Multiple sequence alignment - TraesCS4A01G199700

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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 TraesCS4A01G199700 chr4A 100.000 2642 0 0 1 2642 487869991 487867350 0.000000e+00 4879.0
1 TraesCS4A01G199700 chr4A 83.951 405 22 12 2003 2402 742542768 742542402 5.410000e-92 348.0
2 TraesCS4A01G199700 chr4A 83.333 408 27 12 2000 2402 701625851 701626222 3.260000e-89 339.0
3 TraesCS4A01G199700 chr4D 90.700 1914 84 40 724 2586 93840942 93842812 0.000000e+00 2462.0
4 TraesCS4A01G199700 chr4D 86.842 304 38 2 82 383 93838608 93838911 3.260000e-89 339.0
5 TraesCS4A01G199700 chr4D 81.111 270 28 9 375 622 93838775 93839043 7.460000e-46 195.0
6 TraesCS4A01G199700 chr4D 90.323 62 6 0 1 62 93838547 93838608 6.060000e-12 82.4
7 TraesCS4A01G199700 chr4D 95.238 42 2 0 2601 2642 93842799 93842840 1.700000e-07 67.6
8 TraesCS4A01G199700 chr4B 88.838 1953 93 62 687 2586 132331258 132333138 0.000000e+00 2283.0
9 TraesCS4A01G199700 chr4B 90.000 380 36 1 1 378 132330595 132330974 8.500000e-135 490.0
10 TraesCS4A01G199700 chr4B 84.874 119 18 0 375 493 132330843 132330961 1.280000e-23 121.0
11 TraesCS4A01G199700 chr4B 97.619 42 1 0 2601 2642 132333125 132333166 3.650000e-09 73.1
12 TraesCS4A01G199700 chr5D 84.923 650 73 14 998 1642 213129205 213129834 3.710000e-178 634.0
13 TraesCS4A01G199700 chr5D 82.126 649 93 10 998 1642 212627253 212627882 3.870000e-148 534.0
14 TraesCS4A01G199700 chr5B 84.900 649 75 12 998 1642 227120977 227121606 3.710000e-178 634.0
15 TraesCS4A01G199700 chr5B 80.556 648 105 12 998 1642 226759281 226759910 1.840000e-131 479.0
16 TraesCS4A01G199700 chr5B 84.065 433 25 15 2003 2430 696669690 696669297 6.900000e-101 377.0
17 TraesCS4A01G199700 chr5B 74.373 359 72 17 1228 1575 664998552 664998203 4.590000e-28 135.0
18 TraesCS4A01G199700 chr5A 84.438 649 78 12 998 1642 276980834 276980205 3.740000e-173 617.0
19 TraesCS4A01G199700 chr5A 82.944 557 72 12 998 1550 276111785 276112322 5.110000e-132 481.0
20 TraesCS4A01G199700 chr3B 84.198 405 23 12 2003 2402 805032028 805031660 3.230000e-94 355.0
21 TraesCS4A01G199700 chr7B 83.105 438 24 20 2003 2430 655427453 655427056 1.160000e-93 353.0
22 TraesCS4A01G199700 chr7B 84.365 307 22 12 1991 2291 655433989 655433703 7.200000e-71 278.0
23 TraesCS4A01G199700 chr7B 97.297 37 0 1 2464 2500 655427039 655427004 7.900000e-06 62.1
24 TraesCS4A01G199700 chr2B 83.010 412 19 18 2000 2402 714391764 714392133 2.540000e-85 326.0
25 TraesCS4A01G199700 chr2B 90.625 128 7 2 2304 2427 103687696 103687822 5.850000e-37 165.0
26 TraesCS4A01G199700 chr1B 85.632 174 14 5 2000 2172 276586902 276587065 3.500000e-39 172.0
27 TraesCS4A01G199700 chr6B 86.719 128 8 3 2304 2427 36689251 36689373 1.650000e-27 134.0


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 TraesCS4A01G199700 chr4A 487867350 487869991 2641 True 4879.000 4879 100.00000 1 2642 1 chr4A.!!$R1 2641
1 TraesCS4A01G199700 chr4D 93838547 93842840 4293 False 629.200 2462 88.84280 1 2642 5 chr4D.!!$F1 2641
2 TraesCS4A01G199700 chr4B 132330595 132333166 2571 False 741.775 2283 90.33275 1 2642 4 chr4B.!!$F1 2641
3 TraesCS4A01G199700 chr5D 213129205 213129834 629 False 634.000 634 84.92300 998 1642 1 chr5D.!!$F2 644
4 TraesCS4A01G199700 chr5D 212627253 212627882 629 False 534.000 534 82.12600 998 1642 1 chr5D.!!$F1 644
5 TraesCS4A01G199700 chr5B 227120977 227121606 629 False 634.000 634 84.90000 998 1642 1 chr5B.!!$F2 644
6 TraesCS4A01G199700 chr5B 226759281 226759910 629 False 479.000 479 80.55600 998 1642 1 chr5B.!!$F1 644
7 TraesCS4A01G199700 chr5A 276980205 276980834 629 True 617.000 617 84.43800 998 1642 1 chr5A.!!$R1 644
8 TraesCS4A01G199700 chr5A 276111785 276112322 537 False 481.000 481 82.94400 998 1550 1 chr5A.!!$F1 552

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
672 865 0.036306 AGGTCGGGCGTTTCAATCTT 59.964 50.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2601 4618 0.034574 ATAACGCAATCTGGGCCACA 60.035 50.0 0.0 0.0 33.1 4.17 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
72 73 8.495949 CAGTGGTATATTTTCAATATGTCGGAC 58.504 37.037 0.00 0.00 0.00 4.79
85 86 1.002201 TGTCGGACGCCCTAAAATTGA 59.998 47.619 3.34 0.00 0.00 2.57
97 98 7.929245 ACGCCCTAAAATTGAAATTTGTTAGTT 59.071 29.630 0.00 0.00 38.53 2.24
283 288 9.911788 ATCTTATGTCATTATCTTGTTCAAGGT 57.088 29.630 11.82 7.96 0.00 3.50
