTTGACTTT 57.158 34.783 0.00 0.00 43.37 2.66
553 554 5.841957 ATGAGTTCTGCAACTTGACTTTT 57.158 34.783 0.00 0.00 43.37 2.27
554 555 4.985413 TGAGTTCTGCAACTTGACTTTTG 58.015 39.130 0.00 0.00 43.37 2.44
555 556 4.458989 TGAGTTCTGCAACTTGACTTTTGT 59.541 37.500 0.00 0.00 43.37 2.83
556 557 5.048083 TGAGTTCTGCAACTTGACTTTTGTT 60.048 36.000 0.00 0.00 43.37 2.83
557 558 5.163513 AGTTCTGCAACTTGACTTTTGTTG 58.836 37.500 0.00 0.00 40.16 3.33
564 565 6.226988 CAACTTGACTTTTGTTGCAAAACT 57.773 33.333 0.00 0.00 35.39 2.66
565 566 7.344910 CAACTTGACTTTTGTTGCAAAACTA 57.655 32.000 0.00 0.00 35.39 2.24
566 567 7.447430 CAACTTGACTTTTGTTGCAAAACTAG 58.553 34.615 0.00 0.00 35.39 2.57
567 568 6.919721 ACTTGACTTTTGTTGCAAAACTAGA 58.080 32.000 0.00 0.00 0.00 2.43
568 569 7.375053 ACTTGACTTTTGTTGCAAAACTAGAA 58.625 30.769 0.00 0.00 0.00 2.10
569 570 7.542130 ACTTGACTTTTGTTGCAAAACTAGAAG 59.458 33.333 0.00 2.95 0.00 2.85
570 571 7.151999 TGACTTTTGTTGCAAAACTAGAAGA 57.848 32.000 0.00 0.00 0.00 2.87
571 572 7.027161 TGACTTTTGTTGCAAAACTAGAAGAC 58.973 34.615 0.00 1.90 0.00 3.01
572 573 6.919721 ACTTTTGTTGCAAAACTAGAAGACA 58.080 32.000 0.00 0.00 0.00 3.41
573 574 7.375053 ACTTTTGTTGCAAAACTAGAAGACAA 58.625 30.769 0.00 0.00 0.00 3.18
574 575 7.542130 ACTTTTGTTGCAAAACTAGAAGACAAG 59.458 33.333 0.00 0.00 0.00 3.16
575 576 4.920376 TGTTGCAAAACTAGAAGACAAGC 58.080 39.130 0.00 0.00 0.00 4.01
576 577 4.640201 TGTTGCAAAACTAGAAGACAAGCT 59.360 37.500 0.00 0.00 0.00 3.74
577 578 4.818534 TGCAAAACTAGAAGACAAGCTG 57.181 40.909 0.00 0.00 0.00 4.24
578 579 4.199310 TGCAAAACTAGAAGACAAGCTGT 58.801 39.130 0.00 0.00 0.00 4.40
579 580 4.035558 TGCAAAACTAGAAGACAAGCTGTG 59.964 41.667 0.00 0.00 0.00 3.66
580 581 4.035675 GCAAAACTAGAAGACAAGCTGTGT 59.964 41.667 0.00 0.00 45.74 3.72
581 582 5.449177 GCAAAACTAGAAGACAAGCTGTGTT 60.449 40.000 0.00 0.00 41.96 3.32
582 583 5.741388 AAACTAGAAGACAAGCTGTGTTG 57.259 39.130 0.00 0.00 41.96 3.33
583 584 3.134458 ACTAGAAGACAAGCTGTGTTGC 58.866 45.455 0.00 0.00 41.96 4.17
584 585 2.338577 AGAAGACAAGCTGTGTTGCT 57.661 45.000 3.96 0.00 46.40 3.91
585 586 3.475566 AGAAGACAAGCTGTGTTGCTA 57.524 42.857 3.96 0.00 43.24 3.49
586 587 3.397482 AGAAGACAAGCTGTGTTGCTAG 58.603 45.455 3.96 0.00 43.24 3.42
587 588 3.070159 AGAAGACAAGCTGTGTTGCTAGA 59.930 43.478 0.00 0.00 43.24 2.43
588 589 3.692257 AGACAAGCTGTGTTGCTAGAT 57.308 42.857 0.00 0.00 43.24 1.98
589 590 4.013267 AGACAAGCTGTGTTGCTAGATT 57.987 40.909 0.00 0.00 43.24 2.40
590 591 4.392940 AGACAAGCTGTGTTGCTAGATTT 58.607 39.130 0.00 0.00 43.24 2.17
591 592 4.823989 AGACAAGCTGTGTTGCTAGATTTT 59.176 37.500 0.00 0.00 43.24 1.82
592 593 5.300286 AGACAAGCTGTGTTGCTAGATTTTT 59.700 36.000 0.00 0.00 43.24 1.94
611 612 4.736126 TTTTAGATCAGATGGCTCACGA 57.264 40.909 0.00 0.00 0.00 4.35
612 613 3.998099 TTAGATCAGATGGCTCACGAG 57.002 47.619 0.00 0.00 0.00 4.18
613 614 1.039068 AGATCAGATGGCTCACGAGG 58.961 55.000 0.00 0.00 0.00 4.63
620 621 4.162690 GGCTCACGAGGCGGGATT 62.163 66.667 4.73 0.00 39.06 3.01
