Multiple sequence alignment - TraesCS4B01G196800

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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 TraesCS4B01G196800 chr4B 100.000 5097 0 0 1 5097 423778849 423773753 0.000000e+00 9413.0
1 TraesCS4B01G196800 chr4B 96.711 973 31 1 2663 3635 424061293 424062264 0.000000e+00 1618.0
2 TraesCS4B01G196800 chr4B 97.835 508 11 0 1698 2205 424060249 424060756 0.000000e+00 878.0
3 TraesCS4B01G196800 chr4D 94.527 3581 130 30 683 4221 341698083 341694527 0.000000e+00 5467.0
4 TraesCS4B01G196800 chr4D 96.095 973 37 1 2663 3635 341923947 341924918 0.000000e+00 1585.0
5 TraesCS4B01G196800 chr4D 92.673 737 31 7 4361 5097 341694420 341693707 0.000000e+00 1040.0
6 TraesCS4B01G196800 chr4D 97.835 508 11 0 1698 2205 341922808 341923315 0.000000e+00 878.0
7 TraesCS4B01G196800 chr4D 91.511 483 37 4 1 481 341698583 341698103 0.000000e+00 662.0
8 TraesCS4B01G196800 chr4D 95.946 74 2 1 4216 4289 341694491 341694419 8.960000e-23 119.0
9 TraesCS4B01G196800 chr4D 96.078 51 2 0 2275 2325 341696466 341696416 3.270000e-12 84.2
10 TraesCS4B01G196800 chr4A 90.756 2737 144 52 1529 4191 125027775 125030476 0.000000e+00 3552.0
11 TraesCS4B01G196800 chr4A 91.722 1353 59 16 2318 3635 124405314 124403980 0.000000e+00 1829.0
12 TraesCS4B01G196800 chr4A 93.564 808 49 2 731 1536 125027015 125027821 0.000000e+00 1201.0
13 TraesCS4B01G196800 chr4A 95.016 622 22 2 1698 2319 124405884 124405272 0.000000e+00 968.0
14 TraesCS4B01G196800 chr4A 90.489 736 38 12 4392 5097 125038758 125039491 0.000000e+00 942.0
15 TraesCS4B01G196800 chr4A 91.097 483 37 5 1 481 125026438 125026916 0.000000e+00 649.0
16 TraesCS4B01G196800 chr4A 95.556 45 2 0 4296 4340 125030894 125030938 7.080000e-09 73.1
17 TraesCS4B01G196800 chr5D 95.051 889 43 1 2756 3644 483227761 483226874 0.000000e+00 1397.0
18 TraesCS4B01G196800 chr5D 94.689 885 47 0 2756 3640 483371377 483370493 0.000000e+00 1375.0
19 TraesCS4B01G196800 chr5D 96.234 478 17 1 1697 2174 483228782 483228306 0.000000e+00 782.0
20 TraesCS4B01G196800 chr5D 96.008 476 18 1 1698 2173 483372418 483371944 0.000000e+00 773.0
21 TraesCS4B01G196800 chr5B 94.927 887 44 1 2756 3642 593659272 593658387 0.000000e+00 1387.0
22 TraesCS4B01G196800 chr5B 94.576 885 48 0 2756 3640 593944221 593943337 0.000000e+00 1369.0
23 TraesCS4B01G196800 chr5B 96.639 476 15 1 1698 2173 593945331 593944857 0.000000e+00 789.0
24 TraesCS4B01G196800 chr5A 96.017 477 18 1 1698 2174 604312714 604312239 0.000000e+00 774.0
25 TraesCS4B01G196800 chr6B 95.161 186 4 3 498 679 675396127 675395943 6.460000e-74 289.0
26 TraesCS4B01G196800 chr1D 94.624 186 6 2 497 679 83163041 83163225 8.350000e-73 285.0
27 TraesCS4B01G196800 chr1D 89.573 211 18 2 474 680 439859955 439860165 1.090000e-66 265.0
28 TraesCS4B01G196800 chr6A 94.595 185 6 2 498 679 36495931 36496114 3.000000e-72 283.0
29 TraesCS4B01G196800 chrUn 94.086 186 7 2 497 679 258180625 258180441 3.890000e-71 279.0
30 TraesCS4B01G196800 chrUn 94.086 186 7 2 497 679 451986881 451986697 3.890000e-71 279.0
31 TraesCS4B01G196800 chr7B 94.536 183 6 2 498 677 663837743 663837924 3.890000e-71 279.0
32 TraesCS4B01G196800 chr7B 83.186 226 35 3 1 224 684968984 684969208 2.410000e-48 204.0
