Multiple sequence alignment - TraesCS6D01G296500

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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 TraesCS6D01G296500 chr6D 100.000 2477 0 0 1 2477 407827984 407830460 0.000000e+00 4575
1 TraesCS6D01G296500 chr6D 93.506 231 14 1 256 485 377567911 377567681 2.360000e-90 342
2 TraesCS6D01G296500 chr6A 91.725 1994 80 34 506 2441 553188028 553189994 0.000000e+00 2689
3 TraesCS6D01G296500 chr6A 88.716 257 24 2 1 257 553187777 553188028 2.390000e-80 309
4 TraesCS6D01G296500 chr6B 91.370 1993 97 39 508 2477 612132927 612134867 0.000000e+00 2658
5 TraesCS6D01G296500 chr6B 93.822 259 14 2 1 257 612132667 612132925 2.990000e-104 388
6 TraesCS6D01G296500 chr2D 94.372 231 12 1 256 485 522748528 522748758 1.090000e-93 353
7 TraesCS6D01G296500 chr2D 92.623 244 15 3 245 485 35028790 35029033 5.070000e-92 348
8 TraesCS6D01G296500 chr2D 93.939 231 13 1 256 485 36275112 36275342 5.070000e-92 348
9 TraesCS6D01G296500 chr3A 93.133 233 14 2 254 485 45864846 45864615 8.480000e-90 340
10 TraesCS6D01G296500 chr4A 93.450 229 14 1 258 485 689623989 689623761 3.050000e-89 339
11 TraesCS6D01G296500 chr7D 93.450 229 12 3 258 485 161992027 161991801 1.100000e-88 337
12 TraesCS6D01G296500 chr2A 92.735 234 14 3 254 485 572799473 572799705 3.950000e-88 335
13 TraesCS6D01G296500 chr7A 93.013 229 15 1 258 485 35356695 35356467 1.420000e-87 333


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 TraesCS6D01G296500 chr6D 407827984 407830460 2476 False 4575 4575 100.0000 1 2477 1 chr6D.!!$F1 2476
1 TraesCS6D01G296500 chr6A 553187777 553189994 2217 False 1499 2689 90.2205 1 2441 2 chr6A.!!$F1 2440
2 TraesCS6D01G296500 chr6B 612132667 612134867 2200 False 1523 2658 92.5960 1 2477 2 chr6B.!!$F1 2476

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
379 382 0.180171 CACCTGACCACACCTTCACA 59.82 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2416 0.039074 ACCTGCATCGTCGCTATAGC 60.039 55.0 15.09 15.09 37.78 2.97 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
35 36 2.755469 CCTTTGGATGGCCCACGG 60.755 66.667 0.00 0.00 46.62 4.94
38 39 3.280938 TTTGGATGGCCCACGGGAG 62.281 63.158 6.21 0.00 46.62 4.30
72 73 8.367156 CAGAAATTTTAGAGGATAGAGGAGAGG 58.633 40.741 0.00 0.00 0.00 3.69
103 106 8.058847 AGAGAGAGATAGAGTGTATTGGACTTT 58.941 37.037 0.00 0.00 0.00 2.66
257 260 4.030913 CAATCTAGGGAGGGTGACACTAA 58.969 47.826 5.39 0.00 0.00 2.24
258 261 3.383698 TCTAGGGAGGGTGACACTAAG 57.616 52.381 5.39 0.00 0.00 2.18
259 262 2.024273 TCTAGGGAGGGTGACACTAAGG 60.024 54.545 5.39 0.00 0.00 2.69
260 263 0.252742 AGGGAGGGTGACACTAAGGG 60.253 60.000 5.39 0.00 0.00 3.95
261 264 1.602771 GGAGGGTGACACTAAGGGC 59.397 63.158 5.39 0.00 0.00 5.19
262 265 1.602771 GAGGGTGACACTAAGGGCC 59.397 63.158 5.39 0.00 0.00 5.80
263 266 0.910088 GAGGGTGACACTAAGGGCCT 60.910 60.000 0.00 0.00 0.00 5.19
264 267 1.201429 AGGGTGACACTAAGGGCCTG 61.201 60.000 6.92 0.00 0.00 4.85
265 268 1.489560 GGGTGACACTAAGGGCCTGT 61.490 60.000 6.92 0.00 0.00 4.00
266 269 0.400594 GGTGACACTAAGGGCCTGTT 59.599 55.000 6.92 0.00 0.00 3.16
267 270 1.202891 GGTGACACTAAGGGCCTGTTT 60.203 52.381 6.92 0.00 0.00 2.83
268 271 1.880027 GTGACACTAAGGGCCTGTTTG 59.120 52.381 6.92 6.92 0.00 2.93
269 272 1.202879 TGACACTAAGGGCCTGTTTGG 60.203 52.381 6.92 0.00 39.35 3.28
270 273 0.850784 ACACTAAGGGCCTGTTTGGT 59.149 50.000 6.92 0.00 38.35 3.67
271 274 1.216930 ACACTAAGGGCCTGTTTGGTT 59.783 47.619 6.92 0.00 38.35 3.67
272 275 2.316108 CACTAAGGGCCTGTTTGGTTT 58.684 47.619 6.92 0.00 38.35 3.27
273 276 2.296190 CACTAAGGGCCTGTTTGGTTTC 59.704 50.000 6.92 0.00 38.35 2.78
274 277 2.091555 ACTAAGGGCCTGTTTGGTTTCA 60.092 45.455 6.92 0.00 38.35 2.69
275 278 1.872773 AAGGGCCTGTTTGGTTTCAA 58.127 45.000 6.92 0.00 38.35 2.69
276 279 2.101640 AGGGCCTGTTTGGTTTCAAT 57.898 45.000 4.50 0.00 38.35 2.57
277 280 3.252554 AGGGCCTGTTTGGTTTCAATA 57.747 42.857 4.50 0.00 38.35 1.90
278 281 3.582164 AGGGCCTGTTTGGTTTCAATAA 58.418 40.909 4.50 0.00 38.35 1.40
279 282 3.578282 AGGGCCTGTTTGGTTTCAATAAG 59.422 43.478 4.50 0.00 38.35 1.73
280 283 3.323691 GGGCCTGTTTGGTTTCAATAAGT 59.676 43.478 0.84 0.00 38.35 2.24
281 284 4.556233 GGCCTGTTTGGTTTCAATAAGTC 58.444 43.478 0.00 0.00 38.35 3.01
282 285 4.038642 GGCCTGTTTGGTTTCAATAAGTCA 59.961 41.667 0.00 0.00 38.35 3.41
283 286 4.982295 GCCTGTTTGGTTTCAATAAGTCAC 59.018 41.667 0.00 0.00 38.35 3.67
284 287 5.528870 CCTGTTTGGTTTCAATAAGTCACC 58.471 41.667 0.00 0.00 32.28 4.02
285 288 5.508994 CCTGTTTGGTTTCAATAAGTCACCC 60.509 44.000 0.00 0.00 32.28 4.61
286 289 4.036971 TGTTTGGTTTCAATAAGTCACCCG 59.963 41.667 0.00 0.00 32.28 5.28