621 622 2.586357 GCTCACGAGGCGGGATTC 60.586 66.667 0.00 0.00 39.06 2.52
622 623 2.278857 CTCACGAGGCGGGATTCG 60.279 66.667 0.00 0.00 39.06 3.34
646 647 4.163552 CGGTCGACGCATATGTTATATGT 58.836 43.478 9.92 0.00 34.82 2.29
648 649 5.796437 CGGTCGACGCATATGTTATATGTAA 59.204 40.000 9.92 0.00 34.82 2.41
670 671 9.476202 TGTAATAGACGGTCATAATTTGATCAG 57.524 33.333 11.27 0.00 34.94 2.90
673 674 8.768957 ATAGACGGTCATAATTTGATCAGATG 57.231 34.615 11.27 1.69 34.94 2.90
676 677 7.011763 AGACGGTCATAATTTGATCAGATGTTG 59.988 37.037 11.27 1.55 34.94 3.33
722 723 1.107945 GAGGGAGTACTCTGTGAGCC 58.892 60.000 21.88 13.28 34.65 4.70
748 749 7.602517 AATTTCTCACTTTGGATACGAGAAG 57.397 36.000 0.00 0.00 42.07 2.85
760 761 0.338814 ACGAGAAGGGGGACACCTAT 59.661 55.000 0.00 0.00 40.87 2.57
763 764 2.321719 GAGAAGGGGGACACCTATCTC 58.678 57.143 11.82 11.82 40.87 2.75
775 776 0.312416 CCTATCTCGGAAGCGAGTGG 59.688 60.000 0.00 0.00 37.30 4.00
880 881 5.010282 AGGGTTTTAACATCAGTGATGGAC 58.990 41.667 31.41 21.02 43.60 4.02
1491 1503 1.342074 TGTCAGTCTCCAGGTTCCTG 58.658 55.000 11.52 11.52 0.00 3.86
1515 1527 2.514458 ACCACCCCATCAATGAGTTC 57.486 50.000 0.00 0.00 0.00 3.01
1739 1751 5.819379 TCTCGAAATTGCAAGAATATGAGCT 59.181 36.000 4.94 0.00 0.00 4.09
2088 2100 6.183347 TCAGATAGATAGCATGCTACAGCTA 58.817 40.000 29.11 26.17 46.28 3.32
2243 2255 3.243907 GGTGCTAGTTCTTGTCAGAGTGT 60.244 47.826 0.00 0.00 0.00 3.55
2304 2316 7.959651 GCGAGGTTATGCAATATCATAAAAGAG 59.040 37.037 0.00 0.00 39.70 2.85
2677 2703 1.001633 TCGGGTACAGTTTGGAGAAGC 59.998 52.381 0.00 0.00 0.00 3.86
2857 2883 1.474077 GTGGACTGGATCAATGGCAAC 59.526 52.381 0.00 0.00 0.00 4.17
2961 2987 3.694926 AGCTTTATTTCTTCAGCTGCCT 58.305 40.909 9.47 0.00 41.17 4.75
3029 3055 5.733620 AATGCCATGTCTGAAAACTCAAT 57.266 34.783 0.00 0.00 0.00 2.57
3212 3261 0.401738 CCCATGTGAGGTTGACCAGT 59.598 55.000 2.56 0.00 38.89 4.00
3215 3264 1.072173 CATGTGAGGTTGACCAGTGGA 59.928 52.381 18.40 0.00 38.89 4.02
3303 3353 7.405292 TCTATGAAATCACCAAAGTCCATTCT 58.595 34.615 0.00 0.00 0.00 2.40
3577 3635 0.252761 TTGATCTGCATCTGCCGGAA 59.747 50.000 5.05 0.00 41.18 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.561069 GAAGGAAATATGCCTTAGAGACAATAA 57.439 33.333 9.47 0.00 45.43 1.40
23 24 8.713971 TGAAGGAAATATGCCTTAGAGACAATA 58.286 33.333 9.47 0.00 45.43 1.90
24 25 7.577303 TGAAGGAAATATGCCTTAGAGACAAT 58.423 34.615 9.47 0.00 45.43 2.71
25 26 6.957631 TGAAGGAAATATGCCTTAGAGACAA 58.042 36.000 9.47 0.00 45.43 3.18
26 27 6.156949 ACTGAAGGAAATATGCCTTAGAGACA 59.843 38.462 9.47 3.95 45.43 3.41
27 28 6.587273 ACTGAAGGAAATATGCCTTAGAGAC 58.413 40.000 9.47 0.21 45.43 3.36
28 29 6.814954 ACTGAAGGAAATATGCCTTAGAGA 57.185 37.500 9.47 0.00 45.43 3.10
29 30 7.278875 AGAACTGAAGGAAATATGCCTTAGAG 58.721 38.462 9.47 10.48 45.43 2.43
30 31 7.200434 AGAACTGAAGGAAATATGCCTTAGA 57.800 36.000 9.47 1.23 45.43 2.10
31 32 7.872113 AAGAACTGAAGGAAATATGCCTTAG 57.128 36.000 9.47 9.66 45.43 2.18
32 33 7.499232 GCTAAGAACTGAAGGAAATATGCCTTA 59.501 37.037 9.47 0.00 45.43 2.69
34 35 5.825151 GCTAAGAACTGAAGGAAATATGCCT 59.175 40.000 0.00 0.00 37.35 4.75
