Multiple sequence alignment - TraesCS2D01G114400

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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 TraesCS2D01G114400 chr2D 100.000 2768 0 0 1 2768 63568363 63571130 0.000000e+00 5112.0
1 TraesCS2D01G114400 chr2A 93.027 1305 50 12 600 1893 65182267 65183541 0.000000e+00 1868.0
2 TraesCS2D01G114400 chr2A 94.103 390 15 6 2379 2766 65184100 65184483 1.100000e-163 586.0
3 TraesCS2D01G114400 chr2A 91.667 384 22 5 4 383 65181885 65182262 8.780000e-145 523.0
4 TraesCS2D01G114400 chr2A 94.828 116 5 1 1895 2009 65183610 65183725 2.190000e-41 180.0
5 TraesCS2D01G114400 chr2A 79.000 100 18 3 2211 2307 610997896 610997995 6.400000e-07 65.8
6 TraesCS2D01G114400 chr2B 97.243 544 13 1 1352 1893 99266491 99267034 0.000000e+00 920.0
7 TraesCS2D01G114400 chr2B 90.803 685 35 16 593 1267 99265774 99266440 0.000000e+00 891.0
8 TraesCS2D01G114400 chr2B 93.515 478 17 8 1892 2359 99267108 99267581 0.000000e+00 699.0
9 TraesCS2D01G114400 chr2B 95.078 386 15 4 2376 2759 99267671 99268054 3.050000e-169 604.0
10 TraesCS2D01G114400 chr2B 90.526 285 15 7 1 282 99265432 99265707 1.570000e-97 366.0
11 TraesCS2D01G114400 chr2B 91.549 213 15 2 374 586 501901028 501900819 9.700000e-75 291.0
12 TraesCS2D01G114400 chr4A 96.354 192 5 2 370 561 15128868 15128679 5.750000e-82 315.0
13 TraesCS2D01G114400 chr7D 92.344 209 13 2 378 586 125335104 125334899 7.500000e-76 294.0
14 TraesCS2D01G114400 chr3A 92.344 209 13 2 378 586 385575342 385575137 7.500000e-76 294.0
15 TraesCS2D01G114400 chr3A 97.674 43 1 0 2726 2768 269394315 269394357 1.060000e-09 75.0
16 TraesCS2D01G114400 chr5A 91.244 217 16 2 370 586 584970169 584969956 2.700000e-75 292.0
17 TraesCS2D01G114400 chr5A 91.866 209 14 2 378 586 608041430 608041635 3.490000e-74 289.0
18 TraesCS2D01G114400 chr5A 94.231 52 2 1 2718 2768 48732324 48732375 8.220000e-11 78.7
19 TraesCS2D01G114400 chr7A 91.509 212 15 2 375 586 501318405 501318197 3.490000e-74 289.0
20 TraesCS2D01G114400 chr3D 91.866 209 14 2 378 586 505973685 505973480 3.490000e-74 289.0
21 TraesCS2D01G114400 chr3D 91.121 214 16 2 374 587 1327594 1327384 1.250000e-73 287.0
22 TraesCS2D01G114400 chr6A 97.826 46 1 0 2723 2768 8173705 8173750 2.290000e-11 80.5
23 TraesCS2D01G114400 chr1D 94.340 53 2 1 2716 2768 261260643 261260694 2.290000e-11 80.5
24 TraesCS2D01G114400 chr7B 97.727 44 1 0 2725 2768 501308795 501308838 2.960000e-10 76.8
25 TraesCS2D01G114400 chr1B 97.674 43 1 0 2725 2767 678293606 678293648 1.060000e-09 75.0
26 TraesCS2D01G114400 chr6B 93.878 49 2 1 2718 2766 36040397 36040444 3.820000e-09 73.1
27 TraesCS2D01G114400 chr5D 100.000 29 0 0 2191 2219 558917475 558917503 1.000000e-03 54.7
28 TraesCS2D01G114400 chr6D 100.000 28 0 0 2192 2219 47932243 47932270 5.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G114400 chr2D 63568363 63571130 2767 False 5112.00 5112 100.00000 1 2768 1 chr2D.!!$F1 2767
1 TraesCS2D01G114400 chr2A 65181885 65184483 2598 False 789.25 1868 93.40625 4 2766 4 chr2A.!!$F2 2762
2 TraesCS2D01G114400 chr2B 99265432 99268054 2622 False 696.00 920 93.43300 1 2759 5 chr2B.!!$F1 2758

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
594 603 0.25316 TCCCCACTATGACCAGCCTT 60.253 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2218 0.98989 GACCTGACGAAACGGAATCG 59.01 55.0 5.41 5.41 45.47 3.34 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
92 93 4.640647 ACATCTCGTACTGATCTACTTGCA 59.359 41.667 0.00 0.00 0.00 4.08
95 96 6.208988 TCTCGTACTGATCTACTTGCATTT 57.791 37.500 0.00 0.00 0.00 2.32
126 127 5.009010 CGCTTCTAATCCACATTATTGCCTT 59.991 40.000 0.00 0.00 0.00 4.35
127 128 6.460123 CGCTTCTAATCCACATTATTGCCTTT 60.460 38.462 0.00 0.00 0.00 3.11
135 139 8.823220 ATCCACATTATTGCCTTTTAAGTAGT 57.177 30.769 0.00 0.00 0.00 2.73
136 140 9.914834 ATCCACATTATTGCCTTTTAAGTAGTA 57.085 29.630 0.00 0.00 0.00 1.82
137 141 9.391006 TCCACATTATTGCCTTTTAAGTAGTAG 57.609 33.333 0.00 0.00 0.00 2.57
138 142 9.174166 CCACATTATTGCCTTTTAAGTAGTAGT 57.826 33.333 0.00 0.00 0.00 2.73
146 150 9.902196 TTGCCTTTTAAGTAGTAGTAAAATTGC 57.098 29.630 10.31 10.31 32.74 3.56
161 165 1.522668 ATTGCTGCTGTTGCTTCGTA 58.477 45.000 0.00 0.00 40.48 3.43
182 186 1.571460 GTCAGCAACTGCAGTTCCG 59.429 57.895 28.97 19.51 45.16 4.30
187 192 1.949257 CAACTGCAGTTCCGAACCC 59.051 57.895 28.97 0.58 35.83 4.11
195 200 1.068333 CAGTTCCGAACCCATGCAAAG 60.068 52.381 7.68 0.00 0.00 2.77