33 TraesCS4B01G196800 chr7B 82.511 223 37 2 1 223 697371978 697372198 1.450000e-45 195.0
34 TraesCS4B01G196800 chr2D 94.536 183 6 2 498 677 618294669 618294488 3.890000e-71 279.0
35 TraesCS4B01G196800 chr1B 94.536 183 6 2 498 677 507923051 507923232 3.890000e-71 279.0
36 TraesCS4B01G196800 chr2A 84.722 216 27 4 1 215 3293245 3293035 1.440000e-50 211.0
37 TraesCS4B01G196800 chr3B 87.681 138 13 4 2 136 17146520 17146656 1.900000e-34 158.0
38 TraesCS4B01G196800 chr7D 87.879 132 16 0 18 149 104945571 104945702 6.830000e-34 156.0
39 TraesCS4B01G196800 chr3D 85.526 152 16 6 2 148 11928055 11928205 2.460000e-33 154.0
40 TraesCS4B01G196800 chr3A 82.840 169 25 3 7 175 712456048 712456212 1.140000e-31 148.0
41 TraesCS4B01G196800 chr7A 81.250 160 29 1 125 284 121639359 121639517 1.490000e-25 128.0


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 TraesCS4B01G196800 chr4B 423773753 423778849 5096 True 9413.000 9413 100.00000 1 5097 1 chr4B.!!$R1 5096
1 TraesCS4B01G196800 chr4B 424060249 424062264 2015 False 1248.000 1618 97.27300 1698 3635 2 chr4B.!!$F1 1937
2 TraesCS4B01G196800 chr4D 341693707 341698583 4876 True 1474.440 5467 94.14700 1 5097 5 chr4D.!!$R1 5096
3 TraesCS4B01G196800 chr4D 341922808 341924918 2110 False 1231.500 1585 96.96500 1698 3635 2 chr4D.!!$F1 1937
4 TraesCS4B01G196800 chr4A 124403980 124405884 1904 True 1398.500 1829 93.36900 1698 3635 2 chr4A.!!$R1 1937
5 TraesCS4B01G196800 chr4A 125026438 125030938 4500 False 1368.775 3552 92.74325 1 4340 4 chr4A.!!$F2 4339
6 TraesCS4B01G196800 chr4A 125038758 125039491 733 False 942.000 942 90.48900 4392 5097 1 chr4A.!!$F1 705
7 TraesCS4B01G196800 chr5D 483226874 483228782 1908 True 1089.500 1397 95.64250 1697 3644 2 chr5D.!!$R1 1947
8 TraesCS4B01G196800 chr5D 483370493 483372418 1925 True 1074.000 1375 95.34850 1698 3640 2 chr5D.!!$R2 1942
9 TraesCS4B01G196800 chr5B 593658387 593659272 885 True 1387.000 1387 94.92700 2756 3642 1 chr5B.!!$R1 886
10 TraesCS4B01G196800 chr5B 593943337 593945331 1994 True 1079.000 1369 95.60750 1698 3640 2 chr5B.!!$R2 1942

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
652 658 0.034477 CCTGGTGGGTTGTGGATACC 60.034 60.000 0.0 0.0 34.82 2.73 F
653 659 0.695924 CTGGTGGGTTGTGGATACCA 59.304 55.000 0.0 0.0 38.98 3.25 F
954 992 0.991920 CCAGGAAGGAACCCTAGCAA 59.008 55.000 0.0 0.0 41.22 3.91 F
1013 1051 0.995675 CCCACCCCCATCCTCAATCT 60.996 60.000 0.0 0.0 0.00 2.40 F
1076 1114 1.003233 GGTCAGTTTCCCGATCCAGTT 59.997 52.381 0.0 0.0 0.00 3.16 F
3515 4201 2.570302 GGAGACCTTTGCTACTTACCCA 59.430 50.000 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1604 1.339711 CTAACCCGTGACGGTAAACG 58.660 55.000 23.73 9.52 46.80 3.60 R
1567 1608 1.745087 CTTAGCTAACCCGTGACGGTA 59.255 52.381 23.73 8.73 46.80 4.02 R
2602 3022 3.961480 ATCAACTAGCACAGCAGTACA 57.039 42.857 0.00 0.00 0.00 2.90 R
3765 4459 1.487976 TCCATGTTTTGCCAAAAGCCA 59.512 42.857 2.15 0.00 42.71 4.75 R
3881 4592 6.128282 ACAACCTGCTATTATCACGACAAAAG 60.128 38.462 0.00 0.00 0.00 2.27 R
4793 5892 2.217112 GCACATGCCGATAGACGAC 58.783 57.895 0.00 0.00 45.77 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 175 4.142881 GCCCGAAGAAAGTATGAAGTGAAC 60.143 45.833 0.00 0.00 0.00 3.18