35 36 5.590259 TGCTAAGAACTGAAGGAAATATGCC 59.410 40.000 0.00 0.00 0.00 4.40
36 37 6.683974 TGCTAAGAACTGAAGGAAATATGC 57.316 37.500 0.00 0.00 0.00 3.14
41 42 9.912634 CATTTAAATGCTAAGAACTGAAGGAAA 57.087 29.630 14.96 0.00 0.00 3.13
42 43 9.295825 TCATTTAAATGCTAAGAACTGAAGGAA 57.704 29.630 21.15 0.00 36.36 3.36
43 44 8.862325 TCATTTAAATGCTAAGAACTGAAGGA 57.138 30.769 21.15 0.00 36.36 3.36
97 98 8.185505 GCGGAGTATTTTCCATATAACAAACAA 58.814 33.333 0.00 0.00 37.05 2.83
98 99 7.554835 AGCGGAGTATTTTCCATATAACAAACA 59.445 33.333 0.00 0.00 37.05 2.83
99 100 7.927048 AGCGGAGTATTTTCCATATAACAAAC 58.073 34.615 0.00 0.00 37.05 2.93
100 101 8.514330 AAGCGGAGTATTTTCCATATAACAAA 57.486 30.769 0.00 0.00 37.05 2.83
101 102 7.771361 TGAAGCGGAGTATTTTCCATATAACAA 59.229 33.333 0.00 0.00 37.05 2.83
102 103 7.276658 TGAAGCGGAGTATTTTCCATATAACA 58.723 34.615 0.00 0.00 37.05 2.41
103 104 7.724305 TGAAGCGGAGTATTTTCCATATAAC 57.276 36.000 0.00 0.00 37.05 1.89
104 105 7.227910 GGTTGAAGCGGAGTATTTTCCATATAA 59.772 37.037 0.00 0.00 37.05 0.98
105 106 6.708949 GGTTGAAGCGGAGTATTTTCCATATA 59.291 38.462 0.00 0.00 37.05 0.86
106 107 5.531287 GGTTGAAGCGGAGTATTTTCCATAT 59.469 40.000 0.00 0.00 37.05 1.78
107 108 4.879545 GGTTGAAGCGGAGTATTTTCCATA 59.120 41.667 0.00 0.00 37.05 2.74
108 109 3.694566 GGTTGAAGCGGAGTATTTTCCAT 59.305 43.478 0.00 0.00 37.05 3.41
109 110 3.078837 GGTTGAAGCGGAGTATTTTCCA 58.921 45.455 0.00 0.00 37.05 3.53
110 111 2.095372 CGGTTGAAGCGGAGTATTTTCC 59.905 50.000 9.15 0.00 35.16 3.13
111 112 2.475685 GCGGTTGAAGCGGAGTATTTTC 60.476 50.000 18.75 0.00 39.82 2.29
112 113 1.467342 GCGGTTGAAGCGGAGTATTTT 59.533 47.619 18.75 0.00 39.82 1.82
113 114 1.084289 GCGGTTGAAGCGGAGTATTT 58.916 50.000 18.75 0.00 39.82 1.40
114 115 0.743345 GGCGGTTGAAGCGGAGTATT 60.743 55.000 18.75 0.00 39.82 1.89
115 116 1.153429 GGCGGTTGAAGCGGAGTAT 60.153 57.895 18.75 0.00 39.82 2.12
116 117 2.263540 GGCGGTTGAAGCGGAGTA 59.736 61.111 18.75 0.00 39.82 2.59
117 118 4.699522 GGGCGGTTGAAGCGGAGT 62.700 66.667 18.75 0.00 39.82 3.85
132 133 1.535462 GATAATGGCGTGGAAATCGGG 59.465 52.381 0.00 0.00 0.00 5.14
144 145 3.050275 GAGGCGGCGGATAATGGC 61.050 66.667 9.78 0.00 0.00 4.40
173 174 0.468226 TGGTCCCACTCAAGACACAC 59.532 55.000 0.00 0.00 34.58 3.82
183 184 2.923837 GTGGTTGGTGGTCCCACT 59.076 61.111 15.67 0.00 45.19 4.00
218 219 6.766944 CACTTGCAGAGATATTGAAGAGGAAT 59.233 38.462 3.37 0.00 0.00 3.01
235 236 3.191371 GGACCTTAACCATTCACTTGCAG 59.809 47.826 0.00 0.00 0.00 4.41
236 237 3.153919 GGACCTTAACCATTCACTTGCA 58.846 45.455 0.00 0.00 0.00 4.08
242 243 1.065709 GCTCGGGACCTTAACCATTCA 60.066 52.381 0.00 0.00 0.00 2.57
248 249 1.153429 ATGCGCTCGGGACCTTAAC 60.153 57.895 9.73 0.00 0.00 2.01
249 250 1.153449 CATGCGCTCGGGACCTTAA 60.153 57.895 9.73 0.00 0.00 1.85
251 252 3.376935 CTCATGCGCTCGGGACCTT 62.377 63.158 9.73 0.00 0.00 3.50
280 281 2.632602 TTTTGCCCGCTTCCAGACCA 62.633 55.000 0.00 0.00 0.00 4.02
282 283 0.603065 AATTTTGCCCGCTTCCAGAC 59.397 50.000 0.00 0.00 0.00 3.51
