Multiple sequence alignment - TraesCS4D01G324700

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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 TraesCS4D01G324700 chr4D 100.000 2837 0 0 1 2837 485378438 485381274 0.000000e+00 5240.0
1 TraesCS4D01G324700 chr5A 93.176 2125 93 13 725 2834 666225506 666227593 0.000000e+00 3073.0
2 TraesCS4D01G324700 chr4B 91.708 808 53 8 765 1560 618587517 618588322 0.000000e+00 1109.0
3 TraesCS4D01G324700 chr4B 86.404 456 49 8 1 451 618587073 618587520 1.180000e-133 486.0
4 TraesCS4D01G324700 chr4B 84.906 371 52 4 2470 2837 668757324 668757693 3.450000e-99 372.0
5 TraesCS4D01G324700 chr4B 87.619 315 34 5 457 768 63795072 63794760 7.470000e-96 361.0
6 TraesCS4D01G324700 chr4B 88.421 190 11 2 1621 1799 618588335 618588524 4.760000e-53 219.0
7 TraesCS4D01G324700 chr4B 93.636 110 7 0 1860 1969 618588531 618588640 6.290000e-37 165.0
8 TraesCS4D01G324700 chr5B 81.228 863 131 25 1999 2837 656711785 656712640 0.000000e+00 667.0
9 TraesCS4D01G324700 chr5B 75.812 616 124 19 2243 2837 446878174 446878785 3.580000e-74 289.0
10 TraesCS4D01G324700 chr5B 71.220 549 104 33 2249 2773 188016425 188016943 3.890000e-14 89.8
11 TraesCS4D01G324700 chr2B 81.997 711 115 12 2136 2837 186944872 186944166 2.430000e-165 592.0
12 TraesCS4D01G324700 chr5D 88.462 312 32 4 456 765 127069192 127068883 9.600000e-100 374.0
13 TraesCS4D01G324700 chr2A 88.254 315 33 4 456 768 20010721 20010409 9.600000e-100 374.0
14 TraesCS4D01G324700 chr2A 82.514 366 60 4 2470 2835 42338558 42338919 4.560000e-83 318.0
15 TraesCS4D01G324700 chr3D 88.141 312 32 5 456 765 301532901 301533209 1.610000e-97 366.0
16 TraesCS4D01G324700 chr7D 87.898 314 32 5 456 765 476826619 476826930 5.780000e-97 364.0
17 TraesCS4D01G324700 chr6D 87.156 327 35 7 443 765 459039884 459040207 5.780000e-97 364.0
18 TraesCS4D01G324700 chr2D 87.898 314 31 7 456 765 256866042 256866352 2.080000e-96 363.0
19 TraesCS4D01G324700 chr2D 81.279 438 70 8 2406 2835 37476099 37476532 7.520000e-91 344.0
20 TraesCS4D01G324700 chr1B 87.342 316 34 2 450 765 464102871 464103180 9.670000e-95 357.0
21 TraesCS4D01G324700 chr1B 87.302 315 35 5 457 768 536041823 536042135 3.480000e-94 355.0
22 TraesCS4D01G324700 chr3A 78.094 598 101 19 2244 2816 700742461 700743053 4.500000e-93 351.0
23 TraesCS4D01G324700 chr3A 76.797 612 113 21 2249 2837 685361725 685361120 1.640000e-82 316.0
24 TraesCS4D01G324700 chr6A 77.087 611 112 20 2249 2837 563499609 563500213 7.580000e-86 327.0
25 TraesCS4D01G324700 chr1A 79.115 407 73 11 2134 2532 427456268 427456670 1.300000e-68 270.0
26 TraesCS4D01G324700 chr3B 85.417 192 26 2 2244 2435 64279523 64279334 6.200000e-47 198.0


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 TraesCS4D01G324700 chr4D 485378438 485381274 2836 False 5240.00 5240 100.00000 1 2837 1 chr4D.!!$F1 2836
1 TraesCS4D01G324700 chr5A 666225506 666227593 2087 False 3073.00 3073 93.17600 725 2834 1 chr5A.!!$F1 2109
2 TraesCS4D01G324700 chr4B 618587073 618588640 1567 False 494.75 1109 90.04225 1 1969 4 chr4B.!!$F2 1968
3 TraesCS4D01G324700 chr5B 656711785 656712640 855 False 667.00 667 81.22800 1999 2837 1 chr5B.!!$F3 838
4 TraesCS4D01G324700 chr5B 446878174 446878785 611 False 289.00 289 75.81200 2243 2837 1 chr5B.!!$F2 594
5 TraesCS4D01G324700 chr2B 186944166 186944872 706 True 592.00 592 81.99700 2136 2837 1 chr2B.!!$R1 701
6 TraesCS4D01G324700 chr3A 700742461 700743053 592 False 351.00 351 78.09400 2244 2816 1 chr3A.!!$F1 572
7 TraesCS4D01G324700 chr3A 685361120 685361725 605 True 316.00 316 76.79700 2249 2837 1 chr3A.!!$R1 588
8 TraesCS4D01G324700 chr6A 563499609 563500213 604 False 327.00 327 77.08700 2249 2837 1 chr6A.!!$F1 588

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
468 472 0.036010 AGACCTCTTCCAATGCACGG 60.036 55.0 0.00 0.0 0.0 4.94 F
525 529 0.108186 GCAACTAAAGCCCCCAATGC 60.108 55.0 0.00 0.0 0.0 3.56 F
531 535 0.339510 AAAGCCCCCAATGCATAGGT 59.660 50.0 13.23 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1636 1.187974 TACATGTACGGTGGTGGAGG 58.812 55.0 0.08 0.00 0.00 4.30 R
1803 1832 1.358877 CATCGTTGAATCCAGCGTCA 58.641 50.0 0.00 0.00 45.35 4.35 R
2228 2276 1.482621 AAGCATGTATCAGACGCGCG 61.483 55.0 30.96 30.96 34.00 6.86 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
62 63 4.033358 CACGAGCATCTTGGATGTCTAAAC 59.967 45.833 8.93 0.00 29.58 2.01
65 66 5.295292 CGAGCATCTTGGATGTCTAAACAAT 59.705 40.000 8.93 0.00 39.30 2.71
67 68 7.011389 CGAGCATCTTGGATGTCTAAACAATTA 59.989 37.037 8.93 0.00 39.30 1.40
69 70 9.023962 AGCATCTTGGATGTCTAAACAATTAAA 57.976 29.630 8.93 0.00 39.30 1.52
70 71 9.294030 GCATCTTGGATGTCTAAACAATTAAAG 57.706 33.333 8.93 0.00 39.30 1.85
122 124 3.416277 CGAGTTTATTGTTCACATGCGG 58.584 45.455 0.00 0.00 0.00 5.69
125 127 3.440173 AGTTTATTGTTCACATGCGGGAG 59.560 43.478 0.00 0.00 0.00 4.30
140 142 1.759881 GGAGCATATGAGCCTGGCT 59.240 57.895 23.64 23.64 43.88 4.75
167 170 0.817013 CTGCTCTCGCTCTTCTTCCT 59.183 55.000 0.00 0.00 36.97 3.36
192 195 8.768957 TCTTCTATTATATTCACATGCAGCTC 57.231 34.615 0.00 0.00 0.00 4.09
197 200 2.039818 ATTCACATGCAGCTCTCCTG 57.960 50.000 0.00 0.00 44.67 3.86
277 280 4.497291 TGAACATAGGGTGTATGGGAAC 57.503 45.455 0.00 0.00 41.14 3.62
287 291 4.270008 GGTGTATGGGAACTAGTTGCAAT 58.730 43.478 25.90 22.72 32.17 3.56
