Multiple sequence alignment - TraesCS4A01G338400

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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 TraesCS4A01G338400 chr4A 100.000 2762 0 0 1 2762 620461118 620463879 0.000000e+00 5101
1 TraesCS4A01G338400 chr5B 96.002 1851 50 12 816 2643 700573944 700575793 0.000000e+00 2987
2 TraesCS4A01G338400 chr5B 87.608 347 39 2 3 347 700573159 700573503 1.540000e-107 399
3 TraesCS4A01G338400 chr5B 85.556 180 6 4 658 817 700573712 700573891 1.320000e-38 171
4 TraesCS4A01G338400 chr5B 95.833 96 4 0 2667 2762 700575787 700575882 3.680000e-34 156
5 TraesCS4A01G338400 chr5D 97.155 1441 35 3 816 2255 549019026 549020461 0.000000e+00 2429
6 TraesCS4A01G338400 chr5D 84.588 571 56 19 1755 2311 549031216 549031768 3.130000e-149 538
7 TraesCS4A01G338400 chr5D 87.931 348 39 2 1 347 549018240 549018585 9.210000e-110 407
8 TraesCS4A01G338400 chr5D 90.123 243 10 2 2533 2761 549020748 549020990 1.240000e-78 303
9 TraesCS4A01G338400 chr5D 88.235 221 16 4 2254 2474 549020539 549020749 3.530000e-64 255
10 TraesCS4A01G338400 chr5D 86.592 179 5 4 658 817 549018794 549018972 2.190000e-41 180
11 TraesCS4A01G338400 chr6D 90.208 337 14 4 499 817 22107583 22107248 3.290000e-114 422


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 TraesCS4A01G338400 chr4A 620461118 620463879 2761 False 5101.00 5101 100.00000 1 2762 1 chr4A.!!$F1 2761
1 TraesCS4A01G338400 chr5B 700573159 700575882 2723 False 928.25 2987 91.24975 3 2762 4 chr5B.!!$F1 2759
2 TraesCS4A01G338400 chr5D 549018240 549020990 2750 False 714.80 2429 90.00720 1 2761 5 chr5D.!!$F2 2760
3 TraesCS4A01G338400 chr5D 549031216 549031768 552 False 538.00 538 84.58800 1755 2311 1 chr5D.!!$F1 556

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
523 526 0.179134 GGTGATCTAGTGTCGCGCTT 60.179 55.0 5.56 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2336 2533 0.107361 GTACCATGGTACCACAGCCC 60.107 60.0 35.68 14.98 43.6 5.19 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
17 18 2.598467 TTTGACCACCGCCAACCT 59.402 55.556 0.00 0.00 0.00 3.50
46 47 1.677052 TCGGGGTTTAACTTGTTGCAC 59.323 47.619 0.00 0.00 0.00 4.57
48 49 2.036387 GGGGTTTAACTTGTTGCACCT 58.964 47.619 12.58 0.00 0.00 4.00
61 62 0.392461 TGCACCTCTAAACCCGCATC 60.392 55.000 0.00 0.00 0.00 3.91
62 63 0.392461 GCACCTCTAAACCCGCATCA 60.392 55.000 0.00 0.00 0.00 3.07
88 89 0.831288 CAACTTGCCATTCCCCACCA 60.831 55.000 0.00 0.00 0.00 4.17
103 104 0.808453 CACCACTTGAACCGACACGT 60.808 55.000 0.00 0.00 0.00 4.49
138 139 0.821517 TACCCACCACGCAGACATAG 59.178 55.000 0.00 0.00 0.00 2.23
154 155 1.041437 ATAGCGCAACTCTAGGGGAC 58.959 55.000 11.47 0.00 0.00 4.46
175 176 2.423088 CCGTATAGTGGGAGTGAGGAGT 60.423 54.545 0.00 0.00 0.00 3.85
186 187 0.395312 GTGAGGAGTTTCGGTCCCAA 59.605 55.000 0.00 0.00 34.21 4.12
187 188 1.133363 TGAGGAGTTTCGGTCCCAAA 58.867 50.000 0.00 0.00 34.21 3.28
188 189 1.202722 TGAGGAGTTTCGGTCCCAAAC 60.203 52.381 4.05 4.05 34.21 2.93
190 191 2.301009 GAGGAGTTTCGGTCCCAAACTA 59.699 50.000 13.87 0.00 42.84 2.24
192 193 2.064014 GAGTTTCGGTCCCAAACTACG 58.936 52.381 13.87 0.00 42.84 3.51
193 194 0.514255 GTTTCGGTCCCAAACTACGC 59.486 55.000 4.95 0.00 32.01 4.42
194 195 0.945265 TTTCGGTCCCAAACTACGCG 60.945 55.000 3.53 3.53 0.00 6.01
196 197 2.658422 GGTCCCAAACTACGCGGA 59.342 61.111 12.47 0.00 0.00 5.54
197 198 1.004679 GGTCCCAAACTACGCGGAA 60.005 57.895 12.47 0.00 0.00 4.30
198 199 1.293963 GGTCCCAAACTACGCGGAAC 61.294 60.000 12.47 0.00 0.00 3.62
199 200 1.004679 TCCCAAACTACGCGGAACC 60.005 57.895 12.47 0.00 0.00 3.62
200 201 2.385091 CCCAAACTACGCGGAACCG 61.385 63.158 12.47 9.00 43.09 4.44
216 217 0.666577 ACCGCTAGCGTCTTGTTGAC 60.667 55.000 33.18 0.00 42.06 3.18
232 233 8.511321 GTCTTGTTGACCATATTTGTTGACATA 58.489 33.333 0.00 0.00 39.69 2.29
240 241 8.613060 ACCATATTTGTTGACATATCAGCTAG 57.387 34.615 0.00 0.00 37.01 3.42
248 249 7.234355 TGTTGACATATCAGCTAGGAGAGATA 58.766 38.462 0.00 0.00 37.01 1.98
290 291 7.624360 AAGCAATAATCATAAACCTCGACAA 57.376 32.000 0.00 0.00 0.00 3.18
291 292 7.016361 AGCAATAATCATAAACCTCGACAAC 57.984 36.000 0.00 0.00 0.00 3.32