283 284 1.337118 AAATTTTGCCCGCTTCCAGA 58.663 45.000 0.00 0.00 0.00 3.86
284 285 2.068519 GAAAATTTTGCCCGCTTCCAG 58.931 47.619 8.47 0.00 0.00 3.86
285 286 1.691434 AGAAAATTTTGCCCGCTTCCA 59.309 42.857 8.47 0.00 0.00 3.53
286 287 2.068519 CAGAAAATTTTGCCCGCTTCC 58.931 47.619 8.47 0.00 0.00 3.46
287 288 1.460743 GCAGAAAATTTTGCCCGCTTC 59.539 47.619 8.47 0.00 34.28 3.86
288 289 1.202627 TGCAGAAAATTTTGCCCGCTT 60.203 42.857 8.47 0.00 39.54 4.68
289 290 0.392336 TGCAGAAAATTTTGCCCGCT 59.608 45.000 8.47 0.00 39.54 5.52
290 291 1.069973 GTTGCAGAAAATTTTGCCCGC 60.070 47.619 8.47 5.91 39.54 6.13
291 292 2.208431 TGTTGCAGAAAATTTTGCCCG 58.792 42.857 8.47 0.00 39.54 6.13
292 293 4.834357 AATGTTGCAGAAAATTTTGCCC 57.166 36.364 8.47 1.93 39.54 5.36
293 294 5.469760 AGGTAATGTTGCAGAAAATTTTGCC 59.530 36.000 8.47 0.00 39.54 4.52
294 295 6.544038 AGGTAATGTTGCAGAAAATTTTGC 57.456 33.333 8.47 8.04 40.67 3.68
303 304 9.764363 CTTCTACAATATAGGTAATGTTGCAGA 57.236 33.333 0.00 0.00 39.59 4.26
304 305 9.547753 ACTTCTACAATATAGGTAATGTTGCAG 57.452 33.333 0.00 0.00 39.59 4.41
305 306 9.899661 AACTTCTACAATATAGGTAATGTTGCA 57.100 29.630 0.00 0.00 39.59 4.08
409 410 7.853524 ACATTGTTTTTGCAACATAAGTGATG 58.146 30.769 0.00 0.00 41.79 3.07
410 411 9.195411 CTACATTGTTTTTGCAACATAAGTGAT 57.805 29.630 0.00 0.00 0.00 3.06
411 412 7.168972 GCTACATTGTTTTTGCAACATAAGTGA 59.831 33.333 0.00 0.00 0.00 3.41
412 413 7.169645 AGCTACATTGTTTTTGCAACATAAGTG 59.830 33.333 0.00 0.00 0.00 3.16
413 414 7.209475 AGCTACATTGTTTTTGCAACATAAGT 58.791 30.769 0.00 0.00 0.00 2.24
414 415 7.381948 TGAGCTACATTGTTTTTGCAACATAAG 59.618 33.333 0.00 0.00 0.00 1.73
415 416 7.205992 TGAGCTACATTGTTTTTGCAACATAA 58.794 30.769 0.00 0.00 0.00 1.90
416 417 6.743110 TGAGCTACATTGTTTTTGCAACATA 58.257 32.000 0.00 0.00 0.00 2.29
417 418 5.599732 TGAGCTACATTGTTTTTGCAACAT 58.400 33.333 0.00 0.00 0.00 2.71
418 419 5.003692 TGAGCTACATTGTTTTTGCAACA 57.996 34.783 0.00 0.00 0.00 3.33
419 420 5.964887 TTGAGCTACATTGTTTTTGCAAC 57.035 34.783 0.00 0.00 0.00 4.17
420 421 6.974932 TTTTGAGCTACATTGTTTTTGCAA 57.025 29.167 0.00 0.00 0.00 4.08
421 422 6.369890 TGTTTTTGAGCTACATTGTTTTTGCA 59.630 30.769 0.00 0.00 0.00 4.08
422 423 6.770076 TGTTTTTGAGCTACATTGTTTTTGC 58.230 32.000 0.00 0.00 0.00 3.68
423 424 9.771915 AAATGTTTTTGAGCTACATTGTTTTTG 57.228 25.926 11.56 0.00 40.54 2.44
424 425 9.986833 GAAATGTTTTTGAGCTACATTGTTTTT 57.013 25.926 11.56 0.00 40.54 1.94
425 426 9.382275 AGAAATGTTTTTGAGCTACATTGTTTT 57.618 25.926 11.56 0.00 40.54 2.43
426 427 8.819974 CAGAAATGTTTTTGAGCTACATTGTTT 58.180 29.630 11.56 0.00 40.54 2.83
427 428 7.042523 GCAGAAATGTTTTTGAGCTACATTGTT 60.043 33.333 11.56 0.00 40.54 2.83
428 429 6.421801 GCAGAAATGTTTTTGAGCTACATTGT 59.578 34.615 11.56 0.00 40.54 2.71
429 430 6.421501 TGCAGAAATGTTTTTGAGCTACATTG 59.578 34.615 11.56 3.30 40.54 2.82
430 431 6.514947 TGCAGAAATGTTTTTGAGCTACATT 58.485 32.000 6.06 6.06 42.55 2.71
431 432 6.088016 TGCAGAAATGTTTTTGAGCTACAT 57.912 33.333 0.00 0.00 34.14 2.29