287 290 3.773418 TGGTTTCAATAAGTCACCCGA 57.227 42.857 0.00 0.00 0.00 5.14
288 291 3.404899 TGGTTTCAATAAGTCACCCGAC 58.595 45.455 0.00 0.00 42.95 4.79
289 292 5.920880 TTTGGTTTCAATAAGTCACCCGACT 60.921 40.000 0.00 0.00 42.49 4.18
301 304 5.019785 GTCACCCGACTTATAAATCAGGT 57.980 43.478 0.00 0.00 39.22 4.00
302 305 4.809426 GTCACCCGACTTATAAATCAGGTG 59.191 45.833 18.99 18.99 42.49 4.00
303 306 4.712829 TCACCCGACTTATAAATCAGGTGA 59.287 41.667 22.22 22.22 45.82 4.02
304 307 4.809426 CACCCGACTTATAAATCAGGTGAC 59.191 45.833 19.96 0.00 43.40 3.67
305 308 4.715297 ACCCGACTTATAAATCAGGTGACT 59.285 41.667 1.06 0.00 46.44 3.41
306 309 5.189145 ACCCGACTTATAAATCAGGTGACTT 59.811 40.000 1.06 0.00 40.21 3.01
307 310 6.381994 ACCCGACTTATAAATCAGGTGACTTA 59.618 38.462 1.06 0.00 40.21 2.24
308 311 7.093201 ACCCGACTTATAAATCAGGTGACTTAA 60.093 37.037 1.06 0.00 40.21 1.85
309 312 7.767198 CCCGACTTATAAATCAGGTGACTTAAA 59.233 37.037 0.00 0.00 40.21 1.52
310 313 9.158233 CCGACTTATAAATCAGGTGACTTAAAA 57.842 33.333 0.00 0.00 40.21 1.52
311 314 9.968743 CGACTTATAAATCAGGTGACTTAAAAC 57.031 33.333 0.00 0.00 40.21 2.43
313 316 9.802039 ACTTATAAATCAGGTGACTTAAAACCA 57.198 29.630 4.87 0.00 40.21 3.67
315 318 9.802039 TTATAAATCAGGTGACTTAAAACCAGT 57.198 29.630 4.87 0.00 40.21 4.00
316 319 6.391227 AAATCAGGTGACTTAAAACCAGTG 57.609 37.500 4.87 0.00 40.21 3.66
317 320 4.764050 TCAGGTGACTTAAAACCAGTGA 57.236 40.909 0.00 0.00 40.21 3.41
318 321 4.448210 TCAGGTGACTTAAAACCAGTGAC 58.552 43.478 0.00 0.00 40.21 3.67
319 322 4.163458 TCAGGTGACTTAAAACCAGTGACT 59.837 41.667 0.00 0.00 40.21 3.41
320 323 4.881850 CAGGTGACTTAAAACCAGTGACTT 59.118 41.667 0.00 0.00 40.21 3.01
321 324 6.053005 CAGGTGACTTAAAACCAGTGACTTA 58.947 40.000 0.00 0.00 40.21 2.24
322 325 6.710744 CAGGTGACTTAAAACCAGTGACTTAT 59.289 38.462 0.00 0.00 40.21 1.73
323 326 7.876068 CAGGTGACTTAAAACCAGTGACTTATA 59.124 37.037 0.00 0.00 40.21 0.98
324 327 8.434392 AGGTGACTTAAAACCAGTGACTTATAA 58.566 33.333 0.00 0.00 37.44 0.98
325 328 8.718734 GGTGACTTAAAACCAGTGACTTATAAG 58.281 37.037 11.05 11.05 36.41 1.73
326 329 9.269453 GTGACTTAAAACCAGTGACTTATAAGT 57.731 33.333 18.05 18.05 43.16 2.24
340 343 6.034161 ACTTATAAGTCACGCCTGTTTAGT 57.966 37.500 12.50 0.00 32.86 2.24
341 344 6.461640 ACTTATAAGTCACGCCTGTTTAGTT 58.538 36.000 12.50 0.00 32.86 2.24
342 345 6.367969 ACTTATAAGTCACGCCTGTTTAGTTG 59.632 38.462 12.50 0.00 32.86 3.16
343 346 2.614829 AGTCACGCCTGTTTAGTTGT 57.385 45.000 0.00 0.00 0.00 3.32
344 347 2.480845 AGTCACGCCTGTTTAGTTGTC 58.519 47.619 0.00 0.00 0.00 3.18
345 348 2.159014 AGTCACGCCTGTTTAGTTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
346 349 2.806244 GTCACGCCTGTTTAGTTGTCAT 59.194 45.455 0.00 0.00 0.00 3.06
347 350 3.064207 TCACGCCTGTTTAGTTGTCATC 58.936 45.455 0.00 0.00 0.00 2.92
348 351 3.067106 CACGCCTGTTTAGTTGTCATCT 58.933 45.455 0.00 0.00 0.00 2.90
349 352 3.067106 ACGCCTGTTTAGTTGTCATCTG 58.933 45.455 0.00 0.00 0.00 2.90
350 353 3.244078 ACGCCTGTTTAGTTGTCATCTGA 60.244 43.478 0.00 0.00 0.00 3.27
351 354 3.123621 CGCCTGTTTAGTTGTCATCTGAC 59.876 47.826 3.34 3.34 44.97 3.51
352 355 4.319177 GCCTGTTTAGTTGTCATCTGACT 58.681 43.478 11.35 0.00 44.99 3.41
353 356 4.757149 GCCTGTTTAGTTGTCATCTGACTT 59.243 41.667 11.35 1.05 44.99 3.01
354 357 5.932303 GCCTGTTTAGTTGTCATCTGACTTA 59.068 40.000 11.35 0.00 44.99 2.24
355 358 6.595716 GCCTGTTTAGTTGTCATCTGACTTAT 59.404 38.462 11.35 0.66 44.99 1.73
356 359 7.764443 GCCTGTTTAGTTGTCATCTGACTTATA 59.236 37.037 11.35 0.00 44.99 0.98
357 360 9.653287 CCTGTTTAGTTGTCATCTGACTTATAA 57.347 33.333 11.35 5.19 44.99 0.98
372 375 5.148651 ACTTATAAGTCACCTGACCACAC 57.851 43.478 12.50 0.00 45.85 3.82
373 376 4.020485 ACTTATAAGTCACCTGACCACACC 60.020 45.833 12.50 0.00 45.85 4.16
374 377 2.097110 TAAGTCACCTGACCACACCT 57.903 50.000 1.66 0.00 45.85 4.00
375 378 1.213296 AAGTCACCTGACCACACCTT 58.787 50.000 1.66 0.00 45.85 3.50
376 379 0.759346 AGTCACCTGACCACACCTTC 59.241 55.000 1.66 0.00 45.85 3.46
377 380 0.468226 GTCACCTGACCACACCTTCA 59.532 55.000 0.00 0.00 39.07 3.02
378 381 0.468226 TCACCTGACCACACCTTCAC 59.532 55.000 0.00 0.00 0.00 3.18
379 382 0.180171 CACCTGACCACACCTTCACA 59.820 55.000 0.00 0.00 0.00 3.58
380 383 0.180406 ACCTGACCACACCTTCACAC 59.820 55.000 0.00 0.00 0.00 3.82
381 384 0.535102 CCTGACCACACCTTCACACC 60.535 60.000 0.00 0.00 0.00 4.16
382 385 0.469917 CTGACCACACCTTCACACCT 59.530 55.000 0.00 0.00 0.00 4.00
383 386 0.916086 TGACCACACCTTCACACCTT 59.084 50.000 0.00 0.00 0.00 3.50
384 387 1.308998 GACCACACCTTCACACCTTG 58.691 55.000 0.00 0.00 0.00 3.61
385 388 0.623723 ACCACACCTTCACACCTTGT 59.376 50.000 0.00 0.00 0.00 3.16