312 313 9.988350 GACAACGAGTATGACATAATTTTGATT 57.012 29.630 17.96 4.34 0.00 2.57
333 336 0.409876 AGAGTGCCACTACCCTCTCA 59.590 55.000 0.00 0.00 28.22 3.27
424 427 8.650143 TTTGAGGGATAAAAGAAAGCATAACT 57.350 30.769 0.00 0.00 0.00 2.24
442 445 7.282450 AGCATAACTAAAATAGCAGTTGGGTAC 59.718 37.037 0.00 0.00 35.79 3.34
443 446 7.066525 GCATAACTAAAATAGCAGTTGGGTACA 59.933 37.037 0.00 0.00 35.79 2.90
445 448 9.695155 ATAACTAAAATAGCAGTTGGGTACAAT 57.305 29.630 0.00 0.00 39.13 2.71
451 454 4.382386 AGCAGTTGGGTACAATAAAGGT 57.618 40.909 0.00 0.00 39.13 3.50
452 455 4.079253 AGCAGTTGGGTACAATAAAGGTG 58.921 43.478 0.00 0.00 39.13 4.00
455 458 5.313712 CAGTTGGGTACAATAAAGGTGACT 58.686 41.667 0.00 0.00 40.30 3.41
456 459 6.469410 CAGTTGGGTACAATAAAGGTGACTA 58.531 40.000 0.00 0.00 38.35 2.59
458 461 6.938596 AGTTGGGTACAATAAAGGTGACTAAC 59.061 38.462 0.00 0.00 38.35 2.34
459 462 6.436738 TGGGTACAATAAAGGTGACTAACA 57.563 37.500 0.00 0.00 42.68 2.41
460 463 6.839454 TGGGTACAATAAAGGTGACTAACAA 58.161 36.000 0.00 0.00 42.68 2.83
461 464 7.288560 TGGGTACAATAAAGGTGACTAACAAA 58.711 34.615 0.00 0.00 42.68 2.83
462 465 7.778853 TGGGTACAATAAAGGTGACTAACAAAA 59.221 33.333 0.00 0.00 42.68 2.44
463 466 8.077991 GGGTACAATAAAGGTGACTAACAAAAC 58.922 37.037 0.00 0.00 42.68 2.43
464 467 8.077991 GGTACAATAAAGGTGACTAACAAAACC 58.922 37.037 0.00 0.00 42.68 3.27
469 472 5.641789 AAGGTGACTAACAAAACCTAGGT 57.358 39.130 9.21 9.21 42.25 3.08
490 493 7.856145 AGGTAAACTAATCATTGCAAGAGAG 57.144 36.000 4.94 7.06 0.00 3.20
519 522 3.444703 AAGATGGTGATCTAGTGTCGC 57.555 47.619 0.00 0.00 38.03 5.19
523 526 0.179134 GGTGATCTAGTGTCGCGCTT 60.179 55.000 5.56 0.00 0.00 4.68
524 527 1.630148 GTGATCTAGTGTCGCGCTTT 58.370 50.000 5.56 0.00 0.00 3.51
525 528 2.479049 GGTGATCTAGTGTCGCGCTTTA 60.479 50.000 5.56 0.00 0.00 1.85
526 529 2.784380 GTGATCTAGTGTCGCGCTTTAG 59.216 50.000 5.56 0.66 0.00 1.85
527 530 2.681344 TGATCTAGTGTCGCGCTTTAGA 59.319 45.455 5.56 6.58 0.00 2.10
532 535 3.724295 AGTGTCGCGCTTTAGAAAATC 57.276 42.857 5.56 0.00 0.00 2.17
533 536 3.326747 AGTGTCGCGCTTTAGAAAATCT 58.673 40.909 5.56 0.00 0.00 2.40
534 537 3.123621 AGTGTCGCGCTTTAGAAAATCTG 59.876 43.478 5.56 0.00 0.00 2.90
535 538 3.064207 TGTCGCGCTTTAGAAAATCTGT 58.936 40.909 5.56 0.00 0.00 3.41
536 539 4.090930 GTGTCGCGCTTTAGAAAATCTGTA 59.909 41.667 5.56 0.00 0.00 2.74
537 540 4.868171 TGTCGCGCTTTAGAAAATCTGTAT 59.132 37.500 5.56 0.00 0.00 2.29
538 541 5.350365 TGTCGCGCTTTAGAAAATCTGTATT 59.650 36.000 5.56 0.00 0.00 1.89
539 542 6.532302 TGTCGCGCTTTAGAAAATCTGTATTA 59.468 34.615 5.56 0.00 0.00 0.98
541 544 7.901377 GTCGCGCTTTAGAAAATCTGTATTAAA 59.099 33.333 5.56 0.00 0.00 1.52
542 545 8.114290 TCGCGCTTTAGAAAATCTGTATTAAAG 58.886 33.333 5.56 0.00 0.00 1.85
544 547 8.182227 GCGCTTTAGAAAATCTGTATTAAAGGT 58.818 33.333 0.00 0.00 0.00 3.50
550 553 8.635765 AGAAAATCTGTATTAAAGGTCAAGCA 57.364 30.769 0.00 0.00 0.00 3.91
551 554 9.077885 AGAAAATCTGTATTAAAGGTCAAGCAA 57.922 29.630 0.00 0.00 0.00 3.91
552 555 9.691362 GAAAATCTGTATTAAAGGTCAAGCAAA 57.309 29.630 0.00 0.00 0.00 3.68
593 596 9.321562 ACATAAGTAAGATAACATTTGGGTACG 57.678 33.333 0.00 0.00 0.00 3.67
599 602 7.619964 AAGATAACATTTGGGTACGTAAAGG 57.380 36.000 0.00 0.00 0.00 3.11
600 603 6.714278 AGATAACATTTGGGTACGTAAAGGT 58.286 36.000 0.00 0.00 33.12 3.50
601 604 6.596497 AGATAACATTTGGGTACGTAAAGGTG 59.404 38.462 10.23 0.00 32.40 4.00
602 605 4.354893 ACATTTGGGTACGTAAAGGTGA 57.645 40.909 0.00 0.00 31.27 4.02
603 606 4.320870 ACATTTGGGTACGTAAAGGTGAG 58.679 43.478 0.00 0.00 31.27 3.51
604 607 4.202388 ACATTTGGGTACGTAAAGGTGAGT 60.202 41.667 0.00 0.00 31.27 3.41
605 608 3.389925 TTGGGTACGTAAAGGTGAGTG 57.610 47.619 0.00 0.00 0.00 3.51
606 609 2.596346 TGGGTACGTAAAGGTGAGTGA 58.404 47.619 0.00 0.00 0.00 3.41
607 610 2.297033 TGGGTACGTAAAGGTGAGTGAC 59.703 50.000 0.00 0.00 0.00 3.67
608 611 2.589014 GGTACGTAAAGGTGAGTGACG 58.411 52.381 0.00 0.00 39.37 4.35
609 612 2.226437 GGTACGTAAAGGTGAGTGACGA 59.774 50.000 0.00 0.00 37.00 4.20
610 613 3.304659 GGTACGTAAAGGTGAGTGACGAA 60.305 47.826 0.00 0.00 37.00 3.85
611 614 3.441496 ACGTAAAGGTGAGTGACGAAA 57.559 42.857 0.00 0.00 37.00 3.46