313 322 1.179152 CCTTTCAGGCATGCATGTCA 58.821 50.000 31.47 16.24 34.11 3.58
336 345 2.987547 AACGCCTCCGGTTCGAGA 60.988 61.111 16.72 0.00 39.22 4.04
378 387 6.549952 CCATTTTGAGCTAGCTTTGTCTTAG 58.450 40.000 20.42 5.46 0.00 2.18
383 392 2.093235 AGCTAGCTTTGTCTTAGGCTGG 60.093 50.000 12.68 0.00 36.40 4.85
384 393 2.284190 CTAGCTTTGTCTTAGGCTGGC 58.716 52.381 0.00 0.00 36.40 4.85
385 394 0.322906 AGCTTTGTCTTAGGCTGGCC 60.323 55.000 3.00 3.00 33.50 5.36
387 396 1.957113 GCTTTGTCTTAGGCTGGCCAT 60.957 52.381 5.51 0.00 38.92 4.40
388 397 2.683742 GCTTTGTCTTAGGCTGGCCATA 60.684 50.000 5.51 0.00 38.92 2.74
389 398 3.209410 CTTTGTCTTAGGCTGGCCATAG 58.791 50.000 5.51 9.98 38.92 2.23
390 399 1.879575 TGTCTTAGGCTGGCCATAGT 58.120 50.000 5.51 0.00 38.92 2.12
391 400 1.486310 TGTCTTAGGCTGGCCATAGTG 59.514 52.381 5.51 0.00 38.92 2.74
392 401 1.762957 GTCTTAGGCTGGCCATAGTGA 59.237 52.381 5.51 0.00 38.92 3.41
393 402 2.042464 TCTTAGGCTGGCCATAGTGAG 58.958 52.381 5.51 2.26 38.92 3.51
394 403 2.042464 CTTAGGCTGGCCATAGTGAGA 58.958 52.381 5.51 0.00 38.92 3.27
395 404 1.709578 TAGGCTGGCCATAGTGAGAG 58.290 55.000 5.51 0.00 38.92 3.20
396 405 0.326048 AGGCTGGCCATAGTGAGAGT 60.326 55.000 5.51 0.00 38.92 3.24
397 406 1.062886 AGGCTGGCCATAGTGAGAGTA 60.063 52.381 5.51 0.00 38.92 2.59
398 407 1.762957 GGCTGGCCATAGTGAGAGTAA 59.237 52.381 5.51 0.00 35.81 2.24
399 408 2.483889 GGCTGGCCATAGTGAGAGTAAC 60.484 54.545 5.51 0.00 35.81 2.50
400 409 2.168521 GCTGGCCATAGTGAGAGTAACA 59.831 50.000 5.51 0.00 0.00 2.41
401 410 3.181461 GCTGGCCATAGTGAGAGTAACAT 60.181 47.826 5.51 0.00 0.00 2.71
402 411 4.039245 GCTGGCCATAGTGAGAGTAACATA 59.961 45.833 5.51 0.00 0.00 2.29
403 412 5.453339 GCTGGCCATAGTGAGAGTAACATAA 60.453 44.000 5.51 0.00 0.00 1.90
404 413 5.914033 TGGCCATAGTGAGAGTAACATAAC 58.086 41.667 0.00 0.00 0.00 1.89
405 414 5.661312 TGGCCATAGTGAGAGTAACATAACT 59.339 40.000 0.00 0.00 0.00 2.24
406 415 6.837048 TGGCCATAGTGAGAGTAACATAACTA 59.163 38.462 0.00 0.00 0.00 2.24
407 416 7.014326 TGGCCATAGTGAGAGTAACATAACTAG 59.986 40.741 0.00 0.00 0.00 2.57
408 417 7.014422 GGCCATAGTGAGAGTAACATAACTAGT 59.986 40.741 0.00 0.00 0.00 2.57
409 418 9.064706 GCCATAGTGAGAGTAACATAACTAGTA 57.935 37.037 0.00 0.00 0.00 1.82
427 436 7.925043 ACTAGTATCATATACTTGGGACTCG 57.075 40.000 4.99 0.00 0.00 4.18
428 437 7.460071 ACTAGTATCATATACTTGGGACTCGT 58.540 38.462 4.99 0.00 0.00 4.18
429 438 8.600668 ACTAGTATCATATACTTGGGACTCGTA 58.399 37.037 4.99 0.00 0.00 3.43
430 439 9.445878 CTAGTATCATATACTTGGGACTCGTAA 57.554 37.037 4.99 0.00 0.00 3.18
431 440 8.701908 AGTATCATATACTTGGGACTCGTAAA 57.298 34.615 0.00 0.00 0.00 2.01
432 441 8.574737 AGTATCATATACTTGGGACTCGTAAAC 58.425 37.037 0.00 0.00 0.00 2.01
433 442 6.778834 TCATATACTTGGGACTCGTAAACA 57.221 37.500 0.00 0.00 0.00 2.83
434 443 7.356089 TCATATACTTGGGACTCGTAAACAT 57.644 36.000 0.00 0.00 0.00 2.71
435 444 7.207383 TCATATACTTGGGACTCGTAAACATG 58.793 38.462 0.00 0.00 0.00 3.21
436 445 2.423577 ACTTGGGACTCGTAAACATGC 58.576 47.619 0.00 0.00 0.00 4.06
437 446 2.038557 ACTTGGGACTCGTAAACATGCT 59.961 45.455 0.00 0.00 0.00 3.79
438 447 2.851263 TGGGACTCGTAAACATGCTT 57.149 45.000 0.00 0.00 0.00 3.91
439 448 3.965379 TGGGACTCGTAAACATGCTTA 57.035 42.857 0.00 0.00 0.00 3.09
440 449 3.592059 TGGGACTCGTAAACATGCTTAC 58.408 45.455 8.65 8.65 0.00 2.34
445 454 2.153680 CGTAAACATGCTTACGTGGC 57.846 50.000 25.83 3.00 45.73 5.01
446 455 1.461512 CGTAAACATGCTTACGTGGCA 59.538 47.619 25.83 17.67 45.73 4.92
447 456 2.473868 CGTAAACATGCTTACGTGGCAG 60.474 50.000 25.83 14.54 45.73 4.85
448 457 1.890876 AAACATGCTTACGTGGCAGA 58.109 45.000 19.47 2.04 43.15 4.26
449 458 1.890876 AACATGCTTACGTGGCAGAA 58.109 45.000 19.47 0.00 43.15 3.02
450 459 1.890876 ACATGCTTACGTGGCAGAAA 58.109 45.000 19.47 0.00 43.15 2.52
451 460 2.226330 ACATGCTTACGTGGCAGAAAA 58.774 42.857 19.47 0.82 43.15 2.29
452 461 2.819608 ACATGCTTACGTGGCAGAAAAT 59.180 40.909 19.47 4.06 43.15 1.82
453 462 3.255642 ACATGCTTACGTGGCAGAAAATT 59.744 39.130 19.47 3.47 43.15 1.82
454 463 4.457603 ACATGCTTACGTGGCAGAAAATTA 59.542 37.500 19.47 0.00 43.15 1.40
455 464 5.048364 ACATGCTTACGTGGCAGAAAATTAA 60.048 36.000 19.47 0.00 43.15 1.40
456 465 5.440234 TGCTTACGTGGCAGAAAATTAAA 57.560 34.783 12.76 0.00 34.56 1.52
457 466 5.457140 TGCTTACGTGGCAGAAAATTAAAG 58.543 37.500 12.76 0.00 34.56 1.85
458 467 5.239744 TGCTTACGTGGCAGAAAATTAAAGA 59.760 36.000 12.76 0.00 34.56 2.52