296 300 7.957002 TGGGAACTAGTTGCAATAAAAATTGA 58.043 30.769 25.90 0.00 33.55 2.57
346 350 6.835488 ACTACATTCCTGGATGTTGCATTAAT 59.165 34.615 14.17 0.00 40.54 1.40
376 380 3.915437 AGTGGGTTTCAAGTTAATGCG 57.085 42.857 0.00 0.00 0.00 4.73
378 382 2.554893 GTGGGTTTCAAGTTAATGCGGA 59.445 45.455 0.00 0.00 0.00 5.54
386 390 4.181578 TCAAGTTAATGCGGAGTAAGAGC 58.818 43.478 0.00 0.00 0.00 4.09
408 412 5.356751 AGCGGTTGCATTAATTTAGTCATGA 59.643 36.000 0.00 0.00 46.23 3.07
412 416 7.112009 CGGTTGCATTAATTTAGTCATGAATCG 59.888 37.037 0.00 0.00 0.00 3.34
413 417 7.379529 GGTTGCATTAATTTAGTCATGAATCGG 59.620 37.037 0.00 0.00 0.00 4.18
434 438 4.873259 CGGAAACAAAGAAACAAACCCAAT 59.127 37.500 0.00 0.00 0.00 3.16
436 440 6.535508 CGGAAACAAAGAAACAAACCCAATAA 59.464 34.615 0.00 0.00 0.00 1.40
437 441 7.225734 CGGAAACAAAGAAACAAACCCAATAAT 59.774 33.333 0.00 0.00 0.00 1.28
439 443 6.859420 ACAAAGAAACAAACCCAATAATGC 57.141 33.333 0.00 0.00 0.00 3.56
447 451 3.625649 AACCCAATAATGCGGCATTTT 57.374 38.095 30.74 21.28 35.54 1.82
448 452 2.903798 ACCCAATAATGCGGCATTTTG 58.096 42.857 30.74 27.86 35.54 2.44
449 453 2.499289 ACCCAATAATGCGGCATTTTGA 59.501 40.909 30.74 15.49 35.54 2.69
450 454 3.125316 CCCAATAATGCGGCATTTTGAG 58.875 45.455 30.74 20.23 35.54 3.02
451 455 3.181477 CCCAATAATGCGGCATTTTGAGA 60.181 43.478 30.74 14.76 35.54 3.27
452 456 3.798337 CCAATAATGCGGCATTTTGAGAC 59.202 43.478 30.74 0.00 35.54 3.36
453 457 3.715628 ATAATGCGGCATTTTGAGACC 57.284 42.857 30.74 0.00 35.54 3.85
454 458 1.549203 AATGCGGCATTTTGAGACCT 58.451 45.000 21.87 0.00 28.76 3.85
455 459 1.098050 ATGCGGCATTTTGAGACCTC 58.902 50.000 10.23 0.00 0.00 3.85
456 460 0.036732 TGCGGCATTTTGAGACCTCT 59.963 50.000 0.00 0.00 0.00 3.69
457 461 1.168714 GCGGCATTTTGAGACCTCTT 58.831 50.000 0.00 0.00 0.00 2.85
458 462 1.131315 GCGGCATTTTGAGACCTCTTC 59.869 52.381 0.00 0.00 0.00 2.87
459 463 1.740025 CGGCATTTTGAGACCTCTTCC 59.260 52.381 0.00 0.00 0.00 3.46
460 464 2.795329 GGCATTTTGAGACCTCTTCCA 58.205 47.619 0.00 0.00 0.00 3.53
461 465 3.157087 GGCATTTTGAGACCTCTTCCAA 58.843 45.455 0.00 0.00 0.00 3.53
462 466 3.766051 GGCATTTTGAGACCTCTTCCAAT 59.234 43.478 0.00 0.00 0.00 3.16
463 467 4.381292 GGCATTTTGAGACCTCTTCCAATG 60.381 45.833 0.00 3.64 0.00 2.82
464 468 4.741342 CATTTTGAGACCTCTTCCAATGC 58.259 43.478 0.00 0.00 0.00 3.56
465 469 3.507162 TTTGAGACCTCTTCCAATGCA 57.493 42.857 0.00 0.00 0.00 3.96
466 470 2.479566 TGAGACCTCTTCCAATGCAC 57.520 50.000 0.00 0.00 0.00 4.57
467 471 1.338105 TGAGACCTCTTCCAATGCACG 60.338 52.381 0.00 0.00 0.00 5.34
468 472 0.036010 AGACCTCTTCCAATGCACGG 60.036 55.000 0.00 0.00 0.00 4.94
469 473 1.002134 ACCTCTTCCAATGCACGGG 60.002 57.895 4.22 1.63 0.00 5.28
470 474 1.002134 CCTCTTCCAATGCACGGGT 60.002 57.895 4.22 0.00 0.00 5.28
471 475 1.308069 CCTCTTCCAATGCACGGGTG 61.308 60.000 4.22 0.00 0.00 4.61
481 485 4.509756 CACGGGTGCTCAGATGAG 57.490 61.111 5.45 5.45 44.75 2.90
482 486 1.153489 CACGGGTGCTCAGATGAGG 60.153 63.158 11.63 0.00 42.29 3.86
483 487 1.610673 ACGGGTGCTCAGATGAGGT 60.611 57.895 11.63 0.00 42.29 3.85
484 488 1.153489 CGGGTGCTCAGATGAGGTG 60.153 63.158 11.63 0.00 42.29 4.00
485 489 1.451028 GGGTGCTCAGATGAGGTGC 60.451 63.158 11.63 0.00 42.29 5.01
486 490 1.601171 GGTGCTCAGATGAGGTGCT 59.399 57.895 11.63 0.00 42.29 4.40
487 491 0.826715 GGTGCTCAGATGAGGTGCTA 59.173 55.000 11.63 0.00 42.29 3.49
488 492 1.208052 GGTGCTCAGATGAGGTGCTAA 59.792 52.381 11.63 0.00 42.29 3.09
489 493 2.548875 GTGCTCAGATGAGGTGCTAAG 58.451 52.381 11.63 0.00 42.29 2.18
490 494 1.134580 TGCTCAGATGAGGTGCTAAGC 60.135 52.381 11.63 0.00 42.29 3.09
491 495 1.134580 GCTCAGATGAGGTGCTAAGCA 60.135 52.381 11.63 0.00 42.29 3.91
507 511 5.920273 TGCTAAGCACATTAAAAACTTGAGC 59.080 36.000 0.00 0.00 31.71 4.26
508 512 5.920273 GCTAAGCACATTAAAAACTTGAGCA 59.080 36.000 0.00 0.00 30.66 4.26
509 513 6.420604 GCTAAGCACATTAAAAACTTGAGCAA 59.579 34.615 0.00 0.00 30.66 3.91
510 514 6.588348 AAGCACATTAAAAACTTGAGCAAC 57.412 33.333 0.00 0.00 30.66 4.17
511 515 5.906073 AGCACATTAAAAACTTGAGCAACT 58.094 33.333 0.00 0.00 30.66 3.16
512 516 7.038154 AGCACATTAAAAACTTGAGCAACTA 57.962 32.000 0.00 0.00 30.66 2.24
513 517 7.488322 AGCACATTAAAAACTTGAGCAACTAA 58.512 30.769 0.00 0.00 30.66 2.24
514 518 7.978975 AGCACATTAAAAACTTGAGCAACTAAA 59.021 29.630 0.00 0.00 30.66 1.85
515 519 8.268738 GCACATTAAAAACTTGAGCAACTAAAG 58.731 33.333 0.00 0.00 0.00 1.85
516 520 8.268738 CACATTAAAAACTTGAGCAACTAAAGC 58.731 33.333 0.00 0.00 0.00 3.51
517 521 7.438160 ACATTAAAAACTTGAGCAACTAAAGCC 59.562 33.333 0.00 0.00 0.00 4.35
518 522 4.322080 AAAACTTGAGCAACTAAAGCCC 57.678 40.909 0.00 0.00 0.00 5.19
519 523 1.911057 ACTTGAGCAACTAAAGCCCC 58.089 50.000 0.00 0.00 0.00 5.80
520 524 1.177401 CTTGAGCAACTAAAGCCCCC 58.823 55.000 0.00 0.00 0.00 5.40
521 525 0.480690 TTGAGCAACTAAAGCCCCCA 59.519 50.000 0.00 0.00 0.00 4.96
522 526 0.480690 TGAGCAACTAAAGCCCCCAA 59.519 50.000 0.00 0.00 0.00 4.12
523 527 1.077005 TGAGCAACTAAAGCCCCCAAT 59.923 47.619 0.00 0.00 0.00 3.16
524 528 1.478105 GAGCAACTAAAGCCCCCAATG 59.522 52.381 0.00 0.00 0.00 2.82
525 529 0.108186 GCAACTAAAGCCCCCAATGC 60.108 55.000 0.00 0.00 0.00 3.56
526 530 1.265236 CAACTAAAGCCCCCAATGCA 58.735 50.000 0.00 0.00 0.00 3.96