347 352 3.795101 GCCAGCAATCAAGATGAAAATCG 59.205 43.478 0.00 0.00 0.00 3.34
355 360 6.573664 ATCAAGATGAAAATCGTTGTCCAA 57.426 33.333 0.00 0.00 0.00 3.53
387 392 3.362851 GAACGTGGCGGCGACAATC 62.363 63.158 21.17 13.29 35.59 2.67
389 394 3.118454 CGTGGCGGCGACAATCTT 61.118 61.111 21.17 0.00 0.00 2.40
390 395 2.480555 GTGGCGGCGACAATCTTG 59.519 61.111 21.17 0.00 0.00 3.02
393 401 3.788766 GCGGCGACAATCTTGCGT 61.789 61.111 12.98 0.00 32.85 5.24
395 403 1.962092 GCGGCGACAATCTTGCGTTA 61.962 55.000 12.98 0.00 32.85 3.18
396 404 0.650512 CGGCGACAATCTTGCGTTAT 59.349 50.000 0.00 0.00 32.85 1.89
398 406 2.283086 CGGCGACAATCTTGCGTTATTA 59.717 45.455 0.00 0.00 32.85 0.98
403 411 5.617187 GCGACAATCTTGCGTTATTATCTTG 59.383 40.000 0.00 0.00 32.85 3.02
406 414 7.370836 CGACAATCTTGCGTTATTATCTTGTTC 59.629 37.037 0.00 0.00 0.00 3.18
416 424 6.608610 GTTATTATCTTGTTCAAGGCGTTGT 58.391 36.000 17.96 0.65 34.98 3.32
418 426 2.325583 TCTTGTTCAAGGCGTTGTCT 57.674 45.000 17.96 0.00 34.98 3.41
419 427 3.462483 TCTTGTTCAAGGCGTTGTCTA 57.538 42.857 17.96 9.20 34.98 2.59
420 428 3.128349 TCTTGTTCAAGGCGTTGTCTAC 58.872 45.455 17.96 14.34 34.98 2.59
421 429 2.902705 TGTTCAAGGCGTTGTCTACT 57.097 45.000 17.96 0.00 34.98 2.57
422 430 3.188159 TGTTCAAGGCGTTGTCTACTT 57.812 42.857 17.96 0.00 34.98 2.24
423 431 2.869801 TGTTCAAGGCGTTGTCTACTTG 59.130 45.455 17.96 4.09 41.14 3.16
424 432 2.870411 GTTCAAGGCGTTGTCTACTTGT 59.130 45.455 17.96 0.00 40.74 3.16
425 433 3.188159 TCAAGGCGTTGTCTACTTGTT 57.812 42.857 17.96 0.00 40.74 2.83
426 434 2.869801 TCAAGGCGTTGTCTACTTGTTG 59.130 45.455 17.96 0.00 40.74 3.33
427 435 2.612212 CAAGGCGTTGTCTACTTGTTGT 59.388 45.455 10.97 0.00 36.47 3.32
428 436 2.210116 AGGCGTTGTCTACTTGTTGTG 58.790 47.619 0.00 0.00 0.00 3.33
429 437 2.159014 AGGCGTTGTCTACTTGTTGTGA 60.159 45.455 0.00 0.00 0.00 3.58
430 438 2.806244 GGCGTTGTCTACTTGTTGTGAT 59.194 45.455 0.00 0.00 0.00 3.06
431 439 3.363970 GGCGTTGTCTACTTGTTGTGATG 60.364 47.826 0.00 0.00 0.00 3.07
432 440 3.493129 GCGTTGTCTACTTGTTGTGATGA 59.507 43.478 0.00 0.00 0.00 2.92
433 441 4.152402 GCGTTGTCTACTTGTTGTGATGAT 59.848 41.667 0.00 0.00 0.00 2.45
434 442 5.611919 CGTTGTCTACTTGTTGTGATGATG 58.388 41.667 0.00 0.00 0.00 3.07
435 443 5.389830 CGTTGTCTACTTGTTGTGATGATGG 60.390 44.000 0.00 0.00 0.00 3.51
436 444 5.227569 TGTCTACTTGTTGTGATGATGGT 57.772 39.130 0.00 0.00 0.00 3.55
437 445 5.237815 TGTCTACTTGTTGTGATGATGGTC 58.762 41.667 0.00 0.00 0.00 4.02
438 446 5.012046 TGTCTACTTGTTGTGATGATGGTCT 59.988 40.000 0.00 0.00 0.00 3.85
439 447 5.934625 GTCTACTTGTTGTGATGATGGTCTT 59.065 40.000 0.00 0.00 0.00 3.01
440 448 6.091441 GTCTACTTGTTGTGATGATGGTCTTC 59.909 42.308 0.00 0.00 0.00 2.87
441 449 4.717877 ACTTGTTGTGATGATGGTCTTCA 58.282 39.130 0.00 0.00 0.00 3.02
442 450 5.319453 ACTTGTTGTGATGATGGTCTTCAT 58.681 37.500 0.00 0.00 39.04 2.57
443 451 5.771666 ACTTGTTGTGATGATGGTCTTCATT 59.228 36.000 1.73 0.00 36.48 2.57
444 452 5.632244 TGTTGTGATGATGGTCTTCATTG 57.368 39.130 1.73 0.00 36.48 2.82
445 453 5.072055 TGTTGTGATGATGGTCTTCATTGT 58.928 37.500 1.73 0.00 36.48 2.71
446 454 5.181811 TGTTGTGATGATGGTCTTCATTGTC 59.818 40.000 1.73 0.00 36.48 3.18
447 455 4.264253 TGTGATGATGGTCTTCATTGTCC 58.736 43.478 1.73 0.00 36.48 4.02
448 456 3.310774 GTGATGATGGTCTTCATTGTCCG 59.689 47.826 1.73 0.00 36.48 4.79
449 457 2.401583 TGATGGTCTTCATTGTCCGG 57.598 50.000 0.00 0.00 35.97 5.14
450 458 1.628340 TGATGGTCTTCATTGTCCGGT 59.372 47.619 0.00 0.00 35.97 5.28
451 459 2.280628 GATGGTCTTCATTGTCCGGTC 58.719 52.381 0.00 0.00 35.97 4.79
452 460 1.052617 TGGTCTTCATTGTCCGGTCA 58.947 50.000 0.00 0.00 0.00 4.02
453 461 1.001974 TGGTCTTCATTGTCCGGTCAG 59.998 52.381 0.00 0.00 0.00 3.51
454 462 1.079503 GTCTTCATTGTCCGGTCAGC 58.920 55.000 0.00 0.00 0.00 4.26
455 463 0.684535 TCTTCATTGTCCGGTCAGCA 59.315 50.000 0.00 0.00 0.00 4.41
456 464 1.071542 TCTTCATTGTCCGGTCAGCAA 59.928 47.619 0.00 3.65 0.00 3.91
457 465 1.879380 CTTCATTGTCCGGTCAGCAAA 59.121 47.619 0.00 0.00 0.00 3.68
458 466 1.234821 TCATTGTCCGGTCAGCAAAC 58.765 50.000 0.00 0.00 0.00 2.93
459 467 0.950836 CATTGTCCGGTCAGCAAACA 59.049 50.000 0.00 0.00 0.00 2.83
460 468 1.336440 CATTGTCCGGTCAGCAAACAA 59.664 47.619 0.00 2.80 34.64 2.83
461 469 1.686355 TTGTCCGGTCAGCAAACAAT 58.314 45.000 0.00 0.00 0.00 2.71
462 470 2.552599 TGTCCGGTCAGCAAACAATA 57.447 45.000 0.00 0.00 0.00 1.90