432 433 5.512753 TGCAGAAATGTTTTTGAGCTACA 57.487 34.783 0.00 0.00 0.00 2.74
433 434 5.748152 TGTTGCAGAAATGTTTTTGAGCTAC 59.252 36.000 0.00 0.00 32.65 3.58
434 435 5.900425 TGTTGCAGAAATGTTTTTGAGCTA 58.100 33.333 0.00 0.00 0.00 3.32
435 436 4.757594 TGTTGCAGAAATGTTTTTGAGCT 58.242 34.783 0.00 0.00 0.00 4.09
436 437 5.234757 TCATGTTGCAGAAATGTTTTTGAGC 59.765 36.000 0.72 0.00 0.00 4.26
437 438 6.256104 TGTCATGTTGCAGAAATGTTTTTGAG 59.744 34.615 0.72 0.00 0.00 3.02
438 439 6.104665 TGTCATGTTGCAGAAATGTTTTTGA 58.895 32.000 0.72 0.00 0.00 2.69
439 440 6.347270 TGTCATGTTGCAGAAATGTTTTTG 57.653 33.333 0.00 0.00 0.00 2.44
440 441 8.714179 CATATGTCATGTTGCAGAAATGTTTTT 58.286 29.630 0.00 0.00 0.00 1.94
441 442 7.874016 ACATATGTCATGTTGCAGAAATGTTTT 59.126 29.630 1.41 0.00 0.00 2.43
442 443 7.380536 ACATATGTCATGTTGCAGAAATGTTT 58.619 30.769 1.41 0.00 0.00 2.83
443 444 6.927416 ACATATGTCATGTTGCAGAAATGTT 58.073 32.000 1.41 0.00 0.00 2.71
444 445 6.519679 ACATATGTCATGTTGCAGAAATGT 57.480 33.333 1.41 1.28 0.00 2.71
459 460 5.003778 GCGAAAGACATTTGCAACATATGTC 59.996 40.000 25.30 25.30 45.91 3.06
460 461 4.858692 GCGAAAGACATTTGCAACATATGT 59.141 37.500 13.70 13.70 46.14 2.29
461 462 5.365766 GCGAAAGACATTTGCAACATATG 57.634 39.130 0.00 2.98 46.14 1.78
469 470 3.608073 GGTGTATTGCGAAAGACATTTGC 59.392 43.478 6.91 0.00 46.90 3.68
470 471 5.046910 AGGTGTATTGCGAAAGACATTTG 57.953 39.130 6.91 0.00 0.00 2.32
471 472 5.473504 AGAAGGTGTATTGCGAAAGACATTT 59.526 36.000 6.91 5.19 0.00 2.32
472 473 5.003804 AGAAGGTGTATTGCGAAAGACATT 58.996 37.500 6.91 0.00 0.00 2.71
473 474 4.393062 CAGAAGGTGTATTGCGAAAGACAT 59.607 41.667 6.91 0.00 0.00 3.06
474 475 3.745975 CAGAAGGTGTATTGCGAAAGACA 59.254 43.478 0.00 0.00 0.00 3.41
475 476 3.746492 ACAGAAGGTGTATTGCGAAAGAC 59.254 43.478 0.00 0.00 37.75 3.01
476 477 4.002906 ACAGAAGGTGTATTGCGAAAGA 57.997 40.909 0.00 0.00 37.75 2.52
477 478 4.688879 TGTACAGAAGGTGTATTGCGAAAG 59.311 41.667 0.00 0.00 43.70 2.62
478 479 4.633175 TGTACAGAAGGTGTATTGCGAAA 58.367 39.130 0.00 0.00 43.70 3.46
479 480 4.260139 TGTACAGAAGGTGTATTGCGAA 57.740 40.909 0.00 0.00 43.70 4.70
480 481 3.945981 TGTACAGAAGGTGTATTGCGA 57.054 42.857 0.00 0.00 43.70 5.10
481 482 5.545658 ATTTGTACAGAAGGTGTATTGCG 57.454 39.130 0.00 0.00 43.70 4.85
482 483 9.503427 GAAATATTTGTACAGAAGGTGTATTGC 57.497 33.333 5.17 0.00 43.70 3.56
485 486 8.893727 GCAGAAATATTTGTACAGAAGGTGTAT 58.106 33.333 5.17 0.00 43.70 2.29
486 487 7.880713 TGCAGAAATATTTGTACAGAAGGTGTA 59.119 33.333 5.17 0.00 40.94 2.90
487 488 6.714810 TGCAGAAATATTTGTACAGAAGGTGT 59.285 34.615 5.17 0.00 43.86 4.16
488 489 7.144722 TGCAGAAATATTTGTACAGAAGGTG 57.855 36.000 5.17 0.00 0.00 4.00
489 490 7.230510 TGTTGCAGAAATATTTGTACAGAAGGT 59.769 33.333 5.17 0.00 0.00 3.50
490 491 7.592938 TGTTGCAGAAATATTTGTACAGAAGG 58.407 34.615 5.17 0.00 0.00 3.46
491 492 9.121517 CTTGTTGCAGAAATATTTGTACAGAAG 57.878 33.333 5.17 5.48 0.00 2.85
492 493 8.845227 TCTTGTTGCAGAAATATTTGTACAGAA 58.155 29.630 5.17 0.00 0.00 3.02
493 494 8.389779 TCTTGTTGCAGAAATATTTGTACAGA 57.610 30.769 5.17 0.00 0.00 3.41