527 531 1.832998 CAACTAAAGCCCCCAATGCAT 59.167 47.619 0.00 0.00 0.00 3.96
528 532 3.030291 CAACTAAAGCCCCCAATGCATA 58.970 45.455 0.00 0.00 0.00 3.14
529 533 2.949447 ACTAAAGCCCCCAATGCATAG 58.051 47.619 0.00 0.00 0.00 2.23
530 534 2.242043 CTAAAGCCCCCAATGCATAGG 58.758 52.381 0.00 3.90 0.00 2.57
531 535 0.339510 AAAGCCCCCAATGCATAGGT 59.660 50.000 13.23 0.00 0.00 3.08
532 536 0.397535 AAGCCCCCAATGCATAGGTG 60.398 55.000 13.23 4.69 0.00 4.00
547 551 5.046910 CATAGGTGCTTAACTTGTTGTGG 57.953 43.478 0.00 0.00 0.00 4.17
548 552 1.681264 AGGTGCTTAACTTGTTGTGGC 59.319 47.619 0.00 0.00 0.00 5.01
549 553 1.681264 GGTGCTTAACTTGTTGTGGCT 59.319 47.619 0.00 0.00 0.00 4.75
550 554 2.882137 GGTGCTTAACTTGTTGTGGCTA 59.118 45.455 0.00 0.00 0.00 3.93
551 555 3.316868 GGTGCTTAACTTGTTGTGGCTAA 59.683 43.478 0.00 0.00 0.00 3.09
552 556 4.537015 GTGCTTAACTTGTTGTGGCTAAG 58.463 43.478 0.00 0.00 0.00 2.18
553 557 3.004315 TGCTTAACTTGTTGTGGCTAAGC 59.996 43.478 8.58 8.58 40.34 3.09
554 558 3.253432 GCTTAACTTGTTGTGGCTAAGCT 59.747 43.478 8.36 0.00 38.49 3.74
555 559 4.613850 GCTTAACTTGTTGTGGCTAAGCTC 60.614 45.833 8.36 0.00 38.49 4.09
556 560 1.897560 ACTTGTTGTGGCTAAGCTCC 58.102 50.000 0.00 0.00 0.00 4.70
557 561 1.421646 ACTTGTTGTGGCTAAGCTCCT 59.578 47.619 0.00 0.00 0.00 3.69
558 562 2.158608 ACTTGTTGTGGCTAAGCTCCTT 60.159 45.455 0.00 0.00 0.00 3.36
559 563 2.185004 TGTTGTGGCTAAGCTCCTTC 57.815 50.000 0.00 0.00 0.00 3.46
560 564 1.419762 TGTTGTGGCTAAGCTCCTTCA 59.580 47.619 0.00 0.00 0.00 3.02
561 565 2.040278 TGTTGTGGCTAAGCTCCTTCAT 59.960 45.455 0.00 0.00 0.00 2.57
562 566 3.084786 GTTGTGGCTAAGCTCCTTCATT 58.915 45.455 0.00 0.00 0.00 2.57
563 567 3.439857 TGTGGCTAAGCTCCTTCATTT 57.560 42.857 0.00 0.00 0.00 2.32
564 568 4.568072 TGTGGCTAAGCTCCTTCATTTA 57.432 40.909 0.00 0.00 0.00 1.40
565 569 4.917385 TGTGGCTAAGCTCCTTCATTTAA 58.083 39.130 0.00 0.00 0.00 1.52
566 570 5.509498 TGTGGCTAAGCTCCTTCATTTAAT 58.491 37.500 0.00 0.00 0.00 1.40
567 571 5.357878 TGTGGCTAAGCTCCTTCATTTAATG 59.642 40.000 0.00 0.00 0.00 1.90
568 572 5.590259 GTGGCTAAGCTCCTTCATTTAATGA 59.410 40.000 3.20 3.20 37.55 2.57
569 573 6.264067 GTGGCTAAGCTCCTTCATTTAATGAT 59.736 38.462 8.56 0.00 39.39 2.45
570 574 6.835488 TGGCTAAGCTCCTTCATTTAATGATT 59.165 34.615 8.56 1.93 39.39 2.57
571 575 7.342799 TGGCTAAGCTCCTTCATTTAATGATTT 59.657 33.333 8.56 0.97 39.39 2.17
572 576 8.850156 GGCTAAGCTCCTTCATTTAATGATTTA 58.150 33.333 8.56 0.00 39.39 1.40
573 577 9.890352 GCTAAGCTCCTTCATTTAATGATTTAG 57.110 33.333 8.56 7.36 39.39 1.85
574 578 9.890352 CTAAGCTCCTTCATTTAATGATTTAGC 57.110 33.333 19.29 19.29 39.39 3.09
575 579 7.886629 AGCTCCTTCATTTAATGATTTAGCA 57.113 32.000 24.32 6.63 38.65 3.49
576 580 8.297470 AGCTCCTTCATTTAATGATTTAGCAA 57.703 30.769 24.32 6.09 38.65 3.91
577 581 8.193438 AGCTCCTTCATTTAATGATTTAGCAAC 58.807 33.333 24.32 8.70 38.65 4.17
578 582 8.193438 GCTCCTTCATTTAATGATTTAGCAACT 58.807 33.333 20.76 0.00 39.39 3.16
591 595 9.976511 ATGATTTAGCAACTAAATTCATCCATG 57.023 29.630 12.50 0.00 43.84 3.66
592 596 7.922278 TGATTTAGCAACTAAATTCATCCATGC 59.078 33.333 12.50 0.00 43.84 4.06
593 597 6.772360 TTAGCAACTAAATTCATCCATGCA 57.228 33.333 0.00 0.00 35.11 3.96
594 598 5.864418 AGCAACTAAATTCATCCATGCAT 57.136 34.783 0.00 0.00 35.11 3.96
595 599 6.229936 AGCAACTAAATTCATCCATGCATT 57.770 33.333 0.00 0.00 35.11 3.56
596 600 6.046593 AGCAACTAAATTCATCCATGCATTG 58.953 36.000 0.00 0.00 35.11 2.82
598 602 6.342906 CAACTAAATTCATCCATGCATTGGT 58.657 36.000 0.00 0.00 46.52 3.67
599 603 5.909477 ACTAAATTCATCCATGCATTGGTG 58.091 37.500 4.65 4.65 46.52 4.17
600 604 3.830744 AATTCATCCATGCATTGGTGG 57.169 42.857 10.89 4.45 46.52 4.61
606 610 3.104519 TCCATGCATTGGTGGATTTCT 57.895 42.857 2.53 0.00 46.52 2.52
607 611 3.443052 TCCATGCATTGGTGGATTTCTT 58.557 40.909 2.53 0.00 46.52 2.52
608 612 3.839490 TCCATGCATTGGTGGATTTCTTT 59.161 39.130 2.53 0.00 46.52 2.52
609 613 4.081531 TCCATGCATTGGTGGATTTCTTTC 60.082 41.667 2.53 0.00 46.52 2.62
610 614 4.322877 CCATGCATTGGTGGATTTCTTTCA 60.323 41.667 0.00 0.00 40.99 2.69
611 615 5.424757 CATGCATTGGTGGATTTCTTTCAT 58.575 37.500 0.00 0.00 33.74 2.57
612 616 5.486735 TGCATTGGTGGATTTCTTTCATT 57.513 34.783 0.00 0.00 0.00 2.57
613 617 5.867330 TGCATTGGTGGATTTCTTTCATTT 58.133 33.333 0.00 0.00 0.00 2.32
614 618 7.002250 TGCATTGGTGGATTTCTTTCATTTA 57.998 32.000 0.00 0.00 0.00 1.40
615 619 7.448420 TGCATTGGTGGATTTCTTTCATTTAA 58.552 30.769 0.00 0.00 0.00 1.52
616 620 8.102047 TGCATTGGTGGATTTCTTTCATTTAAT 58.898 29.630 0.00 0.00 0.00 1.40
617 621 8.949177 GCATTGGTGGATTTCTTTCATTTAATT 58.051 29.630 0.00 0.00 0.00 1.40
620 624 9.844257 TTGGTGGATTTCTTTCATTTAATTGTT 57.156 25.926 0.00 0.00 0.00 2.83
621 625 9.844257 TGGTGGATTTCTTTCATTTAATTGTTT 57.156 25.926 0.00 0.00 0.00 2.83
625 629 9.611284 GGATTTCTTTCATTTAATTGTTTTGCC 57.389 29.630 0.00 0.00 0.00 4.52
629 633 9.487790 TTCTTTCATTTAATTGTTTTGCCTAGG 57.512 29.630 3.67 3.67 0.00 3.02
630 634 8.646900 TCTTTCATTTAATTGTTTTGCCTAGGT 58.353 29.630 11.31 0.00 0.00 3.08
631 635 9.271828 CTTTCATTTAATTGTTTTGCCTAGGTT 57.728 29.630 11.31 0.00 0.00 3.50
632 636 8.825667 TTCATTTAATTGTTTTGCCTAGGTTC 57.174 30.769 11.31 0.00 0.00 3.62
633 637 7.957002 TCATTTAATTGTTTTGCCTAGGTTCA 58.043 30.769 11.31 0.00 0.00 3.18
634 638 8.592809 TCATTTAATTGTTTTGCCTAGGTTCAT 58.407 29.630 11.31 0.00 0.00 2.57