386 389 1.005450 ACCACACCTTCACACCTTGTT 59.995 47.619 0.00 0.00 0.00 2.83
387 390 2.099405 CCACACCTTCACACCTTGTTT 58.901 47.619 0.00 0.00 0.00 2.83
388 391 2.495669 CCACACCTTCACACCTTGTTTT 59.504 45.455 0.00 0.00 0.00 2.43
389 392 3.056179 CCACACCTTCACACCTTGTTTTT 60.056 43.478 0.00 0.00 0.00 1.94
411 414 5.440207 TTTATGTAAAGGTAGTGGGACCC 57.560 43.478 2.45 2.45 40.74 4.46
412 415 2.419457 TGTAAAGGTAGTGGGACCCA 57.581 50.000 9.95 9.95 40.74 4.51
420 423 3.039134 GTGGGACCCACGCAAAAG 58.961 61.111 27.79 0.00 44.95 2.27
421 424 2.203422 TGGGACCCACGCAAAAGG 60.203 61.111 9.95 0.00 38.47 3.11
430 433 2.414750 ACGCAAAAGGGGTGACTTG 58.585 52.632 0.00 0.00 41.74 3.16
431 434 1.007387 CGCAAAAGGGGTGACTTGC 60.007 57.895 0.00 0.00 40.58 4.01
432 435 1.733402 CGCAAAAGGGGTGACTTGCA 61.733 55.000 7.17 0.00 43.43 4.08
433 436 0.463620 GCAAAAGGGGTGACTTGCAA 59.536 50.000 0.00 0.00 42.91 4.08
434 437 1.538849 GCAAAAGGGGTGACTTGCAAG 60.539 52.381 24.84 24.84 42.91 4.01
435 438 1.756538 CAAAAGGGGTGACTTGCAAGT 59.243 47.619 31.57 31.57 43.16 3.16
436 439 2.159179 AAAGGGGTGACTTGCAAGTT 57.841 45.000 31.58 16.43 39.88 2.66
437 440 2.159179 AAGGGGTGACTTGCAAGTTT 57.841 45.000 31.58 18.35 39.88 2.66
438 441 2.159179 AGGGGTGACTTGCAAGTTTT 57.841 45.000 31.58 10.81 39.88 2.43
439 442 3.306472 AGGGGTGACTTGCAAGTTTTA 57.694 42.857 31.58 18.60 39.88 1.52
440 443 3.637769 AGGGGTGACTTGCAAGTTTTAA 58.362 40.909 31.58 15.75 39.88 1.52
441 444 3.636764 AGGGGTGACTTGCAAGTTTTAAG 59.363 43.478 31.58 5.60 39.88 1.85
442 445 3.383505 GGGGTGACTTGCAAGTTTTAAGT 59.616 43.478 31.58 9.26 39.88 2.24
443 446 4.142026 GGGGTGACTTGCAAGTTTTAAGTT 60.142 41.667 31.58 7.62 39.88 2.66
444 447 4.803613 GGGTGACTTGCAAGTTTTAAGTTG 59.196 41.667 31.58 3.44 39.88 3.16
445 448 5.393678 GGGTGACTTGCAAGTTTTAAGTTGA 60.394 40.000 31.58 0.00 40.88 3.18
446 449 5.743872 GGTGACTTGCAAGTTTTAAGTTGAG 59.256 40.000 31.58 2.39 40.88 3.02
447 450 5.743872 GTGACTTGCAAGTTTTAAGTTGAGG 59.256 40.000 31.58 2.22 40.88 3.86
448 451 5.417580 TGACTTGCAAGTTTTAAGTTGAGGT 59.582 36.000 31.58 5.72 40.88 3.85
449 452 5.650543 ACTTGCAAGTTTTAAGTTGAGGTG 58.349 37.500 26.36 0.00 40.88 4.00
450 453 4.647424 TGCAAGTTTTAAGTTGAGGTGG 57.353 40.909 12.91 0.00 40.88 4.61
451 454 4.274147 TGCAAGTTTTAAGTTGAGGTGGA 58.726 39.130 12.91 0.00 40.88 4.02
452 455 4.338118 TGCAAGTTTTAAGTTGAGGTGGAG 59.662 41.667 12.91 0.00 40.88 3.86
453 456 4.793028 GCAAGTTTTAAGTTGAGGTGGAGC 60.793 45.833 12.91 0.00 40.88 4.70
454 457 4.164843 AGTTTTAAGTTGAGGTGGAGCA 57.835 40.909 0.00 0.00 0.00 4.26
455 458 4.532834 AGTTTTAAGTTGAGGTGGAGCAA 58.467 39.130 0.00 0.00 0.00 3.91
456 459 4.338400 AGTTTTAAGTTGAGGTGGAGCAAC 59.662 41.667 0.00 0.00 43.48 4.17
462 465 3.674997 GTTGAGGTGGAGCAACTTATGA 58.325 45.455 0.00 0.00 40.79 2.15
463 466 3.334583 TGAGGTGGAGCAACTTATGAC 57.665 47.619 0.00 0.00 28.17 3.06
464 467 2.906389 TGAGGTGGAGCAACTTATGACT 59.094 45.455 0.00 0.00 28.17 3.41
465 468 3.327757 TGAGGTGGAGCAACTTATGACTT 59.672 43.478 0.00 0.00 28.17 3.01
466 469 4.530553 TGAGGTGGAGCAACTTATGACTTA 59.469 41.667 0.00 0.00 28.17 2.24
467 470 5.189736 TGAGGTGGAGCAACTTATGACTTAT 59.810 40.000 0.00 0.00 28.17 1.73
468 471 6.382859 TGAGGTGGAGCAACTTATGACTTATA 59.617 38.462 0.00 0.00 28.17 0.98
469 472 7.093068 TGAGGTGGAGCAACTTATGACTTATAA 60.093 37.037 0.00 0.00 28.17 0.98
470 473 7.630082 AGGTGGAGCAACTTATGACTTATAAA 58.370 34.615 0.00 0.00 31.12 1.40
471 474 8.275040 AGGTGGAGCAACTTATGACTTATAAAT 58.725 33.333 0.00 0.00 31.12 1.40
472 475 8.903820 GGTGGAGCAACTTATGACTTATAAATT 58.096 33.333 0.00 0.00 31.12 1.82
473 476 9.722056 GTGGAGCAACTTATGACTTATAAATTG 57.278 33.333 0.00 0.00 39.96 2.32
474 477 8.902806 TGGAGCAACTTATGACTTATAAATTGG 58.097 33.333 0.00 0.00 38.35 3.16
475 478 8.352942 GGAGCAACTTATGACTTATAAATTGGG 58.647 37.037 0.00 0.00 38.35 4.12
476 479 8.237811 AGCAACTTATGACTTATAAATTGGGG 57.762 34.615 0.00 0.00 38.35 4.96
477 480 7.839200 AGCAACTTATGACTTATAAATTGGGGT 59.161 33.333 0.00 0.00 38.35 4.95
478 481 7.920682 GCAACTTATGACTTATAAATTGGGGTG 59.079 37.037 0.00 0.00 38.35 4.61
479 482 9.184523 CAACTTATGACTTATAAATTGGGGTGA 57.815 33.333 0.00 0.00 35.74 4.02
480 483 8.747538 ACTTATGACTTATAAATTGGGGTGAC 57.252 34.615 0.00 0.00 31.12 3.67
481 484 8.557450 ACTTATGACTTATAAATTGGGGTGACT 58.443 33.333 0.00 0.00 31.12 3.41
482 485 9.408648 CTTATGACTTATAAATTGGGGTGACTT 57.591 33.333 0.00 0.00 31.12 3.01
485 488 9.936329 ATGACTTATAAATTGGGGTGACTTATT 57.064 29.630 0.00 0.00 0.00 1.40
486 489 9.762381 TGACTTATAAATTGGGGTGACTTATTT 57.238 29.630 0.00 0.00 0.00 1.40
488 491 9.762381 ACTTATAAATTGGGGTGACTTATTTGA 57.238 29.630 0.00 0.00 0.00 2.69