494 495 9.069078 CATCTTGTTGCAGAAATATTTGTACAG 57.931 33.333 5.17 0.00 0.00 2.74
495 496 8.575589 ACATCTTGTTGCAGAAATATTTGTACA 58.424 29.630 5.17 0.00 0.00 2.90
496 497 8.970691 ACATCTTGTTGCAGAAATATTTGTAC 57.029 30.769 5.17 0.00 0.00 2.90
497 498 9.013229 AGACATCTTGTTGCAGAAATATTTGTA 57.987 29.630 5.17 0.00 0.00 2.41
498 499 7.811236 CAGACATCTTGTTGCAGAAATATTTGT 59.189 33.333 5.17 0.00 0.00 2.83
499 500 7.811236 ACAGACATCTTGTTGCAGAAATATTTG 59.189 33.333 5.17 0.00 0.00 2.32
500 501 7.889469 ACAGACATCTTGTTGCAGAAATATTT 58.111 30.769 0.00 0.00 0.00 1.40
501 502 7.458409 ACAGACATCTTGTTGCAGAAATATT 57.542 32.000 0.00 0.00 0.00 1.28
502 503 7.310664 CAACAGACATCTTGTTGCAGAAATAT 58.689 34.615 5.32 0.00 36.86 1.28
503 504 6.671190 CAACAGACATCTTGTTGCAGAAATA 58.329 36.000 5.32 0.00 36.86 1.40
504 505 5.526115 CAACAGACATCTTGTTGCAGAAAT 58.474 37.500 5.32 0.00 36.86 2.17
505 506 4.923893 CAACAGACATCTTGTTGCAGAAA 58.076 39.130 5.32 0.00 36.86 2.52
506 507 4.556942 CAACAGACATCTTGTTGCAGAA 57.443 40.909 5.32 0.00 36.86 3.02
511 512 5.283294 TCATTTGCAACAGACATCTTGTTG 58.717 37.500 12.40 12.40 43.90 3.33
512 513 5.068198 ACTCATTTGCAACAGACATCTTGTT 59.932 36.000 0.00 0.00 0.00 2.83
513 514 4.581824 ACTCATTTGCAACAGACATCTTGT 59.418 37.500 0.00 0.00 0.00 3.16
514 515 5.117355 ACTCATTTGCAACAGACATCTTG 57.883 39.130 0.00 0.00 0.00 3.02
515 516 5.533903 AGAACTCATTTGCAACAGACATCTT 59.466 36.000 0.00 0.00 0.00 2.40
516 517 5.048921 CAGAACTCATTTGCAACAGACATCT 60.049 40.000 0.00 1.94 0.00 2.90
517 518 5.152097 CAGAACTCATTTGCAACAGACATC 58.848 41.667 0.00 0.00 0.00 3.06
518 519 4.558095 GCAGAACTCATTTGCAACAGACAT 60.558 41.667 0.00 0.00 37.75 3.06
519 520 3.243168 GCAGAACTCATTTGCAACAGACA 60.243 43.478 0.00 0.00 37.75 3.41
520 521 3.243168 TGCAGAACTCATTTGCAACAGAC 60.243 43.478 0.00 0.00 44.13 3.51
521 522 2.950975 TGCAGAACTCATTTGCAACAGA 59.049 40.909 0.00 0.00 44.13 3.41
522 523 3.358707 TGCAGAACTCATTTGCAACAG 57.641 42.857 0.00 0.00 44.13 3.16
526 527 3.380954 TCAAGTTGCAGAACTCATTTGCA 59.619 39.130 0.00 0.00 41.87 4.08
527 528 3.732721 GTCAAGTTGCAGAACTCATTTGC 59.267 43.478 0.00 0.00 41.87 3.68
528 529 5.179045 AGTCAAGTTGCAGAACTCATTTG 57.821 39.130 0.00 0.00 41.87 2.32
529 530 5.841957 AAGTCAAGTTGCAGAACTCATTT 57.158 34.783 0.00 0.00 41.87 2.32
530 531 5.841957 AAAGTCAAGTTGCAGAACTCATT 57.158 34.783 0.00 0.00 41.87 2.57
531 532 5.126061 ACAAAAGTCAAGTTGCAGAACTCAT 59.874 36.000 0.00 0.00 41.87 2.90
532 533 4.458989 ACAAAAGTCAAGTTGCAGAACTCA 59.541 37.500 0.00 0.00 41.87 3.41
533 534 4.986622 ACAAAAGTCAAGTTGCAGAACTC 58.013 39.130 0.00 0.00 41.87 3.01
534 535 5.163513 CAACAAAAGTCAAGTTGCAGAACT 58.836 37.500 0.00 0.00 44.79 3.01
535 536 5.440260 CAACAAAAGTCAAGTTGCAGAAC 57.560 39.130 0.00 0.00 36.59 3.01
541 542 6.226988 AGTTTTGCAACAAAAGTCAAGTTG 57.773 33.333 0.00 0.00 44.01 3.16
542 543 7.375053 TCTAGTTTTGCAACAAAAGTCAAGTT 58.625 30.769 14.57 0.00 35.05 2.66
543 544 6.919721 TCTAGTTTTGCAACAAAAGTCAAGT 58.080 32.000 14.57 0.00 35.05 3.16