612 615 3.118542 ACGTAAAGGTGAGTGACGAAAC 58.881 45.455 0.00 0.00 37.00 2.78
613 616 3.117794 CGTAAAGGTGAGTGACGAAACA 58.882 45.455 0.00 0.00 35.59 2.83
614 617 3.739300 CGTAAAGGTGAGTGACGAAACAT 59.261 43.478 0.00 0.00 35.59 2.71
615 618 4.919168 CGTAAAGGTGAGTGACGAAACATA 59.081 41.667 0.00 0.00 35.59 2.29
616 619 5.575606 CGTAAAGGTGAGTGACGAAACATAT 59.424 40.000 0.00 0.00 35.59 1.78
617 620 6.748658 CGTAAAGGTGAGTGACGAAACATATA 59.251 38.462 0.00 0.00 35.59 0.86
618 621 7.044249 CGTAAAGGTGAGTGACGAAACATATAG 60.044 40.741 0.00 0.00 35.59 1.31
619 622 5.263968 AGGTGAGTGACGAAACATATAGG 57.736 43.478 0.00 0.00 0.00 2.57
620 623 4.954202 AGGTGAGTGACGAAACATATAGGA 59.046 41.667 0.00 0.00 0.00 2.94
621 624 5.421056 AGGTGAGTGACGAAACATATAGGAA 59.579 40.000 0.00 0.00 0.00 3.36
622 625 6.070995 AGGTGAGTGACGAAACATATAGGAAA 60.071 38.462 0.00 0.00 0.00 3.13
623 626 6.592607 GGTGAGTGACGAAACATATAGGAAAA 59.407 38.462 0.00 0.00 0.00 2.29
624 627 7.412672 GGTGAGTGACGAAACATATAGGAAAAC 60.413 40.741 0.00 0.00 0.00 2.43
625 628 7.331193 GTGAGTGACGAAACATATAGGAAAACT 59.669 37.037 0.00 0.00 0.00 2.66
626 629 8.525316 TGAGTGACGAAACATATAGGAAAACTA 58.475 33.333 0.00 0.00 35.80 2.24
627 630 9.362539 GAGTGACGAAACATATAGGAAAACTAA 57.637 33.333 0.00 0.00 34.79 2.24
628 631 9.148104 AGTGACGAAACATATAGGAAAACTAAC 57.852 33.333 0.00 0.00 34.79 2.34
629 632 8.385858 GTGACGAAACATATAGGAAAACTAACC 58.614 37.037 0.00 0.00 34.79 2.85
630 633 8.095792 TGACGAAACATATAGGAAAACTAACCA 58.904 33.333 0.00 0.00 34.79 3.67
631 634 9.106070 GACGAAACATATAGGAAAACTAACCAT 57.894 33.333 0.00 0.00 34.79 3.55
632 635 9.457436 ACGAAACATATAGGAAAACTAACCATT 57.543 29.630 0.00 0.00 34.79 3.16
633 636 9.716507 CGAAACATATAGGAAAACTAACCATTG 57.283 33.333 0.00 0.00 34.79 2.82
634 637 9.516314 GAAACATATAGGAAAACTAACCATTGC 57.484 33.333 0.00 0.00 34.79 3.56
635 638 8.588290 AACATATAGGAAAACTAACCATTGCA 57.412 30.769 0.00 0.00 34.79 4.08
636 639 8.588290 ACATATAGGAAAACTAACCATTGCAA 57.412 30.769 0.00 0.00 34.79 4.08
637 640 8.686334 ACATATAGGAAAACTAACCATTGCAAG 58.314 33.333 4.94 0.00 34.79 4.01
638 641 8.902806 CATATAGGAAAACTAACCATTGCAAGA 58.097 33.333 4.94 0.00 34.79 3.02
639 642 5.453567 AGGAAAACTAACCATTGCAAGAC 57.546 39.130 4.94 0.00 0.00 3.01
640 643 4.892934 AGGAAAACTAACCATTGCAAGACA 59.107 37.500 4.94 0.00 0.00 3.41
641 644 5.362430 AGGAAAACTAACCATTGCAAGACAA 59.638 36.000 4.94 0.00 44.01 3.18
642 645 5.691754 GGAAAACTAACCATTGCAAGACAAG 59.308 40.000 4.94 1.29 42.87 3.16
643 646 5.852282 AAACTAACCATTGCAAGACAAGT 57.148 34.783 4.94 1.94 42.87 3.16
644 647 6.952773 AAACTAACCATTGCAAGACAAGTA 57.047 33.333 4.94 0.00 42.87 2.24
645 648 6.560253 AACTAACCATTGCAAGACAAGTAG 57.440 37.500 4.94 4.45 42.87 2.57
646 649 5.865085 ACTAACCATTGCAAGACAAGTAGA 58.135 37.500 4.94 0.00 42.87 2.59
647 650 6.296026 ACTAACCATTGCAAGACAAGTAGAA 58.704 36.000 4.94 0.00 42.87 2.10
648 651 6.770785 ACTAACCATTGCAAGACAAGTAGAAA 59.229 34.615 4.94 0.00 42.87 2.52
649 652 6.463995 AACCATTGCAAGACAAGTAGAAAA 57.536 33.333 4.94 0.00 42.87 2.29
650 653 6.463995 ACCATTGCAAGACAAGTAGAAAAA 57.536 33.333 4.94 0.00 42.87 1.94
677 680 8.125978 AGATATTGCCTCAGAAAAACAAATGA 57.874 30.769 0.00 0.00 0.00 2.57
687 690 8.925161 TCAGAAAAACAAATGATTCTTTTCGT 57.075 26.923 11.26 0.00 39.71 3.85
723 740 0.949105 TGACTCCGAAGAAAAGGCGC 60.949 55.000 0.00 0.00 0.00 6.53
755 772 4.900684 AGAAGGCTAGGAAAGAAAGTCAC 58.099 43.478 0.00 0.00 0.00 3.67
784 807 3.173151 TGAAGCCCATCTCAGTCAGTTA 58.827 45.455 0.00 0.00 0.00 2.24
944 1034 2.093288 TGGGAGTGAGATCATCAGTTGC 60.093 50.000 0.00 0.00 41.87 4.17
1866 1965 2.276732 TGAGGGCATTAGCTTATGGC 57.723 50.000 26.05 26.05 46.93 4.40
1906 2009 6.625362 AGTGTGTATATAGGCTTGATGATCG 58.375 40.000 0.00 0.00 0.00 3.69
1907 2010 6.434340 AGTGTGTATATAGGCTTGATGATCGA 59.566 38.462 0.00 0.00 0.00 3.59
1908 2011 7.123397 AGTGTGTATATAGGCTTGATGATCGAT 59.877 37.037 0.00 0.00 0.00 3.59
1909 2012 7.433719 GTGTGTATATAGGCTTGATGATCGATC 59.566 40.741 18.72 18.72 0.00 3.69
2053 2167 8.781196 GTTATGTGCTCATAATGAATGTCATCT 58.219 33.333 20.67 0.00 44.78 2.90
2124 2238 4.254492 ACTTCTGATTCGGCTAAAACCTC 58.746 43.478 0.00 0.00 0.00 3.85