463 471 2.852449 TGTCCGGTCAGCAAACAATAA 58.148 42.857 0.00 0.00 0.00 1.40
464 472 3.215151 TGTCCGGTCAGCAAACAATAAA 58.785 40.909 0.00 0.00 0.00 1.40
465 473 3.252215 TGTCCGGTCAGCAAACAATAAAG 59.748 43.478 0.00 0.00 0.00 1.85
466 474 3.500680 GTCCGGTCAGCAAACAATAAAGA 59.499 43.478 0.00 0.00 0.00 2.52
467 475 4.156008 GTCCGGTCAGCAAACAATAAAGAT 59.844 41.667 0.00 0.00 0.00 2.40
468 476 4.155826 TCCGGTCAGCAAACAATAAAGATG 59.844 41.667 0.00 0.00 0.00 2.90
469 477 4.155826 CCGGTCAGCAAACAATAAAGATGA 59.844 41.667 0.00 0.00 0.00 2.92
470 478 5.335583 CCGGTCAGCAAACAATAAAGATGAA 60.336 40.000 0.00 0.00 0.00 2.57
471 479 6.148948 CGGTCAGCAAACAATAAAGATGAAA 58.851 36.000 0.00 0.00 0.00 2.69
472 480 6.640499 CGGTCAGCAAACAATAAAGATGAAAA 59.360 34.615 0.00 0.00 0.00 2.29
473 481 7.329226 CGGTCAGCAAACAATAAAGATGAAAAT 59.671 33.333 0.00 0.00 0.00 1.82
474 482 8.650714 GGTCAGCAAACAATAAAGATGAAAATC 58.349 33.333 0.00 0.00 0.00 2.17
475 483 8.650714 GTCAGCAAACAATAAAGATGAAAATCC 58.349 33.333 0.00 0.00 0.00 3.01
476 484 7.818930 TCAGCAAACAATAAAGATGAAAATCCC 59.181 33.333 0.00 0.00 0.00 3.85
477 485 7.820872 CAGCAAACAATAAAGATGAAAATCCCT 59.179 33.333 0.00 0.00 0.00 4.20
478 486 7.820872 AGCAAACAATAAAGATGAAAATCCCTG 59.179 33.333 0.00 0.00 0.00 4.45
479 487 7.603784 GCAAACAATAAAGATGAAAATCCCTGT 59.396 33.333 0.00 0.00 0.00 4.00
482 490 8.877864 ACAATAAAGATGAAAATCCCTGTACA 57.122 30.769 0.00 0.00 0.00 2.90
483 491 8.960591 ACAATAAAGATGAAAATCCCTGTACAG 58.039 33.333 16.34 16.34 0.00 2.74
484 492 9.177608 CAATAAAGATGAAAATCCCTGTACAGA 57.822 33.333 24.68 5.81 0.00 3.41
485 493 8.738645 ATAAAGATGAAAATCCCTGTACAGAC 57.261 34.615 24.68 6.86 0.00 3.51
486 494 5.104259 AGATGAAAATCCCTGTACAGACC 57.896 43.478 24.68 5.49 0.00 3.85
487 495 3.328382 TGAAAATCCCTGTACAGACCG 57.672 47.619 24.68 10.90 0.00 4.79
488 496 2.635915 TGAAAATCCCTGTACAGACCGT 59.364 45.455 24.68 3.95 0.00 4.83
489 497 3.259902 GAAAATCCCTGTACAGACCGTC 58.740 50.000 24.68 9.48 0.00 4.79
490 498 2.233305 AATCCCTGTACAGACCGTCT 57.767 50.000 24.68 0.00 0.00 4.18
491 499 2.233305 ATCCCTGTACAGACCGTCTT 57.767 50.000 24.68 0.00 0.00 3.01
492 500 1.542492 TCCCTGTACAGACCGTCTTC 58.458 55.000 24.68 0.00 0.00 2.87
493 501 1.202964 TCCCTGTACAGACCGTCTTCA 60.203 52.381 24.68 0.00 0.00 3.02
494 502 1.202582 CCCTGTACAGACCGTCTTCAG 59.797 57.143 24.68 7.98 0.00 3.02
495 503 1.202582 CCTGTACAGACCGTCTTCAGG 59.797 57.143 24.68 20.41 33.94 3.86
496 504 0.601558 TGTACAGACCGTCTTCAGGC 59.398 55.000 0.00 0.00 0.00 4.85
497 505 0.601558 GTACAGACCGTCTTCAGGCA 59.398 55.000 0.00 0.00 0.00 4.75
498 506 1.000506 GTACAGACCGTCTTCAGGCAA 59.999 52.381 0.00 0.00 0.00 4.52
499 507 0.468226 ACAGACCGTCTTCAGGCAAA 59.532 50.000 0.00 0.00 0.00 3.68
500 508 0.868406 CAGACCGTCTTCAGGCAAAC 59.132 55.000 0.00 0.00 0.00 2.93
501 509 0.468226 AGACCGTCTTCAGGCAAACA 59.532 50.000 0.00 0.00 0.00 2.83
502 510 1.072331 AGACCGTCTTCAGGCAAACAT 59.928 47.619 0.00 0.00 0.00 2.71
503 511 1.197721 GACCGTCTTCAGGCAAACATG 59.802 52.381 0.00 0.00 0.00 3.21
504 512 1.202758 ACCGTCTTCAGGCAAACATGA 60.203 47.619 0.00 0.00 0.00 3.07
505 513 2.086869 CCGTCTTCAGGCAAACATGAT 58.913 47.619 0.00 0.00 0.00 2.45
506 514 2.159476 CCGTCTTCAGGCAAACATGATG 60.159 50.000 0.00 0.00 0.00 3.07
507 515 2.743664 CGTCTTCAGGCAAACATGATGA 59.256 45.455 0.00 0.00 0.00 2.92
508 516 3.425359 CGTCTTCAGGCAAACATGATGAC 60.425 47.826 13.49 13.49 42.63 3.06
509 517 3.503363 GTCTTCAGGCAAACATGATGACA 59.497 43.478 16.77 0.00 44.15 3.58
510 518 4.022935 GTCTTCAGGCAAACATGATGACAA 60.023 41.667 16.77 0.00 44.15 3.18
511 519 4.768448 TCTTCAGGCAAACATGATGACAAT 59.232 37.500 0.00 0.00 0.00 2.71
512 520 4.443913 TCAGGCAAACATGATGACAATG 57.556 40.909 0.00 0.00 0.00 2.82
513 521 3.193903 TCAGGCAAACATGATGACAATGG 59.806 43.478 0.00 0.00 0.00 3.16
514 522 3.056393 CAGGCAAACATGATGACAATGGT 60.056 43.478 0.00 0.00 0.00 3.55
515 523 3.056393 AGGCAAACATGATGACAATGGTG 60.056 43.478 0.00 0.00 0.00 4.17
516 524 3.306225 GGCAAACATGATGACAATGGTGT 60.306 43.478 0.00 0.00 42.10 4.16
517 525 3.676172 GCAAACATGATGACAATGGTGTG 59.324 43.478 0.00 0.00 38.41 3.82
518 526 4.559099 GCAAACATGATGACAATGGTGTGA 60.559 41.667 0.00 0.00 38.41 3.58
519 527 5.158494 CAAACATGATGACAATGGTGTGAG 58.842 41.667 0.00 0.00 38.41 3.51
520 528 4.290711 ACATGATGACAATGGTGTGAGA 57.709 40.909 0.00 0.00 38.41 3.27
