Multiple sequence alignment - TraesCS5D01G566900

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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 TraesCS5D01G566900 chr5D 100.000 3572 0 0 1 3572 564975204 564978775 0.000000e+00 6597.0
1 TraesCS5D01G566900 chr4A 91.097 2707 141 34 858 3522 606411121 606413769 0.000000e+00 3572.0
2 TraesCS5D01G566900 chr4A 90.977 133 9 1 731 860 606410886 606411018 3.670000e-40 176.0
3 TraesCS5D01G566900 chr5B 92.797 2360 128 21 570 2906 708338536 708336196 0.000000e+00 3378.0
4 TraesCS5D01G566900 chr5B 85.821 536 52 17 3016 3530 708335332 708334800 6.740000e-152 547.0
5 TraesCS5D01G566900 chr5B 87.917 240 21 3 1 233 708338921 708338683 3.510000e-70 276.0
6 TraesCS5D01G566900 chr7B 86.640 247 27 4 303 546 511300565 511300808 5.880000e-68 268.0
7 TraesCS5D01G566900 chr6D 89.048 210 19 2 337 545 402347115 402347321 1.270000e-64 257.0
8 TraesCS5D01G566900 chr6D 86.147 231 26 4 305 532 45485282 45485509 9.910000e-61 244.0
9 TraesCS5D01G566900 chr3D 85.542 249 28 5 303 546 104811451 104811206 1.650000e-63 254.0
10 TraesCS5D01G566900 chr3D 84.711 242 32 4 307 545 354012501 354012740 1.660000e-58 237.0
11 TraesCS5D01G566900 chr3A 84.677 248 30 5 303 546 550635190 550635433 1.280000e-59 241.0
12 TraesCS5D01G566900 chr5A 84.774 243 29 4 307 545 341717473 341717235 1.660000e-58 237.0
13 TraesCS5D01G566900 chr5A 92.222 90 6 1 175 264 479748999 479748911 3.740000e-25 126.0
14 TraesCS5D01G566900 chr2B 84.016 244 33 6 306 545 163570698 163570457 2.770000e-56 230.0
15 TraesCS5D01G566900 chr2B 84.298 242 31 4 307 545 610844506 610844743 2.770000e-56 230.0
16 TraesCS5D01G566900 chr2B 89.000 100 9 2 171 269 63783816 63783718 4.840000e-24 122.0
17 TraesCS5D01G566900 chr2D 80.932 236 21 8 1321 1556 263488329 263488540 7.930000e-37 165.0
18 TraesCS5D01G566900 chr2A 91.089 101 7 2 172 271 102692164 102692065 6.220000e-28 135.0
19 TraesCS5D01G566900 chr7D 90.722 97 7 2 174 269 22959753 22959658 1.040000e-25 128.0
20 TraesCS5D01G566900 chr7D 90.323 93 7 2 177 268 426558983 426558892 1.740000e-23 121.0
21 TraesCS5D01G566900 chr6A 91.398 93 7 1 177 269 557970132 557970041 3.740000e-25 126.0
22 TraesCS5D01G566900 chr7A 90.426 94 7 2 173 265 686783298 686783206 4.840000e-24 122.0
23 TraesCS5D01G566900 chr4D 89.796 98 7 2 167 262 478671840 478671936 4.840000e-24 122.0
24 TraesCS5D01G566900 chr4B 85.965 57 8 0 3014 3070 652763208 652763152 1.070000e-05 62.1


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 TraesCS5D01G566900 chr5D 564975204 564978775 3571 False 6597.000000 6597 100.000 1 3572 1 chr5D.!!$F1 3571
1 TraesCS5D01G566900 chr4A 606410886 606413769 2883 False 1874.000000 3572 91.037 731 3522 2 chr4A.!!$F1 2791
2 TraesCS5D01G566900 chr5B 708334800 708338921 4121 True 1400.333333 3378 88.845 1 3530 3 chr5B.!!$R1 3529

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
944 1107 0.529833 TTGCTCTGCTCCTCTTCTCG 59.47 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2668 2861 0.251297 TCACCTCCCTTGTGGCAATG 60.251 55.0 0.0 0.0 34.46 2.82 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
25 26 7.792925 TCTAAAAATGTACTCATCACGTTGTG 58.207 34.615 0.00 0.00 32.56 3.33
30 31 6.801539 ATGTACTCATCACGTTGTGAAAAT 57.198 33.333 3.47 0.00 45.96 1.82
32 33 7.716768 TGTACTCATCACGTTGTGAAAATTA 57.283 32.000 3.47 0.00 45.96 1.40
95 96 4.098960 TGCGGATAATTTCTCGGTCTACTT 59.901 41.667 0.00 0.00 0.00 2.24
100 101 9.903682 CGGATAATTTCTCGGTCTACTTTATAA 57.096 33.333 0.00 0.00 0.00 0.98
156 164 7.124347 TCAACATGTTAGTACGAATTTGTCC 57.876 36.000 11.53 0.00 0.00 4.02
161 169 4.688879 TGTTAGTACGAATTTGTCCAGCTG 59.311 41.667 6.78 6.78 0.00 4.24
207 261 6.175471 TCCGTCCTCATAATATAAGAGCGTA 58.825 40.000 0.00 0.00 0.00 4.42
269 324 3.678548 GCGAAGGCGGGAGTAATATTTAG 59.321 47.826 0.00 0.00 38.16 1.85
276 331 5.465724 GGCGGGAGTAATATTTAGTCTTGTG 59.534 44.000 0.00 0.00 0.00 3.33
288 343 3.705043 AGTCTTGTGTTAGAACGACGT 57.295 42.857 0.00 0.00 0.00 4.34
293 348 7.533426 AGTCTTGTGTTAGAACGACGTAATAT 58.467 34.615 0.00 0.00 0.00 1.28