2139 2253 7.255625 GGCTAAAACCTCCCATAATTGAAGATC 60.256 40.741 0.00 0.00 0.00 2.75
2396 2594 3.659786 TGACGGAAATTGACAGTAGTGG 58.340 45.455 1.92 0.00 0.00 4.00
2398 2596 4.062991 GACGGAAATTGACAGTAGTGGTT 58.937 43.478 1.92 0.00 0.00 3.67
2432 2630 3.307339 GGAGGAGAAAGCACTCATCTTGT 60.307 47.826 15.55 0.00 44.00 3.16
2434 2632 3.326006 AGGAGAAAGCACTCATCTTGTGA 59.674 43.478 0.00 0.00 38.51 3.58
2480 2738 2.481289 GCTTTCAGCAGTTACCCTCT 57.519 50.000 0.00 0.00 41.89 3.69
2481 2739 3.611766 GCTTTCAGCAGTTACCCTCTA 57.388 47.619 0.00 0.00 41.89 2.43
2482 2740 4.143986 GCTTTCAGCAGTTACCCTCTAT 57.856 45.455 0.00 0.00 41.89 1.98
2483 2741 4.123506 GCTTTCAGCAGTTACCCTCTATC 58.876 47.826 0.00 0.00 41.89 2.08
2484 2742 4.698575 CTTTCAGCAGTTACCCTCTATCC 58.301 47.826 0.00 0.00 0.00 2.59
2485 2743 3.398318 TCAGCAGTTACCCTCTATCCA 57.602 47.619 0.00 0.00 0.00 3.41
2486 2744 3.719871 TCAGCAGTTACCCTCTATCCAA 58.280 45.455 0.00 0.00 0.00 3.53
2487 2745 4.298626 TCAGCAGTTACCCTCTATCCAAT 58.701 43.478 0.00 0.00 0.00 3.16
2488 2746 5.464069 TCAGCAGTTACCCTCTATCCAATA 58.536 41.667 0.00 0.00 0.00 1.90
2489 2747 6.084738 TCAGCAGTTACCCTCTATCCAATAT 58.915 40.000 0.00 0.00 0.00 1.28
2490 2748 6.014242 TCAGCAGTTACCCTCTATCCAATATG 60.014 42.308 0.00 0.00 0.00 1.78
2491 2749 5.249393 AGCAGTTACCCTCTATCCAATATGG 59.751 44.000 0.00 0.00 39.43 2.74
2492 2750 5.571658 GCAGTTACCCTCTATCCAATATGGG 60.572 48.000 0.00 0.00 38.32 4.00
2493 2751 5.045578 CAGTTACCCTCTATCCAATATGGGG 60.046 48.000 0.00 0.00 38.32 4.96
2494 2752 3.674358 ACCCTCTATCCAATATGGGGT 57.326 47.619 0.00 0.00 40.47 4.95
2495 2753 3.532102 ACCCTCTATCCAATATGGGGTC 58.468 50.000 0.00 0.00 41.30 4.46
2496 2754 3.115962 ACCCTCTATCCAATATGGGGTCA 60.116 47.826 0.00 0.00 41.30 4.02
2497 2755 3.521126 CCCTCTATCCAATATGGGGTCAG 59.479 52.174 0.00 0.00 38.32 3.51
2498 2756 4.429505 CCTCTATCCAATATGGGGTCAGA 58.570 47.826 0.00 0.00 38.32 3.27
2499 2757 5.035556 CCTCTATCCAATATGGGGTCAGAT 58.964 45.833 0.00 0.00 38.32 2.90
2500 2758 5.490357 CCTCTATCCAATATGGGGTCAGATT 59.510 44.000 0.00 0.00 38.32 2.40
2501 2759 6.378661 TCTATCCAATATGGGGTCAGATTG 57.621 41.667 0.00 6.72 46.44 2.67
2502 2760 5.851693 TCTATCCAATATGGGGTCAGATTGT 59.148 40.000 11.21 0.00 45.83 2.71
2503 2761 4.437682 TCCAATATGGGGTCAGATTGTC 57.562 45.455 11.21 0.00 45.83 3.18
2504 2762 3.785325 TCCAATATGGGGTCAGATTGTCA 59.215 43.478 11.21 0.00 45.83 3.58
2505 2763 4.416513 TCCAATATGGGGTCAGATTGTCAT 59.583 41.667 11.21 0.00 45.83 3.06
2506 2764 4.521639 CCAATATGGGGTCAGATTGTCATG 59.478 45.833 11.21 0.00 45.83 3.07
2507 2765 5.135383 CAATATGGGGTCAGATTGTCATGT 58.865 41.667 5.79 0.00 43.65 3.21
2508 2766 3.744940 ATGGGGTCAGATTGTCATGTT 57.255 42.857 0.00 0.00 0.00 2.71
2509 2767 3.524095 TGGGGTCAGATTGTCATGTTT 57.476 42.857 0.00 0.00 0.00 2.83
2510 2768 3.843422 TGGGGTCAGATTGTCATGTTTT 58.157 40.909 0.00 0.00 0.00 2.43
2511 2769 4.222336 TGGGGTCAGATTGTCATGTTTTT 58.778 39.130 0.00 0.00 0.00 1.94
2512 2770 4.280677 TGGGGTCAGATTGTCATGTTTTTC 59.719 41.667 0.00 0.00 0.00 2.29
2513 2771 4.280677 GGGGTCAGATTGTCATGTTTTTCA 59.719 41.667 0.00 0.00 0.00 2.69
2514 2772 5.464168 GGGTCAGATTGTCATGTTTTTCAG 58.536 41.667 0.00 0.00 0.00 3.02
2515 2773 5.010012 GGGTCAGATTGTCATGTTTTTCAGT 59.990 40.000 0.00 0.00 0.00 3.41
2516 2774 6.461509 GGGTCAGATTGTCATGTTTTTCAGTT 60.462 38.462 0.00 0.00 0.00 3.16
2517 2775 7.255451 GGGTCAGATTGTCATGTTTTTCAGTTA 60.255 37.037 0.00 0.00 0.00 2.24
2518 2776 8.299570 GGTCAGATTGTCATGTTTTTCAGTTAT 58.700 33.333 0.00 0.00 0.00 1.89
2519 2777 9.683069 GTCAGATTGTCATGTTTTTCAGTTATT 57.317 29.630 0.00 0.00 0.00 1.40
2520 2778 9.897744 TCAGATTGTCATGTTTTTCAGTTATTC 57.102 29.630 0.00 0.00 0.00 1.75
2521 2779 8.843733 CAGATTGTCATGTTTTTCAGTTATTCG 58.156 33.333 0.00 0.00 0.00 3.34
2522 2780 8.567948 AGATTGTCATGTTTTTCAGTTATTCGT 58.432 29.630 0.00 0.00 0.00 3.85
2523 2781 8.728088 ATTGTCATGTTTTTCAGTTATTCGTC 57.272 30.769 0.00 0.00 0.00 4.20
2524 2782 7.252965 TGTCATGTTTTTCAGTTATTCGTCA 57.747 32.000 0.00 0.00 0.00 4.35
2525 2783 7.129622 TGTCATGTTTTTCAGTTATTCGTCAC 58.870 34.615 0.00 0.00 0.00 3.67
2526 2784 7.129622 GTCATGTTTTTCAGTTATTCGTCACA 58.870 34.615 0.00 0.00 0.00 3.58