521 529 4.005650 ACATGATGACAATGGTGTGAGAC 58.994 43.478 0.00 0.00 38.41 3.36
522 530 2.687370 TGATGACAATGGTGTGAGACG 58.313 47.619 0.00 0.00 38.41 4.18
523 531 2.298729 TGATGACAATGGTGTGAGACGA 59.701 45.455 0.00 0.00 38.41 4.20
524 532 3.055891 TGATGACAATGGTGTGAGACGAT 60.056 43.478 0.00 0.00 38.41 3.73
525 533 3.401033 TGACAATGGTGTGAGACGATT 57.599 42.857 0.00 0.00 38.41 3.34
526 534 4.529109 TGACAATGGTGTGAGACGATTA 57.471 40.909 0.00 0.00 38.41 1.75
527 535 5.084818 TGACAATGGTGTGAGACGATTAT 57.915 39.130 0.00 0.00 38.41 1.28
528 536 5.109210 TGACAATGGTGTGAGACGATTATC 58.891 41.667 0.00 0.00 38.41 1.75
529 537 4.112634 ACAATGGTGTGAGACGATTATCG 58.887 43.478 13.43 13.43 40.54 2.92
606 737 9.491675 TTTATCATGATTCACTTTGTTTTGCAT 57.508 25.926 14.65 0.00 0.00 3.96
661 854 0.179129 CAATGATGCAAAGGTCGGGC 60.179 55.000 0.00 0.00 0.00 6.13
672 865 0.036306 AGGTCGGGCGTTTCAATCTT 59.964 50.000 0.00 0.00 0.00 2.40
678 871 3.058501 TCGGGCGTTTCAATCTTCTTTTC 60.059 43.478 0.00 0.00 0.00 2.29
679 872 3.304391 CGGGCGTTTCAATCTTCTTTTCA 60.304 43.478 0.00 0.00 0.00 2.69
680 873 4.229876 GGGCGTTTCAATCTTCTTTTCAG 58.770 43.478 0.00 0.00 0.00 3.02
681 874 4.023193 GGGCGTTTCAATCTTCTTTTCAGA 60.023 41.667 0.00 0.00 0.00 3.27
712 905 1.442769 ACTCTTTGTATGGCACTGCG 58.557 50.000 0.00 0.00 0.00 5.18
761 2693 1.542915 CAATCTCTGCCCCACACAAAG 59.457 52.381 0.00 0.00 0.00 2.77
817 2749 3.244976 CCAAAGAACCATGACGCAATTC 58.755 45.455 0.00 0.00 0.00 2.17
901 2833 4.459089 GAGCGGCCACCTCAGTCC 62.459 72.222 13.95 0.00 0.00 3.85
928 2860 3.003763 ACACCGCCCCTCCTCTTC 61.004 66.667 0.00 0.00 0.00 2.87
933 2865 2.430610 CGCCCCTCCTCTTCCTCTG 61.431 68.421 0.00 0.00 0.00 3.35
964 2913 1.445582 CTCCCACACGCGTCCTAAC 60.446 63.158 9.86 0.00 0.00 2.34
974 2923 3.657537 CGTCCTAACGCAAGCAAAG 57.342 52.632 0.00 0.00 42.82 2.77
975 2924 0.452784 CGTCCTAACGCAAGCAAAGC 60.453 55.000 0.00 0.00 42.82 3.51
976 2925 0.875059 GTCCTAACGCAAGCAAAGCT 59.125 50.000 0.00 0.00 42.56 3.74
977 2926 1.135944 GTCCTAACGCAAGCAAAGCTC 60.136 52.381 0.00 0.00 38.25 4.09
978 2927 0.179215 CCTAACGCAAGCAAAGCTCG 60.179 55.000 0.00 0.00 38.25 5.03
979 2928 0.179215 CTAACGCAAGCAAAGCTCGG 60.179 55.000 5.34 0.00 38.25 4.63
980 2929 2.182614 TAACGCAAGCAAAGCTCGGC 62.183 55.000 1.50 1.50 38.25 5.54
982 2931 4.766088 GCAAGCAAAGCTCGGCGG 62.766 66.667 7.21 0.00 38.25 6.13
983 2932 3.049674 CAAGCAAAGCTCGGCGGA 61.050 61.111 7.21 0.00 38.25 5.54
984 2933 2.281484 AAGCAAAGCTCGGCGGAA 60.281 55.556 7.21 0.00 38.25 4.30
985 2934 1.896660 AAGCAAAGCTCGGCGGAAA 60.897 52.632 7.21 0.00 38.25 3.13
986 2935 1.856265 AAGCAAAGCTCGGCGGAAAG 61.856 55.000 7.21 0.00 38.25 2.62
1476 3425 2.769602 GGTACCTCATCCTCCAGGTA 57.230 55.000 4.06 0.00 41.55 3.08
1677 3626 1.999024 CGCTCTGCTTCTTCTTCTTCC 59.001 52.381 0.00 0.00 0.00 3.46
1680 3632 3.055891 GCTCTGCTTCTTCTTCTTCCTCT 60.056 47.826 0.00 0.00 0.00 3.69
1683 3635 4.020662 TCTGCTTCTTCTTCTTCCTCTTCC 60.021 45.833 0.00 0.00 0.00 3.46
1699 3651 2.438614 CCTCCTCTGCTCCGTCGA 60.439 66.667 0.00 0.00 0.00 4.20
1760 3712 2.517450 GCGTCGCCAAGAAGGATCG 61.517 63.158 5.75 0.00 41.22 3.69
1822 3776 2.555757 GTGTTAGCGTCGAGGGGTATAT 59.444 50.000 7.31 0.00 0.00 0.86
1827 3781 1.881973 GCGTCGAGGGGTATATGTGTA 59.118 52.381 7.31 0.00 0.00 2.90
1882 3839 6.770785 ACTCCTACTAAATTGTGTTTTGCTCA 59.229 34.615 0.00 0.00 0.00 4.26
1890 3847 9.848172 CTAAATTGTGTTTTGCTCATGTTTAAC 57.152 29.630 0.00 0.00 0.00 2.01
1912 3869 5.183228 ACTGTTGGTGAGGTATTTATTCCG 58.817 41.667 0.00 0.00 0.00 4.30
1961 3918 6.938030 ACCTGTTGTTACGATGGAATTAAAGA 59.062 34.615 0.00 0.00 0.00 2.52
1988 3946 3.830178 GGTTAATGCTGGGGTTACAAGTT 59.170 43.478 0.00 0.00 0.00 2.66
2000 3978 4.167268 GGTTACAAGTTGTTTTGTTGCGA 58.833 39.130 14.90 0.00 41.31 5.10
2076 4059 2.120312 GGAAGGGTCCTAGCTTAGCTT 58.880 52.381 13.44 0.00 41.24 3.74
2077 4060 3.306613 GGAAGGGTCCTAGCTTAGCTTA 58.693 50.000 13.44 0.00 41.24 3.09
2078 4061 3.322541 GGAAGGGTCCTAGCTTAGCTTAG 59.677 52.174 13.44 7.79 41.24 2.18
2079 4062 2.321719 AGGGTCCTAGCTTAGCTTAGC 58.678 52.381 16.83 16.83 40.44 3.09
2080 4063 1.345089 GGGTCCTAGCTTAGCTTAGCC 59.655 57.143 20.52 13.49 42.20 3.93
2287 4293 2.492012 CATCTATGGAAGCACCTCTGC 58.508 52.381 1.91 0.00 44.63 4.26
2288 4294 1.571955 TCTATGGAAGCACCTCTGCA 58.428 50.000 0.00 0.00 46.97 4.41
2289 4295 2.121948 TCTATGGAAGCACCTCTGCAT 58.878 47.619 0.00 0.00 46.97 3.96