544 545 7.754924 TCTTCTAGTTTTGCAACAAAAGTCAAG 59.245 33.333 14.57 15.96 35.05 3.02
545 546 7.540745 GTCTTCTAGTTTTGCAACAAAAGTCAA 59.459 33.333 14.57 9.36 35.05 3.18
546 547 7.027161 GTCTTCTAGTTTTGCAACAAAAGTCA 58.973 34.615 14.57 3.24 35.05 3.41
547 548 7.027161 TGTCTTCTAGTTTTGCAACAAAAGTC 58.973 34.615 14.57 1.85 35.05 3.01
548 549 6.919721 TGTCTTCTAGTTTTGCAACAAAAGT 58.080 32.000 15.27 15.27 35.05 2.66
549 550 7.463251 GCTTGTCTTCTAGTTTTGCAACAAAAG 60.463 37.037 0.00 0.00 35.05 2.27
550 551 6.310224 GCTTGTCTTCTAGTTTTGCAACAAAA 59.690 34.615 0.00 1.50 35.05 2.44
551 552 5.804979 GCTTGTCTTCTAGTTTTGCAACAAA 59.195 36.000 0.00 0.00 35.05 2.83
552 553 5.125417 AGCTTGTCTTCTAGTTTTGCAACAA 59.875 36.000 0.00 0.00 35.05 2.83
553 554 4.640201 AGCTTGTCTTCTAGTTTTGCAACA 59.360 37.500 0.00 0.00 35.05 3.33
554 555 4.972440 CAGCTTGTCTTCTAGTTTTGCAAC 59.028 41.667 0.00 0.00 0.00 4.17
555 556 4.640201 ACAGCTTGTCTTCTAGTTTTGCAA 59.360 37.500 0.00 0.00 0.00 4.08
556 557 4.035558 CACAGCTTGTCTTCTAGTTTTGCA 59.964 41.667 0.00 0.00 0.00 4.08
557 558 4.035675 ACACAGCTTGTCTTCTAGTTTTGC 59.964 41.667 0.00 0.00 29.79 3.68
558 559 5.741388 ACACAGCTTGTCTTCTAGTTTTG 57.259 39.130 0.00 0.00 29.79 2.44
559 560 5.449177 GCAACACAGCTTGTCTTCTAGTTTT 60.449 40.000 2.65 0.00 37.51 2.43
560 561 4.035675 GCAACACAGCTTGTCTTCTAGTTT 59.964 41.667 2.65 0.00 37.51 2.66
561 562 3.561725 GCAACACAGCTTGTCTTCTAGTT 59.438 43.478 2.65 0.00 37.51 2.24
562 563 3.134458 GCAACACAGCTTGTCTTCTAGT 58.866 45.455 2.65 0.00 37.51 2.57
563 564 3.397482 AGCAACACAGCTTGTCTTCTAG 58.603 45.455 2.65 0.00 43.70 2.43
564 565 3.475566 AGCAACACAGCTTGTCTTCTA 57.524 42.857 2.65 0.00 43.70 2.10
565 566 2.338577 AGCAACACAGCTTGTCTTCT 57.661 45.000 2.65 0.00 43.70 2.85
566 567 3.393800 TCTAGCAACACAGCTTGTCTTC 58.606 45.455 0.00 0.00 43.70 2.87
567 568 3.475566 TCTAGCAACACAGCTTGTCTT 57.524 42.857 0.00 0.00 43.70 3.01
568 569 3.692257 ATCTAGCAACACAGCTTGTCT 57.308 42.857 0.00 0.67 43.70 3.41
569 570 4.756084 AAATCTAGCAACACAGCTTGTC 57.244 40.909 0.00 0.00 43.70 3.18
570 571 5.520376 AAAAATCTAGCAACACAGCTTGT 57.480 34.783 0.00 0.00 43.70 3.16
589 590 5.084818 TCGTGAGCCATCTGATCTAAAAA 57.915 39.130 0.00 0.00 0.00 1.94
590 591 4.442052 CCTCGTGAGCCATCTGATCTAAAA 60.442 45.833 0.00 0.00 0.00 1.52
591 592 3.068732 CCTCGTGAGCCATCTGATCTAAA 59.931 47.826 0.00 0.00 0.00 1.85
592 593 2.625314 CCTCGTGAGCCATCTGATCTAA 59.375 50.000 0.00 0.00 0.00 2.10
593 594 2.234143 CCTCGTGAGCCATCTGATCTA 58.766 52.381 0.00 0.00 0.00 1.98
594 595 1.039068 CCTCGTGAGCCATCTGATCT 58.961 55.000 0.00 0.00 0.00 2.75
595 596 0.599728 GCCTCGTGAGCCATCTGATC 60.600 60.000 0.00 0.00 0.00 2.92
596 597 1.445095 GCCTCGTGAGCCATCTGAT 59.555 57.895 0.00 0.00 0.00 2.90
597 598 2.895680 GCCTCGTGAGCCATCTGA 59.104 61.111 0.00 0.00 0.00 3.27
598 599 2.584418 CGCCTCGTGAGCCATCTG 60.584 66.667 0.00 0.00 0.00 2.90
599 600 3.842923 CCGCCTCGTGAGCCATCT 61.843 66.667 0.00 0.00 0.00 2.90
600 601 4.899239 CCCGCCTCGTGAGCCATC 62.899 72.222 0.00 0.00 0.00 3.51
603 604 4.162690 AATCCCGCCTCGTGAGCC 62.163 66.667 0.00 0.00 0.00 4.70