2527 2785 7.642194 GTCATGTTTTTCAGTTATTCGTCACAA 59.358 33.333 0.00 0.00 0.00 3.33
2528 2786 7.642194 TCATGTTTTTCAGTTATTCGTCACAAC 59.358 33.333 0.00 0.00 0.00 3.32
2529 2787 6.259638 TGTTTTTCAGTTATTCGTCACAACC 58.740 36.000 0.00 0.00 0.00 3.77
2530 2788 5.427036 TTTTCAGTTATTCGTCACAACCC 57.573 39.130 0.00 0.00 0.00 4.11
2531 2789 4.345859 TTCAGTTATTCGTCACAACCCT 57.654 40.909 0.00 0.00 0.00 4.34
2532 2790 4.345859 TCAGTTATTCGTCACAACCCTT 57.654 40.909 0.00 0.00 0.00 3.95
2533 2791 4.710324 TCAGTTATTCGTCACAACCCTTT 58.290 39.130 0.00 0.00 0.00 3.11
2541 2799 2.031870 GTCACAACCCTTTTCCTTGCT 58.968 47.619 0.00 0.00 0.00 3.91
2547 2805 0.101219 CCCTTTTCCTTGCTATGCGC 59.899 55.000 0.00 0.00 39.77 6.09
2551 2809 0.672091 TTTCCTTGCTATGCGCGTGA 60.672 50.000 13.61 0.00 43.27 4.35
2569 2827 0.249447 GAGCCCTGTTGCACCAAAAC 60.249 55.000 0.00 0.00 0.00 2.43
2584 2842 5.050023 GCACCAAAACTGTAGAAGAGTTCTC 60.050 44.000 0.00 0.00 41.14 2.87
2609 2867 8.002459 TCCTTTGTTAACTTAGTTTTCCCTGAT 58.998 33.333 1.94 0.00 0.00 2.90
2646 2904 2.452600 TGGAACTTGAAGTTGGCCTT 57.547 45.000 16.25 0.00 38.80 4.35
2737 3009 7.004086 TGAAACATTCCTATAATAGGGGCAAG 58.996 38.462 0.00 0.00 46.24 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.887387 GCGGGTTTAGAGGTGCAACA 60.887 55.000 3.64 0.00 39.98 3.33
40 41 0.887387 TGCGGGTTTAGAGGTGCAAC 60.887 55.000 0.00 0.00 0.00 4.17
46 47 1.017387 GCTTGATGCGGGTTTAGAGG 58.983 55.000 0.00 0.00 0.00 3.69
61 62 2.438951 AATGGCAAGTTGGGCGCTTG 62.439 55.000 7.64 4.42 44.34 4.01
62 63 2.158561 GAATGGCAAGTTGGGCGCTT 62.159 55.000 7.64 0.00 35.84 4.68
88 89 2.967740 GACACGTGTCGGTTCAAGT 58.032 52.632 31.03 0.00 35.12 3.16
103 104 1.888512 GGGTAGTGTAAGACCACGACA 59.111 52.381 6.84 0.00 41.14 4.35
108 109 1.972795 GTGGTGGGTAGTGTAAGACCA 59.027 52.381 0.00 0.00 37.47 4.02
138 139 2.187163 GGTCCCCTAGAGTTGCGC 59.813 66.667 0.00 0.00 0.00 6.09
154 155 2.231529 CTCCTCACTCCCACTATACGG 58.768 57.143 0.00 0.00 0.00 4.02
155 156 2.933573 ACTCCTCACTCCCACTATACG 58.066 52.381 0.00 0.00 0.00 3.06
175 176 0.945265 CGCGTAGTTTGGGACCGAAA 60.945 55.000 0.00 0.00 0.00 3.46
193 194 2.158959 CAAGACGCTAGCGGTTCCG 61.159 63.158 37.66 19.56 44.69 4.30
194 195 0.669625 AACAAGACGCTAGCGGTTCC 60.670 55.000 37.66 23.46 44.69 3.62
196 197 0.032952 TCAACAAGACGCTAGCGGTT 59.967 50.000 37.66 27.88 44.69 4.44
197 198 0.666577 GTCAACAAGACGCTAGCGGT 60.667 55.000 37.66 24.10 44.69 5.68
198 199 2.070861 GTCAACAAGACGCTAGCGG 58.929 57.895 37.66 23.44 44.69 5.52
216 217 7.879677 TCCTAGCTGATATGTCAACAAATATGG 59.120 37.037 0.00 0.00 33.05 2.74
248 249 6.594788 TTGCTTTTTATGCCAGAAGAGAAT 57.405 33.333 0.00 0.00 0.00 2.40
257 258 9.323985 GGTTTATGATTATTGCTTTTTATGCCA 57.676 29.630 0.00 0.00 0.00 4.92
263 264 8.519526 TGTCGAGGTTTATGATTATTGCTTTTT 58.480 29.630 0.00 0.00 0.00 1.94
264 265 8.050778 TGTCGAGGTTTATGATTATTGCTTTT 57.949 30.769 0.00 0.00 0.00 2.27
268 269 5.901884 CGTTGTCGAGGTTTATGATTATTGC 59.098 40.000 0.00 0.00 39.71 3.56
285 286 7.671827 TCAAAATTATGTCATACTCGTTGTCG 58.328 34.615 0.00 0.00 38.55 4.35
302 303 7.338449 GGGTAGTGGCACTCTAAATCAAAATTA 59.662 37.037 25.80 0.00 36.13 1.40
312 313 2.921834 AGAGGGTAGTGGCACTCTAA 57.078 50.000 25.80 3.46 46.48 2.10
397 400 9.705290 GTTATGCTTTCTTTTATCCCTCAAAAA 57.295 29.630 0.00 0.00 0.00 1.94
398 401 9.088987 AGTTATGCTTTCTTTTATCCCTCAAAA 57.911 29.630 0.00 0.00 0.00 2.44
399 402 8.650143 AGTTATGCTTTCTTTTATCCCTCAAA 57.350 30.769 0.00 0.00 0.00 2.69
400 403 9.747898 TTAGTTATGCTTTCTTTTATCCCTCAA 57.252 29.630 0.00 0.00 0.00 3.02
401 404 9.747898 TTTAGTTATGCTTTCTTTTATCCCTCA 57.252 29.630 0.00 0.00 0.00 3.86
411 414 9.846248 CAACTGCTATTTTAGTTATGCTTTCTT 57.154 29.630 0.00 0.00 35.50 2.52
412 415 8.462016 CCAACTGCTATTTTAGTTATGCTTTCT 58.538 33.333 0.00 0.00 35.50 2.52
413 416 7.702348 CCCAACTGCTATTTTAGTTATGCTTTC 59.298 37.037 0.00 0.00 35.50 2.62
417 420 6.451064 ACCCAACTGCTATTTTAGTTATGC 57.549 37.500 0.00 0.00 35.50 3.14
424 427 8.962679 CCTTTATTGTACCCAACTGCTATTTTA 58.037 33.333 0.00 0.00 32.26 1.52
434 437 6.711645 TGTTAGTCACCTTTATTGTACCCAAC 59.288 38.462 0.00 0.00 32.26 3.77