492 495 5.738619 ATTGGGGTGACTTATTTGAAACC 57.261 39.130 0.00 0.00 0.00 3.27
493 496 4.186077 TGGGGTGACTTATTTGAAACCA 57.814 40.909 0.00 0.00 0.00 3.67
494 497 4.547671 TGGGGTGACTTATTTGAAACCAA 58.452 39.130 0.00 0.00 0.00 3.67
495 498 4.962995 TGGGGTGACTTATTTGAAACCAAA 59.037 37.500 0.00 0.00 37.85 3.28
496 499 5.163395 TGGGGTGACTTATTTGAAACCAAAC 60.163 40.000 0.00 0.00 36.48 2.93
497 500 5.069914 GGGGTGACTTATTTGAAACCAAACT 59.930 40.000 0.00 0.00 36.48 2.66
498 501 5.983118 GGGTGACTTATTTGAAACCAAACTG 59.017 40.000 0.00 0.00 36.48 3.16
499 502 5.983118 GGTGACTTATTTGAAACCAAACTGG 59.017 40.000 0.00 0.00 45.02 4.00
500 503 5.462068 GTGACTTATTTGAAACCAAACTGGC 59.538 40.000 0.00 0.00 42.67 4.85
501 504 4.956085 ACTTATTTGAAACCAAACTGGCC 58.044 39.130 0.00 0.00 42.67 5.36
502 505 2.928801 ATTTGAAACCAAACTGGCCC 57.071 45.000 0.00 0.00 42.67 5.80
503 506 1.872773 TTTGAAACCAAACTGGCCCT 58.127 45.000 0.00 0.00 42.67 5.19
504 507 2.757894 TTGAAACCAAACTGGCCCTA 57.242 45.000 0.00 0.00 42.67 3.53
505 508 2.757894 TGAAACCAAACTGGCCCTAA 57.242 45.000 0.00 0.00 42.67 2.69
506 509 2.593026 TGAAACCAAACTGGCCCTAAG 58.407 47.619 0.00 0.00 42.67 2.18
523 526 1.040339 AAGAAGCCGTGGGTTTGCAA 61.040 50.000 4.63 0.00 35.84 4.08
716 725 1.198713 CTCATAGGCCACTGACCACT 58.801 55.000 5.01 0.00 0.00 4.00
722 731 1.202818 AGGCCACTGACCACTTTCTTC 60.203 52.381 5.01 0.00 0.00 2.87
797 806 1.000396 GGCCACCTTGAGCTCCAAT 60.000 57.895 12.15 0.00 33.68 3.16
803 812 3.529533 CACCTTGAGCTCCAATAGAGTG 58.470 50.000 12.15 5.59 45.21 3.51
849 859 0.616964 AGCTCTGGCCAGTCTGATCA 60.617 55.000 31.58 10.30 39.73 2.92
851 861 1.743091 GCTCTGGCCAGTCTGATCAAG 60.743 57.143 31.58 19.52 0.00 3.02
948 958 4.754322 CTTCTCTTCTCTTTAGCCTCACC 58.246 47.826 0.00 0.00 0.00 4.02
955 965 1.819288 TCTTTAGCCTCACCTCTCACG 59.181 52.381 0.00 0.00 0.00 4.35
1123 1133 2.161855 TCTCCGCTTTTCAGGTACGTA 58.838 47.619 0.00 0.00 0.00 3.57
1125 1135 2.858344 CTCCGCTTTTCAGGTACGTATG 59.142 50.000 0.00 0.00 0.00 2.39
1131 1141 3.770263 TTTCAGGTACGTATGTCCTCG 57.230 47.619 0.00 0.00 0.00 4.63
1155 1165 3.642377 AGCATAGATGACAGAGCATCACT 59.358 43.478 0.00 0.00 45.52 3.41
1167 1190 1.481772 AGCATCACTCTCTCTCCTTGC 59.518 52.381 0.00 0.00 0.00 4.01
1169 1192 2.354503 GCATCACTCTCTCTCCTTGCAA 60.355 50.000 0.00 0.00 0.00 4.08
1191 1214 4.196971 ACTCCATTAATTTACGTGGCTCC 58.803 43.478 0.00 0.00 0.00 4.70
1193 1222 4.196193 TCCATTAATTTACGTGGCTCCAG 58.804 43.478 0.00 0.00 0.00 3.86
1217 1246 1.626654 CTAAACCGCACTGACGCTGG 61.627 60.000 0.00 0.00 0.00 4.85
1296 1325 2.118404 CCACAACCGGTGCAACACT 61.118 57.895 8.52 0.00 46.50 3.55
1570 1614 1.146957 TCGAGACTCGAGAGCTACGC 61.147 60.000 23.27 5.83 44.82 4.42
1571 1615 1.149361 CGAGACTCGAGAGCTACGCT 61.149 60.000 21.68 4.17 43.74 5.07
1572 1616 1.855513 GAGACTCGAGAGCTACGCTA 58.144 55.000 21.68 0.00 39.88 4.26
1573 1617 1.523934 GAGACTCGAGAGCTACGCTAC 59.476 57.143 21.68 0.00 39.88 3.58
1574 1618 0.230260 GACTCGAGAGCTACGCTACG 59.770 60.000 21.68 8.03 39.88 3.51
1575 1619 0.179116 ACTCGAGAGCTACGCTACGA 60.179 55.000 21.68 13.65 39.88 3.43
1596 1640 4.442472 CGATCCCGGTCTAGTTTTGGTTAT 60.442 45.833 0.00 0.00 0.00 1.89
1641 1685 0.248539 GCATCTCGTGTACCGTCCTC 60.249 60.000 4.11 0.00 37.94 3.71
1651 1695 2.759641 TACCGTCCTCGTCCTGCACT 62.760 60.000 0.00 0.00 35.01 4.40
1691 1735 2.800544 GTGTTCTTTCTTGCTACGCTGA 59.199 45.455 0.00 0.00 0.00 4.26
1697 1741 2.299993 TCTTGCTACGCTGATTCCAG 57.700 50.000 0.00 0.00 43.22 3.86
1713 1757 3.688694 TCCAGCATTTTACGGTGTACT 57.311 42.857 0.00 0.00 0.00 2.73
1714 1758 4.804868 TCCAGCATTTTACGGTGTACTA 57.195 40.909 0.00 0.00 0.00 1.82
1715 1759 4.497300 TCCAGCATTTTACGGTGTACTAC 58.503 43.478 0.00 0.00 0.00 2.73
1716 1760 3.305094 CCAGCATTTTACGGTGTACTACG 59.695 47.826 7.97 7.97 0.00 3.51
1717 1761 2.925563 AGCATTTTACGGTGTACTACGC 59.074 45.455 9.19 0.00 0.00 4.42
1718 1762 2.667481 GCATTTTACGGTGTACTACGCA 59.333 45.455 9.19 0.00 0.00 5.24
1719 1763 3.482436 GCATTTTACGGTGTACTACGCAC 60.482 47.826 9.19 0.00 36.22 5.34
1720 1764 3.361794 TTTTACGGTGTACTACGCACA 57.638 42.857 9.19 0.00 38.51 4.57
1721 1765 3.574284 TTTACGGTGTACTACGCACAT 57.426 42.857 9.19 0.00 38.51 3.21
1722 1766 4.693538 TTTACGGTGTACTACGCACATA 57.306 40.909 9.19 0.00 38.51 2.29
1839 1892 0.678950 GGTTAAAAGCCAGGCAAGCA 59.321 50.000 15.80 0.00 0.00 3.91
2179 2245 1.819632 GCTGGGCTGGGTTCGTATG 60.820 63.158 0.00 0.00 0.00 2.39
2180 2246 1.153168 CTGGGCTGGGTTCGTATGG 60.153 63.158 0.00 0.00 0.00 2.74
2181 2247 2.192175 GGGCTGGGTTCGTATGGG 59.808 66.667 0.00 0.00 0.00 4.00
2182 2248 2.676265 GGGCTGGGTTCGTATGGGT 61.676 63.158 0.00 0.00 0.00 4.51
2183 2249 1.451387 GGCTGGGTTCGTATGGGTG 60.451 63.158 0.00 0.00 0.00 4.61