635 639 8.658609 CATTTAATTGTTTTGCCTAGGTTCATG 58.341 33.333 11.31 0.00 0.00 3.07
636 640 5.806654 AATTGTTTTGCCTAGGTTCATGT 57.193 34.783 11.31 0.00 0.00 3.21
637 641 4.582701 TTGTTTTGCCTAGGTTCATGTG 57.417 40.909 11.31 0.00 0.00 3.21
638 642 2.295909 TGTTTTGCCTAGGTTCATGTGC 59.704 45.455 11.31 0.00 0.00 4.57
639 643 2.558359 GTTTTGCCTAGGTTCATGTGCT 59.442 45.455 11.31 0.00 0.00 4.40
640 644 2.584835 TTGCCTAGGTTCATGTGCTT 57.415 45.000 11.31 0.00 0.00 3.91
641 645 3.712016 TTGCCTAGGTTCATGTGCTTA 57.288 42.857 11.31 0.00 0.00 3.09
642 646 3.266510 TGCCTAGGTTCATGTGCTTAG 57.733 47.619 11.31 0.00 0.00 2.18
643 647 2.092968 TGCCTAGGTTCATGTGCTTAGG 60.093 50.000 11.31 16.83 0.00 2.69
644 648 2.565841 CCTAGGTTCATGTGCTTAGGC 58.434 52.381 0.00 0.00 39.26 3.93
658 662 5.125100 TGCTTAGGCATTGTTTCTTTCTG 57.875 39.130 0.00 0.00 44.28 3.02
659 663 4.022068 TGCTTAGGCATTGTTTCTTTCTGG 60.022 41.667 0.00 0.00 44.28 3.86
660 664 4.619160 GCTTAGGCATTGTTTCTTTCTGGG 60.619 45.833 0.00 0.00 38.54 4.45
661 665 2.250924 AGGCATTGTTTCTTTCTGGGG 58.749 47.619 0.00 0.00 0.00 4.96
662 666 1.970640 GGCATTGTTTCTTTCTGGGGT 59.029 47.619 0.00 0.00 0.00 4.95
663 667 2.029020 GGCATTGTTTCTTTCTGGGGTC 60.029 50.000 0.00 0.00 0.00 4.46
664 668 2.627699 GCATTGTTTCTTTCTGGGGTCA 59.372 45.455 0.00 0.00 0.00 4.02
665 669 3.259123 GCATTGTTTCTTTCTGGGGTCAT 59.741 43.478 0.00 0.00 0.00 3.06
666 670 4.619160 GCATTGTTTCTTTCTGGGGTCATC 60.619 45.833 0.00 0.00 0.00 2.92
667 671 3.874383 TGTTTCTTTCTGGGGTCATCA 57.126 42.857 0.00 0.00 0.00 3.07
668 672 3.486383 TGTTTCTTTCTGGGGTCATCAC 58.514 45.455 0.00 0.00 0.00 3.06
669 673 3.117701 TGTTTCTTTCTGGGGTCATCACA 60.118 43.478 0.00 0.00 0.00 3.58
670 674 2.859165 TCTTTCTGGGGTCATCACAC 57.141 50.000 0.00 0.00 0.00 3.82
671 675 2.338809 TCTTTCTGGGGTCATCACACT 58.661 47.619 0.00 0.00 0.00 3.55
672 676 2.303022 TCTTTCTGGGGTCATCACACTC 59.697 50.000 0.00 0.00 0.00 3.51
673 677 1.728323 TTCTGGGGTCATCACACTCA 58.272 50.000 0.00 0.00 0.00 3.41
674 678 1.956869 TCTGGGGTCATCACACTCAT 58.043 50.000 0.00 0.00 0.00 2.90
675 679 1.833630 TCTGGGGTCATCACACTCATC 59.166 52.381 0.00 0.00 0.00 2.92
676 680 1.836166 CTGGGGTCATCACACTCATCT 59.164 52.381 0.00 0.00 0.00 2.90
677 681 1.833630 TGGGGTCATCACACTCATCTC 59.166 52.381 0.00 0.00 0.00 2.75
678 682 1.202463 GGGGTCATCACACTCATCTCG 60.202 57.143 0.00 0.00 0.00 4.04
679 683 1.565305 GGTCATCACACTCATCTCGC 58.435 55.000 0.00 0.00 0.00 5.03
680 684 1.135915 GGTCATCACACTCATCTCGCT 59.864 52.381 0.00 0.00 0.00 4.93
681 685 2.458951 GTCATCACACTCATCTCGCTC 58.541 52.381 0.00 0.00 0.00 5.03
682 686 1.406898 TCATCACACTCATCTCGCTCC 59.593 52.381 0.00 0.00 0.00 4.70
683 687 1.408340 CATCACACTCATCTCGCTCCT 59.592 52.381 0.00 0.00 0.00 3.69
684 688 1.098869 TCACACTCATCTCGCTCCTC 58.901 55.000 0.00 0.00 0.00 3.71
685 689 1.102154 CACACTCATCTCGCTCCTCT 58.898 55.000 0.00 0.00 0.00 3.69
686 690 1.476085 CACACTCATCTCGCTCCTCTT 59.524 52.381 0.00 0.00 0.00 2.85
687 691 2.685388 CACACTCATCTCGCTCCTCTTA 59.315 50.000 0.00 0.00 0.00 2.10
688 692 3.129462 CACACTCATCTCGCTCCTCTTAA 59.871 47.826 0.00 0.00 0.00 1.85
689 693 3.957497 ACACTCATCTCGCTCCTCTTAAT 59.043 43.478 0.00 0.00 0.00 1.40
690 694 4.404073 ACACTCATCTCGCTCCTCTTAATT 59.596 41.667 0.00 0.00 0.00 1.40
691 695 5.594725 ACACTCATCTCGCTCCTCTTAATTA 59.405 40.000 0.00 0.00 0.00 1.40
692 696 5.918011 CACTCATCTCGCTCCTCTTAATTAC 59.082 44.000 0.00 0.00 0.00 1.89
693 697 5.010213 ACTCATCTCGCTCCTCTTAATTACC 59.990 44.000 0.00 0.00 0.00 2.85
694 698 5.141182 TCATCTCGCTCCTCTTAATTACCT 58.859 41.667 0.00 0.00 0.00 3.08
695 699 5.598830 TCATCTCGCTCCTCTTAATTACCTT 59.401 40.000 0.00 0.00 0.00 3.50
696 700 5.263968 TCTCGCTCCTCTTAATTACCTTG 57.736 43.478 0.00 0.00 0.00 3.61
697 701 3.793559 TCGCTCCTCTTAATTACCTTGC 58.206 45.455 0.00 0.00 0.00 4.01
698 702 2.872858 CGCTCCTCTTAATTACCTTGCC 59.127 50.000 0.00 0.00 0.00 4.52
699 703 3.681594 CGCTCCTCTTAATTACCTTGCCA 60.682 47.826 0.00 0.00 0.00 4.92
700 704 4.464947 GCTCCTCTTAATTACCTTGCCAT 58.535 43.478 0.00 0.00 0.00 4.40
701 705 5.621193 GCTCCTCTTAATTACCTTGCCATA 58.379 41.667 0.00 0.00 0.00 2.74
702 706 6.241645 GCTCCTCTTAATTACCTTGCCATAT 58.758 40.000 0.00 0.00 0.00 1.78
703 707 6.372937 GCTCCTCTTAATTACCTTGCCATATC 59.627 42.308 0.00 0.00 0.00 1.63
704 708 7.387265 TCCTCTTAATTACCTTGCCATATCA 57.613 36.000 0.00 0.00 0.00 2.15
705 709 7.453393 TCCTCTTAATTACCTTGCCATATCAG 58.547 38.462 0.00 0.00 0.00 2.90
706 710 7.072454 TCCTCTTAATTACCTTGCCATATCAGT 59.928 37.037 0.00 0.00 0.00 3.41
707 711 7.721399 CCTCTTAATTACCTTGCCATATCAGTT 59.279 37.037 0.00 0.00 0.00 3.16
708 712 9.125026 CTCTTAATTACCTTGCCATATCAGTTT 57.875 33.333 0.00 0.00 0.00 2.66
709 713 9.474313 TCTTAATTACCTTGCCATATCAGTTTT 57.526 29.630 0.00 0.00 0.00 2.43
743 747 5.847304 TGATAGCCTTAGCATCTGTACAAG 58.153 41.667 0.00 0.00 43.56 3.16
744 748 5.598417 TGATAGCCTTAGCATCTGTACAAGA 59.402 40.000 0.00 0.00 43.56 3.02
939 946 2.297315 GAGGGGCCACTTTCAGAAAAAG 59.703 50.000 10.15 0.00 0.00 2.27
943 955 2.035961 GGCCACTTTCAGAAAAAGTCCC 59.964 50.000 0.00 1.80 38.32 4.46
953 965 1.711375 GAAAAAGTCCCCCTCCTCCTT 59.289 52.381 0.00 0.00 0.00 3.36
979 991 3.456277 GTCCTACATCCCTCAACCATCTT 59.544 47.826 0.00 0.00 0.00 2.40
1003 1015 3.487202 CAACGACGTCGGCCATGG 61.487 66.667 37.89 14.30 44.95 3.66