442 445 8.512138 CCTAGGTTTTGTTAGTCACCTTTATTG 58.488 37.037 0.00 0.00 0.00 1.90
443 446 8.222637 ACCTAGGTTTTGTTAGTCACCTTTATT 58.777 33.333 9.21 0.00 0.00 1.40
445 448 7.140522 ACCTAGGTTTTGTTAGTCACCTTTA 57.859 36.000 9.21 0.00 0.00 1.85
446 449 6.009908 ACCTAGGTTTTGTTAGTCACCTTT 57.990 37.500 9.21 0.00 0.00 3.11
449 452 6.994496 AGTTTACCTAGGTTTTGTTAGTCACC 59.006 38.462 22.11 0.00 0.00 4.02
458 461 8.519526 TGCAATGATTAGTTTACCTAGGTTTTG 58.480 33.333 22.11 4.19 0.00 2.44
459 462 8.644374 TGCAATGATTAGTTTACCTAGGTTTT 57.356 30.769 22.11 6.08 0.00 2.43
460 463 8.644374 TTGCAATGATTAGTTTACCTAGGTTT 57.356 30.769 22.11 6.45 0.00 3.27
461 464 8.107095 TCTTGCAATGATTAGTTTACCTAGGTT 58.893 33.333 22.11 4.10 0.00 3.50
462 465 7.630082 TCTTGCAATGATTAGTTTACCTAGGT 58.370 34.615 20.57 20.57 0.00 3.08
463 466 7.987458 TCTCTTGCAATGATTAGTTTACCTAGG 59.013 37.037 7.41 7.41 0.00 3.02
464 467 8.948631 TCTCTTGCAATGATTAGTTTACCTAG 57.051 34.615 0.00 0.00 0.00 3.02
505 508 1.630148 AAAGCGCGACACTAGATCAC 58.370 50.000 12.10 0.00 0.00 3.06
509 512 3.564235 TTTCTAAAGCGCGACACTAGA 57.436 42.857 12.10 6.93 0.00 2.43
510 513 4.563184 AGATTTTCTAAAGCGCGACACTAG 59.437 41.667 12.10 4.37 0.00 2.57
519 522 9.704098 GACCTTTAATACAGATTTTCTAAAGCG 57.296 33.333 0.00 0.00 0.00 4.68
524 527 9.733556 TGCTTGACCTTTAATACAGATTTTCTA 57.266 29.630 0.00 0.00 0.00 2.10
525 528 8.635765 TGCTTGACCTTTAATACAGATTTTCT 57.364 30.769 0.00 0.00 0.00 2.52
526 529 9.691362 TTTGCTTGACCTTTAATACAGATTTTC 57.309 29.630 0.00 0.00 0.00 2.29
567 570 9.321562 CGTACCCAAATGTTATCTTACTTATGT 57.678 33.333 0.00 0.00 0.00 2.29
568 571 9.321562 ACGTACCCAAATGTTATCTTACTTATG 57.678 33.333 0.00 0.00 0.00 1.90
571 574 9.723601 TTTACGTACCCAAATGTTATCTTACTT 57.276 29.630 0.00 0.00 0.00 2.24
572 575 9.374838 CTTTACGTACCCAAATGTTATCTTACT 57.625 33.333 0.00 0.00 0.00 2.24
573 576 8.606602 CCTTTACGTACCCAAATGTTATCTTAC 58.393 37.037 0.00 0.00 0.00 2.34
574 577 8.320617 ACCTTTACGTACCCAAATGTTATCTTA 58.679 33.333 0.00 0.00 0.00 2.10
577 580 6.594937 TCACCTTTACGTACCCAAATGTTATC 59.405 38.462 0.00 0.00 0.00 1.75
578 581 6.474630 TCACCTTTACGTACCCAAATGTTAT 58.525 36.000 0.00 0.00 0.00 1.89
579 582 5.862845 TCACCTTTACGTACCCAAATGTTA 58.137 37.500 0.00 0.00 0.00 2.41
582 585 4.153475 CACTCACCTTTACGTACCCAAATG 59.847 45.833 0.00 0.00 0.00 2.32
583 586 4.040706 TCACTCACCTTTACGTACCCAAAT 59.959 41.667 0.00 0.00 0.00 2.32
585 588 2.964464 TCACTCACCTTTACGTACCCAA 59.036 45.455 0.00 0.00 0.00 4.12
586 589 2.297033 GTCACTCACCTTTACGTACCCA 59.703 50.000 0.00 0.00 0.00 4.51
587 590 2.669391 CGTCACTCACCTTTACGTACCC 60.669 54.545 0.00 0.00 0.00 3.69
588 591 2.226437 TCGTCACTCACCTTTACGTACC 59.774 50.000 0.00 0.00 35.21 3.34
590 593 4.202000 TGTTTCGTCACTCACCTTTACGTA 60.202 41.667 0.00 0.00 35.21 3.57
591 594 3.118542 GTTTCGTCACTCACCTTTACGT 58.881 45.455 0.00 0.00 35.21 3.57
592 595 3.117794 TGTTTCGTCACTCACCTTTACG 58.882 45.455 0.00 0.00 34.99 3.18
593 596 6.963049 ATATGTTTCGTCACTCACCTTTAC 57.037 37.500 0.00 0.00 0.00 2.01
595 598 6.070995 TCCTATATGTTTCGTCACTCACCTTT 60.071 38.462 0.00 0.00 0.00 3.11
599 602 7.331193 AGTTTTCCTATATGTTTCGTCACTCAC 59.669 37.037 0.00 0.00 0.00 3.51
600 603 7.383687 AGTTTTCCTATATGTTTCGTCACTCA 58.616 34.615 0.00 0.00 0.00 3.41
601 604 7.829378 AGTTTTCCTATATGTTTCGTCACTC 57.171 36.000 0.00 0.00 0.00 3.51
602 605 9.148104 GTTAGTTTTCCTATATGTTTCGTCACT 57.852 33.333 0.00 0.00 0.00 3.41
603 606 8.385858 GGTTAGTTTTCCTATATGTTTCGTCAC 58.614 37.037 0.00 0.00 0.00 3.67
604 607 8.095792 TGGTTAGTTTTCCTATATGTTTCGTCA 58.904 33.333 0.00 0.00 0.00 4.35
605 608 8.483307 TGGTTAGTTTTCCTATATGTTTCGTC 57.517 34.615 0.00 0.00 0.00 4.20
606 609 9.457436 AATGGTTAGTTTTCCTATATGTTTCGT 57.543 29.630 0.00 0.00 0.00 3.85
607 610 9.716507 CAATGGTTAGTTTTCCTATATGTTTCG 57.283 33.333 0.00 0.00 0.00 3.46
608 611 9.516314 GCAATGGTTAGTTTTCCTATATGTTTC 57.484 33.333 0.00 0.00 0.00 2.78
609 612 9.030452 TGCAATGGTTAGTTTTCCTATATGTTT 57.970 29.630 0.00 0.00 0.00 2.83
610 613 8.588290 TGCAATGGTTAGTTTTCCTATATGTT 57.412 30.769 0.00 0.00 0.00 2.71
611 614 8.588290 TTGCAATGGTTAGTTTTCCTATATGT 57.412 30.769 0.00 0.00 0.00 2.29