295 350 8.642020 GTCTTGTGTTAGAACGACGTAATATTT 58.358 33.333 0.00 0.00 0.00 1.40
296 351 9.838975 TCTTGTGTTAGAACGACGTAATATTTA 57.161 29.630 0.00 0.00 0.00 1.40
317 372 7.944729 TTTATTCTAACACTACTACCTCCGT 57.055 36.000 0.00 0.00 0.00 4.69
318 373 7.559590 TTATTCTAACACTACTACCTCCGTC 57.440 40.000 0.00 0.00 0.00 4.79
319 374 3.878778 TCTAACACTACTACCTCCGTCC 58.121 50.000 0.00 0.00 0.00 4.79
320 375 2.895242 AACACTACTACCTCCGTCCT 57.105 50.000 0.00 0.00 0.00 3.85
321 376 2.125773 ACACTACTACCTCCGTCCTG 57.874 55.000 0.00 0.00 0.00 3.86
322 377 1.340795 ACACTACTACCTCCGTCCTGG 60.341 57.143 0.00 0.00 40.09 4.45
323 378 0.998145 ACTACTACCTCCGTCCTGGT 59.002 55.000 0.00 0.00 39.52 4.00
324 379 1.357079 ACTACTACCTCCGTCCTGGTT 59.643 52.381 0.00 0.00 39.52 3.67
325 380 2.225217 ACTACTACCTCCGTCCTGGTTT 60.225 50.000 0.00 0.00 39.52 3.27
326 381 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
327 382 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
328 383 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
329 384 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
330 385 2.262637 ACCTCCGTCCTGGTTTATTGA 58.737 47.619 0.00 0.00 39.52 2.57
331 386 2.027469 ACCTCCGTCCTGGTTTATTGAC 60.027 50.000 0.00 0.00 39.52 3.18
332 387 2.629051 CTCCGTCCTGGTTTATTGACC 58.371 52.381 0.00 0.00 39.52 4.02
333 388 1.279846 TCCGTCCTGGTTTATTGACCC 59.720 52.381 0.00 0.00 39.01 4.46
334 389 1.280998 CCGTCCTGGTTTATTGACCCT 59.719 52.381 0.00 0.00 39.01 4.34
335 390 2.502538 CCGTCCTGGTTTATTGACCCTA 59.497 50.000 0.00 0.00 39.01 3.53
336 391 3.054948 CCGTCCTGGTTTATTGACCCTAA 60.055 47.826 0.00 0.00 39.01 2.69
337 392 4.189231 CGTCCTGGTTTATTGACCCTAAG 58.811 47.826 0.00 0.00 39.01 2.18
338 393 4.323257 CGTCCTGGTTTATTGACCCTAAGT 60.323 45.833 0.00 0.00 39.01 2.24
339 394 5.105228 CGTCCTGGTTTATTGACCCTAAGTA 60.105 44.000 0.00 0.00 39.01 2.24
340 395 6.407752 CGTCCTGGTTTATTGACCCTAAGTAT 60.408 42.308 0.00 0.00 39.01 2.12
341 396 7.344134 GTCCTGGTTTATTGACCCTAAGTATT 58.656 38.462 0.00 0.00 39.01 1.89
342 397 7.832685 GTCCTGGTTTATTGACCCTAAGTATTT 59.167 37.037 0.00 0.00 39.01 1.40
343 398 8.395605 TCCTGGTTTATTGACCCTAAGTATTTT 58.604 33.333 0.00 0.00 39.01 1.82
344 399 8.466798 CCTGGTTTATTGACCCTAAGTATTTTG 58.533 37.037 0.00 0.00 39.01 2.44
345 400 8.943594 TGGTTTATTGACCCTAAGTATTTTGT 57.056 30.769 0.00 0.00 39.01 2.83
346 401 8.798402 TGGTTTATTGACCCTAAGTATTTTGTG 58.202 33.333 0.00 0.00 39.01 3.33
347 402 7.758076 GGTTTATTGACCCTAAGTATTTTGTGC 59.242 37.037 0.00 0.00 33.41 4.57
348 403 5.914898 ATTGACCCTAAGTATTTTGTGCC 57.085 39.130 0.00 0.00 0.00 5.01
349 404 4.374689 TGACCCTAAGTATTTTGTGCCA 57.625 40.909 0.00 0.00 0.00 4.92
350 405 4.730966 TGACCCTAAGTATTTTGTGCCAA 58.269 39.130 0.00 0.00 0.00 4.52
351 406 5.329399 TGACCCTAAGTATTTTGTGCCAAT 58.671 37.500 0.00 0.00 0.00 3.16
352 407 5.777732 TGACCCTAAGTATTTTGTGCCAATT 59.222 36.000 0.00 0.00 0.00 2.32
353 408 6.268847 TGACCCTAAGTATTTTGTGCCAATTT 59.731 34.615 0.00 0.00 0.00 1.82
354 409 7.073457 ACCCTAAGTATTTTGTGCCAATTTT 57.927 32.000 0.00 0.00 0.00 1.82
355 410 7.513856 ACCCTAAGTATTTTGTGCCAATTTTT 58.486 30.769 0.00 0.00 0.00 1.94
356 411 7.443879 ACCCTAAGTATTTTGTGCCAATTTTTG 59.556 33.333 0.00 0.00 0.00 2.44
357 412 7.659390 CCCTAAGTATTTTGTGCCAATTTTTGA 59.341 33.333 0.00 0.00 0.00 2.69
358 413 8.495148 CCTAAGTATTTTGTGCCAATTTTTGAC 58.505 33.333 0.00 0.00 0.00 3.18
359 414 6.859420 AGTATTTTGTGCCAATTTTTGACC 57.141 33.333 0.00 0.00 0.00 4.02
360 415 6.352516 AGTATTTTGTGCCAATTTTTGACCA 58.647 32.000 0.00 0.00 0.00 4.02
361 416 6.997476 AGTATTTTGTGCCAATTTTTGACCAT 59.003 30.769 0.00 0.00 0.00 3.55
362 417 6.712179 ATTTTGTGCCAATTTTTGACCATT 57.288 29.167 0.00 0.00 0.00 3.16
363 418 7.814264 ATTTTGTGCCAATTTTTGACCATTA 57.186 28.000 0.00 0.00 0.00 1.90
364 419 7.630242 TTTTGTGCCAATTTTTGACCATTAA 57.370 28.000 0.00 0.00 0.00 1.40
365 420 7.814264 TTTGTGCCAATTTTTGACCATTAAT 57.186 28.000 0.00 0.00 0.00 1.40
366 421 7.814264 TTGTGCCAATTTTTGACCATTAATT 57.186 28.000 0.00 0.00 0.00 1.40