190 193 9.899226 GAAGTGAACAAAGCTCTAAACAATATT 57.101 29.630 0.00 0.00 0.00 1.28
242 245 4.813027 CATCAACAAATGGACCTTCAAGG 58.187 43.478 0.22 0.22 42.49 3.61
243 246 4.177537 TCAACAAATGGACCTTCAAGGA 57.822 40.909 11.59 0.00 37.67 3.36
259 262 7.618512 ACCTTCAAGGAAGAATCATCATCAAAT 59.381 33.333 11.59 0.00 41.71 2.32
293 296 9.463443 AACTGATAATGTTGCTACTTGTTTTTC 57.537 29.630 0.00 0.00 0.00 2.29
417 422 6.038603 TGGCATGAGACACATTTAAATAGCTC 59.961 38.462 0.00 6.19 37.07 4.09
425 430 8.418662 AGACACATTTAAATAGCTCGGTATACA 58.581 33.333 5.01 0.00 0.00 2.29
456 462 8.280497 AGTTTGTTATACAAAGTCGCTACAAAG 58.720 33.333 5.30 0.00 45.68 2.77
500 506 6.729391 TTTAACACAATATAGACGCAAGCA 57.271 33.333 0.00 0.00 45.62 3.91
501 507 4.600012 AACACAATATAGACGCAAGCAC 57.400 40.909 0.00 0.00 45.62 4.40
502 508 2.603110 ACACAATATAGACGCAAGCACG 59.397 45.455 0.00 0.00 45.62 5.34
503 509 2.033747 CACAATATAGACGCAAGCACGG 60.034 50.000 0.00 0.00 45.62 4.94
504 510 1.070577 CAATATAGACGCAAGCACGGC 60.071 52.381 0.00 0.00 43.08 5.68
505 511 0.104120 ATATAGACGCAAGCACGGCA 59.896 50.000 2.43 0.00 46.03 5.69
506 512 0.104120 TATAGACGCAAGCACGGCAT 59.896 50.000 2.43 0.00 46.03 4.40
507 513 0.104120 ATAGACGCAAGCACGGCATA 59.896 50.000 2.43 0.00 46.03 3.14
508 514 0.104120 TAGACGCAAGCACGGCATAT 59.896 50.000 2.43 0.00 46.03 1.78
509 515 1.154205 AGACGCAAGCACGGCATATC 61.154 55.000 2.43 0.00 46.03 1.63
510 516 1.428370 GACGCAAGCACGGCATATCA 61.428 55.000 0.00 0.00 42.03 2.15
511 517 0.815213 ACGCAAGCACGGCATATCAT 60.815 50.000 0.00 0.00 45.62 2.45
512 518 0.110509 CGCAAGCACGGCATATCATC 60.111 55.000 0.00 0.00 0.00 2.92
513 519 1.233019 GCAAGCACGGCATATCATCT 58.767 50.000 0.00 0.00 0.00 2.90
514 520 1.605710 GCAAGCACGGCATATCATCTT 59.394 47.619 0.00 0.00 0.00 2.40
515 521 2.603892 GCAAGCACGGCATATCATCTTG 60.604 50.000 0.00 0.00 34.32 3.02
516 522 2.874086 CAAGCACGGCATATCATCTTGA 59.126 45.455 0.00 0.00 33.34 3.02
517 523 3.198409 AGCACGGCATATCATCTTGAA 57.802 42.857 0.00 0.00 0.00 2.69
518 524 3.544684 AGCACGGCATATCATCTTGAAA 58.455 40.909 0.00 0.00 0.00 2.69
519 525 4.139786 AGCACGGCATATCATCTTGAAAT 58.860 39.130 0.00 0.00 0.00 2.17
520 526 4.581824 AGCACGGCATATCATCTTGAAATT 59.418 37.500 0.00 0.00 0.00 1.82
521 527 5.068198 AGCACGGCATATCATCTTGAAATTT 59.932 36.000 0.00 0.00 0.00 1.82
522 528 6.262944 AGCACGGCATATCATCTTGAAATTTA 59.737 34.615 0.00 0.00 0.00 1.40
523 529 6.360681 GCACGGCATATCATCTTGAAATTTAC 59.639 38.462 0.00 0.00 0.00 2.01
524 530 6.574832 CACGGCATATCATCTTGAAATTTACG 59.425 38.462 0.00 0.00 0.00 3.18
525 531 6.481976 ACGGCATATCATCTTGAAATTTACGA 59.518 34.615 0.00 0.00 0.00 3.43
526 532 7.011950 ACGGCATATCATCTTGAAATTTACGAA 59.988 33.333 0.00 0.00 0.00 3.85
527 533 7.531871 CGGCATATCATCTTGAAATTTACGAAG 59.468 37.037 0.00 0.00 0.00 3.79
529 535 9.374960 GCATATCATCTTGAAATTTACGAAGTC 57.625 33.333 0.00 0.00 43.93 3.01
532 538 7.129109 TCATCTTGAAATTTACGAAGTCACC 57.871 36.000 0.00 0.00 43.93 4.02
533 539 5.585500 TCTTGAAATTTACGAAGTCACCG 57.415 39.130 0.00 0.00 43.93 4.94
534 540 5.051816 TCTTGAAATTTACGAAGTCACCGT 58.948 37.500 0.00 0.00 43.93 4.83
535 541 6.215121 TCTTGAAATTTACGAAGTCACCGTA 58.785 36.000 0.00 0.00 43.93 4.02