459 468 6.146898 GCTTACGTGGCAGAAAATTAAAGAA 58.853 36.000 0.00 0.00 0.00 2.52
460 469 6.639279 GCTTACGTGGCAGAAAATTAAAGAAA 59.361 34.615 0.00 0.00 0.00 2.52
461 470 7.168469 GCTTACGTGGCAGAAAATTAAAGAAAA 59.832 33.333 0.00 0.00 0.00 2.29
462 471 8.568732 TTACGTGGCAGAAAATTAAAGAAAAG 57.431 30.769 0.00 0.00 0.00 2.27
463 472 6.801575 ACGTGGCAGAAAATTAAAGAAAAGA 58.198 32.000 0.00 0.00 0.00 2.52
464 473 6.918022 ACGTGGCAGAAAATTAAAGAAAAGAG 59.082 34.615 0.00 0.00 0.00 2.85
465 474 7.138736 CGTGGCAGAAAATTAAAGAAAAGAGA 58.861 34.615 0.00 0.00 0.00 3.10
466 475 7.324616 CGTGGCAGAAAATTAAAGAAAAGAGAG 59.675 37.037 0.00 0.00 0.00 3.20
467 476 8.352942 GTGGCAGAAAATTAAAGAAAAGAGAGA 58.647 33.333 0.00 0.00 0.00 3.10
468 477 8.571336 TGGCAGAAAATTAAAGAAAAGAGAGAG 58.429 33.333 0.00 0.00 0.00 3.20
469 478 8.026026 GGCAGAAAATTAAAGAAAAGAGAGAGG 58.974 37.037 0.00 0.00 0.00 3.69
470 479 8.026026 GCAGAAAATTAAAGAAAAGAGAGAGGG 58.974 37.037 0.00 0.00 0.00 4.30
471 480 9.072375 CAGAAAATTAAAGAAAAGAGAGAGGGT 57.928 33.333 0.00 0.00 0.00 4.34
472 481 9.290988 AGAAAATTAAAGAAAAGAGAGAGGGTC 57.709 33.333 0.00 0.00 0.00 4.46
473 482 8.410673 AAAATTAAAGAAAAGAGAGAGGGTCC 57.589 34.615 0.00 0.00 0.00 4.46
474 483 6.961361 ATTAAAGAAAAGAGAGAGGGTCCT 57.039 37.500 0.00 0.00 0.00 3.85
475 484 8.450780 AATTAAAGAAAAGAGAGAGGGTCCTA 57.549 34.615 0.00 0.00 0.00 2.94
476 485 7.483580 TTAAAGAAAAGAGAGAGGGTCCTAG 57.516 40.000 0.00 0.00 0.00 3.02
477 486 4.685513 AGAAAAGAGAGAGGGTCCTAGT 57.314 45.455 0.00 0.00 0.00 2.57
478 487 5.799978 AGAAAAGAGAGAGGGTCCTAGTA 57.200 43.478 0.00 0.00 0.00 1.82
479 488 6.155247 AGAAAAGAGAGAGGGTCCTAGTAA 57.845 41.667 0.00 0.00 0.00 2.24
480 489 5.953548 AGAAAAGAGAGAGGGTCCTAGTAAC 59.046 44.000 0.00 0.00 0.00 2.50
481 490 4.949966 AAGAGAGAGGGTCCTAGTAACA 57.050 45.455 0.00 0.00 0.00 2.41
482 491 5.475398 AAGAGAGAGGGTCCTAGTAACAT 57.525 43.478 0.00 0.00 0.00 2.71
483 492 6.593759 AAGAGAGAGGGTCCTAGTAACATA 57.406 41.667 0.00 0.00 0.00 2.29
484 493 6.195600 AGAGAGAGGGTCCTAGTAACATAG 57.804 45.833 0.00 0.00 0.00 2.23
485 494 5.073965 AGAGAGAGGGTCCTAGTAACATAGG 59.926 48.000 0.00 0.00 43.30 2.57
486 495 4.732957 AGAGAGGGTCCTAGTAACATAGGT 59.267 45.833 0.00 0.00 42.63 3.08
487 496 5.915900 AGAGAGGGTCCTAGTAACATAGGTA 59.084 44.000 0.00 0.00 42.63 3.08
488 497 6.044637 AGAGAGGGTCCTAGTAACATAGGTAG 59.955 46.154 0.00 0.00 42.63 3.18
489 498 5.915900 AGAGGGTCCTAGTAACATAGGTAGA 59.084 44.000 0.00 0.00 42.63 2.59
490 499 6.567260 AGAGGGTCCTAGTAACATAGGTAGAT 59.433 42.308 0.00 0.00 42.63 1.98
491 500 7.743139 AGAGGGTCCTAGTAACATAGGTAGATA 59.257 40.741 0.00 0.00 42.63 1.98
492 501 7.697946 AGGGTCCTAGTAACATAGGTAGATAC 58.302 42.308 0.00 0.00 42.63 2.24
493 502 6.889177 GGGTCCTAGTAACATAGGTAGATACC 59.111 46.154 0.43 0.43 46.82 2.73
529 538 6.603237 TTGTTATGCTACTATGTGTCATGC 57.397 37.500 0.00 0.00 0.00 4.06
530 539 5.669477 TGTTATGCTACTATGTGTCATGCA 58.331 37.500 0.00 0.00 35.34 3.96
531 540 6.290605 TGTTATGCTACTATGTGTCATGCAT 58.709 36.000 0.00 0.00 40.50 3.96
532 541 6.203338 TGTTATGCTACTATGTGTCATGCATG 59.797 38.462 21.07 21.07 39.07 4.06
533 542 3.469739 TGCTACTATGTGTCATGCATGG 58.530 45.455 25.97 10.76 0.00 3.66
534 543 2.225019 GCTACTATGTGTCATGCATGGC 59.775 50.000 24.40 24.40 0.00 4.40
535 544 2.423446 ACTATGTGTCATGCATGGCA 57.577 45.000 29.45 29.45 44.86 4.92
536 545 2.725637 ACTATGTGTCATGCATGGCAA 58.274 42.857 34.01 23.37 44.94 4.52
537 546 3.293337 ACTATGTGTCATGCATGGCAAT 58.707 40.909 34.01 27.34 44.94 3.56
538 547 4.463070 ACTATGTGTCATGCATGGCAATA 58.537 39.130 34.01 27.05 44.94 1.90
539 548 4.888823 ACTATGTGTCATGCATGGCAATAA 59.111 37.500 34.01 22.53 44.94 1.40
540 549 4.739587 ATGTGTCATGCATGGCAATAAA 57.260 36.364 34.01 20.14 44.94 1.40
541 550 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
542 551 4.434520 TGTGTCATGCATGGCAATAAATG 58.565 39.130 34.01 2.58 44.94 2.32
543 552 4.159879 TGTGTCATGCATGGCAATAAATGA 59.840 37.500 34.01 7.61 44.94 2.57
544 553 4.743151 GTGTCATGCATGGCAATAAATGAG 59.257 41.667 34.01 0.13 44.94 2.90
545 554 4.645588 TGTCATGCATGGCAATAAATGAGA 59.354 37.500 30.82 3.91 43.62 3.27
546 555 4.980434 GTCATGCATGGCAATAAATGAGAC 59.020 41.667 26.04 8.36 43.62 3.36
547 556 4.038282 TCATGCATGGCAATAAATGAGACC 59.962 41.667 25.97 0.00 43.62 3.85
548 557 3.363627 TGCATGGCAATAAATGAGACCA 58.636 40.909 0.00 0.00 34.76 4.02
549 558 3.130869 TGCATGGCAATAAATGAGACCAC 59.869 43.478 0.00 0.00 34.76 4.16