367 422 7.814264 TGTGCCAATTTTTGACCATTAATTT 57.186 28.000 0.00 0.00 0.00 1.82
368 423 8.908786 TGTGCCAATTTTTGACCATTAATTTA 57.091 26.923 0.00 0.00 0.00 1.40
369 424 9.342308 TGTGCCAATTTTTGACCATTAATTTAA 57.658 25.926 0.00 0.00 0.00 1.52
422 477 7.611213 AAAAACAGTATCATCGGAAACTAGG 57.389 36.000 0.00 0.00 0.00 3.02
423 478 5.934402 AACAGTATCATCGGAAACTAGGT 57.066 39.130 0.00 0.00 0.00 3.08
424 479 5.934402 ACAGTATCATCGGAAACTAGGTT 57.066 39.130 0.00 0.00 0.00 3.50
425 480 6.295719 ACAGTATCATCGGAAACTAGGTTT 57.704 37.500 0.00 0.00 38.54 3.27
426 481 7.414222 ACAGTATCATCGGAAACTAGGTTTA 57.586 36.000 0.00 0.00 35.77 2.01
427 482 7.844009 ACAGTATCATCGGAAACTAGGTTTAA 58.156 34.615 0.00 0.00 35.77 1.52
428 483 8.316214 ACAGTATCATCGGAAACTAGGTTTAAA 58.684 33.333 0.00 0.00 35.77 1.52
429 484 9.326413 CAGTATCATCGGAAACTAGGTTTAAAT 57.674 33.333 0.00 0.00 35.77 1.40
432 487 7.760131 TCATCGGAAACTAGGTTTAAATACG 57.240 36.000 0.00 0.00 35.77 3.06
433 488 7.546358 TCATCGGAAACTAGGTTTAAATACGA 58.454 34.615 0.00 0.00 35.77 3.43
434 489 8.034215 TCATCGGAAACTAGGTTTAAATACGAA 58.966 33.333 0.00 0.00 35.77 3.85
435 490 8.823818 CATCGGAAACTAGGTTTAAATACGAAT 58.176 33.333 0.00 0.00 35.77 3.34
436 491 8.411318 TCGGAAACTAGGTTTAAATACGAATC 57.589 34.615 0.00 0.00 35.77 2.52
437 492 7.492344 TCGGAAACTAGGTTTAAATACGAATCC 59.508 37.037 0.00 0.00 35.77 3.01
438 493 7.278424 CGGAAACTAGGTTTAAATACGAATCCA 59.722 37.037 0.00 0.00 35.77 3.41
439 494 8.949177 GGAAACTAGGTTTAAATACGAATCCAA 58.051 33.333 0.00 0.00 35.77 3.53
440 495 9.764870 GAAACTAGGTTTAAATACGAATCCAAC 57.235 33.333 0.00 0.00 35.77 3.77
441 496 7.529880 ACTAGGTTTAAATACGAATCCAACG 57.470 36.000 0.00 0.00 0.00 4.10
442 497 7.322664 ACTAGGTTTAAATACGAATCCAACGA 58.677 34.615 0.00 0.00 34.70 3.85
443 498 7.983484 ACTAGGTTTAAATACGAATCCAACGAT 59.017 33.333 0.00 0.00 34.70 3.73
444 499 9.467258 CTAGGTTTAAATACGAATCCAACGATA 57.533 33.333 0.00 0.00 34.70 2.92
445 500 8.897872 AGGTTTAAATACGAATCCAACGATAT 57.102 30.769 0.00 0.00 34.70 1.63
446 501 9.985730 AGGTTTAAATACGAATCCAACGATATA 57.014 29.630 0.00 0.00 34.70 0.86
477 532 9.702494 TTTATGACATGCATTAACATTTTGTCA 57.298 25.926 14.34 14.34 38.44 3.58
478 533 9.702494 TTATGACATGCATTAACATTTTGTCAA 57.298 25.926 15.55 5.51 35.43 3.18
479 534 8.780846 ATGACATGCATTAACATTTTGTCAAT 57.219 26.923 15.55 4.91 35.43 2.57
480 535 8.604640 TGACATGCATTAACATTTTGTCAATT 57.395 26.923 10.64 0.00 31.39 2.32
481 536 9.702494 TGACATGCATTAACATTTTGTCAATTA 57.298 25.926 10.64 0.00 31.39 1.40
501 556 9.632807 TCAATTAAATTTATGGTCGAGTTTTGG 57.367 29.630 0.00 0.00 0.00 3.28
502 557 8.379902 CAATTAAATTTATGGTCGAGTTTTGGC 58.620 33.333 0.00 0.00 0.00 4.52
503 558 5.461032 AAATTTATGGTCGAGTTTTGGCA 57.539 34.783 0.00 0.00 0.00 4.92
504 559 3.907894 TTTATGGTCGAGTTTTGGCAC 57.092 42.857 0.00 0.00 0.00 5.01
505 560 2.552599 TATGGTCGAGTTTTGGCACA 57.447 45.000 0.00 0.00 0.00 4.57
519 574 3.410631 TGGCACAAAATACGAAGAGGA 57.589 42.857 0.00 0.00 31.92 3.71
520 575 3.071479 TGGCACAAAATACGAAGAGGAC 58.929 45.455 0.00 0.00 31.92 3.85
521 576 2.418976 GGCACAAAATACGAAGAGGACC 59.581 50.000 0.00 0.00 0.00 4.46
522 577 3.071479 GCACAAAATACGAAGAGGACCA 58.929 45.455 0.00 0.00 0.00 4.02
523 578 3.500680 GCACAAAATACGAAGAGGACCAA 59.499 43.478 0.00 0.00 0.00 3.67
524 579 4.156008 GCACAAAATACGAAGAGGACCAAT 59.844 41.667 0.00 0.00 0.00 3.16
525 580 5.353123 GCACAAAATACGAAGAGGACCAATA 59.647 40.000 0.00 0.00 0.00 1.90
526 581 6.128117 GCACAAAATACGAAGAGGACCAATAA 60.128 38.462 0.00 0.00 0.00 1.40
527 582 7.574217 GCACAAAATACGAAGAGGACCAATAAA 60.574 37.037 0.00 0.00 0.00 1.40
528 583 7.749126 CACAAAATACGAAGAGGACCAATAAAC 59.251 37.037 0.00 0.00 0.00 2.01
529 584 6.997239 AAATACGAAGAGGACCAATAAACC 57.003 37.500 0.00 0.00 0.00 3.27
530 585 5.687166 ATACGAAGAGGACCAATAAACCA 57.313 39.130 0.00 0.00 0.00 3.67
531 586 3.939066 ACGAAGAGGACCAATAAACCAG 58.061 45.455 0.00 0.00 0.00 4.00
532 587 2.678336 CGAAGAGGACCAATAAACCAGC 59.322 50.000 0.00 0.00 0.00 4.85
533 588 3.686016 GAAGAGGACCAATAAACCAGCA 58.314 45.455 0.00 0.00 0.00 4.41