2184 2250 1.298667 GCTGGGTTCGTATGGGTGT 59.701 57.895 0.00 0.00 0.00 4.16
2185 2251 1.024579 GCTGGGTTCGTATGGGTGTG 61.025 60.000 0.00 0.00 0.00 3.82
2186 2252 0.392461 CTGGGTTCGTATGGGTGTGG 60.392 60.000 0.00 0.00 0.00 4.17
2187 2253 1.128809 TGGGTTCGTATGGGTGTGGT 61.129 55.000 0.00 0.00 0.00 4.16
2188 2254 0.675522 GGGTTCGTATGGGTGTGGTG 60.676 60.000 0.00 0.00 0.00 4.17
2189 2255 0.675522 GGTTCGTATGGGTGTGGTGG 60.676 60.000 0.00 0.00 0.00 4.61
2190 2256 0.675522 GTTCGTATGGGTGTGGTGGG 60.676 60.000 0.00 0.00 0.00 4.61
2261 2327 4.787280 CCTGTCGGGCCTCCCTCT 62.787 72.222 0.84 0.00 42.67 3.69
2338 2416 1.588824 TACGGACACACCAGTAGCGG 61.589 60.000 0.00 0.00 38.90 5.52
2340 2418 2.657237 GACACACCAGTAGCGGCT 59.343 61.111 7.98 7.98 0.00 5.52
2341 2419 1.601419 GGACACACCAGTAGCGGCTA 61.601 60.000 5.42 5.42 38.79 3.93
2399 2481 3.507162 TCAAATTGAAGTGAGGCAGGA 57.493 42.857 0.00 0.00 0.00 3.86
2429 2515 3.874543 TCGTCTGCAAATAAGTGTGTGTT 59.125 39.130 0.00 0.00 0.00 3.32
2435 2521 6.540551 TCTGCAAATAAGTGTGTGTTAAGACA 59.459 34.615 0.45 0.45 0.00 3.41
2463 2549 3.294493 TTTTGCGGGGTGCTGCTC 61.294 61.111 0.00 0.00 46.63 4.26
2464 2550 4.577677 TTTGCGGGGTGCTGCTCA 62.578 61.111 0.00 0.00 46.63 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.630037 TCCTCTAAAATTTCTGTGTTTTTCTCC 58.370 33.333 0.00 0.00 0.00 3.71
63 64 3.051341 TCTCTCTCTACTCCCTCTCCTCT 60.051 52.174 0.00 0.00 0.00 3.69
72 73 7.606456 CCAATACACTCTATCTCTCTCTACTCC 59.394 44.444 0.00 0.00 0.00 3.85
121 124 7.778853 AGGAATATGAACATGAGCTCAAATCTT 59.221 33.333 22.50 17.58 0.00 2.40
257 260 2.101640 ATTGAAACCAAACAGGCCCT 57.898 45.000 0.00 0.00 43.14 5.19
258 261 3.323691 ACTTATTGAAACCAAACAGGCCC 59.676 43.478 0.00 0.00 43.14 5.80
259 262 4.038642 TGACTTATTGAAACCAAACAGGCC 59.961 41.667 0.00 0.00 43.14 5.19
260 263 4.982295 GTGACTTATTGAAACCAAACAGGC 59.018 41.667 0.00 0.00 43.14 4.85
261 264 5.508994 GGGTGACTTATTGAAACCAAACAGG 60.509 44.000 0.00 0.00 45.67 4.00
262 265 5.528870 GGGTGACTTATTGAAACCAAACAG 58.471 41.667 0.00 0.00 32.28 3.16
263 266 4.036971 CGGGTGACTTATTGAAACCAAACA 59.963 41.667 0.00 0.00 32.28 2.83
264 267 4.276431 TCGGGTGACTTATTGAAACCAAAC 59.724 41.667 0.00 0.00 32.28 2.93
265 268 4.276431 GTCGGGTGACTTATTGAAACCAAA 59.724 41.667 0.00 0.00 42.08 3.28
266 269 3.816523 GTCGGGTGACTTATTGAAACCAA 59.183 43.478 0.00 0.00 42.08 3.67
267 270 3.404899 GTCGGGTGACTTATTGAAACCA 58.595 45.455 0.00 0.00 42.08 3.67
283 286 5.277857 AGTCACCTGATTTATAAGTCGGG 57.722 43.478 26.38 26.38 44.75 5.14
284 287 8.712285 TTTAAGTCACCTGATTTATAAGTCGG 57.288 34.615 9.32 9.32 0.00 4.79
285 288 9.968743 GTTTTAAGTCACCTGATTTATAAGTCG 57.031 33.333 3.81 0.00 0.00 4.18
287 290 9.802039 TGGTTTTAAGTCACCTGATTTATAAGT 57.198 29.630 3.10 0.00 33.76 2.24
289 292 9.802039 ACTGGTTTTAAGTCACCTGATTTATAA 57.198 29.630 11.87 0.00 35.95 0.98
290 293 9.226606 CACTGGTTTTAAGTCACCTGATTTATA 57.773 33.333 11.87 0.00 35.95 0.98
291 294 7.942341 TCACTGGTTTTAAGTCACCTGATTTAT 59.058 33.333 11.87 0.00 35.95 1.40
292 295 7.227910 GTCACTGGTTTTAAGTCACCTGATTTA 59.772 37.037 11.87 0.00 35.95 1.40
293 296 6.039382 GTCACTGGTTTTAAGTCACCTGATTT 59.961 38.462 11.87 0.00 35.95 2.17
294 297 5.531287 GTCACTGGTTTTAAGTCACCTGATT 59.469 40.000 11.87 0.00 35.95 2.57
295 298 5.063880 GTCACTGGTTTTAAGTCACCTGAT 58.936 41.667 11.87 0.00 35.95 2.90
296 299 4.163458 AGTCACTGGTTTTAAGTCACCTGA 59.837 41.667 11.87 3.02 35.95 3.86
297 300 4.451900 AGTCACTGGTTTTAAGTCACCTG 58.548 43.478 6.12 6.12 37.86 4.00
298 301 4.772886 AGTCACTGGTTTTAAGTCACCT 57.227 40.909 3.10 0.00 33.76 4.00
299 302 8.611654 TTATAAGTCACTGGTTTTAAGTCACC 57.388 34.615 0.00 0.00 0.00 4.02
300 303 9.269453 ACTTATAAGTCACTGGTTTTAAGTCAC 57.731 33.333 12.50 0.00 32.86 3.67
317 320 6.034161 ACTAAACAGGCGTGACTTATAAGT 57.966 37.500 18.05 18.05 43.16 2.24
318 321 6.367969 ACAACTAAACAGGCGTGACTTATAAG 59.632 38.462 14.38 11.05 0.00 1.73
319 322 6.225318 ACAACTAAACAGGCGTGACTTATAA 58.775 36.000 14.38 0.00 0.00 0.98
320 323 5.786311 ACAACTAAACAGGCGTGACTTATA 58.214 37.500 14.38 0.00 0.00 0.98
321 324 4.638304 ACAACTAAACAGGCGTGACTTAT 58.362 39.130 14.38 0.00 0.00 1.73
322 325 4.053295 GACAACTAAACAGGCGTGACTTA 58.947 43.478 14.38 9.07 0.00 2.24
323 326 2.870411 GACAACTAAACAGGCGTGACTT 59.130 45.455 14.38 8.39 0.00 3.01
324 327 2.159014 TGACAACTAAACAGGCGTGACT 60.159 45.455 14.38 1.85 0.00 3.41
325 328 2.206750 TGACAACTAAACAGGCGTGAC 58.793 47.619 14.38 0.00 0.00 3.67
326 329 2.605837 TGACAACTAAACAGGCGTGA 57.394 45.000 14.38 0.00 0.00 4.35
327 330 3.067106 AGATGACAACTAAACAGGCGTG 58.933 45.455 4.53 4.53 0.00 5.34
328 331 3.067106 CAGATGACAACTAAACAGGCGT 58.933 45.455 0.00 0.00 0.00 5.68