550 559 3.491447 GCATGGCAATAAATGAGACCACC 60.491 47.826 0.00 0.00 0.00 4.61
551 560 3.737559 TGGCAATAAATGAGACCACCT 57.262 42.857 0.00 0.00 0.00 4.00
552 561 4.853468 TGGCAATAAATGAGACCACCTA 57.147 40.909 0.00 0.00 0.00 3.08
553 562 5.387113 TGGCAATAAATGAGACCACCTAT 57.613 39.130 0.00 0.00 0.00 2.57
554 563 5.132502 TGGCAATAAATGAGACCACCTATG 58.867 41.667 0.00 0.00 0.00 2.23
555 564 5.104151 TGGCAATAAATGAGACCACCTATGA 60.104 40.000 0.00 0.00 0.00 2.15
556 565 6.006449 GGCAATAAATGAGACCACCTATGAT 58.994 40.000 0.00 0.00 0.00 2.45
557 566 7.168219 GGCAATAAATGAGACCACCTATGATA 58.832 38.462 0.00 0.00 0.00 2.15
558 567 7.119846 GGCAATAAATGAGACCACCTATGATAC 59.880 40.741 0.00 0.00 0.00 2.24
559 568 7.880195 GCAATAAATGAGACCACCTATGATACT 59.120 37.037 0.00 0.00 0.00 2.12
562 571 9.830186 ATAAATGAGACCACCTATGATACTACT 57.170 33.333 0.00 0.00 0.00 2.57
564 573 8.871629 AATGAGACCACCTATGATACTACTAG 57.128 38.462 0.00 0.00 0.00 2.57
565 574 7.390013 TGAGACCACCTATGATACTACTAGT 57.610 40.000 0.00 0.00 0.00 2.57
566 575 7.225011 TGAGACCACCTATGATACTACTAGTG 58.775 42.308 5.39 0.00 0.00 2.74
567 576 7.147355 TGAGACCACCTATGATACTACTAGTGT 60.147 40.741 5.39 4.48 0.00 3.55
568 577 8.272659 AGACCACCTATGATACTACTAGTGTA 57.727 38.462 5.39 6.64 0.00 2.90
569 578 8.892530 AGACCACCTATGATACTACTAGTGTAT 58.107 37.037 5.39 11.07 33.79 2.29
570 579 8.865420 ACCACCTATGATACTACTAGTGTATG 57.135 38.462 17.32 9.01 31.55 2.39
571 580 8.446394 ACCACCTATGATACTACTAGTGTATGT 58.554 37.037 17.32 9.21 31.55 2.29
572 581 9.298250 CCACCTATGATACTACTAGTGTATGTT 57.702 37.037 17.32 10.07 31.55 2.71
578 587 8.915057 TGATACTACTAGTGTATGTTACTCCC 57.085 38.462 17.32 6.32 31.55 4.30
579 588 7.941238 TGATACTACTAGTGTATGTTACTCCCC 59.059 40.741 17.32 5.84 31.55 4.81
580 589 6.083487 ACTACTAGTGTATGTTACTCCCCA 57.917 41.667 5.39 0.00 0.00 4.96
581 590 5.890419 ACTACTAGTGTATGTTACTCCCCAC 59.110 44.000 5.39 0.00 0.00 4.61
582 591 4.944177 ACTAGTGTATGTTACTCCCCACT 58.056 43.478 0.00 0.00 37.04 4.00
583 592 6.083487 ACTAGTGTATGTTACTCCCCACTA 57.917 41.667 0.00 0.00 35.08 2.74
584 593 6.680540 ACTAGTGTATGTTACTCCCCACTAT 58.319 40.000 0.00 0.00 35.54 2.12
585 594 5.871396 AGTGTATGTTACTCCCCACTATG 57.129 43.478 0.00 0.00 31.80 2.23
586 595 5.525484 AGTGTATGTTACTCCCCACTATGA 58.475 41.667 0.00 0.00 31.80 2.15
587 596 5.363005 AGTGTATGTTACTCCCCACTATGAC 59.637 44.000 0.00 0.00 31.80 3.06
588 597 4.652421 TGTATGTTACTCCCCACTATGACC 59.348 45.833 0.00 0.00 0.00 4.02
589 598 3.193395 TGTTACTCCCCACTATGACCA 57.807 47.619 0.00 0.00 0.00 4.02
590 599 3.104512 TGTTACTCCCCACTATGACCAG 58.895 50.000 0.00 0.00 0.00 4.00
591 600 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
592 601 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
593 602 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
594 603 0.253160 TCCCCACTATGACCAGCCTT 60.253 55.000 0.00 0.00 0.00 4.35
595 604 1.009060 TCCCCACTATGACCAGCCTTA 59.991 52.381 0.00 0.00 0.00 2.69
665 679 3.353836 GGCACGAACCACACGCAT 61.354 61.111 0.00 0.00 0.00 4.73
695 709 0.668535 GGCACTGAAACTTGGACACC 59.331 55.000 0.00 0.00 0.00 4.16
709 723 6.180472 ACTTGGACACCAATAGACTATTTGG 58.820 40.000 16.13 16.13 43.07 3.28
730 744 2.533942 GCTAATTAAAATTGCCGCCACG 59.466 45.455 0.00 0.00 0.00 4.94
765 779 4.496360 TGCATGGCATAAATGTGTTTCAG 58.504 39.130 0.00 0.00 31.71 3.02
768 782 3.772387 TGGCATAAATGTGTTTCAGGGA 58.228 40.909 0.00 0.00 0.00 4.20
783 797 9.010029 GTGTTTCAGGGAGTTTTTAATATCTGA 57.990 33.333 0.00 0.00 0.00 3.27
784 798 9.753674 TGTTTCAGGGAGTTTTTAATATCTGAT 57.246 29.630 0.00 0.00 31.35 2.90
875 891 3.345808 CCAGCAACCACGTCACCG 61.346 66.667 0.00 0.00 40.83 4.94
899 915 2.287248 ACTTTTGCGCTTTTGCTCTCTC 60.287 45.455 9.73 0.00 44.80 3.20
900 916 1.597742 TTTGCGCTTTTGCTCTCTCT 58.402 45.000 9.73 0.00 44.80 3.10
931 950 3.952323 TGTGTATATATCGAGCCCTAGCC 59.048 47.826 0.00 0.00 41.25 3.93
1107 1132 2.633657 GTGTTCACGCTGTGGCTG 59.366 61.111 8.46 0.00 33.87 4.85
1167 1192 4.429212 TCCGACGGCCACATCGTG 62.429 66.667 9.66 10.31 41.22 4.35
1290 1315 8.411683 ACATTTTCCTTTGCTGAGAATATCATC 58.588 33.333 0.00 0.00 37.28 2.92
1294 1319 6.892485 TCCTTTGCTGAGAATATCATCAAGA 58.108 36.000 0.00 0.00 43.06 3.02
1339 1364 5.603452 GCTCAAACGAATGTATGATCGATC 58.397 41.667 18.72 18.72 41.43 3.69
1798 1826 8.834749 AACCAGAACAGAATAGAGACTTTTAC 57.165 34.615 0.00 0.00 0.00 2.01
1847 1879 1.199558 ACTGCGAGTAGAACGACTTCC 59.800 52.381 0.00 0.00 0.00 3.46