534 589 3.073274 AGAGGACCAATAAACCAGCAC 57.927 47.619 0.00 0.00 0.00 4.40
535 590 2.644798 AGAGGACCAATAAACCAGCACT 59.355 45.455 0.00 0.00 0.00 4.40
536 591 2.749621 GAGGACCAATAAACCAGCACTG 59.250 50.000 0.00 0.00 0.00 3.66
537 592 2.375174 AGGACCAATAAACCAGCACTGA 59.625 45.455 0.00 0.00 0.00 3.41
538 593 2.749621 GGACCAATAAACCAGCACTGAG 59.250 50.000 0.00 0.00 0.00 3.35
539 594 2.749621 GACCAATAAACCAGCACTGAGG 59.250 50.000 0.00 0.00 0.00 3.86
540 595 2.108250 ACCAATAAACCAGCACTGAGGT 59.892 45.455 0.00 0.00 40.61 3.85
541 596 3.329520 ACCAATAAACCAGCACTGAGGTA 59.670 43.478 0.00 0.00 37.07 3.08
542 597 3.941483 CCAATAAACCAGCACTGAGGTAG 59.059 47.826 0.00 0.00 37.07 3.18
543 598 4.565652 CCAATAAACCAGCACTGAGGTAGT 60.566 45.833 0.00 0.00 41.36 2.73
544 599 5.338056 CCAATAAACCAGCACTGAGGTAGTA 60.338 44.000 0.00 0.00 37.60 1.82
555 610 7.436673 CAGCACTGAGGTAGTATGAAATCTTAC 59.563 40.741 0.00 0.00 37.60 2.34
556 611 7.124298 AGCACTGAGGTAGTATGAAATCTTACA 59.876 37.037 8.59 0.00 37.60 2.41
559 614 8.982723 ACTGAGGTAGTATGAAATCTTACACAT 58.017 33.333 8.59 0.00 38.04 3.21
579 634 8.547967 ACACATATCACAAACTTAACTACTGG 57.452 34.615 0.00 0.00 0.00 4.00
587 642 9.059260 TCACAAACTTAACTACTGGGAATTTAC 57.941 33.333 0.00 0.00 0.00 2.01
591 646 9.511272 AAACTTAACTACTGGGAATTTACGAAT 57.489 29.630 0.00 0.00 0.00 3.34
677 732 9.942526 ATATGGATTAACAAATTTCCCTCTTCT 57.057 29.630 0.00 0.00 0.00 2.85
678 733 7.466746 TGGATTAACAAATTTCCCTCTTCTG 57.533 36.000 0.00 0.00 0.00 3.02
680 735 7.508977 TGGATTAACAAATTTCCCTCTTCTGTT 59.491 33.333 0.00 0.00 0.00 3.16
681 736 8.367911 GGATTAACAAATTTCCCTCTTCTGTTT 58.632 33.333 0.00 0.00 0.00 2.83
682 737 9.411801 GATTAACAAATTTCCCTCTTCTGTTTC 57.588 33.333 0.00 0.00 0.00 2.78
683 738 8.533569 TTAACAAATTTCCCTCTTCTGTTTCT 57.466 30.769 0.00 0.00 0.00 2.52
684 739 7.423844 AACAAATTTCCCTCTTCTGTTTCTT 57.576 32.000 0.00 0.00 0.00 2.52
685 740 7.423844 ACAAATTTCCCTCTTCTGTTTCTTT 57.576 32.000 0.00 0.00 0.00 2.52
701 756 5.128663 TGTTTCTTTCCTTTTCTCCCCAAAG 59.871 40.000 0.00 0.00 0.00 2.77
705 760 2.597455 TCCTTTTCTCCCCAAAGCAAG 58.403 47.619 0.00 0.00 30.94 4.01
725 780 2.559668 AGCACATGCACAAAGTTGCTAT 59.440 40.909 6.64 0.00 43.41 2.97
727 782 4.400251 AGCACATGCACAAAGTTGCTATAT 59.600 37.500 6.64 0.00 43.41 0.86
729 784 6.263842 AGCACATGCACAAAGTTGCTATATAT 59.736 34.615 6.64 0.00 43.41 0.86
758 813 2.954684 GCCTCCGTGTCATCCACCA 61.955 63.158 0.00 0.00 41.26 4.17
779 835 4.460382 CCAACTTGCTCCACATCTATTTGT 59.540 41.667 0.00 0.00 0.00 2.83
935 1098 2.563427 GGCCGTTTTGCTCTGCTC 59.437 61.111 0.00 0.00 0.00 4.26
944 1107 0.529833 TTGCTCTGCTCCTCTTCTCG 59.470 55.000 0.00 0.00 0.00 4.04
959 1122 2.668212 TCGCCGAAGCAAACCCAG 60.668 61.111 0.00 0.00 39.83 4.45
1043 1210 2.863853 CGCACGATCATGGTCAGCG 61.864 63.158 22.92 22.92 36.46 5.18
1060 1227 2.381109 CGTGAGCAAGAGCATCAGG 58.619 57.895 0.00 0.00 45.49 3.86
1062 1232 1.367659 GTGAGCAAGAGCATCAGGAC 58.632 55.000 0.00 0.00 45.49 3.85
1245 1415 2.051435 CTCGGCGATCTCGAGCTG 60.051 66.667 11.27 1.69 45.67 4.24
1777 1947 2.815647 GGAAGAGCGCCAAGACGG 60.816 66.667 2.29 0.00 38.11 4.79
2232 2405 1.451927 GGCGATGAAGGTGATGGCA 60.452 57.895 0.00 0.00 0.00 4.92
2397 2570 3.237741 CTGGGGATCGAGGGGCTC 61.238 72.222 0.00 0.00 0.00 4.70
2413 2586 3.740128 CTCCTGGCCGGGTTCATCG 62.740 68.421 30.31 9.12 0.00 3.84
2632 2822 7.683437 ATGAGTGCAATGTATATGAAGATGG 57.317 36.000 0.00 0.00 0.00 3.51
2668 2861 8.757164 ATTTTGTTTTGAAATCGGTAGAATCC 57.243 30.769 0.00 0.00 0.00 3.01
2699 2892 0.179000 GGAGGTGAGGCGATGAATGT 59.821 55.000 0.00 0.00 0.00 2.71
2726 2919 2.930040 TCGAATGCTTTCTCCGACATTC 59.070 45.455 10.29 0.00 43.08 2.67
2874 3067 1.701847 AGCAAGGTGATGAGTGGACTT 59.298 47.619 0.00 0.00 0.00 3.01
2877 3070 3.070018 CAAGGTGATGAGTGGACTTGTC 58.930 50.000 0.00 0.00 32.79 3.18
2897 3090 1.661112 CGAACATTTTCCTCTCCGAGC 59.339 52.381 0.00 0.00 0.00 5.03
2898 3091 2.675317 CGAACATTTTCCTCTCCGAGCT 60.675 50.000 0.00 0.00 0.00 4.09
2899 3092 2.682155 ACATTTTCCTCTCCGAGCTC 57.318 50.000 2.73 2.73 0.00 4.09
2900 3093 1.134965 ACATTTTCCTCTCCGAGCTCG 60.135 52.381 29.06 29.06 39.44 5.03