329 332 3.123621 GTCAGATGACAACTAAACAGGCG 59.876 47.826 8.09 0.00 44.18 5.52
330 333 4.670227 GTCAGATGACAACTAAACAGGC 57.330 45.455 8.09 0.00 44.18 4.85
350 353 4.020485 GGTGTGGTCAGGTGACTTATAAGT 60.020 45.833 18.05 18.05 44.20 2.24
351 354 4.223032 AGGTGTGGTCAGGTGACTTATAAG 59.777 45.833 11.05 11.05 44.20 1.73
352 355 4.164981 AGGTGTGGTCAGGTGACTTATAA 58.835 43.478 9.90 0.00 44.20 0.98
353 356 3.786553 AGGTGTGGTCAGGTGACTTATA 58.213 45.455 9.90 0.00 44.20 0.98
354 357 2.621070 AGGTGTGGTCAGGTGACTTAT 58.379 47.619 9.90 0.00 44.20 1.73
355 358 2.097110 AGGTGTGGTCAGGTGACTTA 57.903 50.000 9.90 0.00 44.20 2.24
356 359 1.141053 GAAGGTGTGGTCAGGTGACTT 59.859 52.381 9.90 0.00 44.20 3.01
357 360 0.759346 GAAGGTGTGGTCAGGTGACT 59.241 55.000 9.90 0.00 44.20 3.41
358 361 0.468226 TGAAGGTGTGGTCAGGTGAC 59.532 55.000 1.17 1.17 44.04 3.67
359 362 0.468226 GTGAAGGTGTGGTCAGGTGA 59.532 55.000 0.00 0.00 0.00 4.02
360 363 0.180171 TGTGAAGGTGTGGTCAGGTG 59.820 55.000 0.00 0.00 0.00 4.00
361 364 0.180406 GTGTGAAGGTGTGGTCAGGT 59.820 55.000 0.00 0.00 0.00 4.00
362 365 0.535102 GGTGTGAAGGTGTGGTCAGG 60.535 60.000 0.00 0.00 0.00 3.86
363 366 0.469917 AGGTGTGAAGGTGTGGTCAG 59.530 55.000 0.00 0.00 0.00 3.51
364 367 0.916086 AAGGTGTGAAGGTGTGGTCA 59.084 50.000 0.00 0.00 0.00 4.02
365 368 1.308998 CAAGGTGTGAAGGTGTGGTC 58.691 55.000 0.00 0.00 0.00 4.02
366 369 0.623723 ACAAGGTGTGAAGGTGTGGT 59.376 50.000 0.00 0.00 0.00 4.16
367 370 1.762708 AACAAGGTGTGAAGGTGTGG 58.237 50.000 0.00 0.00 0.00 4.17
368 371 3.866883 AAAACAAGGTGTGAAGGTGTG 57.133 42.857 0.00 0.00 0.00 3.82
387 390 6.183361 TGGGTCCCACTACCTTTACATAAAAA 60.183 38.462 6.47 0.00 39.65 1.94
388 391 5.312708 TGGGTCCCACTACCTTTACATAAAA 59.687 40.000 6.47 0.00 39.65 1.52
389 392 4.850963 TGGGTCCCACTACCTTTACATAAA 59.149 41.667 6.47 0.00 39.65 1.40
390 393 4.437023 TGGGTCCCACTACCTTTACATAA 58.563 43.478 6.47 0.00 39.65 1.90
391 394 4.077552 TGGGTCCCACTACCTTTACATA 57.922 45.455 6.47 0.00 39.65 2.29
392 395 2.923908 TGGGTCCCACTACCTTTACAT 58.076 47.619 6.47 0.00 39.65 2.29
393 396 2.419457 TGGGTCCCACTACCTTTACA 57.581 50.000 6.47 0.00 39.65 2.41
404 407 2.203422 CCTTTTGCGTGGGTCCCA 60.203 61.111 6.47 6.47 0.00 4.37
405 408 2.989253 CCCTTTTGCGTGGGTCCC 60.989 66.667 0.00 0.00 38.65 4.46
406 409 2.989253 CCCCTTTTGCGTGGGTCC 60.989 66.667 0.00 0.00 41.82 4.46
409 412 2.203422 TCACCCCTTTTGCGTGGG 60.203 61.111 0.00 0.00 45.34 4.61
410 413 1.106944 AAGTCACCCCTTTTGCGTGG 61.107 55.000 0.00 0.00 0.00 4.94
411 414 0.030638 CAAGTCACCCCTTTTGCGTG 59.969 55.000 0.00 0.00 0.00 5.34
412 415 1.734388 GCAAGTCACCCCTTTTGCGT 61.734 55.000 0.00 0.00 36.89 5.24
413 416 1.007387 GCAAGTCACCCCTTTTGCG 60.007 57.895 0.00 0.00 36.89 4.85
414 417 0.463620 TTGCAAGTCACCCCTTTTGC 59.536 50.000 0.00 1.39 44.56 3.68
415 418 1.756538 ACTTGCAAGTCACCCCTTTTG 59.243 47.619 26.36 0.00 32.86 2.44
416 419 2.159179 ACTTGCAAGTCACCCCTTTT 57.841 45.000 26.36 0.00 32.86 2.27
417 420 2.159179 AACTTGCAAGTCACCCCTTT 57.841 45.000 31.20 11.34 38.57 3.11
418 421 2.159179 AAACTTGCAAGTCACCCCTT 57.841 45.000 31.20 18.03 38.57 3.95
419 422 2.159179 AAAACTTGCAAGTCACCCCT 57.841 45.000 31.20 12.86 38.57 4.79
420 423 3.383505 ACTTAAAACTTGCAAGTCACCCC 59.616 43.478 31.20 0.00 38.57 4.95
421 424 4.649088 ACTTAAAACTTGCAAGTCACCC 57.351 40.909 31.20 0.00 38.57 4.61
422 425 5.646606 TCAACTTAAAACTTGCAAGTCACC 58.353 37.500 31.20 0.00 38.57 4.02
423 426 5.743872 CCTCAACTTAAAACTTGCAAGTCAC 59.256 40.000 31.20 0.00 38.57 3.67
424 427 5.417580 ACCTCAACTTAAAACTTGCAAGTCA 59.582 36.000 31.20 17.02 38.57 3.41
425 428 5.743872 CACCTCAACTTAAAACTTGCAAGTC 59.256 40.000 31.20 0.00 38.57 3.01
426 429 5.394115 CCACCTCAACTTAAAACTTGCAAGT 60.394 40.000 26.36 26.36 42.04 3.16
427 430 5.043248 CCACCTCAACTTAAAACTTGCAAG 58.957 41.667 24.84 24.84 0.00 4.01
428 431 4.707448 TCCACCTCAACTTAAAACTTGCAA 59.293 37.500 0.00 0.00 0.00 4.08
429 432 4.274147 TCCACCTCAACTTAAAACTTGCA 58.726 39.130 0.00 0.00 0.00 4.08
430 433 4.793028 GCTCCACCTCAACTTAAAACTTGC 60.793 45.833 0.00 0.00 0.00 4.01
431 434 4.338118 TGCTCCACCTCAACTTAAAACTTG 59.662 41.667 0.00 0.00 0.00 3.16
432 435 4.532834 TGCTCCACCTCAACTTAAAACTT 58.467 39.130 0.00 0.00 0.00 2.66
433 436 4.164843 TGCTCCACCTCAACTTAAAACT 57.835 40.909 0.00 0.00 0.00 2.66
434 437 4.607955 GTTGCTCCACCTCAACTTAAAAC 58.392 43.478 0.00 0.00 39.41 2.43
435 438 4.911514 GTTGCTCCACCTCAACTTAAAA 57.088 40.909 0.00 0.00 39.41 1.52
441 444 3.437049 GTCATAAGTTGCTCCACCTCAAC 59.563 47.826 0.00 0.00 41.97 3.18
442 445 3.327757 AGTCATAAGTTGCTCCACCTCAA 59.672 43.478 0.00 0.00 0.00 3.02
443 446 2.906389 AGTCATAAGTTGCTCCACCTCA 59.094 45.455 0.00 0.00 0.00 3.86