1893 1926 7.395190 TCTACAAGTGATTTTGATTCCATGG 57.605 36.000 4.97 4.97 0.00 3.66
1933 2040 0.530744 TTCAGCGTCGCCTAAGATGT 59.469 50.000 14.86 0.00 0.00 3.06
1936 2043 0.246635 AGCGTCGCCTAAGATGTGTT 59.753 50.000 14.86 0.00 0.00 3.32
1993 2101 2.897326 GCAAGTTGTTTATTCCCACCCT 59.103 45.455 4.48 0.00 0.00 4.34
2012 2120 3.427243 CCTCTGACTTCAATCGTCGTAC 58.573 50.000 0.00 0.00 34.17 3.67
2028 2136 2.483877 TCGTACGTGAACTCCGTGTAAT 59.516 45.455 16.05 0.00 39.22 1.89
2110 2218 2.124403 CTCTCCACCAGGGCATGC 60.124 66.667 9.90 9.90 36.21 4.06
2139 2248 2.920645 CGTCAGGTCGCTGGACAGT 61.921 63.158 0.82 0.00 45.28 3.55
2176 2285 3.543680 AATCACTGAGGAACATACCGG 57.456 47.619 0.00 0.00 34.73 5.28
2252 2372 4.526438 AGATGCTTAATTAGGCACCCTT 57.474 40.909 22.85 8.61 41.19 3.95
2270 2390 4.021016 ACCCTTTACAGAGACAAGCACTAG 60.021 45.833 0.00 0.00 0.00 2.57
2348 2474 5.527582 GCACTGTATACAAGACCTAAATGGG 59.472 44.000 7.06 0.00 41.11 4.00
2376 2502 3.440173 ACTGGCTGGAACATCAATTAACG 59.560 43.478 0.00 0.00 38.20 3.18
2377 2503 3.680490 TGGCTGGAACATCAATTAACGA 58.320 40.909 0.00 0.00 38.20 3.85
2382 2508 5.795441 GCTGGAACATCAATTAACGAAACTC 59.205 40.000 0.00 0.00 38.20 3.01
2383 2509 6.249035 TGGAACATCAATTAACGAAACTCC 57.751 37.500 0.00 0.00 0.00 3.85
2384 2510 5.106869 TGGAACATCAATTAACGAAACTCCG 60.107 40.000 0.00 0.00 0.00 4.63
2385 2511 5.121142 GGAACATCAATTAACGAAACTCCGA 59.879 40.000 0.00 0.00 0.00 4.55
2386 2512 6.347888 GGAACATCAATTAACGAAACTCCGAA 60.348 38.462 0.00 0.00 0.00 4.30
2390 2516 4.449743 TCAATTAACGAAACTCCGAACTGG 59.550 41.667 0.00 0.00 40.09 4.00
2508 2719 4.278310 TCTGCTCTATGTACAGGCTACAA 58.722 43.478 0.33 0.00 32.19 2.41
2562 2773 1.860641 TTCTAGATCCGCCTTCACCA 58.139 50.000 0.00 0.00 0.00 4.17
2625 2836 6.642540 TCGAATCAGATGATATACTTGCACAC 59.357 38.462 0.00 0.00 33.73 3.82
2742 2955 2.123180 TACTCCCTCCGCCCCAAA 59.877 61.111 0.00 0.00 0.00 3.28
2743 2956 1.993391 TACTCCCTCCGCCCCAAAG 60.993 63.158 0.00 0.00 0.00 2.77
2744 2957 2.758852 TACTCCCTCCGCCCCAAAGT 62.759 60.000 0.00 0.00 0.00 2.66
2766 2979 9.880157 AAAGTAAGTGTCTCAACTTTGTACTAA 57.120 29.630 0.00 0.00 39.89 2.24
2767 2980 8.868635 AGTAAGTGTCTCAACTTTGTACTAAC 57.131 34.615 0.00 0.00 40.77 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.595929 GTCGTCACCAAAGCGGGAA 60.596 57.895 0.00 0.00 40.22 3.97
95 96 6.509418 AATGTGGATTAGAAGCGCTTAAAA 57.491 33.333 25.11 19.89 0.00 1.52
103 104 6.396829 AAGGCAATAATGTGGATTAGAAGC 57.603 37.500 0.00 0.00 0.00 3.86
126 127 9.280174 ACAGCAGCAATTTTACTACTACTTAAA 57.720 29.630 0.00 0.00 0.00 1.52
127 128 8.842358 ACAGCAGCAATTTTACTACTACTTAA 57.158 30.769 0.00 0.00 0.00 1.85
135 139 5.452078 AAGCAACAGCAGCAATTTTACTA 57.548 34.783 0.00 0.00 0.00 1.82
136 140 4.301628 GAAGCAACAGCAGCAATTTTACT 58.698 39.130 0.00 0.00 0.00 2.24
137 141 3.120121 CGAAGCAACAGCAGCAATTTTAC 59.880 43.478 0.00 0.00 0.00 2.01
138 142 3.243367 ACGAAGCAACAGCAGCAATTTTA 60.243 39.130 0.00 0.00 0.00 1.52
139 143 2.129607 CGAAGCAACAGCAGCAATTTT 58.870 42.857 0.00 0.00 0.00 1.82
140 144 1.067516 ACGAAGCAACAGCAGCAATTT 59.932 42.857 0.00 0.00 0.00 1.82
141 145 0.670162 ACGAAGCAACAGCAGCAATT 59.330 45.000 0.00 0.00 0.00 2.32
142 146 1.197721 GTACGAAGCAACAGCAGCAAT 59.802 47.619 0.00 0.00 0.00 3.56
143 147 0.586319 GTACGAAGCAACAGCAGCAA 59.414 50.000 0.00 0.00 0.00 3.91
144 148 1.227999 GGTACGAAGCAACAGCAGCA 61.228 55.000 0.00 0.00 0.00 4.41
145 149 1.497722 GGTACGAAGCAACAGCAGC 59.502 57.895 0.00 0.00 0.00 5.25
161 165 1.153168 AACTGCAGTTGCTGACGGT 60.153 52.632 30.66 3.41 41.71 4.83
182 186 0.169009 GTCGCTCTTTGCATGGGTTC 59.831 55.000 0.00 0.00 43.06 3.62
187 192 2.787249 CCGGTCGCTCTTTGCATG 59.213 61.111 0.00 0.00 43.06 4.06
206 211 1.879884 TGCATGCGTCGAGATGCTC 60.880 57.895 22.60 7.93 44.46 4.26
336 345 6.709018 AAATGGCCGTGCTTAATTAGTAAT 57.291 33.333 0.00 0.00 0.00 1.89
378 387 1.414158 TACTCTCACTATGGCCAGCC 58.586 55.000 13.05 0.38 0.00 4.85
383 392 7.942990 ACTAGTTATGTTACTCTCACTATGGC 58.057 38.462 0.00 0.00 0.00 4.40
401 410 9.445878 CGAGTCCCAAGTATATGATACTAGTTA 57.554 37.037 0.00 0.00 0.00 2.24
402 411 7.943447 ACGAGTCCCAAGTATATGATACTAGTT 59.057 37.037 0.00 0.00 0.00 2.24
403 412 7.460071 ACGAGTCCCAAGTATATGATACTAGT 58.540 38.462 0.00 0.00 0.00 2.57
404 413 7.925043 ACGAGTCCCAAGTATATGATACTAG 57.075 40.000 0.00 0.00 0.00 2.57
405 414 9.797642 TTTACGAGTCCCAAGTATATGATACTA 57.202 33.333 0.00 0.00 0.00 1.82
406 415 8.574737 GTTTACGAGTCCCAAGTATATGATACT 58.425 37.037 0.00 0.00 0.00 2.12