2901 3094 1.134965 CATTTTCCTCTCCGAGCTCGT 60.135 52.381 32.41 9.03 37.74 4.18
2902 3095 0.243907 TTTTCCTCTCCGAGCTCGTG 59.756 55.000 32.41 24.08 37.74 4.35
2903 3096 2.214181 TTTCCTCTCCGAGCTCGTGC 62.214 60.000 32.41 0.07 37.74 5.34
2993 3992 9.625747 TCACATGGATGTATATTACACATGTTT 57.374 29.630 15.58 0.00 45.88 2.83
3104 4112 4.566545 TTTTTGCACATGTCTAGTGTGG 57.433 40.909 12.41 0.00 45.39 4.17
3105 4113 1.522668 TTGCACATGTCTAGTGTGGC 58.477 50.000 12.41 0.00 45.39 5.01
3135 4150 1.261619 GTCAGTTGGAGCACGTTCAAG 59.738 52.381 0.00 0.00 0.00 3.02
3187 4205 8.843262 CCATGATTTCACTATGTACATGAACAT 58.157 33.333 18.81 11.85 42.62 2.71
3220 4238 4.332819 CGGACAAAGACAAGACAAGAAAGT 59.667 41.667 0.00 0.00 0.00 2.66
3354 4377 6.824958 AGGGCCAATAATGTACTAGAGAAA 57.175 37.500 6.18 0.00 0.00 2.52
3400 4423 4.208047 CCTCTTTGATTCGCACGATTCTAG 59.792 45.833 13.96 11.40 0.00 2.43
3440 4471 6.746745 AAAATTGATTGAAATGTCATGCCC 57.253 33.333 0.00 0.00 32.48 5.36
3455 4486 1.917872 TGCCCATTTCAACCCTACAC 58.082 50.000 0.00 0.00 0.00 2.90
3456 4487 1.427368 TGCCCATTTCAACCCTACACT 59.573 47.619 0.00 0.00 0.00 3.55
3464 4495 6.210584 CCATTTCAACCCTACACTATTTTGGT 59.789 38.462 0.00 0.00 0.00 3.67
3530 4561 9.442047 CAAAGAGGTTTGAGTAGATGTTAGAAT 57.558 33.333 0.00 0.00 45.22 2.40
3535 4566 9.793259 AGGTTTGAGTAGATGTTAGAATTTTGA 57.207 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.351981 TGAACTAATTTTCACAACGTGATGAG 58.648 34.615 0.00 0.00 42.40 2.90
53 54 6.223852 TCCGCAGCCAACAAATTTTAAAATA 58.776 32.000 13.68 0.00 0.00 1.40
62 63 4.160252 AGAAATTATCCGCAGCCAACAAAT 59.840 37.500 0.00 0.00 0.00 2.32
65 66 2.682856 GAGAAATTATCCGCAGCCAACA 59.317 45.455 0.00 0.00 0.00 3.33
66 67 2.286418 CGAGAAATTATCCGCAGCCAAC 60.286 50.000 0.00 0.00 0.00 3.77
68 69 1.581934 CGAGAAATTATCCGCAGCCA 58.418 50.000 0.00 0.00 0.00 4.75
70 71 1.527311 GACCGAGAAATTATCCGCAGC 59.473 52.381 0.00 0.00 0.00 5.25
72 73 3.635373 AGTAGACCGAGAAATTATCCGCA 59.365 43.478 0.00 0.00 0.00 5.69
73 74 4.240175 AGTAGACCGAGAAATTATCCGC 57.760 45.455 0.00 0.00 0.00 5.54
135 143 5.121768 GCTGGACAAATTCGTACTAACATGT 59.878 40.000 0.00 0.00 0.00 3.21
143 151 1.130561 GCCAGCTGGACAAATTCGTAC 59.869 52.381 37.21 9.96 37.39 3.67
146 154 0.597568 TTGCCAGCTGGACAAATTCG 59.402 50.000 37.21 6.70 37.39 3.34
156 164 3.655276 ACATCTTTTCTTTGCCAGCTG 57.345 42.857 6.78 6.78 0.00 4.24
161 169 4.336280 AGGGAGTACATCTTTTCTTTGCC 58.664 43.478 0.00 0.00 0.00 4.52
235 289 3.548014 CCCGCCTTCGCATAATGTAAAAG 60.548 47.826 0.00 0.00 34.03 2.27
237 291 1.944024 CCCGCCTTCGCATAATGTAAA 59.056 47.619 0.00 0.00 34.03 2.01
241 295 0.532862 ACTCCCGCCTTCGCATAATG 60.533 55.000 0.00 0.00 34.03 1.90
246 300 1.045407 ATATTACTCCCGCCTTCGCA 58.955 50.000 0.00 0.00 34.03 5.10
248 302 4.879598 ACTAAATATTACTCCCGCCTTCG 58.120 43.478 0.00 0.00 0.00 3.79
250 304 6.126854 ACAAGACTAAATATTACTCCCGCCTT 60.127 38.462 0.00 0.00 0.00 4.35
252 306 5.465724 CACAAGACTAAATATTACTCCCGCC 59.534 44.000 0.00 0.00 0.00 6.13
254 308 9.245962 CTAACACAAGACTAAATATTACTCCCG 57.754 37.037 0.00 0.00 0.00 5.14
269 324 7.731556 ATATTACGTCGTTCTAACACAAGAC 57.268 36.000 1.78 0.00 0.00 3.01
293 348 7.067494 GGACGGAGGTAGTAGTGTTAGAATAAA 59.933 40.741 0.00 0.00 0.00 1.40
295 350 6.058183 GGACGGAGGTAGTAGTGTTAGAATA 58.942 44.000 0.00 0.00 0.00 1.75
296 351 4.886489 GGACGGAGGTAGTAGTGTTAGAAT 59.114 45.833 0.00 0.00 0.00 2.40
297 352 4.018960 AGGACGGAGGTAGTAGTGTTAGAA 60.019 45.833 0.00 0.00 0.00 2.10
298 353 3.521126 AGGACGGAGGTAGTAGTGTTAGA 59.479 47.826 0.00 0.00 0.00 2.10
300 355 3.614092 CAGGACGGAGGTAGTAGTGTTA 58.386 50.000 0.00 0.00 0.00 2.41
307 362 2.610438 TAAACCAGGACGGAGGTAGT 57.390 50.000 0.00 0.00 37.07 2.73
308 363 3.449737 TCAATAAACCAGGACGGAGGTAG 59.550 47.826 0.00 0.00 37.07 3.18
309 364 3.196254 GTCAATAAACCAGGACGGAGGTA 59.804 47.826 0.00 0.00 37.07 3.08
310 365 2.027469 GTCAATAAACCAGGACGGAGGT 60.027 50.000 0.00 0.00 40.61 3.85
311 366 2.629051 GTCAATAAACCAGGACGGAGG 58.371 52.381 0.00 0.00 38.63 4.30
312 367 2.629051 GGTCAATAAACCAGGACGGAG 58.371 52.381 0.00 0.00 39.27 4.63