2290 4296 3.308401 TCTATGGAAGCACCTCTGCATA 58.692 45.455 0.00 0.00 46.97 3.14
2291 4297 2.634815 ATGGAAGCACCTCTGCATAG 57.365 50.000 0.00 0.00 46.97 2.23
2292 4298 1.571955 TGGAAGCACCTCTGCATAGA 58.428 50.000 0.00 0.00 46.97 1.98
2293 4299 1.908619 TGGAAGCACCTCTGCATAGAA 59.091 47.619 0.00 0.00 46.97 2.10
2294 4300 2.305635 TGGAAGCACCTCTGCATAGAAA 59.694 45.455 0.00 0.00 46.97 2.52
2295 4301 3.244875 TGGAAGCACCTCTGCATAGAAAA 60.245 43.478 0.00 0.00 46.97 2.29
2296 4302 3.758554 GGAAGCACCTCTGCATAGAAAAA 59.241 43.478 0.00 0.00 46.97 1.94
2393 4406 1.222936 CTGGTGAGGAGTGGCCATC 59.777 63.158 9.72 7.72 40.02 3.51
2427 4442 7.573968 AAAGTATTCTGTAGCCATGGAATTC 57.426 36.000 18.40 3.05 31.89 2.17
2454 4469 6.146347 GTGCAGGAGAGGAATTATACGAAATC 59.854 42.308 0.00 0.00 0.00 2.17
2458 4473 6.014156 AGGAGAGGAATTATACGAAATCCCAG 60.014 42.308 0.00 0.00 0.00 4.45
2544 4561 0.247460 CAAGGTCTCCATGACGAGCA 59.753 55.000 13.38 0.00 46.24 4.26
2556 4573 2.002963 GACGAGCAGTGACGATTGCG 62.003 60.000 14.99 0.00 44.80 4.85
2575 4592 1.472201 CGTGATATCTGCAGCCTGTGT 60.472 52.381 9.47 0.00 0.00 3.72
2576 4593 1.938577 GTGATATCTGCAGCCTGTGTG 59.061 52.381 9.47 0.00 0.00 3.82
2577 4594 1.134310 TGATATCTGCAGCCTGTGTGG 60.134 52.381 9.47 0.00 39.35 4.17
2586 4603 4.850193 CCTGTGTGGCCCAGATTT 57.150 55.556 8.90 0.00 31.38 2.17
2587 4604 3.056213 CCTGTGTGGCCCAGATTTT 57.944 52.632 8.90 0.00 31.38 1.82
2588 4605 1.341080 CCTGTGTGGCCCAGATTTTT 58.659 50.000 8.90 0.00 31.38 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.833794 ACATCGTTGCACTACTGTTGT 58.166 42.857 0.00 0.00 0.00 3.32
7 8 3.874543 TGAAACATCGTTGCACTACTGTT 59.125 39.130 0.00 0.00 0.00 3.16
14 15 5.888412 AAAGAAATGAAACATCGTTGCAC 57.112 34.783 0.00 0.00 0.00 4.57
48 49 7.507304 CGTCCGACATATTGAAAATATACCAC 58.493 38.462 0.00 0.00 0.00 4.16
65 66 1.002201 TCAATTTTAGGGCGTCCGACA 59.998 47.619 0.00 0.00 38.33 4.35
67 68 2.476126 TTCAATTTTAGGGCGTCCGA 57.524 45.000 0.00 0.00 38.33 4.55
72 73 7.883229 ACTAACAAATTTCAATTTTAGGGCG 57.117 32.000 7.92 0.00 36.52 6.13
262 267 7.231317 ACAACACCTTGAACAAGATAATGACAT 59.769 33.333 14.99 0.00 40.79 3.06
283 288 3.056250 AGCACCACAACAAATTGACAACA 60.056 39.130 0.00 0.00 39.30 3.33
327 332 5.860182 ACAACGATTTTCATCTTGATTGCTG 59.140 36.000 0.00 0.00 0.00 4.41
379 384 5.330271 AGATAATAACGCAAGATTGTCGC 57.670 39.130 8.57 0.00 43.62 5.19
383 388 8.894409 TTGAACAAGATAATAACGCAAGATTG 57.106 30.769 0.00 0.00 43.62 2.67
384 389 8.184192 CCTTGAACAAGATAATAACGCAAGATT 58.816 33.333 14.99 0.00 40.79 2.40
385 390 7.679638 GCCTTGAACAAGATAATAACGCAAGAT 60.680 37.037 14.99 0.00 40.79 2.40
387 392 5.739161 GCCTTGAACAAGATAATAACGCAAG 59.261 40.000 14.99 0.00 40.79 4.01
389 394 4.201773 CGCCTTGAACAAGATAATAACGCA 60.202 41.667 14.99 0.00 40.79 5.24
390 395 4.201783 ACGCCTTGAACAAGATAATAACGC 60.202 41.667 14.99 7.00 40.79 4.84
393 401 6.653320 AGACAACGCCTTGAACAAGATAATAA 59.347 34.615 14.99 0.00 40.79 1.40
395 403 5.003804 AGACAACGCCTTGAACAAGATAAT 58.996 37.500 14.99 0.00 40.79 1.28
396 404 4.385825 AGACAACGCCTTGAACAAGATAA 58.614 39.130 14.99 0.00 40.79 1.75
398 406 2.851195 AGACAACGCCTTGAACAAGAT 58.149 42.857 14.99 0.00 40.79 2.40
403 411 2.870411 ACAAGTAGACAACGCCTTGAAC 59.130 45.455 2.26 0.00 38.11 3.18
406 414 2.612212 ACAACAAGTAGACAACGCCTTG 59.388 45.455 0.00 0.00 40.05 3.61
416 424 5.745312 AGACCATCATCACAACAAGTAGA 57.255 39.130 0.00 0.00 0.00 2.59
418 426 5.863965 TGAAGACCATCATCACAACAAGTA 58.136 37.500 0.00 0.00 0.00 2.24
419 427 4.717877 TGAAGACCATCATCACAACAAGT 58.282 39.130 0.00 0.00 0.00 3.16
420 428 5.892160 ATGAAGACCATCATCACAACAAG 57.108 39.130 0.00 0.00 35.07 3.16
421 429 5.535783 ACAATGAAGACCATCATCACAACAA 59.464 36.000 0.00 0.00 39.08 2.83
422 430 5.072055 ACAATGAAGACCATCATCACAACA 58.928 37.500 0.00 0.00 39.08 3.33
423 431 5.392380 GGACAATGAAGACCATCATCACAAC 60.392 44.000 0.00 0.00 39.08 3.32
424 432 4.701651 GGACAATGAAGACCATCATCACAA 59.298 41.667 0.00 0.00 39.08 3.33
425 433 4.264253 GGACAATGAAGACCATCATCACA 58.736 43.478 0.00 0.00 39.08 3.58
426 434 3.310774 CGGACAATGAAGACCATCATCAC 59.689 47.826 0.00 0.00 39.08 3.06
427 435 3.534554 CGGACAATGAAGACCATCATCA 58.465 45.455 0.00 0.00 39.08 3.07
428 436 2.874701 CCGGACAATGAAGACCATCATC 59.125 50.000 0.00 0.00 39.08 2.92
429 437 2.239654 ACCGGACAATGAAGACCATCAT 59.760 45.455 9.46 0.00 41.74 2.45
430 438 1.628340 ACCGGACAATGAAGACCATCA 59.372 47.619 9.46 0.00 33.53 3.07