1027 1039 2.622436 ACCAGATTCTTGAGCTAACGC 58.378 47.619 0.00 0.00 0.00 4.84
1109 1121 2.851102 CTCCATCTCCGGGGCCAT 60.851 66.667 4.39 0.00 0.00 4.40
1200 1218 2.717485 CATTTGCCGATCCCTGCG 59.283 61.111 0.00 0.00 0.00 5.18
1293 1311 2.664424 CGTTGGTGAAGTATTTGTGCCG 60.664 50.000 0.00 0.00 0.00 5.69
1326 1344 0.965439 TGGCAGGCACAAATAACACC 59.035 50.000 0.00 0.00 0.00 4.16
1353 1371 2.636830 CCAAAGACCATGAGCTACCAG 58.363 52.381 0.00 0.00 0.00 4.00
1483 1501 7.131302 CAGTATGTCAAGTACTCTGGGGACC 62.131 52.000 0.00 0.00 38.64 4.46
1551 1569 0.968405 AACCGCATGCCACATTTTCT 59.032 45.000 13.15 0.00 0.00 2.52
1574 1592 1.535204 CCACCGGGTGTACCTTACGT 61.535 60.000 24.70 0.00 36.97 3.57
1608 1626 3.048600 AGTGTATCCACCACAGCCATAT 58.951 45.455 0.00 0.00 42.88 1.78
1609 1627 3.141398 GTGTATCCACCACAGCCATATG 58.859 50.000 0.00 0.00 35.44 1.78
1610 1628 2.106338 TGTATCCACCACAGCCATATGG 59.894 50.000 18.07 18.07 42.13 2.74
1611 1629 0.479815 ATCCACCACAGCCATATGGG 59.520 55.000 23.30 10.03 40.59 4.00
1618 1636 2.516930 AGCCATATGGGTGTGCGC 60.517 61.111 25.40 7.67 45.50 6.09
1619 1637 3.595758 GCCATATGGGTGTGCGCC 61.596 66.667 23.30 0.00 39.65 6.53
1644 1662 5.010922 TCCACCACCGTACATGTATAATACC 59.989 44.000 9.18 0.00 0.00 2.73
1676 1697 3.243035 CCGGCAACAATGTATGTGTATGG 60.243 47.826 0.00 0.00 42.99 2.74
1680 1701 2.571212 ACAATGTATGTGTATGGGCCG 58.429 47.619 0.00 0.00 41.93 6.13
1803 1832 0.760567 TGGAGTCTGATGCCGCCTAT 60.761 55.000 0.00 0.00 0.00 2.57
1812 1841 4.221422 GCCGCCTATGACGCTGGA 62.221 66.667 0.00 0.00 0.00 3.86
1818 1847 1.599542 GCCTATGACGCTGGATTCAAC 59.400 52.381 0.00 0.00 0.00 3.18
1847 1876 7.119262 TGGGATGAGTTTTTAGTTCTCGAAATC 59.881 37.037 0.00 0.00 0.00 2.17
1894 1923 7.936847 TGTCCTTGTAAATCTGTACTGTGAATT 59.063 33.333 0.00 0.00 0.00 2.17
1926 1955 7.081526 AGTGAGCAAAGTGAAATCATCATAC 57.918 36.000 0.00 0.00 40.97 2.39
2307 2360 1.856265 GCGCACCTCCTTTCCTTGTG 61.856 60.000 0.30 0.00 0.00 3.33
2619 2707 1.075601 TTGACCTTCCTGGAGGCATT 58.924 50.000 10.85 0.00 40.65 3.56
2744 2837 2.586792 CCCTCTTGAGGGCTTCGG 59.413 66.667 21.32 0.00 42.99 4.30
2785 2879 3.897122 GGGACTGGTGGTTGGCCA 61.897 66.667 0.00 0.00 43.73 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.091655 CGCAATGTGCATGCAAAATTTAGA 59.908 37.500 24.58 0.00 45.36 2.10
15 16 3.744942 ACGCAATGTGCATGCAAAATTTA 59.255 34.783 24.58 5.24 45.36 1.40
38 39 1.134580 AGACATCCAAGATGCTCGTGG 60.135 52.381 4.51 10.39 45.57 4.94
40 41 4.184629 GTTTAGACATCCAAGATGCTCGT 58.815 43.478 4.51 0.00 0.00 4.18
96 98 6.375377 GCATGTGAACAATAAACTCGGTAAA 58.625 36.000 0.00 0.00 0.00 2.01
97 99 5.390040 CGCATGTGAACAATAAACTCGGTAA 60.390 40.000 0.00 0.00 0.00 2.85
98 100 4.092237 CGCATGTGAACAATAAACTCGGTA 59.908 41.667 0.00 0.00 0.00 4.02
104 106 3.758300 CTCCCGCATGTGAACAATAAAC 58.242 45.455 8.11 0.00 0.00 2.01
122 124 1.759881 AGCCAGGCTCATATGCTCC 59.240 57.895 8.70 1.40 30.62 4.70
136 138 4.704833 GAGCAGCGGTTGGAGCCA 62.705 66.667 0.00 0.00 34.64 4.75
151 153 3.016736 AGAAGAGGAAGAAGAGCGAGAG 58.983 50.000 0.00 0.00 0.00 3.20
167 170 8.591940 AGAGCTGCATGTGAATATAATAGAAGA 58.408 33.333 1.02 0.00 0.00 2.87
248 251 7.038017 CCCATACACCCTATGTTCATCTCTTAT 60.038 40.741 0.00 0.00 43.19 1.73
263 266 2.238898 GCAACTAGTTCCCATACACCCT 59.761 50.000 4.77 0.00 0.00 4.34
317 321 5.423931 TGCAACATCCAGGAATGTAGTAGTA 59.576 40.000 0.00 0.00 38.92 1.82
318 322 4.225042 TGCAACATCCAGGAATGTAGTAGT 59.775 41.667 0.00 0.00 38.92 2.73
319 323 4.769688 TGCAACATCCAGGAATGTAGTAG 58.230 43.478 0.00 0.00 38.92 2.57
346 350 6.783708 ACTTGAAACCCACTTTAATCAACA 57.216 33.333 0.00 0.00 0.00 3.33
376 380 1.739067 AATGCAACCGCTCTTACTCC 58.261 50.000 0.00 0.00 39.64 3.85
378 382 5.897377 AAATTAATGCAACCGCTCTTACT 57.103 34.783 0.00 0.00 39.64 2.24
386 390 7.112009 CGATTCATGACTAAATTAATGCAACCG 59.888 37.037 0.00 0.00 0.00 4.44
408 412 5.113383 GGGTTTGTTTCTTTGTTTCCGATT 58.887 37.500 0.00 0.00 0.00 3.34
412 416 7.851387 TTATTGGGTTTGTTTCTTTGTTTCC 57.149 32.000 0.00 0.00 0.00 3.13
413 417 7.855409 GCATTATTGGGTTTGTTTCTTTGTTTC 59.145 33.333 0.00 0.00 0.00 2.78
434 438 2.682856 GAGGTCTCAAAATGCCGCATTA 59.317 45.455 18.80 3.07 32.43 1.90
436 440 1.098050 GAGGTCTCAAAATGCCGCAT 58.902 50.000 0.00 0.00 0.00 4.73
437 441 0.036732 AGAGGTCTCAAAATGCCGCA 59.963 50.000 0.00 0.00 0.00 5.69
439 443 1.740025 GGAAGAGGTCTCAAAATGCCG 59.260 52.381 0.55 0.00 0.00 5.69
447 451 1.338105 CGTGCATTGGAAGAGGTCTCA 60.338 52.381 0.00 0.00 0.00 3.27
448 452 1.363744 CGTGCATTGGAAGAGGTCTC 58.636 55.000 0.00 0.00 0.00 3.36
449 453 0.036010 CCGTGCATTGGAAGAGGTCT 60.036 55.000 1.85 0.00 0.00 3.85
450 454 1.026718 CCCGTGCATTGGAAGAGGTC 61.027 60.000 9.37 0.00 0.00 3.85
451 455 1.002134 CCCGTGCATTGGAAGAGGT 60.002 57.895 9.37 0.00 0.00 3.85
452 456 1.002134 ACCCGTGCATTGGAAGAGG 60.002 57.895 11.09 0.00 0.00 3.69
453 457 2.174334 CACCCGTGCATTGGAAGAG 58.826 57.895 11.09 0.00 0.00 2.85
454 458 4.395519 CACCCGTGCATTGGAAGA 57.604 55.556 11.09 0.00 0.00 2.87
464 468 1.153489 CCTCATCTGAGCACCCGTG 60.153 63.158 1.51 0.00 40.75 4.94
465 469 1.610673 ACCTCATCTGAGCACCCGT 60.611 57.895 1.51 0.00 40.75 5.28
466 470 1.153489 CACCTCATCTGAGCACCCG 60.153 63.158 1.51 0.00 40.75 5.28
467 471 1.451028 GCACCTCATCTGAGCACCC 60.451 63.158 1.51 0.00 40.75 4.61