407 416 8.355169 TGTTTACGAGTCCCAAGTATATGATAC 58.645 37.037 0.00 0.00 0.00 2.24
408 417 8.467963 TGTTTACGAGTCCCAAGTATATGATA 57.532 34.615 0.00 0.00 0.00 2.15
409 418 7.356089 TGTTTACGAGTCCCAAGTATATGAT 57.644 36.000 0.00 0.00 0.00 2.45
410 419 6.778834 TGTTTACGAGTCCCAAGTATATGA 57.221 37.500 0.00 0.00 0.00 2.15
411 420 6.073765 GCATGTTTACGAGTCCCAAGTATATG 60.074 42.308 0.00 0.00 0.00 1.78
412 421 5.989777 GCATGTTTACGAGTCCCAAGTATAT 59.010 40.000 0.00 0.00 0.00 0.86
413 422 5.128171 AGCATGTTTACGAGTCCCAAGTATA 59.872 40.000 0.00 0.00 0.00 1.47
414 423 4.081087 AGCATGTTTACGAGTCCCAAGTAT 60.081 41.667 0.00 0.00 0.00 2.12
415 424 3.259876 AGCATGTTTACGAGTCCCAAGTA 59.740 43.478 0.00 0.00 0.00 2.24
416 425 2.038557 AGCATGTTTACGAGTCCCAAGT 59.961 45.455 0.00 0.00 0.00 3.16
417 426 2.699954 AGCATGTTTACGAGTCCCAAG 58.300 47.619 0.00 0.00 0.00 3.61
418 427 2.851263 AGCATGTTTACGAGTCCCAA 57.149 45.000 0.00 0.00 0.00 4.12
419 428 2.851263 AAGCATGTTTACGAGTCCCA 57.149 45.000 0.00 0.00 0.00 4.37
427 436 2.739913 TCTGCCACGTAAGCATGTTTAC 59.260 45.455 19.30 19.30 40.04 2.01
428 437 3.046968 TCTGCCACGTAAGCATGTTTA 57.953 42.857 12.34 0.00 40.04 2.01
429 438 1.890876 TCTGCCACGTAAGCATGTTT 58.109 45.000 12.34 0.00 40.04 2.83
430 439 1.890876 TTCTGCCACGTAAGCATGTT 58.109 45.000 12.34 0.00 40.04 2.71
431 440 1.890876 TTTCTGCCACGTAAGCATGT 58.109 45.000 12.34 0.00 40.04 3.21
432 441 2.987413 TTTTCTGCCACGTAAGCATG 57.013 45.000 12.34 7.59 40.04 4.06
433 442 5.637006 TTAATTTTCTGCCACGTAAGCAT 57.363 34.783 12.34 0.60 40.04 3.79
434 443 5.239744 TCTTTAATTTTCTGCCACGTAAGCA 59.760 36.000 11.51 11.51 45.62 3.91
435 444 5.695818 TCTTTAATTTTCTGCCACGTAAGC 58.304 37.500 2.88 2.88 45.62 3.09
437 446 8.407064 TCTTTTCTTTAATTTTCTGCCACGTAA 58.593 29.630 0.00 0.00 0.00 3.18
438 447 7.932335 TCTTTTCTTTAATTTTCTGCCACGTA 58.068 30.769 0.00 0.00 0.00 3.57
439 448 6.801575 TCTTTTCTTTAATTTTCTGCCACGT 58.198 32.000 0.00 0.00 0.00 4.49
440 449 7.138736 TCTCTTTTCTTTAATTTTCTGCCACG 58.861 34.615 0.00 0.00 0.00 4.94
441 450 8.352942 TCTCTCTTTTCTTTAATTTTCTGCCAC 58.647 33.333 0.00 0.00 0.00 5.01
442 451 8.463930 TCTCTCTTTTCTTTAATTTTCTGCCA 57.536 30.769 0.00 0.00 0.00 4.92
443 452 8.026026 CCTCTCTCTTTTCTTTAATTTTCTGCC 58.974 37.037 0.00 0.00 0.00 4.85
444 453 8.026026 CCCTCTCTCTTTTCTTTAATTTTCTGC 58.974 37.037 0.00 0.00 0.00 4.26
445 454 9.072375 ACCCTCTCTCTTTTCTTTAATTTTCTG 57.928 33.333 0.00 0.00 0.00 3.02
446 455 9.290988 GACCCTCTCTCTTTTCTTTAATTTTCT 57.709 33.333 0.00 0.00 0.00 2.52
447 456 8.516234 GGACCCTCTCTCTTTTCTTTAATTTTC 58.484 37.037 0.00 0.00 0.00 2.29
448 457 8.228206 AGGACCCTCTCTCTTTTCTTTAATTTT 58.772 33.333 0.00 0.00 0.00 1.82
449 458 7.760607 AGGACCCTCTCTCTTTTCTTTAATTT 58.239 34.615 0.00 0.00 0.00 1.82
450 459 7.336475 AGGACCCTCTCTCTTTTCTTTAATT 57.664 36.000 0.00 0.00 0.00 1.40
451 460 6.961361 AGGACCCTCTCTCTTTTCTTTAAT 57.039 37.500 0.00 0.00 0.00 1.40
452 461 7.017531 ACTAGGACCCTCTCTCTTTTCTTTAA 58.982 38.462 0.00 0.00 0.00 1.52
453 462 6.563163 ACTAGGACCCTCTCTCTTTTCTTTA 58.437 40.000 0.00 0.00 0.00 1.85
454 463 5.407936 ACTAGGACCCTCTCTCTTTTCTTT 58.592 41.667 0.00 0.00 0.00 2.52
455 464 5.018374 ACTAGGACCCTCTCTCTTTTCTT 57.982 43.478 0.00 0.00 0.00 2.52
456 465 4.685513 ACTAGGACCCTCTCTCTTTTCT 57.314 45.455 0.00 0.00 0.00 2.52
457 466 5.715753 TGTTACTAGGACCCTCTCTCTTTTC 59.284 44.000 0.00 0.00 0.00 2.29
458 467 5.652324 TGTTACTAGGACCCTCTCTCTTTT 58.348 41.667 0.00 0.00 0.00 2.27
459 468 5.272405 TGTTACTAGGACCCTCTCTCTTT 57.728 43.478 0.00 0.00 0.00 2.52
460 469 4.949966 TGTTACTAGGACCCTCTCTCTT 57.050 45.455 0.00 0.00 0.00 2.85
461 470 5.073965 CCTATGTTACTAGGACCCTCTCTCT 59.926 48.000 0.00 0.00 40.76 3.10
462 471 5.163066 ACCTATGTTACTAGGACCCTCTCTC 60.163 48.000 12.51 0.00 40.76 3.20
463 472 4.732957 ACCTATGTTACTAGGACCCTCTCT 59.267 45.833 12.51 0.00 40.76 3.10
464 473 5.064314 ACCTATGTTACTAGGACCCTCTC 57.936 47.826 12.51 0.00 40.76 3.20
465 474 5.915900 TCTACCTATGTTACTAGGACCCTCT 59.084 44.000 12.51 0.00 40.76 3.69
466 475 6.198237 TCTACCTATGTTACTAGGACCCTC 57.802 45.833 12.51 0.00 40.76 4.30
467 476 6.800223 ATCTACCTATGTTACTAGGACCCT 57.200 41.667 12.51 0.00 40.76 4.34
468 477 6.889177 GGTATCTACCTATGTTACTAGGACCC 59.111 46.154 12.51 0.00 43.10 4.46
469 478 6.597280 CGGTATCTACCTATGTTACTAGGACC 59.403 46.154 12.51 8.93 44.25 4.46
470 479 7.164803 ACGGTATCTACCTATGTTACTAGGAC 58.835 42.308 12.51 0.00 44.25 3.85