313 368 1.279846 GGGTCAATAAACCAGGACGGA 59.720 52.381 0.00 0.00 41.40 4.69
314 369 1.280998 AGGGTCAATAAACCAGGACGG 59.719 52.381 0.00 0.00 41.40 4.79
315 370 2.781681 AGGGTCAATAAACCAGGACG 57.218 50.000 0.00 0.00 41.40 4.79
316 371 5.175388 ACTTAGGGTCAATAAACCAGGAC 57.825 43.478 0.00 0.00 41.40 3.85
317 372 7.519347 AATACTTAGGGTCAATAAACCAGGA 57.481 36.000 0.00 0.00 41.40 3.86
318 373 8.466798 CAAAATACTTAGGGTCAATAAACCAGG 58.533 37.037 0.00 0.00 41.40 4.45
319 374 9.020731 ACAAAATACTTAGGGTCAATAAACCAG 57.979 33.333 0.00 0.00 41.40 4.00
320 375 8.798402 CACAAAATACTTAGGGTCAATAAACCA 58.202 33.333 0.00 0.00 41.40 3.67
321 376 7.758076 GCACAAAATACTTAGGGTCAATAAACC 59.242 37.037 0.00 0.00 38.69 3.27
322 377 7.758076 GGCACAAAATACTTAGGGTCAATAAAC 59.242 37.037 0.00 0.00 0.00 2.01
323 378 7.451877 TGGCACAAAATACTTAGGGTCAATAAA 59.548 33.333 0.00 0.00 31.92 1.40
324 379 6.948886 TGGCACAAAATACTTAGGGTCAATAA 59.051 34.615 0.00 0.00 31.92 1.40
325 380 6.486056 TGGCACAAAATACTTAGGGTCAATA 58.514 36.000 0.00 0.00 31.92 1.90
326 381 5.329399 TGGCACAAAATACTTAGGGTCAAT 58.671 37.500 0.00 0.00 31.92 2.57
327 382 4.730966 TGGCACAAAATACTTAGGGTCAA 58.269 39.130 0.00 0.00 31.92 3.18
328 383 4.374689 TGGCACAAAATACTTAGGGTCA 57.625 40.909 0.00 0.00 31.92 4.02
343 398 7.814264 AAATTAATGGTCAAAAATTGGCACA 57.186 28.000 0.00 0.00 36.88 4.57
398 453 7.166167 ACCTAGTTTCCGATGATACTGTTTTT 58.834 34.615 0.00 0.00 34.97 1.94
399 454 6.708285 ACCTAGTTTCCGATGATACTGTTTT 58.292 36.000 0.00 0.00 34.97 2.43
400 455 6.295719 ACCTAGTTTCCGATGATACTGTTT 57.704 37.500 0.00 0.00 34.97 2.83
401 456 5.934402 ACCTAGTTTCCGATGATACTGTT 57.066 39.130 0.00 0.00 34.97 3.16
402 457 5.934402 AACCTAGTTTCCGATGATACTGT 57.066 39.130 0.00 0.00 34.97 3.55
403 458 8.712285 TTTAAACCTAGTTTCCGATGATACTG 57.288 34.615 0.00 0.00 37.01 2.74
406 461 9.467258 CGTATTTAAACCTAGTTTCCGATGATA 57.533 33.333 0.00 0.00 37.01 2.15
407 462 8.199449 TCGTATTTAAACCTAGTTTCCGATGAT 58.801 33.333 0.00 0.00 37.01 2.45
408 463 7.546358 TCGTATTTAAACCTAGTTTCCGATGA 58.454 34.615 0.00 0.00 37.01 2.92
409 464 7.760131 TCGTATTTAAACCTAGTTTCCGATG 57.240 36.000 0.00 0.00 37.01 3.84
410 465 8.953368 ATTCGTATTTAAACCTAGTTTCCGAT 57.047 30.769 0.00 0.00 37.01 4.18
411 466 7.492344 GGATTCGTATTTAAACCTAGTTTCCGA 59.508 37.037 0.00 0.00 37.01 4.55
412 467 7.278424 TGGATTCGTATTTAAACCTAGTTTCCG 59.722 37.037 0.00 0.00 37.01 4.30
413 468 8.496707 TGGATTCGTATTTAAACCTAGTTTCC 57.503 34.615 0.00 0.00 37.01 3.13
414 469 9.764870 GTTGGATTCGTATTTAAACCTAGTTTC 57.235 33.333 0.00 0.00 37.01 2.78
415 470 8.445493 CGTTGGATTCGTATTTAAACCTAGTTT 58.555 33.333 0.00 0.00 39.24 2.66
416 471 7.818930 TCGTTGGATTCGTATTTAAACCTAGTT 59.181 33.333 0.00 0.00 0.00 2.24
417 472 7.322664 TCGTTGGATTCGTATTTAAACCTAGT 58.677 34.615 0.00 0.00 0.00 2.57
418 473 7.760131 TCGTTGGATTCGTATTTAAACCTAG 57.240 36.000 0.00 0.00 0.00 3.02
419 474 9.985730 ATATCGTTGGATTCGTATTTAAACCTA 57.014 29.630 0.00 0.00 34.00 3.08
420 475 8.897872 ATATCGTTGGATTCGTATTTAAACCT 57.102 30.769 0.00 0.00 34.00 3.50
451 506 9.702494 TGACAAAATGTTAATGCATGTCATAAA 57.298 25.926 0.00 0.00 34.33 1.40
452 507 9.702494 TTGACAAAATGTTAATGCATGTCATAA 57.298 25.926 13.10 0.34 32.86 1.90
453 508 9.872721 ATTGACAAAATGTTAATGCATGTCATA 57.127 25.926 13.10 6.69 35.60 2.15
454 509 8.780846 ATTGACAAAATGTTAATGCATGTCAT 57.219 26.923 13.10 9.42 35.60 3.06
455 510 8.604640 AATTGACAAAATGTTAATGCATGTCA 57.395 26.923 0.00 4.80 36.80 3.58
475 530 9.632807 CCAAAACTCGACCATAAATTTAATTGA 57.367 29.630 1.21 0.56 0.00 2.57
476 531 8.379902 GCCAAAACTCGACCATAAATTTAATTG 58.620 33.333 1.21 0.00 0.00 2.32
477 532 8.091449 TGCCAAAACTCGACCATAAATTTAATT 58.909 29.630 1.21 0.00 0.00 1.40
478 533 7.544217 GTGCCAAAACTCGACCATAAATTTAAT 59.456 33.333 1.21 0.00 0.00 1.40
479 534 6.864165 GTGCCAAAACTCGACCATAAATTTAA 59.136 34.615 1.21 0.00 0.00 1.52
480 535 6.016192 TGTGCCAAAACTCGACCATAAATTTA 60.016 34.615 0.00 0.00 0.00 1.40
481 536 5.221342 TGTGCCAAAACTCGACCATAAATTT 60.221 36.000 0.00 0.00 0.00 1.82