431 439 2.280628 GACCGGACAATGAAGACCATC 58.719 52.381 9.46 0.00 33.53 3.51
432 440 1.628340 TGACCGGACAATGAAGACCAT 59.372 47.619 9.46 0.00 36.99 3.55
433 441 1.001974 CTGACCGGACAATGAAGACCA 59.998 52.381 9.46 0.00 0.00 4.02
434 442 1.726853 CTGACCGGACAATGAAGACC 58.273 55.000 9.46 0.00 0.00 3.85
435 443 1.079503 GCTGACCGGACAATGAAGAC 58.920 55.000 9.46 0.00 0.00 3.01
436 444 0.684535 TGCTGACCGGACAATGAAGA 59.315 50.000 9.46 0.00 0.00 2.87
437 445 1.522668 TTGCTGACCGGACAATGAAG 58.477 50.000 9.46 0.00 0.00 3.02
438 446 1.606668 GTTTGCTGACCGGACAATGAA 59.393 47.619 9.46 0.00 0.00 2.57
439 447 1.234821 GTTTGCTGACCGGACAATGA 58.765 50.000 9.46 0.00 0.00 2.57
440 448 0.950836 TGTTTGCTGACCGGACAATG 59.049 50.000 9.46 0.00 0.00 2.82
441 449 1.686355 TTGTTTGCTGACCGGACAAT 58.314 45.000 9.46 0.00 0.00 2.71
442 450 1.686355 ATTGTTTGCTGACCGGACAA 58.314 45.000 9.46 6.79 35.04 3.18
443 451 2.552599 TATTGTTTGCTGACCGGACA 57.447 45.000 9.46 7.70 0.00 4.02
444 452 3.500680 TCTTTATTGTTTGCTGACCGGAC 59.499 43.478 9.46 1.07 0.00 4.79
445 453 3.745799 TCTTTATTGTTTGCTGACCGGA 58.254 40.909 9.46 0.00 0.00 5.14
446 454 4.155826 TCATCTTTATTGTTTGCTGACCGG 59.844 41.667 0.00 0.00 0.00 5.28
447 455 5.295431 TCATCTTTATTGTTTGCTGACCG 57.705 39.130 0.00 0.00 0.00 4.79
448 456 7.945033 TTTTCATCTTTATTGTTTGCTGACC 57.055 32.000 0.00 0.00 0.00 4.02
449 457 8.650714 GGATTTTCATCTTTATTGTTTGCTGAC 58.349 33.333 0.00 0.00 0.00 3.51
450 458 7.818930 GGGATTTTCATCTTTATTGTTTGCTGA 59.181 33.333 0.00 0.00 0.00 4.26
451 459 7.820872 AGGGATTTTCATCTTTATTGTTTGCTG 59.179 33.333 0.00 0.00 0.00 4.41
452 460 7.820872 CAGGGATTTTCATCTTTATTGTTTGCT 59.179 33.333 0.00 0.00 0.00 3.91
453 461 7.603784 ACAGGGATTTTCATCTTTATTGTTTGC 59.396 33.333 0.00 0.00 0.00 3.68
456 464 9.308000 TGTACAGGGATTTTCATCTTTATTGTT 57.692 29.630 0.00 0.00 0.00 2.83
457 465 8.877864 TGTACAGGGATTTTCATCTTTATTGT 57.122 30.769 0.00 0.00 0.00 2.71
458 466 9.177608 TCTGTACAGGGATTTTCATCTTTATTG 57.822 33.333 22.48 0.00 0.00 1.90
459 467 9.178758 GTCTGTACAGGGATTTTCATCTTTATT 57.821 33.333 22.48 0.00 0.00 1.40
460 468 7.775561 GGTCTGTACAGGGATTTTCATCTTTAT 59.224 37.037 22.48 0.00 0.00 1.40
461 469 7.110155 GGTCTGTACAGGGATTTTCATCTTTA 58.890 38.462 22.48 0.00 0.00 1.85
462 470 5.946377 GGTCTGTACAGGGATTTTCATCTTT 59.054 40.000 22.48 0.00 0.00 2.52
463 471 5.501156 GGTCTGTACAGGGATTTTCATCTT 58.499 41.667 22.48 0.00 0.00 2.40
464 472 4.383118 CGGTCTGTACAGGGATTTTCATCT 60.383 45.833 22.48 0.00 0.00 2.90
465 473 3.871594 CGGTCTGTACAGGGATTTTCATC 59.128 47.826 22.48 0.16 0.00 2.92
466 474 3.263425 ACGGTCTGTACAGGGATTTTCAT 59.737 43.478 22.48 0.00 0.00 2.57
467 475 2.635915 ACGGTCTGTACAGGGATTTTCA 59.364 45.455 22.48 0.00 0.00 2.69
468 476 3.056035 AGACGGTCTGTACAGGGATTTTC 60.056 47.826 22.48 11.41 0.00 2.29
469 477 2.904434 AGACGGTCTGTACAGGGATTTT 59.096 45.455 22.48 2.94 0.00 1.82
470 478 2.537143 AGACGGTCTGTACAGGGATTT 58.463 47.619 22.48 4.00 0.00 2.17
471 479 2.233305 AGACGGTCTGTACAGGGATT 57.767 50.000 22.48 5.43 0.00 3.01
472 480 2.100989 GAAGACGGTCTGTACAGGGAT 58.899 52.381 22.48 6.31 0.00 3.85
473 481 1.202964 TGAAGACGGTCTGTACAGGGA 60.203 52.381 22.48 1.52 0.00 4.20
474 482 1.202582 CTGAAGACGGTCTGTACAGGG 59.797 57.143 22.48 14.13 0.00 4.45
475 483 1.202582 CCTGAAGACGGTCTGTACAGG 59.797 57.143 27.90 27.90 37.07 4.00
476 484 1.402984 GCCTGAAGACGGTCTGTACAG 60.403 57.143 17.17 17.17 0.00 2.74
477 485 0.601558 GCCTGAAGACGGTCTGTACA 59.398 55.000 12.12 11.25 0.00 2.90
478 486 0.601558 TGCCTGAAGACGGTCTGTAC 59.398 55.000 12.12 7.28 0.00 2.90
479 487 1.334160 TTGCCTGAAGACGGTCTGTA 58.666 50.000 12.12 3.01 0.00 2.74
480 488 0.468226 TTTGCCTGAAGACGGTCTGT 59.532 50.000 12.12 2.01 0.00 3.41
481 489 0.868406 GTTTGCCTGAAGACGGTCTG 59.132 55.000 12.12 0.00 0.00 3.51
482 490 0.468226 TGTTTGCCTGAAGACGGTCT 59.532 50.000 4.45 4.45 0.00 3.85
483 491 1.197721 CATGTTTGCCTGAAGACGGTC 59.802 52.381 0.00 0.00 0.00 4.79
484 492 1.202758 TCATGTTTGCCTGAAGACGGT 60.203 47.619 0.00 0.00 0.00 4.83
485 493 1.522668 TCATGTTTGCCTGAAGACGG 58.477 50.000 0.00 0.00 0.00 4.79
486 494 2.743664 TCATCATGTTTGCCTGAAGACG 59.256 45.455 0.00 0.00 0.00 4.18
487 495 3.503363 TGTCATCATGTTTGCCTGAAGAC 59.497 43.478 0.00 0.00 37.97 3.01
488 496 3.753815 TGTCATCATGTTTGCCTGAAGA 58.246 40.909 0.00 0.00 0.00 2.87
489 497 4.508461 TTGTCATCATGTTTGCCTGAAG 57.492 40.909 0.00 0.00 0.00 3.02