612 615 8.902806 TCTTGCAATGGTTAGTTTTCCTATATG 58.097 33.333 0.00 0.00 0.00 1.78
613 616 8.903820 GTCTTGCAATGGTTAGTTTTCCTATAT 58.096 33.333 0.00 0.00 0.00 0.86
614 617 7.885922 TGTCTTGCAATGGTTAGTTTTCCTATA 59.114 33.333 0.00 0.00 0.00 1.31
615 618 6.719370 TGTCTTGCAATGGTTAGTTTTCCTAT 59.281 34.615 0.00 0.00 0.00 2.57
616 619 6.065374 TGTCTTGCAATGGTTAGTTTTCCTA 58.935 36.000 0.00 0.00 0.00 2.94
617 620 4.892934 TGTCTTGCAATGGTTAGTTTTCCT 59.107 37.500 0.00 0.00 0.00 3.36
618 621 5.195001 TGTCTTGCAATGGTTAGTTTTCC 57.805 39.130 0.00 0.00 0.00 3.13
619 622 6.273071 ACTTGTCTTGCAATGGTTAGTTTTC 58.727 36.000 0.00 0.00 36.36 2.29
620 623 6.220726 ACTTGTCTTGCAATGGTTAGTTTT 57.779 33.333 0.00 0.00 36.36 2.43
621 624 5.852282 ACTTGTCTTGCAATGGTTAGTTT 57.148 34.783 0.00 0.00 36.36 2.66
622 625 6.296026 TCTACTTGTCTTGCAATGGTTAGTT 58.704 36.000 0.00 0.00 36.36 2.24
623 626 5.865085 TCTACTTGTCTTGCAATGGTTAGT 58.135 37.500 0.00 3.29 36.36 2.24
624 627 6.801539 TTCTACTTGTCTTGCAATGGTTAG 57.198 37.500 0.00 0.00 36.36 2.34
625 628 7.575414 TTTTCTACTTGTCTTGCAATGGTTA 57.425 32.000 0.00 0.00 36.36 2.85
626 629 6.463995 TTTTCTACTTGTCTTGCAATGGTT 57.536 33.333 0.00 0.00 36.36 3.67
627 630 6.463995 TTTTTCTACTTGTCTTGCAATGGT 57.536 33.333 0.00 0.00 36.36 3.55
648 651 9.612066 TTTGTTTTTCTGAGGCAATATCTTTTT 57.388 25.926 0.00 0.00 0.00 1.94
649 652 9.783081 ATTTGTTTTTCTGAGGCAATATCTTTT 57.217 25.926 0.00 0.00 0.00 2.27
650 653 9.211485 CATTTGTTTTTCTGAGGCAATATCTTT 57.789 29.630 0.00 0.00 0.00 2.52
651 654 8.587608 TCATTTGTTTTTCTGAGGCAATATCTT 58.412 29.630 0.00 0.00 0.00 2.40
652 655 8.125978 TCATTTGTTTTTCTGAGGCAATATCT 57.874 30.769 0.00 0.00 0.00 1.98
653 656 8.937634 ATCATTTGTTTTTCTGAGGCAATATC 57.062 30.769 0.00 0.00 0.00 1.63
654 657 9.374838 GAATCATTTGTTTTTCTGAGGCAATAT 57.625 29.630 0.00 0.00 0.00 1.28
655 658 8.587608 AGAATCATTTGTTTTTCTGAGGCAATA 58.412 29.630 0.00 0.00 0.00 1.90
656 659 7.447594 AGAATCATTTGTTTTTCTGAGGCAAT 58.552 30.769 0.00 0.00 0.00 3.56
677 680 4.816385 TGACTCAAAGCTCACGAAAAGAAT 59.184 37.500 0.00 0.00 0.00 2.40
723 740 0.105039 CTAGCCTTCTTAGCCCACCG 59.895 60.000 0.00 0.00 0.00 4.94
1866 1965 2.416547 CACACTAGGATTGGTGAAAGCG 59.583 50.000 0.00 0.00 36.92 4.68
1906 2009 6.971602 TCATTACGACAGAGATAAGGTGATC 58.028 40.000 0.00 0.00 0.00 2.92
1907 2010 6.961360 TCATTACGACAGAGATAAGGTGAT 57.039 37.500 0.00 0.00 0.00 3.06
1908 2011 6.961360 ATCATTACGACAGAGATAAGGTGA 57.039 37.500 0.00 0.00 0.00 4.02
1909 2012 7.274468 GCATATCATTACGACAGAGATAAGGTG 59.726 40.741 0.00 0.00 0.00 4.00
2100 2214 5.990668 AGGTTTTAGCCGAATCAGAAGTAT 58.009 37.500 0.00 0.00 0.00 2.12
2117 2231 9.413734 CTAAGATCTTCAATTATGGGAGGTTTT 57.586 33.333 12.24 0.00 0.00 2.43
2118 2232 8.781951 TCTAAGATCTTCAATTATGGGAGGTTT 58.218 33.333 12.24 0.00 0.00 3.27
2119 2233 8.337118 TCTAAGATCTTCAATTATGGGAGGTT 57.663 34.615 12.24 0.00 0.00 3.50
2120 2234 7.937700 TCTAAGATCTTCAATTATGGGAGGT 57.062 36.000 12.24 0.00 0.00 3.85
2124 2238 9.393512 GATCCATCTAAGATCTTCAATTATGGG 57.606 37.037 12.24 4.81 37.69 4.00
2156 2270 6.985117 ACAGCTTTCAGAAATAAAATCTGCA 58.015 32.000 0.00 0.00 43.19 4.41
2334 2531 1.140134 ACCATGGTACCACAGCCCTT 61.140 55.000 19.09 0.00 0.00 3.95
2336 2533 0.107361 GTACCATGGTACCACAGCCC 60.107 60.000 35.68 14.98 43.60 5.19
2396 2594 6.293571 GCTTTCTCCTCCGACTATAGTAGAAC 60.294 46.154 13.96 0.00 0.00 3.01
2398 2596 5.163227 TGCTTTCTCCTCCGACTATAGTAGA 60.163 44.000 13.96 9.27 0.00 2.59
2432 2630 0.179468 GTAAGCCCGTAAGCCCATCA 59.821 55.000 0.00 0.00 0.00 3.07
2434 2632 0.180406 CAGTAAGCCCGTAAGCCCAT 59.820 55.000 0.00 0.00 0.00 4.00
2474 2732 3.115962 TGACCCCATATTGGATAGAGGGT 60.116 47.826 9.35 9.35 43.33 4.34
2475 2733 3.521126 CTGACCCCATATTGGATAGAGGG 59.479 52.174 0.00 0.00 40.96 4.30
2476 2734 4.429505 TCTGACCCCATATTGGATAGAGG 58.570 47.826 0.00 0.00 40.96 3.69
2477 2735 6.013032 ACAATCTGACCCCATATTGGATAGAG 60.013 42.308 0.00 0.00 40.96 2.43
2478 2736 5.851693 ACAATCTGACCCCATATTGGATAGA 59.148 40.000 0.00 0.00 40.96 1.98
2479 2737 6.131972 ACAATCTGACCCCATATTGGATAG 57.868 41.667 0.00 0.00 40.96 2.08
2480 2738 5.610557 TGACAATCTGACCCCATATTGGATA 59.389 40.000 0.00 0.00 40.96 2.59