482 537 4.279671 TGTGCCAAAACTCGACCATAAATT 59.720 37.500 0.00 0.00 0.00 1.82
483 538 3.823873 TGTGCCAAAACTCGACCATAAAT 59.176 39.130 0.00 0.00 0.00 1.40
484 539 3.215151 TGTGCCAAAACTCGACCATAAA 58.785 40.909 0.00 0.00 0.00 1.40
485 540 2.852449 TGTGCCAAAACTCGACCATAA 58.148 42.857 0.00 0.00 0.00 1.90
486 541 2.552599 TGTGCCAAAACTCGACCATA 57.447 45.000 0.00 0.00 0.00 2.74
487 542 1.686355 TTGTGCCAAAACTCGACCAT 58.314 45.000 0.00 0.00 0.00 3.55
488 543 1.464734 TTTGTGCCAAAACTCGACCA 58.535 45.000 0.00 0.00 0.00 4.02
489 544 2.570442 TTTTGTGCCAAAACTCGACC 57.430 45.000 8.46 0.00 0.00 4.79
490 545 3.662186 CGTATTTTGTGCCAAAACTCGAC 59.338 43.478 20.38 13.61 0.00 4.20
491 546 3.560481 TCGTATTTTGTGCCAAAACTCGA 59.440 39.130 21.88 21.88 0.00 4.04
492 547 3.879427 TCGTATTTTGTGCCAAAACTCG 58.121 40.909 19.72 19.72 0.00 4.18
493 548 5.516090 TCTTCGTATTTTGTGCCAAAACTC 58.484 37.500 13.15 9.40 0.00 3.01
494 549 5.507315 CCTCTTCGTATTTTGTGCCAAAACT 60.507 40.000 13.15 7.45 0.00 2.66
495 550 4.679654 CCTCTTCGTATTTTGTGCCAAAAC 59.320 41.667 13.15 4.58 0.00 2.43
496 551 4.580995 TCCTCTTCGTATTTTGTGCCAAAA 59.419 37.500 13.22 13.22 0.00 2.44
497 552 4.023536 GTCCTCTTCGTATTTTGTGCCAAA 60.024 41.667 0.00 0.00 0.00 3.28
498 553 3.500680 GTCCTCTTCGTATTTTGTGCCAA 59.499 43.478 0.00 0.00 0.00 4.52
499 554 3.071479 GTCCTCTTCGTATTTTGTGCCA 58.929 45.455 0.00 0.00 0.00 4.92
500 555 2.418976 GGTCCTCTTCGTATTTTGTGCC 59.581 50.000 0.00 0.00 0.00 5.01
501 556 3.071479 TGGTCCTCTTCGTATTTTGTGC 58.929 45.455 0.00 0.00 0.00 4.57
502 557 5.880054 ATTGGTCCTCTTCGTATTTTGTG 57.120 39.130 0.00 0.00 0.00 3.33
503 558 7.094506 GGTTTATTGGTCCTCTTCGTATTTTGT 60.095 37.037 0.00 0.00 0.00 2.83
504 559 7.094549 TGGTTTATTGGTCCTCTTCGTATTTTG 60.095 37.037 0.00 0.00 0.00 2.44
505 560 6.943718 TGGTTTATTGGTCCTCTTCGTATTTT 59.056 34.615 0.00 0.00 0.00 1.82
506 561 6.478129 TGGTTTATTGGTCCTCTTCGTATTT 58.522 36.000 0.00 0.00 0.00 1.40
507 562 6.057321 TGGTTTATTGGTCCTCTTCGTATT 57.943 37.500 0.00 0.00 0.00 1.89
508 563 5.671493 CTGGTTTATTGGTCCTCTTCGTAT 58.329 41.667 0.00 0.00 0.00 3.06
509 564 4.622220 GCTGGTTTATTGGTCCTCTTCGTA 60.622 45.833 0.00 0.00 0.00 3.43
510 565 3.868754 GCTGGTTTATTGGTCCTCTTCGT 60.869 47.826 0.00 0.00 0.00 3.85
511 566 2.678336 GCTGGTTTATTGGTCCTCTTCG 59.322 50.000 0.00 0.00 0.00 3.79
512 567 3.440522 GTGCTGGTTTATTGGTCCTCTTC 59.559 47.826 0.00 0.00 0.00 2.87
513 568 3.074538 AGTGCTGGTTTATTGGTCCTCTT 59.925 43.478 0.00 0.00 0.00 2.85
514 569 2.644798 AGTGCTGGTTTATTGGTCCTCT 59.355 45.455 0.00 0.00 0.00 3.69
515 570 2.749621 CAGTGCTGGTTTATTGGTCCTC 59.250 50.000 0.00 0.00 0.00 3.71
516 571 2.375174 TCAGTGCTGGTTTATTGGTCCT 59.625 45.455 0.00 0.00 0.00 3.85
517 572 2.749621 CTCAGTGCTGGTTTATTGGTCC 59.250 50.000 0.00 0.00 0.00 4.46
518 573 2.749621 CCTCAGTGCTGGTTTATTGGTC 59.250 50.000 0.00 0.00 0.00 4.02
519 574 2.108250 ACCTCAGTGCTGGTTTATTGGT 59.892 45.455 2.37 0.00 31.62 3.67
520 575 2.795329 ACCTCAGTGCTGGTTTATTGG 58.205 47.619 2.37 0.00 31.62 3.16
521 576 4.579869 ACTACCTCAGTGCTGGTTTATTG 58.420 43.478 11.86 3.17 35.62 1.90
522 577 4.910458 ACTACCTCAGTGCTGGTTTATT 57.090 40.909 11.86 0.00 35.62 1.40
523 578 5.661312 TCATACTACCTCAGTGCTGGTTTAT 59.339 40.000 11.86 7.60 38.24 1.40
524 579 5.020795 TCATACTACCTCAGTGCTGGTTTA 58.979 41.667 11.86 6.02 38.24 2.01
525 580 3.838317 TCATACTACCTCAGTGCTGGTTT 59.162 43.478 11.86 4.36 38.24 3.27
526 581 3.441101 TCATACTACCTCAGTGCTGGTT 58.559 45.455 11.86 0.27 38.24 3.67
527 582 3.101643 TCATACTACCTCAGTGCTGGT 57.898 47.619 11.44 11.44 38.24 4.00
528 583 4.471904 TTTCATACTACCTCAGTGCTGG 57.528 45.455 0.00 1.19 38.24 4.85
529 584 5.911752 AGATTTCATACTACCTCAGTGCTG 58.088 41.667 0.00 0.00 38.24 4.41
530 585 6.552445 AAGATTTCATACTACCTCAGTGCT 57.448 37.500 0.00 0.00 38.24 4.40
531 586 7.222999 GTGTAAGATTTCATACTACCTCAGTGC 59.777 40.741 0.00 0.00 38.24 4.40
532 587 8.251026 TGTGTAAGATTTCATACTACCTCAGTG 58.749 37.037 0.00 0.00 38.24 3.66
533 588 8.362464 TGTGTAAGATTTCATACTACCTCAGT 57.638 34.615 0.00 0.00 41.62 3.41
555 610 7.822334 TCCCAGTAGTTAAGTTTGTGATATGTG 59.178 37.037 0.00 0.00 0.00 3.21