468 472 0.826715 TAGCACCTCATCTGAGCACC 59.173 55.000 1.51 0.00 40.75 5.01
469 473 2.548875 CTTAGCACCTCATCTGAGCAC 58.451 52.381 1.51 0.00 40.75 4.40
470 474 1.134580 GCTTAGCACCTCATCTGAGCA 60.135 52.381 0.00 0.00 40.39 4.26
471 475 1.134580 TGCTTAGCACCTCATCTGAGC 60.135 52.381 1.39 0.00 40.86 4.26
472 476 2.975732 TGCTTAGCACCTCATCTGAG 57.024 50.000 1.39 0.00 36.34 3.35
483 487 5.920273 GCTCAAGTTTTTAATGTGCTTAGCA 59.080 36.000 1.39 1.39 35.60 3.49
484 488 5.920273 TGCTCAAGTTTTTAATGTGCTTAGC 59.080 36.000 0.00 0.00 35.30 3.09
485 489 7.649306 AGTTGCTCAAGTTTTTAATGTGCTTAG 59.351 33.333 0.00 0.00 35.30 2.18
486 490 7.488322 AGTTGCTCAAGTTTTTAATGTGCTTA 58.512 30.769 0.00 0.00 35.30 3.09
487 491 6.340522 AGTTGCTCAAGTTTTTAATGTGCTT 58.659 32.000 0.00 0.00 35.30 3.91
488 492 5.906073 AGTTGCTCAAGTTTTTAATGTGCT 58.094 33.333 0.00 0.00 35.30 4.40
489 493 7.692908 TTAGTTGCTCAAGTTTTTAATGTGC 57.307 32.000 0.00 0.00 34.95 4.57
490 494 8.268738 GCTTTAGTTGCTCAAGTTTTTAATGTG 58.731 33.333 0.00 0.00 0.00 3.21
491 495 7.438160 GGCTTTAGTTGCTCAAGTTTTTAATGT 59.562 33.333 0.00 0.00 0.00 2.71
492 496 7.095649 GGGCTTTAGTTGCTCAAGTTTTTAATG 60.096 37.037 0.00 0.00 0.00 1.90
493 497 6.929049 GGGCTTTAGTTGCTCAAGTTTTTAAT 59.071 34.615 0.00 0.00 0.00 1.40
494 498 6.277605 GGGCTTTAGTTGCTCAAGTTTTTAA 58.722 36.000 0.00 0.00 0.00 1.52
495 499 5.221362 GGGGCTTTAGTTGCTCAAGTTTTTA 60.221 40.000 0.00 0.00 31.40 1.52
496 500 4.442893 GGGGCTTTAGTTGCTCAAGTTTTT 60.443 41.667 0.00 0.00 31.40 1.94
497 501 3.069586 GGGGCTTTAGTTGCTCAAGTTTT 59.930 43.478 0.00 0.00 31.40 2.43
498 502 2.628178 GGGGCTTTAGTTGCTCAAGTTT 59.372 45.455 0.00 0.00 31.40 2.66
499 503 2.239400 GGGGCTTTAGTTGCTCAAGTT 58.761 47.619 0.00 0.00 31.40 2.66
500 504 1.547901 GGGGGCTTTAGTTGCTCAAGT 60.548 52.381 0.00 0.00 31.40 3.16
501 505 1.177401 GGGGGCTTTAGTTGCTCAAG 58.823 55.000 0.00 0.00 31.40 3.02
502 506 0.480690 TGGGGGCTTTAGTTGCTCAA 59.519 50.000 0.00 0.00 31.40 3.02
503 507 0.480690 TTGGGGGCTTTAGTTGCTCA 59.519 50.000 0.00 0.00 31.40 4.26
504 508 1.478105 CATTGGGGGCTTTAGTTGCTC 59.522 52.381 0.00 0.00 0.00 4.26
505 509 1.560505 CATTGGGGGCTTTAGTTGCT 58.439 50.000 0.00 0.00 0.00 3.91
506 510 0.108186 GCATTGGGGGCTTTAGTTGC 60.108 55.000 0.00 0.00 0.00 4.17
507 511 1.265236 TGCATTGGGGGCTTTAGTTG 58.735 50.000 0.00 0.00 0.00 3.16
508 512 2.252535 ATGCATTGGGGGCTTTAGTT 57.747 45.000 0.00 0.00 0.00 2.24
509 513 2.424812 CCTATGCATTGGGGGCTTTAGT 60.425 50.000 18.33 0.00 0.00 2.24
510 514 2.242043 CCTATGCATTGGGGGCTTTAG 58.758 52.381 18.33 0.00 0.00 1.85
511 515 1.573376 ACCTATGCATTGGGGGCTTTA 59.427 47.619 27.42 0.00 0.00 1.85
512 516 0.339510 ACCTATGCATTGGGGGCTTT 59.660 50.000 27.42 6.06 0.00 3.51
513 517 0.397535 CACCTATGCATTGGGGGCTT 60.398 55.000 27.42 6.76 0.00 4.35
514 518 1.231068 CACCTATGCATTGGGGGCT 59.769 57.895 27.42 7.11 0.00 5.19
515 519 3.860681 CACCTATGCATTGGGGGC 58.139 61.111 27.42 0.00 0.00 5.80
525 529 4.615912 GCCACAACAAGTTAAGCACCTATG 60.616 45.833 0.00 0.00 0.00 2.23
526 530 3.506067 GCCACAACAAGTTAAGCACCTAT 59.494 43.478 0.00 0.00 0.00 2.57
527 531 2.882137 GCCACAACAAGTTAAGCACCTA 59.118 45.455 0.00 0.00 0.00 3.08
528 532 1.681264 GCCACAACAAGTTAAGCACCT 59.319 47.619 0.00 0.00 0.00 4.00
529 533 1.681264 AGCCACAACAAGTTAAGCACC 59.319 47.619 0.00 0.00 0.00 5.01
530 534 4.537015 CTTAGCCACAACAAGTTAAGCAC 58.463 43.478 0.00 0.00 0.00 4.40
531 535 3.004315 GCTTAGCCACAACAAGTTAAGCA 59.996 43.478 11.98 0.00 40.93 3.91
532 536 3.253432 AGCTTAGCCACAACAAGTTAAGC 59.747 43.478 0.00 9.67 41.29 3.09
533 537 4.083271 GGAGCTTAGCCACAACAAGTTAAG 60.083 45.833 0.00 0.00 0.00 1.85
534 538 3.818773 GGAGCTTAGCCACAACAAGTTAA 59.181 43.478 0.00 0.00 0.00 2.01
535 539 3.072476 AGGAGCTTAGCCACAACAAGTTA 59.928 43.478 0.00 0.00 0.00 2.24
536 540 2.158608 AGGAGCTTAGCCACAACAAGTT 60.159 45.455 0.00 0.00 0.00 2.66
537 541 1.421646 AGGAGCTTAGCCACAACAAGT 59.578 47.619 0.00 0.00 0.00 3.16
538 542 2.191128 AGGAGCTTAGCCACAACAAG 57.809 50.000 0.00 0.00 0.00 3.16
539 543 2.158682 TGAAGGAGCTTAGCCACAACAA 60.159 45.455 0.00 0.00 0.00 2.83
540 544 1.419762 TGAAGGAGCTTAGCCACAACA 59.580 47.619 0.00 0.00 0.00 3.33
541 545 2.185004 TGAAGGAGCTTAGCCACAAC 57.815 50.000 0.00 0.00 0.00 3.32
542 546 3.439857 AATGAAGGAGCTTAGCCACAA 57.560 42.857 0.00 0.00 0.00 3.33
543 547 3.439857 AAATGAAGGAGCTTAGCCACA 57.560 42.857 0.00 0.00 0.00 4.17
544 548 5.590259 TCATTAAATGAAGGAGCTTAGCCAC 59.410 40.000 0.00 0.00 36.11 5.01
545 549 5.754782 TCATTAAATGAAGGAGCTTAGCCA 58.245 37.500 0.00 0.00 36.11 4.75
546 550 6.890979 ATCATTAAATGAAGGAGCTTAGCC 57.109 37.500 0.00 0.00 43.50 3.93
547 551 9.890352 CTAAATCATTAAATGAAGGAGCTTAGC 57.110 33.333 0.00 0.00 43.50 3.09
548 552 9.890352 GCTAAATCATTAAATGAAGGAGCTTAG 57.110 33.333 0.00 7.93 43.50 2.18
549 553 9.407380 TGCTAAATCATTAAATGAAGGAGCTTA 57.593 29.630 2.99 3.64 43.50 3.09
550 554 8.297470 TGCTAAATCATTAAATGAAGGAGCTT 57.703 30.769 2.99 0.00 43.50 3.74
551 555 7.886629 TGCTAAATCATTAAATGAAGGAGCT 57.113 32.000 2.99 0.00 43.50 4.09
552 556 8.193438 AGTTGCTAAATCATTAAATGAAGGAGC 58.807 33.333 0.00 0.00 43.50 4.70
565 569 9.976511 CATGGATGAATTTAGTTGCTAAATCAT 57.023 29.630 12.69 15.09 43.27 2.45
566 570 7.922278 GCATGGATGAATTTAGTTGCTAAATCA 59.078 33.333 12.69 12.23 43.27 2.57
567 571 7.922278 TGCATGGATGAATTTAGTTGCTAAATC 59.078 33.333 12.69 8.41 43.27 2.17