604 605 2.586357 GAATCCCGCCTCGTGAGC 60.586 66.667 0.00 0.00 0.00 4.26
605 606 2.278857 CGAATCCCGCCTCGTGAG 60.279 66.667 0.00 0.00 0.00 3.51
621 622 3.394874 CATATGCGTCGACCGGCG 61.395 66.667 12.28 12.28 46.98 6.46
622 623 0.595567 TAACATATGCGTCGACCGGC 60.596 55.000 10.58 9.30 36.94 6.13
623 624 2.060326 ATAACATATGCGTCGACCGG 57.940 50.000 10.58 0.00 36.94 5.28
624 625 4.163552 ACATATAACATATGCGTCGACCG 58.836 43.478 10.58 6.51 40.40 4.79
625 626 7.751047 ATTACATATAACATATGCGTCGACC 57.249 36.000 10.58 3.43 0.00 4.79
626 627 9.712359 TCTATTACATATAACATATGCGTCGAC 57.288 33.333 5.18 5.18 0.00 4.20
627 628 9.712359 GTCTATTACATATAACATATGCGTCGA 57.288 33.333 1.58 0.00 0.00 4.20
628 629 8.670668 CGTCTATTACATATAACATATGCGTCG 58.329 37.037 1.58 0.00 0.00 5.12
629 630 8.955002 CCGTCTATTACATATAACATATGCGTC 58.045 37.037 1.58 0.00 0.00 5.19
630 631 8.464404 ACCGTCTATTACATATAACATATGCGT 58.536 33.333 1.58 0.00 0.00 5.24
631 632 8.851960 ACCGTCTATTACATATAACATATGCG 57.148 34.615 1.58 0.00 0.00 4.73
632 633 9.797556 TGACCGTCTATTACATATAACATATGC 57.202 33.333 1.58 0.00 0.00 3.14
648 649 8.370940 ACATCTGATCAAATTATGACCGTCTAT 58.629 33.333 11.75 0.00 41.93 1.98
659 660 7.000472 GGATCTCCCAACATCTGATCAAATTA 59.000 38.462 0.00 0.00 36.28 1.40
670 671 4.200092 GGTTTACTGGATCTCCCAACATC 58.800 47.826 0.00 0.00 46.07 3.06
673 674 3.713826 TGGTTTACTGGATCTCCCAAC 57.286 47.619 0.00 0.00 46.07 3.77
676 677 3.199946 TGTCATGGTTTACTGGATCTCCC 59.800 47.826 0.00 0.00 34.29 4.30
694 695 1.285373 GAGTACTCCCTCCCTCTGTCA 59.715 57.143 12.13 0.00 0.00 3.58
722 723 7.364522 TCTCGTATCCAAAGTGAGAAATTTG 57.635 36.000 0.00 0.00 36.40 2.32
748 749 0.398098 TTCCGAGATAGGTGTCCCCC 60.398 60.000 0.00 0.00 0.00 5.40
763 764 2.027625 GGTCAACCACTCGCTTCCG 61.028 63.158 0.00 0.00 35.64 4.30
1271 1283 1.531748 GAATCCGGGATCTTGGCCA 59.468 57.895 10.56 0.00 0.00 5.36
1491 1503 2.624838 CTCATTGATGGGGTGGTATTGC 59.375 50.000 0.00 0.00 0.00 3.56
1515 1527 1.870016 GCTCTCGAAGAACGGCTCG 60.870 63.158 0.00 0.00 42.82 5.03
2088 2100 2.048023 CCATGGGCACTGCACGAAT 61.048 57.895 2.85 0.00 32.76 3.34
2243 2255 5.555966 TCATGGTAGACAACACAATAGCAA 58.444 37.500 0.00 0.00 0.00 3.91
2304 2316 2.238898 AGTACCAAACTGCATAGGGTCC 59.761 50.000 3.14 0.00 36.93 4.46
2349 2361 4.607293 ACTGTCTATCTTTGTCACAGCA 57.393 40.909 0.00 0.00 38.44 4.41
2677 2703 6.047231 TGTACATCATGAATCTCAGCTTCAG 58.953 40.000 0.00 0.00 36.16 3.02
2961 2987 0.680921 GTAGCCCTGCATTGCAAGGA 60.681 55.000 26.87 6.99 42.28 3.36
2980 3006 8.291740 TGTGAAGATGTGTCAAGATTTGTATTG 58.708 33.333 0.00 0.00 0.00 1.90
3274 3324 8.055279 TGGACTTTGGTGATTTCATAGAAATC 57.945 34.615 20.11 20.11 37.21 2.17
3303 3353 0.766131 TCGGGGCCAACAAAGAGTTA 59.234 50.000 4.39 0.00 38.74 2.24
3559 3617 0.462581 GTTCCGGCAGATGCAGATCA 60.463 55.000 7.19 0.00 44.36 2.92
3577 3635 3.391382 GGTAGCTCCCGCACTGGT 61.391 66.667 0.00 0.00 39.10 4.00
3620 3678 8.914328 TCACAAGCATTAATCACAATACAATG 57.086 30.769 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.