471 480 7.321717 ACGGTATCTACCTATGTTACTAGGA 57.678 40.000 12.51 0.00 44.25 2.94
472 481 8.940952 GTTACGGTATCTACCTATGTTACTAGG 58.059 40.741 4.93 6.41 44.25 3.02
473 482 9.494271 TGTTACGGTATCTACCTATGTTACTAG 57.506 37.037 4.93 0.00 44.25 2.57
475 484 8.930846 ATGTTACGGTATCTACCTATGTTACT 57.069 34.615 4.93 0.00 44.25 2.24
503 512 8.773645 GCATGACACATAGTAGCATAACAATTA 58.226 33.333 0.00 0.00 0.00 1.40
504 513 7.282901 TGCATGACACATAGTAGCATAACAATT 59.717 33.333 0.00 0.00 30.65 2.32
505 514 6.767423 TGCATGACACATAGTAGCATAACAAT 59.233 34.615 0.00 0.00 30.65 2.71
506 515 6.112058 TGCATGACACATAGTAGCATAACAA 58.888 36.000 0.00 0.00 30.65 2.83
507 516 5.669477 TGCATGACACATAGTAGCATAACA 58.331 37.500 0.00 0.00 30.65 2.41
508 517 6.347969 CCATGCATGACACATAGTAGCATAAC 60.348 42.308 28.31 0.00 39.67 1.89
509 518 5.702209 CCATGCATGACACATAGTAGCATAA 59.298 40.000 28.31 0.00 39.67 1.90
510 519 5.240121 CCATGCATGACACATAGTAGCATA 58.760 41.667 28.31 0.00 39.67 3.14
511 520 4.070009 CCATGCATGACACATAGTAGCAT 58.930 43.478 28.31 0.00 41.24 3.79
512 521 3.469739 CCATGCATGACACATAGTAGCA 58.530 45.455 28.31 0.00 37.13 3.49
513 522 2.225019 GCCATGCATGACACATAGTAGC 59.775 50.000 28.31 14.15 0.00 3.58
514 523 3.469739 TGCCATGCATGACACATAGTAG 58.530 45.455 28.31 8.01 31.71 2.57
515 524 3.557228 TGCCATGCATGACACATAGTA 57.443 42.857 28.31 5.91 31.71 1.82
516 525 2.423446 TGCCATGCATGACACATAGT 57.577 45.000 28.31 0.00 31.71 2.12
517 526 5.441709 TTATTGCCATGCATGACACATAG 57.558 39.130 28.31 10.23 38.76 2.23
518 527 5.848833 TTTATTGCCATGCATGACACATA 57.151 34.783 28.31 17.78 38.76 2.29
519 528 4.739587 TTTATTGCCATGCATGACACAT 57.260 36.364 28.31 18.68 38.76 3.21
520 529 4.159879 TCATTTATTGCCATGCATGACACA 59.840 37.500 28.31 18.81 38.76 3.72
521 530 4.684877 TCATTTATTGCCATGCATGACAC 58.315 39.130 28.31 16.49 38.76 3.67
522 531 4.645588 TCTCATTTATTGCCATGCATGACA 59.354 37.500 28.31 20.53 38.76 3.58
523 532 4.980434 GTCTCATTTATTGCCATGCATGAC 59.020 41.667 28.31 17.77 38.76 3.06
524 533 4.038282 GGTCTCATTTATTGCCATGCATGA 59.962 41.667 28.31 8.76 38.76 3.07
525 534 4.202172 TGGTCTCATTTATTGCCATGCATG 60.202 41.667 20.19 20.19 38.76 4.06
526 535 3.962063 TGGTCTCATTTATTGCCATGCAT 59.038 39.130 0.00 0.00 38.76 3.96
527 536 3.130869 GTGGTCTCATTTATTGCCATGCA 59.869 43.478 0.00 0.00 36.47 3.96
528 537 3.491447 GGTGGTCTCATTTATTGCCATGC 60.491 47.826 0.00 0.00 0.00 4.06
529 538 3.956199 AGGTGGTCTCATTTATTGCCATG 59.044 43.478 0.00 0.00 0.00 3.66
530 539 4.255510 AGGTGGTCTCATTTATTGCCAT 57.744 40.909 0.00 0.00 0.00 4.40
531 540 3.737559 AGGTGGTCTCATTTATTGCCA 57.262 42.857 0.00 0.00 0.00 4.92
532 541 5.376625 TCATAGGTGGTCTCATTTATTGCC 58.623 41.667 0.00 0.00 0.00 4.52
533 542 7.880195 AGTATCATAGGTGGTCTCATTTATTGC 59.120 37.037 0.00 0.00 0.00 3.56
536 545 9.830186 AGTAGTATCATAGGTGGTCTCATTTAT 57.170 33.333 0.00 0.00 0.00 1.40
538 547 9.303116 CTAGTAGTATCATAGGTGGTCTCATTT 57.697 37.037 0.00 0.00 0.00 2.32
539 548 8.449625 ACTAGTAGTATCATAGGTGGTCTCATT 58.550 37.037 0.00 0.00 0.00 2.57
540 549 7.885922 CACTAGTAGTATCATAGGTGGTCTCAT 59.114 40.741 1.57 0.00 0.00 2.90
541 550 7.147355 ACACTAGTAGTATCATAGGTGGTCTCA 60.147 40.741 1.57 0.00 0.00 3.27
542 551 7.225725 ACACTAGTAGTATCATAGGTGGTCTC 58.774 42.308 1.57 0.00 0.00 3.36
543 552 7.151694 ACACTAGTAGTATCATAGGTGGTCT 57.848 40.000 1.57 0.00 0.00 3.85
544 553 8.948145 CATACACTAGTAGTATCATAGGTGGTC 58.052 40.741 1.57 0.00 32.86 4.02
545 554 8.446394 ACATACACTAGTAGTATCATAGGTGGT 58.554 37.037 1.57 0.00 32.86 4.16
546 555 8.865420 ACATACACTAGTAGTATCATAGGTGG 57.135 38.462 1.57 0.00 32.86 4.61
552 561 9.517868 GGGAGTAACATACACTAGTAGTATCAT 57.482 37.037 1.57 8.60 32.86 2.45
553 562 7.941238 GGGGAGTAACATACACTAGTAGTATCA 59.059 40.741 1.57 0.00 32.86 2.15
554 563 7.941238 TGGGGAGTAACATACACTAGTAGTATC 59.059 40.741 1.57 4.90 32.86 2.24
555 564 7.723172 GTGGGGAGTAACATACACTAGTAGTAT 59.277 40.741 1.57 3.75 32.86 2.12
556 565 7.056635 GTGGGGAGTAACATACACTAGTAGTA 58.943 42.308 1.57 1.31 32.86 1.82
557 566 5.890419 GTGGGGAGTAACATACACTAGTAGT 59.110 44.000 0.00 0.00 32.86 2.73
558 567 6.127793 AGTGGGGAGTAACATACACTAGTAG 58.872 44.000 0.00 0.00 37.41 2.57
559 568 6.083487 AGTGGGGAGTAACATACACTAGTA 57.917 41.667 0.00 0.00 37.41 1.82
560 569 4.944177 AGTGGGGAGTAACATACACTAGT 58.056 43.478 0.00 0.00 37.41 2.57
561 570 6.776116 TCATAGTGGGGAGTAACATACACTAG 59.224 42.308 0.00 0.00 42.51 2.57
562 571 6.548622 GTCATAGTGGGGAGTAACATACACTA 59.451 42.308 0.00 0.00 43.13 2.74