568 572 7.784037 TGCATGGATGAATTTAGTTGCTAAAT 58.216 30.769 7.96 7.96 45.15 1.40
569 573 7.167924 TGCATGGATGAATTTAGTTGCTAAA 57.832 32.000 4.14 4.14 39.73 1.85
570 574 6.772360 TGCATGGATGAATTTAGTTGCTAA 57.228 33.333 0.00 0.00 0.00 3.09
571 575 6.964807 ATGCATGGATGAATTTAGTTGCTA 57.035 33.333 0.00 0.00 0.00 3.49
572 576 5.864418 ATGCATGGATGAATTTAGTTGCT 57.136 34.783 0.00 0.00 0.00 3.91
573 577 6.281848 CAATGCATGGATGAATTTAGTTGC 57.718 37.500 0.00 0.00 33.76 4.17
588 592 4.823157 TGAAAGAAATCCACCAATGCATG 58.177 39.130 0.00 0.00 0.00 4.06
589 593 5.687166 ATGAAAGAAATCCACCAATGCAT 57.313 34.783 0.00 0.00 0.00 3.96
590 594 5.486735 AATGAAAGAAATCCACCAATGCA 57.513 34.783 0.00 0.00 0.00 3.96
591 595 7.903995 TTAAATGAAAGAAATCCACCAATGC 57.096 32.000 0.00 0.00 0.00 3.56
594 598 9.844257 AACAATTAAATGAAAGAAATCCACCAA 57.156 25.926 0.00 0.00 0.00 3.67
595 599 9.844257 AAACAATTAAATGAAAGAAATCCACCA 57.156 25.926 0.00 0.00 0.00 4.17
599 603 9.611284 GGCAAAACAATTAAATGAAAGAAATCC 57.389 29.630 0.00 0.00 0.00 3.01
603 607 9.487790 CCTAGGCAAAACAATTAAATGAAAGAA 57.512 29.630 0.00 0.00 0.00 2.52
604 608 8.646900 ACCTAGGCAAAACAATTAAATGAAAGA 58.353 29.630 9.30 0.00 0.00 2.52
605 609 8.831715 ACCTAGGCAAAACAATTAAATGAAAG 57.168 30.769 9.30 0.00 0.00 2.62
606 610 9.267084 GAACCTAGGCAAAACAATTAAATGAAA 57.733 29.630 9.30 0.00 0.00 2.69
607 611 8.424918 TGAACCTAGGCAAAACAATTAAATGAA 58.575 29.630 9.30 0.00 0.00 2.57
608 612 7.957002 TGAACCTAGGCAAAACAATTAAATGA 58.043 30.769 9.30 0.00 0.00 2.57
609 613 8.658609 CATGAACCTAGGCAAAACAATTAAATG 58.341 33.333 9.30 0.00 0.00 2.32
610 614 8.374743 ACATGAACCTAGGCAAAACAATTAAAT 58.625 29.630 9.30 0.00 0.00 1.40
611 615 7.655328 CACATGAACCTAGGCAAAACAATTAAA 59.345 33.333 9.30 0.00 0.00 1.52
612 616 7.151308 CACATGAACCTAGGCAAAACAATTAA 58.849 34.615 9.30 0.00 0.00 1.40
613 617 6.686630 CACATGAACCTAGGCAAAACAATTA 58.313 36.000 9.30 0.00 0.00 1.40
614 618 5.540911 CACATGAACCTAGGCAAAACAATT 58.459 37.500 9.30 0.00 0.00 2.32
615 619 4.561326 GCACATGAACCTAGGCAAAACAAT 60.561 41.667 9.30 0.00 0.00 2.71
616 620 3.243704 GCACATGAACCTAGGCAAAACAA 60.244 43.478 9.30 0.00 0.00 2.83
617 621 2.295909 GCACATGAACCTAGGCAAAACA 59.704 45.455 9.30 2.58 0.00 2.83
618 622 2.558359 AGCACATGAACCTAGGCAAAAC 59.442 45.455 9.30 0.00 0.00 2.43
619 623 2.875296 AGCACATGAACCTAGGCAAAA 58.125 42.857 9.30 0.00 0.00 2.44
620 624 2.584835 AGCACATGAACCTAGGCAAA 57.415 45.000 9.30 0.00 0.00 3.68
621 625 2.584835 AAGCACATGAACCTAGGCAA 57.415 45.000 9.30 0.00 0.00 4.52
622 626 2.092968 CCTAAGCACATGAACCTAGGCA 60.093 50.000 9.30 0.00 0.00 4.75
623 627 2.565841 CCTAAGCACATGAACCTAGGC 58.434 52.381 9.30 0.00 0.00 3.93
624 628 2.092968 TGCCTAAGCACATGAACCTAGG 60.093 50.000 7.41 7.41 46.52 3.02
625 629 3.266510 TGCCTAAGCACATGAACCTAG 57.733 47.619 0.00 0.00 46.52 3.02
637 641 4.488879 CCAGAAAGAAACAATGCCTAAGC 58.511 43.478 0.00 0.00 40.48 3.09
638 642 4.082026 CCCCAGAAAGAAACAATGCCTAAG 60.082 45.833 0.00 0.00 0.00 2.18
639 643 3.831911 CCCCAGAAAGAAACAATGCCTAA 59.168 43.478 0.00 0.00 0.00 2.69
640 644 3.181423 ACCCCAGAAAGAAACAATGCCTA 60.181 43.478 0.00 0.00 0.00 3.93
641 645 2.250924 CCCCAGAAAGAAACAATGCCT 58.749 47.619 0.00 0.00 0.00 4.75
642 646 1.970640 ACCCCAGAAAGAAACAATGCC 59.029 47.619 0.00 0.00 0.00 4.40
643 647 2.627699 TGACCCCAGAAAGAAACAATGC 59.372 45.455 0.00 0.00 0.00 3.56
644 648 4.523943 TGATGACCCCAGAAAGAAACAATG 59.476 41.667 0.00 0.00 0.00 2.82
645 649 4.524328 GTGATGACCCCAGAAAGAAACAAT 59.476 41.667 0.00 0.00 0.00 2.71
646 650 3.888930 GTGATGACCCCAGAAAGAAACAA 59.111 43.478 0.00 0.00 0.00 2.83
647 651 3.117701 TGTGATGACCCCAGAAAGAAACA 60.118 43.478 0.00 0.00 0.00 2.83
648 652 3.253432 GTGTGATGACCCCAGAAAGAAAC 59.747 47.826 0.00 0.00 0.00 2.78
649 653 3.138283 AGTGTGATGACCCCAGAAAGAAA 59.862 43.478 0.00 0.00 0.00 2.52
650 654 2.711009 AGTGTGATGACCCCAGAAAGAA 59.289 45.455 0.00 0.00 0.00 2.52
651 655 2.303022 GAGTGTGATGACCCCAGAAAGA 59.697 50.000 0.00 0.00 0.00 2.52
652 656 2.038952 TGAGTGTGATGACCCCAGAAAG 59.961 50.000 0.00 0.00 0.00 2.62
653 657 2.054021 TGAGTGTGATGACCCCAGAAA 58.946 47.619 0.00 0.00 0.00 2.52
654 658 1.728323 TGAGTGTGATGACCCCAGAA 58.272 50.000 0.00 0.00 0.00 3.02
655 659 1.833630 GATGAGTGTGATGACCCCAGA 59.166 52.381 0.00 0.00 0.00 3.86
656 660 1.836166 AGATGAGTGTGATGACCCCAG 59.164 52.381 0.00 0.00 0.00 4.45
657 661 1.833630 GAGATGAGTGTGATGACCCCA 59.166 52.381 0.00 0.00 0.00 4.96
658 662 1.202463 CGAGATGAGTGTGATGACCCC 60.202 57.143 0.00 0.00 0.00 4.95
659 663 1.804372 GCGAGATGAGTGTGATGACCC 60.804 57.143 0.00 0.00 0.00 4.46
660 664 1.135915 AGCGAGATGAGTGTGATGACC 59.864 52.381 0.00 0.00 0.00 4.02
661 665 2.458951 GAGCGAGATGAGTGTGATGAC 58.541 52.381 0.00 0.00 0.00 3.06
662 666 1.406898 GGAGCGAGATGAGTGTGATGA 59.593 52.381 0.00 0.00 0.00 2.92
663 667 1.408340 AGGAGCGAGATGAGTGTGATG 59.592 52.381 0.00 0.00 0.00 3.07
664 668 1.680735 GAGGAGCGAGATGAGTGTGAT 59.319 52.381 0.00 0.00 0.00 3.06
665 669 1.098869 GAGGAGCGAGATGAGTGTGA 58.901 55.000 0.00 0.00 0.00 3.58
666 670 1.102154 AGAGGAGCGAGATGAGTGTG 58.898 55.000 0.00 0.00 0.00 3.82
667 671 1.846007 AAGAGGAGCGAGATGAGTGT 58.154 50.000 0.00 0.00 0.00 3.55
668 672 4.582701 ATTAAGAGGAGCGAGATGAGTG 57.417 45.455 0.00 0.00 0.00 3.51