556 611 7.913789 TCCCAGTAGTTAAGTTTGTGATATGT 58.086 34.615 0.00 0.00 0.00 2.29
559 614 9.802039 AAATTCCCAGTAGTTAAGTTTGTGATA 57.198 29.630 0.00 0.00 0.00 2.15
562 617 8.013378 CGTAAATTCCCAGTAGTTAAGTTTGTG 58.987 37.037 0.00 0.00 0.00 3.33
563 618 7.933033 TCGTAAATTCCCAGTAGTTAAGTTTGT 59.067 33.333 0.00 0.00 0.00 2.83
564 619 8.314143 TCGTAAATTCCCAGTAGTTAAGTTTG 57.686 34.615 0.00 0.00 0.00 2.93
566 621 9.159364 GATTCGTAAATTCCCAGTAGTTAAGTT 57.841 33.333 0.00 0.00 0.00 2.66
568 623 8.712285 TGATTCGTAAATTCCCAGTAGTTAAG 57.288 34.615 0.00 0.00 0.00 1.85
660 715 7.423844 AAGAAACAGAAGAGGGAAATTTGTT 57.576 32.000 0.00 0.00 0.00 2.83
661 716 7.417911 GGAAAGAAACAGAAGAGGGAAATTTGT 60.418 37.037 0.00 0.00 0.00 2.83
670 725 6.016693 GGAGAAAAGGAAAGAAACAGAAGAGG 60.017 42.308 0.00 0.00 0.00 3.69
671 726 6.016693 GGGAGAAAAGGAAAGAAACAGAAGAG 60.017 42.308 0.00 0.00 0.00 2.85
674 729 4.893524 GGGGAGAAAAGGAAAGAAACAGAA 59.106 41.667 0.00 0.00 0.00 3.02
676 731 4.215109 TGGGGAGAAAAGGAAAGAAACAG 58.785 43.478 0.00 0.00 0.00 3.16
677 732 4.258457 TGGGGAGAAAAGGAAAGAAACA 57.742 40.909 0.00 0.00 0.00 2.83
678 733 5.601662 CTTTGGGGAGAAAAGGAAAGAAAC 58.398 41.667 0.00 0.00 32.15 2.78
680 735 3.641436 GCTTTGGGGAGAAAAGGAAAGAA 59.359 43.478 0.00 0.00 35.57 2.52
681 736 3.230976 GCTTTGGGGAGAAAAGGAAAGA 58.769 45.455 0.00 0.00 35.57 2.52
682 737 2.965147 TGCTTTGGGGAGAAAAGGAAAG 59.035 45.455 0.00 0.00 35.57 2.62
683 738 3.039252 TGCTTTGGGGAGAAAAGGAAA 57.961 42.857 0.00 0.00 35.57 3.13
684 739 2.765689 TGCTTTGGGGAGAAAAGGAA 57.234 45.000 0.00 0.00 35.57 3.36
685 740 2.597455 CTTGCTTTGGGGAGAAAAGGA 58.403 47.619 0.00 0.00 35.57 3.36
701 756 1.259507 CAACTTTGTGCATGTGCTTGC 59.740 47.619 6.55 3.50 42.66 4.01
758 813 5.633830 CACAAATAGATGTGGAGCAAGTT 57.366 39.130 0.00 0.00 45.47 2.66
779 835 5.362143 TGCCATACCAGCAATTTATTTAGCA 59.638 36.000 0.00 0.00 37.28 3.49
829 887 3.993081 GAGATATGCTGATCCAAACGGAG 59.007 47.826 0.00 0.00 35.52 4.63
832 890 5.998454 AAAGAGATATGCTGATCCAAACG 57.002 39.130 0.00 0.00 0.00 3.60
944 1107 0.597377 CAAACTGGGTTTGCTTCGGC 60.597 55.000 9.66 0.00 44.59 5.54
959 1122 1.530293 CTCAGTGTGAGCAGAGCAAAC 59.470 52.381 0.00 0.00 37.72 2.93
1043 1210 1.367659 GTCCTGATGCTCTTGCTCAC 58.632 55.000 0.00 0.00 40.48 3.51
1759 1929 3.181967 CGTCTTGGCGCTCTTCCG 61.182 66.667 7.64 0.65 0.00 4.30
1881 2054 2.022129 CCACTCGAGGCACGTGTTC 61.022 63.158 18.41 13.99 44.41 3.18
2232 2405 3.241530 TTCACCACCTCCAGCGCT 61.242 61.111 2.64 2.64 0.00 5.92
2397 2570 4.096003 ACGATGAACCCGGCCAGG 62.096 66.667 2.45 2.45 40.63 4.45
2533 2706 2.282462 GGGTGCCTCCTTGTGGTG 60.282 66.667 0.00 0.00 36.25 4.17
2535 2708 2.655077 TTTGGGGTGCCTCCTTGTGG 62.655 60.000 0.00 0.00 36.25 4.17
2608 2785 7.455891 TCCATCTTCATATACATTGCACTCAT 58.544 34.615 0.00 0.00 0.00 2.90
2622 2799 8.742777 CAAAATCTCCAAAGTTCCATCTTCATA 58.257 33.333 0.00 0.00 0.00 2.15
2632 2822 9.920826 GATTTCAAAACAAAATCTCCAAAGTTC 57.079 29.630 0.00 0.00 39.14 3.01
2668 2861 0.251297 TCACCTCCCTTGTGGCAATG 60.251 55.000 0.00 0.00 34.46 2.82
2699 2892 2.738643 CGGAGAAAGCATTCGAAGGCTA 60.739 50.000 34.44 0.00 46.49 3.93
2726 2919 4.313277 TGAGTGAGTGAGTGAGTGAAAG 57.687 45.455 0.00 0.00 0.00 2.62
2844 3037 6.373774 CACTCATCACCTTGCTAATCTTCTTT 59.626 38.462 0.00 0.00 0.00 2.52
2874 3067 2.297880 TCGGAGAGGAAAATGTTCGACA 59.702 45.455 0.00 0.00 34.28 4.35
3104 4112 3.428045 GCTCCAACTGACACCATATTTGC 60.428 47.826 0.00 0.00 0.00 3.68
3105 4113 3.758023 TGCTCCAACTGACACCATATTTG 59.242 43.478 0.00 0.00 0.00 2.32
3135 4150 4.612033 GCATGGCAGCAAAAATTCACTTTC 60.612 41.667 0.00 0.00 0.00 2.62
3175 4192 3.433957 GTGCCAACGTATGTTCATGTACA 59.566 43.478 7.67 7.67 35.72 2.90
3227 4245 2.165234 GGCCTCTCTTGCTCAATTTTCC 59.835 50.000 0.00 0.00 0.00 3.13
3354 4377 4.141959 GCCCCAATGTTGTAATGCATAGTT 60.142 41.667 0.00 0.00 0.00 2.24
3421 4449 5.423704 AATGGGCATGACATTTCAATCAA 57.576 34.783 0.00 0.00 35.11 2.57
3440 4471 7.227049 ACCAAAATAGTGTAGGGTTGAAATG 57.773 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.