444 447 3.618690 AGTCATAAGTTGCTCCACCTC 57.381 47.619 0.00 0.00 0.00 3.85
445 448 5.700402 ATAAGTCATAAGTTGCTCCACCT 57.300 39.130 0.00 0.00 0.00 4.00
446 449 7.859325 TTTATAAGTCATAAGTTGCTCCACC 57.141 36.000 0.00 0.00 30.75 4.61
447 450 9.722056 CAATTTATAAGTCATAAGTTGCTCCAC 57.278 33.333 0.00 0.00 38.91 4.02
448 451 8.902806 CCAATTTATAAGTCATAAGTTGCTCCA 58.097 33.333 6.69 0.00 41.78 3.86
449 452 8.352942 CCCAATTTATAAGTCATAAGTTGCTCC 58.647 37.037 6.69 0.00 41.78 4.70
450 453 8.352942 CCCCAATTTATAAGTCATAAGTTGCTC 58.647 37.037 6.69 0.00 41.78 4.26
451 454 7.839200 ACCCCAATTTATAAGTCATAAGTTGCT 59.161 33.333 6.69 0.00 41.78 3.91
452 455 7.920682 CACCCCAATTTATAAGTCATAAGTTGC 59.079 37.037 6.69 0.00 41.78 4.17
453 456 9.184523 TCACCCCAATTTATAAGTCATAAGTTG 57.815 33.333 5.67 5.67 42.32 3.16
454 457 9.185680 GTCACCCCAATTTATAAGTCATAAGTT 57.814 33.333 0.00 0.00 31.23 2.66
455 458 8.557450 AGTCACCCCAATTTATAAGTCATAAGT 58.443 33.333 0.00 0.00 30.75 2.24
456 459 8.980481 AGTCACCCCAATTTATAAGTCATAAG 57.020 34.615 0.00 0.00 30.75 1.73
459 462 9.936329 AATAAGTCACCCCAATTTATAAGTCAT 57.064 29.630 0.00 0.00 0.00 3.06
460 463 9.762381 AAATAAGTCACCCCAATTTATAAGTCA 57.238 29.630 0.00 0.00 0.00 3.41
462 465 9.762381 TCAAATAAGTCACCCCAATTTATAAGT 57.238 29.630 0.00 0.00 0.00 2.24
466 469 8.318412 GGTTTCAAATAAGTCACCCCAATTTAT 58.682 33.333 0.00 0.00 0.00 1.40
467 470 7.290248 TGGTTTCAAATAAGTCACCCCAATTTA 59.710 33.333 0.00 0.00 0.00 1.40
468 471 6.100424 TGGTTTCAAATAAGTCACCCCAATTT 59.900 34.615 0.00 0.00 0.00 1.82
469 472 5.604650 TGGTTTCAAATAAGTCACCCCAATT 59.395 36.000 0.00 0.00 0.00 2.32
470 473 5.151454 TGGTTTCAAATAAGTCACCCCAAT 58.849 37.500 0.00 0.00 0.00 3.16
471 474 4.547671 TGGTTTCAAATAAGTCACCCCAA 58.452 39.130 0.00 0.00 0.00 4.12
472 475 4.186077 TGGTTTCAAATAAGTCACCCCA 57.814 40.909 0.00 0.00 0.00 4.96
473 476 5.069914 AGTTTGGTTTCAAATAAGTCACCCC 59.930 40.000 0.00 0.00 43.73 4.95
474 477 5.983118 CAGTTTGGTTTCAAATAAGTCACCC 59.017 40.000 0.00 0.00 43.73 4.61
475 478 5.983118 CCAGTTTGGTTTCAAATAAGTCACC 59.017 40.000 0.00 0.00 43.73 4.02
476 479 5.462068 GCCAGTTTGGTTTCAAATAAGTCAC 59.538 40.000 0.00 0.00 43.73 3.67
477 480 5.452636 GGCCAGTTTGGTTTCAAATAAGTCA 60.453 40.000 0.00 0.00 43.73 3.41
478 481 4.988540 GGCCAGTTTGGTTTCAAATAAGTC 59.011 41.667 0.00 0.00 43.73 3.01
479 482 4.202315 GGGCCAGTTTGGTTTCAAATAAGT 60.202 41.667 4.39 0.00 43.73 2.24
480 483 4.040339 AGGGCCAGTTTGGTTTCAAATAAG 59.960 41.667 6.18 0.00 43.73 1.73
481 484 3.970640 AGGGCCAGTTTGGTTTCAAATAA 59.029 39.130 6.18 0.00 43.73 1.40
482 485 3.582164 AGGGCCAGTTTGGTTTCAAATA 58.418 40.909 6.18 0.00 43.73 1.40
483 486 2.407562 AGGGCCAGTTTGGTTTCAAAT 58.592 42.857 6.18 0.00 43.73 2.32
484 487 1.872773 AGGGCCAGTTTGGTTTCAAA 58.127 45.000 6.18 0.00 40.46 2.69
485 488 2.757894 TAGGGCCAGTTTGGTTTCAA 57.242 45.000 6.18 0.00 40.46 2.69
486 489 2.175931 TCTTAGGGCCAGTTTGGTTTCA 59.824 45.455 6.18 0.00 40.46 2.69
487 490 2.871453 TCTTAGGGCCAGTTTGGTTTC 58.129 47.619 6.18 0.00 40.46 2.78
488 491 3.230976 CTTCTTAGGGCCAGTTTGGTTT 58.769 45.455 6.18 0.00 40.46 3.27
489 492 2.876581 CTTCTTAGGGCCAGTTTGGTT 58.123 47.619 6.18 0.00 40.46 3.67
490 493 1.547901 GCTTCTTAGGGCCAGTTTGGT 60.548 52.381 6.18 0.00 40.46 3.67
491 494 1.177401 GCTTCTTAGGGCCAGTTTGG 58.823 55.000 6.18 0.00 41.55 3.28
492 495 1.177401 GGCTTCTTAGGGCCAGTTTG 58.823 55.000 6.18 0.00 46.84 2.93
493 496 3.672066 GGCTTCTTAGGGCCAGTTT 57.328 52.632 6.18 0.00 46.84 2.66
498 501 2.124695 CCACGGCTTCTTAGGGCC 60.125 66.667 0.00 0.00 44.43 5.80
499 502 2.124695 CCCACGGCTTCTTAGGGC 60.125 66.667 0.00 0.00 31.81 5.19
500 503 0.037734 AAACCCACGGCTTCTTAGGG 59.962 55.000 0.00 0.00 45.20 3.53
501 504 1.165270 CAAACCCACGGCTTCTTAGG 58.835 55.000 0.00 0.00 0.00 2.69
502 505 0.521735 GCAAACCCACGGCTTCTTAG 59.478 55.000 0.00 0.00 0.00 2.18
503 506 0.179015 TGCAAACCCACGGCTTCTTA 60.179 50.000 0.00 0.00 0.00 2.10
504 507 1.040339 TTGCAAACCCACGGCTTCTT 61.040 50.000 0.00 0.00 0.00 2.52
505 508 1.454847 TTGCAAACCCACGGCTTCT 60.455 52.632 0.00 0.00 0.00 2.85
506 509 1.299850 GTTGCAAACCCACGGCTTC 60.300 57.895 0.00 0.00 42.21 3.86
523 526 1.271054 ACGTACTACCACTCCACTCGT 60.271 52.381 0.00 0.00 0.00 4.18
716 725 3.447586 CGGACATCAGAGGGTAGAAGAAA 59.552 47.826 0.00 0.00 0.00 2.52
722 731 1.889829 GGATCGGACATCAGAGGGTAG 59.110 57.143 0.00 0.00 0.00 3.18
849 859 1.493022 TGCCTTGTGTGTAGGTTCCTT 59.507 47.619 0.00 0.00 35.13 3.36
851 861 1.880027 CTTGCCTTGTGTGTAGGTTCC 59.120 52.381 0.00 0.00 35.13 3.62
948 958 3.680786 TGCCGGTGACCGTGAGAG 61.681 66.667 23.73 8.11 46.80 3.20
955 965 1.299541 CAGATTATGTGCCGGTGACC 58.700 55.000 1.90 0.00 0.00 4.02