2481 2739 4.416513 TGACAATCTGACCCCATATTGGAT 59.583 41.667 0.00 0.00 40.96 3.41
2482 2740 3.785325 TGACAATCTGACCCCATATTGGA 59.215 43.478 0.00 0.00 40.96 3.53
2483 2741 4.169059 TGACAATCTGACCCCATATTGG 57.831 45.455 0.00 0.00 39.66 3.16
2484 2742 5.135383 ACATGACAATCTGACCCCATATTG 58.865 41.667 0.00 0.00 40.56 1.90
2485 2743 5.393068 ACATGACAATCTGACCCCATATT 57.607 39.130 0.00 0.00 0.00 1.28
2486 2744 5.393068 AACATGACAATCTGACCCCATAT 57.607 39.130 0.00 0.00 0.00 1.78
2487 2745 4.860802 AACATGACAATCTGACCCCATA 57.139 40.909 0.00 0.00 0.00 2.74
2488 2746 3.744940 AACATGACAATCTGACCCCAT 57.255 42.857 0.00 0.00 0.00 4.00
2489 2747 3.524095 AAACATGACAATCTGACCCCA 57.476 42.857 0.00 0.00 0.00 4.96
2490 2748 4.280677 TGAAAAACATGACAATCTGACCCC 59.719 41.667 0.00 0.00 0.00 4.95
2491 2749 5.010012 ACTGAAAAACATGACAATCTGACCC 59.990 40.000 0.00 0.00 0.00 4.46
2492 2750 6.076981 ACTGAAAAACATGACAATCTGACC 57.923 37.500 0.00 0.00 0.00 4.02
2493 2751 9.683069 AATAACTGAAAAACATGACAATCTGAC 57.317 29.630 0.00 0.00 0.00 3.51
2494 2752 9.897744 GAATAACTGAAAAACATGACAATCTGA 57.102 29.630 0.00 0.00 0.00 3.27
2495 2753 8.843733 CGAATAACTGAAAAACATGACAATCTG 58.156 33.333 0.00 0.00 0.00 2.90
2496 2754 8.567948 ACGAATAACTGAAAAACATGACAATCT 58.432 29.630 0.00 0.00 0.00 2.40
2497 2755 8.728088 ACGAATAACTGAAAAACATGACAATC 57.272 30.769 0.00 0.00 0.00 2.67
2498 2756 8.349245 TGACGAATAACTGAAAAACATGACAAT 58.651 29.630 0.00 0.00 0.00 2.71
2499 2757 7.642194 GTGACGAATAACTGAAAAACATGACAA 59.358 33.333 0.00 0.00 0.00 3.18
2500 2758 7.129622 GTGACGAATAACTGAAAAACATGACA 58.870 34.615 0.00 0.00 0.00 3.58
2501 2759 7.129622 TGTGACGAATAACTGAAAAACATGAC 58.870 34.615 0.00 0.00 0.00 3.06
2502 2760 7.252965 TGTGACGAATAACTGAAAAACATGA 57.747 32.000 0.00 0.00 0.00 3.07
2503 2761 7.096640 GGTTGTGACGAATAACTGAAAAACATG 60.097 37.037 0.00 0.00 30.98 3.21
2504 2762 6.915843 GGTTGTGACGAATAACTGAAAAACAT 59.084 34.615 0.00 0.00 30.98 2.71
2505 2763 6.259638 GGTTGTGACGAATAACTGAAAAACA 58.740 36.000 0.00 0.00 30.98 2.83
2506 2764 5.684184 GGGTTGTGACGAATAACTGAAAAAC 59.316 40.000 0.00 0.00 30.98 2.43
2507 2765 5.591067 AGGGTTGTGACGAATAACTGAAAAA 59.409 36.000 0.00 0.00 30.98 1.94
2508 2766 5.127491 AGGGTTGTGACGAATAACTGAAAA 58.873 37.500 0.00 0.00 30.98 2.29
2509 2767 4.710324 AGGGTTGTGACGAATAACTGAAA 58.290 39.130 0.00 0.00 30.98 2.69
2510 2768 4.345859 AGGGTTGTGACGAATAACTGAA 57.654 40.909 0.00 0.00 30.98 3.02
2511 2769 4.345859 AAGGGTTGTGACGAATAACTGA 57.654 40.909 0.00 0.00 30.98 3.41
2512 2770 5.432885 AAAAGGGTTGTGACGAATAACTG 57.567 39.130 0.00 0.00 30.98 3.16
2513 2771 4.517832 GGAAAAGGGTTGTGACGAATAACT 59.482 41.667 0.00 0.00 30.98 2.24
2514 2772 4.517832 AGGAAAAGGGTTGTGACGAATAAC 59.482 41.667 0.00 0.00 0.00 1.89
2515 2773 4.721132 AGGAAAAGGGTTGTGACGAATAA 58.279 39.130 0.00 0.00 0.00 1.40
2516 2774 4.360951 AGGAAAAGGGTTGTGACGAATA 57.639 40.909 0.00 0.00 0.00 1.75
2517 2775 3.223674 AGGAAAAGGGTTGTGACGAAT 57.776 42.857 0.00 0.00 0.00 3.34
2518 2776 2.685897 CAAGGAAAAGGGTTGTGACGAA 59.314 45.455 0.00 0.00 0.00 3.85
2519 2777 2.294074 CAAGGAAAAGGGTTGTGACGA 58.706 47.619 0.00 0.00 0.00 4.20
2520 2778 1.269051 GCAAGGAAAAGGGTTGTGACG 60.269 52.381 0.00 0.00 0.00 4.35
2521 2779 2.031870 AGCAAGGAAAAGGGTTGTGAC 58.968 47.619 0.00 0.00 0.00 3.67
2522 2780 2.452600 AGCAAGGAAAAGGGTTGTGA 57.547 45.000 0.00 0.00 0.00 3.58
2523 2781 3.614870 GCATAGCAAGGAAAAGGGTTGTG 60.615 47.826 0.00 0.00 0.00 3.33
2524 2782 2.562738 GCATAGCAAGGAAAAGGGTTGT 59.437 45.455 0.00 0.00 0.00 3.32
2525 2783 2.415893 CGCATAGCAAGGAAAAGGGTTG 60.416 50.000 0.00 0.00 0.00 3.77
2526 2784 1.818674 CGCATAGCAAGGAAAAGGGTT 59.181 47.619 0.00 0.00 0.00 4.11
2527 2785 1.463674 CGCATAGCAAGGAAAAGGGT 58.536 50.000 0.00 0.00 0.00 4.34
2547 2805 3.357079 GGTGCAACAGGGCTCACG 61.357 66.667 0.00 0.00 39.98 4.35
2551 2809 0.687427 AGTTTTGGTGCAACAGGGCT 60.687 50.000 3.79 1.02 39.98 5.19
2569 2827 8.145122 AGTTAACAAAGGAGAACTCTTCTACAG 58.855 37.037 8.61 0.00 43.38 2.74
2584 2842 7.576861 TCAGGGAAAACTAAGTTAACAAAGG 57.423 36.000 8.61 0.00 0.00 3.11
2609 2867 8.739039 CAAGTTCCATCAAACCATAACATCTTA 58.261 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.