490 498 4.322123 CCATTGTCATCATGTTTGCCTGAA 60.322 41.667 0.00 0.00 0.00 3.02
491 499 3.193903 CCATTGTCATCATGTTTGCCTGA 59.806 43.478 0.00 0.00 0.00 3.86
492 500 3.056393 ACCATTGTCATCATGTTTGCCTG 60.056 43.478 0.00 0.00 0.00 4.85
493 501 3.056393 CACCATTGTCATCATGTTTGCCT 60.056 43.478 0.00 0.00 0.00 4.75
494 502 3.255725 CACCATTGTCATCATGTTTGCC 58.744 45.455 0.00 0.00 0.00 4.52
495 503 3.676172 CACACCATTGTCATCATGTTTGC 59.324 43.478 0.00 0.00 31.66 3.68
496 504 5.048573 TCTCACACCATTGTCATCATGTTTG 60.049 40.000 0.00 0.00 31.66 2.93
497 505 5.048504 GTCTCACACCATTGTCATCATGTTT 60.049 40.000 0.00 0.00 31.66 2.83
498 506 4.456911 GTCTCACACCATTGTCATCATGTT 59.543 41.667 0.00 0.00 31.66 2.71
499 507 4.005650 GTCTCACACCATTGTCATCATGT 58.994 43.478 0.00 0.00 31.66 3.21
500 508 3.063045 CGTCTCACACCATTGTCATCATG 59.937 47.826 0.00 0.00 31.66 3.07
501 509 3.055891 TCGTCTCACACCATTGTCATCAT 60.056 43.478 0.00 0.00 31.66 2.45
502 510 2.298729 TCGTCTCACACCATTGTCATCA 59.701 45.455 0.00 0.00 31.66 3.07
503 511 2.959516 TCGTCTCACACCATTGTCATC 58.040 47.619 0.00 0.00 31.66 2.92
504 512 3.616956 ATCGTCTCACACCATTGTCAT 57.383 42.857 0.00 0.00 31.66 3.06
505 513 3.401033 AATCGTCTCACACCATTGTCA 57.599 42.857 0.00 0.00 31.66 3.58
506 514 4.207224 CGATAATCGTCTCACACCATTGTC 59.793 45.833 0.00 0.00 34.72 3.18
507 515 4.112634 CGATAATCGTCTCACACCATTGT 58.887 43.478 0.00 0.00 34.72 2.71
508 516 3.490896 CCGATAATCGTCTCACACCATTG 59.509 47.826 0.00 0.00 38.40 2.82
509 517 3.383505 TCCGATAATCGTCTCACACCATT 59.616 43.478 0.00 0.00 38.40 3.16
510 518 2.956333 TCCGATAATCGTCTCACACCAT 59.044 45.455 0.00 0.00 38.40 3.55
511 519 2.371306 TCCGATAATCGTCTCACACCA 58.629 47.619 0.00 0.00 38.40 4.17
512 520 3.066342 TCTTCCGATAATCGTCTCACACC 59.934 47.826 0.00 0.00 38.40 4.16
513 521 4.288670 TCTTCCGATAATCGTCTCACAC 57.711 45.455 0.00 0.00 38.40 3.82
514 522 4.398358 ACTTCTTCCGATAATCGTCTCACA 59.602 41.667 0.00 0.00 38.40 3.58
515 523 4.922719 ACTTCTTCCGATAATCGTCTCAC 58.077 43.478 0.00 0.00 38.40 3.51
516 524 4.260661 CGACTTCTTCCGATAATCGTCTCA 60.261 45.833 0.00 0.00 38.40 3.27
517 525 4.025061 TCGACTTCTTCCGATAATCGTCTC 60.025 45.833 0.00 0.00 38.40 3.36
518 526 3.875727 TCGACTTCTTCCGATAATCGTCT 59.124 43.478 0.00 0.00 38.40 4.18
519 527 3.967470 GTCGACTTCTTCCGATAATCGTC 59.033 47.826 8.70 0.00 38.40 4.20
520 528 3.626670 AGTCGACTTCTTCCGATAATCGT 59.373 43.478 13.58 0.00 38.40 3.73
521 529 4.212213 AGTCGACTTCTTCCGATAATCG 57.788 45.455 13.58 0.00 40.07 3.34
522 530 6.727215 ACTAAGTCGACTTCTTCCGATAATC 58.273 40.000 32.86 0.00 37.40 1.75
523 531 6.696441 ACTAAGTCGACTTCTTCCGATAAT 57.304 37.500 32.86 8.61 37.40 1.28
524 532 7.798596 ATACTAAGTCGACTTCTTCCGATAA 57.201 36.000 32.86 12.31 37.40 1.75
525 533 7.798596 AATACTAAGTCGACTTCTTCCGATA 57.201 36.000 32.86 13.03 37.40 2.92
526 534 6.696441 AATACTAAGTCGACTTCTTCCGAT 57.304 37.500 32.86 15.90 37.40 4.18
527 535 6.259608 CCTAATACTAAGTCGACTTCTTCCGA 59.740 42.308 32.86 14.48 37.40 4.55
528 536 6.038050 ACCTAATACTAAGTCGACTTCTTCCG 59.962 42.308 32.86 18.66 37.40 4.30
529 537 7.148103 ACACCTAATACTAAGTCGACTTCTTCC 60.148 40.741 32.86 0.00 37.40 3.46
578 709 9.801714 GCAAAACAAAGTGAATCATGATAAAAG 57.198 29.630 9.04 0.00 0.00 2.27
638 800 2.424601 CCGACCTTTGCATCATTGTGAT 59.575 45.455 0.00 0.00 37.65 3.06
639 801 1.811965 CCGACCTTTGCATCATTGTGA 59.188 47.619 0.00 0.00 0.00 3.58
640 802 1.135315 CCCGACCTTTGCATCATTGTG 60.135 52.381 0.00 0.00 0.00 3.33
641 803 1.176527 CCCGACCTTTGCATCATTGT 58.823 50.000 0.00 0.00 0.00 2.71
642 804 0.179129 GCCCGACCTTTGCATCATTG 60.179 55.000 0.00 0.00 0.00 2.82
643 805 1.656818 CGCCCGACCTTTGCATCATT 61.657 55.000 0.00 0.00 0.00 2.57
644 806 2.114670 CGCCCGACCTTTGCATCAT 61.115 57.895 0.00 0.00 0.00 2.45
646 808 1.862602 AAACGCCCGACCTTTGCATC 61.863 55.000 0.00 0.00 0.00 3.91
647 809 1.862602 GAAACGCCCGACCTTTGCAT 61.863 55.000 0.00 0.00 0.00 3.96
648 810 2.517402 AAACGCCCGACCTTTGCA 60.517 55.556 0.00 0.00 0.00 4.08
650 812 0.596082 ATTGAAACGCCCGACCTTTG 59.404 50.000 0.00 0.00 0.00 2.77
651 813 0.879090 GATTGAAACGCCCGACCTTT 59.121 50.000 0.00 0.00 0.00 3.11
652 814 0.036306 AGATTGAAACGCCCGACCTT 59.964 50.000 0.00 0.00 0.00 3.50
656 849 2.178912 AAGAAGATTGAAACGCCCGA 57.821 45.000 0.00 0.00 0.00 5.14
693 886 1.270839 ACGCAGTGCCATACAAAGAGT 60.271 47.619 10.11 0.00 42.51 3.24
694 887 1.442769 ACGCAGTGCCATACAAAGAG 58.557 50.000 10.11 0.00 42.51 2.85