1057 1067 4.116328 CGTCGCAGCTCCGAGGAA 62.116 66.667 14.39 0.00 43.49 3.36
1123 1133 2.560542 GTCATCTATGCTCCGAGGACAT 59.439 50.000 0.00 10.44 39.83 3.06
1125 1135 1.957177 TGTCATCTATGCTCCGAGGAC 59.043 52.381 0.00 7.29 40.31 3.85
1131 1141 3.006644 TGATGCTCTGTCATCTATGCTCC 59.993 47.826 11.60 0.00 42.44 4.70
1155 1165 2.015456 TGGAGTTGCAAGGAGAGAGA 57.985 50.000 0.00 0.00 0.00 3.10
1167 1190 5.448632 GGAGCCACGTAAATTAATGGAGTTG 60.449 44.000 8.33 0.00 33.80 3.16
1169 1192 4.196971 GGAGCCACGTAAATTAATGGAGT 58.803 43.478 8.33 0.00 33.80 3.85
1191 1214 2.412089 GTCAGTGCGGTTTAGTTAGCTG 59.588 50.000 0.00 0.00 0.00 4.24
1193 1222 1.389106 CGTCAGTGCGGTTTAGTTAGC 59.611 52.381 0.00 0.00 0.00 3.09
1217 1246 1.270550 CCAAGTTCTGCCCATGAACAC 59.729 52.381 8.91 0.00 44.30 3.32
1570 1614 3.490419 CCAAAACTAGACCGGGATCGTAG 60.490 52.174 6.32 1.24 33.95 3.51
1571 1615 2.428171 CCAAAACTAGACCGGGATCGTA 59.572 50.000 6.32 0.00 33.95 3.43
1572 1616 1.206371 CCAAAACTAGACCGGGATCGT 59.794 52.381 6.32 0.00 33.95 3.73
1573 1617 1.206371 ACCAAAACTAGACCGGGATCG 59.794 52.381 6.32 0.00 0.00 3.69
1574 1618 3.345508 AACCAAAACTAGACCGGGATC 57.654 47.619 6.32 0.00 0.00 3.36
1575 1619 5.446260 AATAACCAAAACTAGACCGGGAT 57.554 39.130 6.32 0.00 0.00 3.85
1596 1640 7.393216 CAAGGAATTTATGGGACCAAATGAAA 58.607 34.615 0.00 0.00 0.00 2.69
1691 1735 4.585879 AGTACACCGTAAAATGCTGGAAT 58.414 39.130 0.00 0.00 0.00 3.01
1697 1741 2.667481 TGCGTAGTACACCGTAAAATGC 59.333 45.455 0.38 0.00 0.00 3.56
1713 1757 5.451381 CCCAATCACTCTTACTATGTGCGTA 60.451 44.000 0.00 0.00 0.00 4.42
1714 1758 4.433615 CCAATCACTCTTACTATGTGCGT 58.566 43.478 0.00 0.00 0.00 5.24
1715 1759 3.804325 CCCAATCACTCTTACTATGTGCG 59.196 47.826 0.00 0.00 0.00 5.34
1716 1760 5.023533 TCCCAATCACTCTTACTATGTGC 57.976 43.478 0.00 0.00 0.00 4.57
1717 1761 5.923114 CGATCCCAATCACTCTTACTATGTG 59.077 44.000 0.00 0.00 31.76 3.21
1718 1762 5.833667 TCGATCCCAATCACTCTTACTATGT 59.166 40.000 0.00 0.00 31.76 2.29
1719 1763 6.332735 TCGATCCCAATCACTCTTACTATG 57.667 41.667 0.00 0.00 31.76 2.23
1720 1764 6.071108 CCATCGATCCCAATCACTCTTACTAT 60.071 42.308 0.00 0.00 31.76 2.12
1721 1765 5.243954 CCATCGATCCCAATCACTCTTACTA 59.756 44.000 0.00 0.00 31.76 1.82
1722 1766 4.039730 CCATCGATCCCAATCACTCTTACT 59.960 45.833 0.00 0.00 31.76 2.24
1783 1836 8.974238 ACAGCACTGGTACTGTTATTACTATTA 58.026 33.333 2.21 0.00 44.59 0.98
1784 1837 7.764443 CACAGCACTGGTACTGTTATTACTATT 59.236 37.037 4.08 0.00 44.59 1.73
1785 1838 7.265673 CACAGCACTGGTACTGTTATTACTAT 58.734 38.462 4.08 0.00 44.59 2.12
1801 1854 2.683859 CGCCATCACCACAGCACTG 61.684 63.158 0.00 0.00 0.00 3.66
1802 1855 2.359107 CGCCATCACCACAGCACT 60.359 61.111 0.00 0.00 0.00 4.40
1912 1965 4.256090 CGCTAATTGCTGGGCCGC 62.256 66.667 12.46 12.46 40.11 6.53
1913 1966 4.256090 GCGCTAATTGCTGGGCCG 62.256 66.667 0.00 0.00 40.11 6.13
1915 1968 3.140141 TGGCGCTAATTGCTGGGC 61.140 61.111 7.64 7.92 40.11 5.36
1993 2046 2.096417 ACACAAGCGCAATTACTTCGAC 60.096 45.455 11.47 0.00 0.00 4.20
2138 2197 2.997897 GGCGAGGGAGACACCACT 60.998 66.667 0.00 0.00 41.20 4.00
2164 2223 2.192175 CCCATACGAACCCAGCCC 59.808 66.667 0.00 0.00 0.00 5.19
2169 2228 0.675522 CACCACACCCATACGAACCC 60.676 60.000 0.00 0.00 0.00 4.11
2171 2230 0.675522 CCCACCACACCCATACGAAC 60.676 60.000 0.00 0.00 0.00 3.95
2172 2231 1.680487 CCCACCACACCCATACGAA 59.320 57.895 0.00 0.00 0.00 3.85
2179 2245 3.816090 ACACACCCCACCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
2180 2246 2.518349 CACACACCCCACCACACC 60.518 66.667 0.00 0.00 0.00 4.16
2181 2247 2.518349 CCACACACCCCACCACAC 60.518 66.667 0.00 0.00 0.00 3.82
2182 2248 3.814906 CCCACACACCCCACCACA 61.815 66.667 0.00 0.00 0.00 4.17
2183 2249 4.596585 CCCCACACACCCCACCAC 62.597 72.222 0.00 0.00 0.00 4.16
2185 2251 3.802852 GAACCCCACACACCCCACC 62.803 68.421 0.00 0.00 0.00 4.61
2186 2252 2.203437 GAACCCCACACACCCCAC 60.203 66.667 0.00 0.00 0.00 4.61
2187 2253 3.879885 CGAACCCCACACACCCCA 61.880 66.667 0.00 0.00 0.00 4.96
2338 2416 0.039074 ACCTGCATCGTCGCTATAGC 60.039 55.000 15.09 15.09 37.78 2.97
2340 2418 1.029681 ACACCTGCATCGTCGCTATA 58.970 50.000 0.00 0.00 0.00 1.31
2341 2419 0.175760 AACACCTGCATCGTCGCTAT 59.824 50.000 0.00 0.00 0.00 2.97
2399 2481 6.482308 ACACTTATTTGCAGACGAAAACTACT 59.518 34.615 0.00 0.00 0.00 2.57
2429 2515 3.554324 GCAAAACACTGTCTCGTGTCTTA 59.446 43.478 0.00 0.00 46.71 2.10
2435 2521 1.157870 CCCGCAAAACACTGTCTCGT 61.158 55.000 0.00 0.00 0.00 4.18
2446 2532 3.294493 GAGCAGCACCCCGCAAAA 61.294 61.111 0.00 0.00 46.13 2.44


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

AutoCloner maintained by Alex Coulton.