669 673 5.010213 GGTAATTAAGAGGAGCGAGATGAGT 59.990 44.000 0.00 0.00 0.00 3.41
670 674 5.242838 AGGTAATTAAGAGGAGCGAGATGAG 59.757 44.000 0.00 0.00 0.00 2.90
671 675 5.141182 AGGTAATTAAGAGGAGCGAGATGA 58.859 41.667 0.00 0.00 0.00 2.92
672 676 5.461032 AGGTAATTAAGAGGAGCGAGATG 57.539 43.478 0.00 0.00 0.00 2.90
673 677 5.740513 GCAAGGTAATTAAGAGGAGCGAGAT 60.741 44.000 0.00 0.00 0.00 2.75
674 678 4.441634 GCAAGGTAATTAAGAGGAGCGAGA 60.442 45.833 0.00 0.00 0.00 4.04
675 679 3.804873 GCAAGGTAATTAAGAGGAGCGAG 59.195 47.826 0.00 0.00 0.00 5.03
676 680 3.431766 GGCAAGGTAATTAAGAGGAGCGA 60.432 47.826 0.00 0.00 0.00 4.93
677 681 2.872858 GGCAAGGTAATTAAGAGGAGCG 59.127 50.000 0.00 0.00 0.00 5.03
678 682 3.886123 TGGCAAGGTAATTAAGAGGAGC 58.114 45.455 0.00 0.00 0.00 4.70
679 683 7.453393 TGATATGGCAAGGTAATTAAGAGGAG 58.547 38.462 0.00 0.00 0.00 3.69
680 684 7.072454 ACTGATATGGCAAGGTAATTAAGAGGA 59.928 37.037 0.00 0.00 0.00 3.71
681 685 7.227156 ACTGATATGGCAAGGTAATTAAGAGG 58.773 38.462 0.00 0.00 0.00 3.69
682 686 8.682936 AACTGATATGGCAAGGTAATTAAGAG 57.317 34.615 0.00 0.00 0.00 2.85
683 687 9.474313 AAAACTGATATGGCAAGGTAATTAAGA 57.526 29.630 0.00 0.00 0.00 2.10
708 712 7.109501 TGCTAAGGCTATCATGTAGACAAAAA 58.890 34.615 9.82 0.00 39.59 1.94
709 713 6.649155 TGCTAAGGCTATCATGTAGACAAAA 58.351 36.000 9.82 0.00 39.59 2.44
710 714 6.233905 TGCTAAGGCTATCATGTAGACAAA 57.766 37.500 9.82 0.00 39.59 2.83
711 715 5.869649 TGCTAAGGCTATCATGTAGACAA 57.130 39.130 9.82 0.00 39.59 3.18
712 716 5.777223 AGATGCTAAGGCTATCATGTAGACA 59.223 40.000 9.82 0.00 39.59 3.41
713 717 6.098679 CAGATGCTAAGGCTATCATGTAGAC 58.901 44.000 6.53 3.95 39.59 2.59
714 718 5.777223 ACAGATGCTAAGGCTATCATGTAGA 59.223 40.000 6.53 0.00 39.59 2.59
715 719 6.035368 ACAGATGCTAAGGCTATCATGTAG 57.965 41.667 0.00 0.00 39.59 2.74
716 720 6.493458 TGTACAGATGCTAAGGCTATCATGTA 59.507 38.462 0.00 0.00 39.59 2.29
717 721 4.970860 ACAGATGCTAAGGCTATCATGT 57.029 40.909 0.00 0.00 39.59 3.21
718 722 5.787380 TGTACAGATGCTAAGGCTATCATG 58.213 41.667 0.00 0.00 39.59 3.07
719 723 6.268617 TCTTGTACAGATGCTAAGGCTATCAT 59.731 38.462 0.00 0.00 39.59 2.45
720 724 5.598417 TCTTGTACAGATGCTAAGGCTATCA 59.402 40.000 0.00 0.00 39.59 2.15
721 725 6.090483 TCTTGTACAGATGCTAAGGCTATC 57.910 41.667 0.00 0.00 39.59 2.08
722 726 6.678568 ATCTTGTACAGATGCTAAGGCTAT 57.321 37.500 0.00 0.00 41.13 2.97
743 747 1.034292 GCCCTTCCCAGTGCTTCATC 61.034 60.000 0.00 0.00 0.00 2.92
744 748 1.000396 GCCCTTCCCAGTGCTTCAT 60.000 57.895 0.00 0.00 0.00 2.57
747 751 2.860971 AGGCCCTTCCCAGTGCTT 60.861 61.111 0.00 0.00 34.51 3.91
753 757 2.935481 CACCTCAGGCCCTTCCCA 60.935 66.667 0.00 0.00 34.51 4.37
939 946 0.637743 ACTAGAAGGAGGAGGGGGAC 59.362 60.000 0.00 0.00 0.00 4.46
943 955 2.514582 TGTAGGACTAGAAGGAGGAGGG 59.485 54.545 0.00 0.00 0.00 4.30
953 965 3.271225 TGGTTGAGGGATGTAGGACTAGA 59.729 47.826 0.00 0.00 0.00 2.43
1003 1015 4.210120 CGTTAGCTCAAGAATCTGGTATGC 59.790 45.833 0.00 0.00 0.00 3.14
1109 1121 0.268869 ATGGGTAGGCATCCAGGAGA 59.731 55.000 0.00 0.00 36.38 3.71
1200 1218 1.693083 GCCCGCGAGTATCAACACAC 61.693 60.000 8.23 0.00 33.17 3.82
1293 1311 3.119029 TGCCTGCCAAAAGATCATTAAGC 60.119 43.478 0.00 0.00 0.00 3.09
1326 1344 2.165030 GCTCATGGTCTTTGGGTCATTG 59.835 50.000 0.00 0.00 0.00 2.82
1574 1592 1.265635 GATACACTGCGTTTGGTGCAA 59.734 47.619 0.00 0.00 42.70 4.08
1616 1634 3.014085 ATGTACGGTGGTGGAGGCG 62.014 63.158 0.00 0.00 0.00 5.52
1617 1635 1.449601 CATGTACGGTGGTGGAGGC 60.450 63.158 0.00 0.00 0.00 4.70
1618 1636 1.187974 TACATGTACGGTGGTGGAGG 58.812 55.000 0.08 0.00 0.00 4.30
1619 1637 4.659111 TTATACATGTACGGTGGTGGAG 57.341 45.455 7.96 0.00 0.00 3.86
1676 1697 2.895372 CCATAGTCGTTGCCGGCC 60.895 66.667 26.77 8.57 40.30 6.13
1680 1701 1.745115 TGCAGCCATAGTCGTTGCC 60.745 57.895 0.00 0.00 33.98 4.52
1758 1779 4.592192 AGCATCATCCCGCCGACG 62.592 66.667 0.00 0.00 39.67 5.12
1767 1796 1.493950 CCAAGTCGCCGAGCATCATC 61.494 60.000 0.00 0.00 33.17 2.92
1803 1832 1.358877 CATCGTTGAATCCAGCGTCA 58.641 50.000 0.00 0.00 45.35 4.35
1812 1841 5.982890 AAAAACTCATCCCATCGTTGAAT 57.017 34.783 0.00 0.00 0.00 2.57
1818 1847 5.005779 CGAGAACTAAAAACTCATCCCATCG 59.994 44.000 0.00 0.00 0.00 3.84
1847 1876 3.131709 TCCTCCTTATACGTAGTCCGG 57.868 52.381 0.08 0.00 43.93 5.14
1886 1915 5.765176 TGCTCACTCATTTTCAATTCACAG 58.235 37.500 0.00 0.00 0.00 3.66
1894 1923 5.833406 TTCACTTTGCTCACTCATTTTCA 57.167 34.783 0.00 0.00 0.00 2.69
1926 1955 9.683069 AATTAAGATACAAAAAGACTTGCACAG 57.317 29.630 0.00 0.00 0.00 3.66
2016 2046 3.691342 CTCACGGCCGAACCTCCA 61.691 66.667 35.90 5.68 35.61 3.86
2091 2126 2.124570 GCCACACCAGATCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
2228 2276 1.482621 AAGCATGTATCAGACGCGCG 61.483 55.000 30.96 30.96 34.00 6.86
2619 2707 1.597797 GGTATGGCAGCAAAGCAGCA 61.598 55.000 8.58 0.00 42.80 4.41
2686 2775 3.589988 GCCATCGTCCGATCATAAGATT 58.410 45.455 0.00 0.00 33.72 2.40
2744 2837 2.657944 CGATGCCGAGCTCTGAGC 60.658 66.667 21.72 21.72 42.84 4.26
2784 2878 1.302431 TCTGGATGCCACAACCGTG 60.302 57.895 0.00 0.00 43.21 4.94
2785 2879 1.302511 GTCTGGATGCCACAACCGT 60.303 57.895 0.00 0.00 0.00 4.83
2796 2890 0.674895 GTTGCCGCAGAAGTCTGGAT 60.675 55.000 10.25 0.00 43.94 3.41


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

AutoCloner maintained by Alex Coulton.