695 888 3.623848 ACGCAGTGCCATACAAAGA 57.376 47.368 10.11 0.00 42.51 2.52
712 905 5.009010 AGGCGATCATGTTTAAATCATGGAC 59.991 40.000 20.71 16.04 41.79 4.02
779 2711 0.178975 TGGTGGGTCATCGCCTTTTT 60.179 50.000 0.00 0.00 38.11 1.94
787 2719 2.286365 TGGTTCTTTGGTGGGTCATC 57.714 50.000 0.00 0.00 0.00 2.92
817 2749 9.428363 TCGTGATTTCCGAAATAAAATAAATCG 57.572 29.630 6.34 0.00 36.56 3.34
895 2827 1.416401 GGTGTCTGGTTGAAGGACTGA 59.584 52.381 0.00 0.00 0.00 3.41
901 2833 1.966451 GGGCGGTGTCTGGTTGAAG 60.966 63.158 0.00 0.00 0.00 3.02
923 2855 2.301346 GAGAGGAGAGCAGAGGAAGAG 58.699 57.143 0.00 0.00 0.00 2.85
928 2860 0.552848 AGAGGAGAGGAGAGCAGAGG 59.447 60.000 0.00 0.00 0.00 3.69
933 2865 0.755327 GTGGGAGAGGAGAGGAGAGC 60.755 65.000 0.00 0.00 0.00 4.09
1212 3161 3.226429 GAGCACGGTGGAGAGCACA 62.226 63.158 10.60 0.00 0.00 4.57
1476 3425 4.430765 ACGCGGCCGTCGATCTTT 62.431 61.111 36.24 18.63 46.39 2.52
1657 3606 1.999024 GGAAGAAGAAGAAGCAGAGCG 59.001 52.381 0.00 0.00 0.00 5.03
1677 3626 0.682855 ACGGAGCAGAGGAGGAAGAG 60.683 60.000 0.00 0.00 0.00 2.85
1680 3632 2.046864 CGACGGAGCAGAGGAGGAA 61.047 63.158 0.00 0.00 0.00 3.36
1683 3635 2.795297 GTCGACGGAGCAGAGGAG 59.205 66.667 0.00 0.00 0.00 3.69
1699 3651 2.205243 GAAACCTACCTCGTCGCCGT 62.205 60.000 0.00 0.00 35.01 5.68
1705 3657 0.037605 CCGCAAGAAACCTACCTCGT 60.038 55.000 0.00 0.00 43.02 4.18
1746 3698 1.002366 CTTGACGATCCTTCTTGGCG 58.998 55.000 0.00 0.00 35.26 5.69
1756 3708 2.388347 GCCTTCAGCCTTGACGATC 58.612 57.895 0.00 0.00 34.35 3.69
1777 3729 0.915387 TACCACCATGTACCACCCCC 60.915 60.000 0.00 0.00 0.00 5.40
1882 3839 7.833285 AAATACCTCACCAACAGTTAAACAT 57.167 32.000 0.00 0.00 0.00 2.71
1890 3847 4.035208 GCGGAATAAATACCTCACCAACAG 59.965 45.833 0.00 0.00 0.00 3.16
1961 3918 4.841246 TGTAACCCCAGCATTAACCATTTT 59.159 37.500 0.00 0.00 0.00 1.82
1988 3946 4.789481 GCTCTCTCAAATCGCAACAAAACA 60.789 41.667 0.00 0.00 0.00 2.83
2000 3978 5.127682 ACCACAACAAAAAGCTCTCTCAAAT 59.872 36.000 0.00 0.00 0.00 2.32
2096 4079 3.548770 TCGACGATACTATCTGGTTGGT 58.451 45.455 0.00 0.00 0.00 3.67
2097 4080 4.215613 TCATCGACGATACTATCTGGTTGG 59.784 45.833 10.57 0.00 0.00 3.77
2098 4081 5.358298 TCATCGACGATACTATCTGGTTG 57.642 43.478 10.57 0.00 0.00 3.77
2099 4082 5.705905 TCATCATCGACGATACTATCTGGTT 59.294 40.000 10.57 0.00 0.00 3.67
2346 4352 1.257743 TCACCACTACTCTGCCACTC 58.742 55.000 0.00 0.00 0.00 3.51
2351 4357 2.751166 ACACATCACCACTACTCTGC 57.249 50.000 0.00 0.00 0.00 4.26
2405 4418 6.126652 ACTGAATTCCATGGCTACAGAATACT 60.127 38.462 23.93 7.95 0.00 2.12
2406 4419 6.017605 CACTGAATTCCATGGCTACAGAATAC 60.018 42.308 23.93 5.01 0.00 1.89
2417 4432 2.022195 CTCCTGCACTGAATTCCATGG 58.978 52.381 4.97 4.97 0.00 3.66
2420 4435 1.280133 CCTCTCCTGCACTGAATTCCA 59.720 52.381 2.27 0.00 0.00 3.53
2427 4442 4.038042 TCGTATAATTCCTCTCCTGCACTG 59.962 45.833 0.00 0.00 0.00 3.66
2458 4473 0.404040 TGGAAGTTCCATGGGACACC 59.596 55.000 25.54 24.75 42.67 4.16
2518 4533 0.679002 CATGGAGACCTTGCACCTGG 60.679 60.000 0.00 0.00 0.00 4.45
2556 4573 1.938577 CACACAGGCTGCAGATATCAC 59.061 52.381 20.43 0.00 0.00 3.06
2588 4605 2.838202 TGGGCCACACCTTGTTTAAAAA 59.162 40.909 0.00 0.00 39.10 1.94
2589 4606 2.432510 CTGGGCCACACCTTGTTTAAAA 59.567 45.455 0.00 0.00 39.10 1.52
2590 4607 2.035632 CTGGGCCACACCTTGTTTAAA 58.964 47.619 0.00 0.00 39.10 1.52
2591 4608 1.215673 TCTGGGCCACACCTTGTTTAA 59.784 47.619 0.00 0.00 39.10 1.52
2592 4609 0.847373 TCTGGGCCACACCTTGTTTA 59.153 50.000 0.00 0.00 39.10 2.01
2593 4610 0.188342 ATCTGGGCCACACCTTGTTT 59.812 50.000 0.00 0.00 39.10 2.83
2594 4611 0.188342 AATCTGGGCCACACCTTGTT 59.812 50.000 0.00 0.00 39.10 2.83
2595 4612 0.540365 CAATCTGGGCCACACCTTGT 60.540 55.000 0.00 0.00 39.10 3.16
2596 4613 1.880819 GCAATCTGGGCCACACCTTG 61.881 60.000 0.00 5.21 39.10 3.61
2597 4614 1.607467 GCAATCTGGGCCACACCTT 60.607 57.895 0.00 0.00 39.10 3.50
2598 4615 2.036256 GCAATCTGGGCCACACCT 59.964 61.111 0.00 0.00 39.10 4.00
2599 4616 3.443045 CGCAATCTGGGCCACACC 61.443 66.667 0.00 0.00 37.93 4.16
2600 4617 0.958382 TAACGCAATCTGGGCCACAC 60.958 55.000 0.00 0.00 33.10 3.82
2601 4618 0.034574 ATAACGCAATCTGGGCCACA 60.035 50.000 0.00 0.00 33.10 4.17
2602 4619 1.961793 TATAACGCAATCTGGGCCAC 58.038 50.000 0.00 0.00 33.10 5.01


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

AutoCloner maintained by Alex Coulton.