563 572 5.363005 GTCATAGTGGGGAGTAACATACACT 59.637 44.000 0.00 0.00 41.52 3.55
564 573 5.452917 GGTCATAGTGGGGAGTAACATACAC 60.453 48.000 0.00 0.00 0.00 2.90
565 574 4.652421 GGTCATAGTGGGGAGTAACATACA 59.348 45.833 0.00 0.00 0.00 2.29
566 575 4.652421 TGGTCATAGTGGGGAGTAACATAC 59.348 45.833 0.00 0.00 0.00 2.39
567 576 4.886163 TGGTCATAGTGGGGAGTAACATA 58.114 43.478 0.00 0.00 0.00 2.29
568 577 3.711704 CTGGTCATAGTGGGGAGTAACAT 59.288 47.826 0.00 0.00 0.00 2.71
569 578 3.104512 CTGGTCATAGTGGGGAGTAACA 58.895 50.000 0.00 0.00 0.00 2.41
570 579 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
571 580 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
572 581 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
573 582 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
574 583 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
575 584 0.253160 AAGGCTGGTCATAGTGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
576 585 1.141053 GTAAGGCTGGTCATAGTGGGG 59.859 57.143 0.00 0.00 0.00 4.96
577 586 1.202533 CGTAAGGCTGGTCATAGTGGG 60.203 57.143 0.00 0.00 0.00 4.61
578 587 1.806623 GCGTAAGGCTGGTCATAGTGG 60.807 57.143 0.00 0.00 39.11 4.00
579 588 1.571919 GCGTAAGGCTGGTCATAGTG 58.428 55.000 0.00 0.00 39.11 2.74
590 599 1.135402 CCAACCATTTCAGCGTAAGGC 60.135 52.381 0.00 0.00 44.05 4.35
591 600 1.135402 GCCAACCATTTCAGCGTAAGG 60.135 52.381 0.00 0.00 38.28 2.69
592 601 1.135402 GGCCAACCATTTCAGCGTAAG 60.135 52.381 0.00 0.00 35.26 2.34
593 602 0.885196 GGCCAACCATTTCAGCGTAA 59.115 50.000 0.00 0.00 35.26 3.18
594 603 0.037590 AGGCCAACCATTTCAGCGTA 59.962 50.000 5.01 0.00 39.06 4.42
595 604 1.228552 AGGCCAACCATTTCAGCGT 60.229 52.632 5.01 0.00 39.06 5.07
709 723 2.533942 CGTGGCGGCAATTTTAATTAGC 59.466 45.455 15.50 0.00 0.00 3.09
899 915 6.183360 GCTCGATATATACACAGAGGAGGAAG 60.183 46.154 0.00 0.00 0.00 3.46
900 916 5.648526 GCTCGATATATACACAGAGGAGGAA 59.351 44.000 0.00 0.00 0.00 3.36
931 950 8.564574 GTCTCTCTATGTGATCTGGTTAAGTAG 58.435 40.741 0.00 0.00 0.00 2.57
982 1006 3.679389 CCATCTCTGCCTGTACAAAGTT 58.321 45.455 0.00 0.00 0.00 2.66
987 1012 0.970427 TCGCCATCTCTGCCTGTACA 60.970 55.000 0.00 0.00 0.00 2.90
992 1017 2.589610 TACCCTCGCCATCTCTGCCT 62.590 60.000 0.00 0.00 0.00 4.75
1167 1192 1.122419 CGTAGTTGTCGACGCGGTAC 61.122 60.000 12.47 5.88 36.13 3.34
1290 1315 8.438513 CGCCAACATAGTATTTCATAGATCTTG 58.561 37.037 0.00 0.00 0.00 3.02
1294 1319 6.467677 AGCGCCAACATAGTATTTCATAGAT 58.532 36.000 2.29 0.00 0.00 1.98
1339 1364 7.444183 TCCACAATTAAGTAACCAGTCAGAAAG 59.556 37.037 0.00 0.00 0.00 2.62
1437 1465 3.055719 CGCGCCACCTTGAACCAT 61.056 61.111 0.00 0.00 0.00 3.55
1533 1561 1.146041 GATCCTGTACCGCATGGCA 59.854 57.895 0.00 0.00 39.70 4.92
1798 1826 5.388475 CGGTAATTCACACGAAGAAAGACTG 60.388 44.000 0.00 0.00 33.74 3.51
1847 1879 4.773323 TCAGTCATCTGTGTCACACTAG 57.227 45.455 9.90 5.32 41.91 2.57
1893 1926 3.120041 ACATTTTTGGCAGTACAAACGC 58.880 40.909 0.00 0.00 39.82 4.84
1993 2101 2.481568 ACGTACGACGATTGAAGTCAGA 59.518 45.455 24.41 0.00 46.05 3.27
2012 2120 4.730657 AGACTAATTACACGGAGTTCACG 58.269 43.478 0.00 0.00 41.61 4.35
2050 2158 3.868661 GGCGAAACAACACTTCCAATTTT 59.131 39.130 0.00 0.00 0.00 1.82
2057 2165 1.001706 GGGAAGGCGAAACAACACTTC 60.002 52.381 0.00 0.00 37.43 3.01
2110 2218 0.989890 GACCTGACGAAACGGAATCG 59.010 55.000 5.41 5.41 45.47 3.34
2176 2285 4.723309 AGGCCTTAATCAAGACATGGATC 58.277 43.478 0.00 0.00 33.20 3.36
2348 2474 1.537202 GATGTTCCAGCCAGTGTGAAC 59.463 52.381 0.00 0.00 37.10 3.18
2376 2502 3.071479 TGTAATGCCAGTTCGGAGTTTC 58.929 45.455 0.00 0.00 36.56 2.78
2377 2503 3.134574 TGTAATGCCAGTTCGGAGTTT 57.865 42.857 0.00 0.00 36.56 2.66
2382 2508 3.634568 TGTTTTGTAATGCCAGTTCGG 57.365 42.857 0.00 0.00 38.11 4.30
2383 2509 5.689514 TCAATTGTTTTGTAATGCCAGTTCG 59.310 36.000 5.13 0.00 0.00 3.95
2384 2510 6.701400 AGTCAATTGTTTTGTAATGCCAGTTC 59.299 34.615 5.13 0.00 0.00 3.01
2385 2511 6.581712 AGTCAATTGTTTTGTAATGCCAGTT 58.418 32.000 5.13 0.00 0.00 3.16
2386 2512 6.160576 AGTCAATTGTTTTGTAATGCCAGT 57.839 33.333 5.13 0.00 0.00 4.00
2625 2836 0.033504 ACTTGCCTCGTGTGTAGGTG 59.966 55.000 0.00 0.00 36.43 4.00
2721 2934 1.155624 GGGGCGGAGGGAGTACTAT 59.844 63.158 0.00 0.00 0.00 2.12
2742 2955 8.868635 GTTAGTACAAAGTTGAGACACTTACT 57.131 34.615 0.00 0.00 35.87 2.24


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

AutoCloner maintained by Alex Coulton.