536 542 6.364165 TCTTGAAATTTACGAAGTCACCGTAG 59.636 38.462 0.00 0.00 43.93 3.51
550 556 2.566997 CGTAGGCACTTCGTCATCG 58.433 57.895 0.00 0.00 44.10 3.84
551 557 0.098200 CGTAGGCACTTCGTCATCGA 59.902 55.000 0.00 0.00 44.10 3.59
552 558 1.546834 GTAGGCACTTCGTCATCGAC 58.453 55.000 0.00 0.00 46.03 4.20
571 577 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
572 578 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
573 579 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
574 580 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
575 581 1.550976 GAACGTCTCCTCCCACTGAAT 59.449 52.381 0.00 0.00 0.00 2.57
576 582 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
577 583 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
578 584 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
579 585 1.817099 CTCCTCCCACTGAATGCGC 60.817 63.158 0.00 0.00 0.00 6.09
580 586 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
581 587 1.452651 CCTCCCACTGAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
582 588 1.442526 CCTCCCACTGAATGCGCATC 61.443 60.000 25.53 17.12 0.00 3.91
583 589 1.769098 CTCCCACTGAATGCGCATCG 61.769 60.000 25.53 17.09 0.00 3.84
594 600 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
595 601 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
596 602 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
597 603 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
598 604 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
599 605 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
600 606 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
601 607 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
602 608 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
603 609 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
604 610 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
605 611 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
606 612 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
607 613 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
608 614 5.594317 CCGGAAATCCTGAAATAAATCCAGT 59.406 40.000 0.00 0.00 0.00 4.00
609 615 6.770785 CCGGAAATCCTGAAATAAATCCAGTA 59.229 38.462 0.00 0.00 0.00 2.74
610 616 7.284489 CCGGAAATCCTGAAATAAATCCAGTAA 59.716 37.037 0.00 0.00 0.00 2.24
611 617 8.682710 CGGAAATCCTGAAATAAATCCAGTAAA 58.317 33.333 0.00 0.00 0.00 2.01
614 620 9.822185 AAATCCTGAAATAAATCCAGTAAATGC 57.178 29.630 0.00 0.00 0.00 3.56
615 621 7.026631 TCCTGAAATAAATCCAGTAAATGCG 57.973 36.000 0.00 0.00 0.00 4.73
616 622 6.826231 TCCTGAAATAAATCCAGTAAATGCGA 59.174 34.615 0.00 0.00 0.00 5.10
617 623 7.012327 TCCTGAAATAAATCCAGTAAATGCGAG 59.988 37.037 0.00 0.00 0.00 5.03
618 624 6.494842 TGAAATAAATCCAGTAAATGCGAGC 58.505 36.000 0.00 0.00 0.00 5.03
619 625 6.094742 TGAAATAAATCCAGTAAATGCGAGCA 59.905 34.615 0.00 0.00 0.00 4.26
620 626 3.764885 AAATCCAGTAAATGCGAGCAC 57.235 42.857 0.00 0.00 0.00 4.40
621 627 1.668419 ATCCAGTAAATGCGAGCACC 58.332 50.000 0.00 0.00 0.00 5.01
622 628 0.323302 TCCAGTAAATGCGAGCACCA 59.677 50.000 0.00 0.00 0.00 4.17
623 629 0.729116 CCAGTAAATGCGAGCACCAG 59.271 55.000 0.00 0.00 0.00 4.00
624 630 0.729116 CAGTAAATGCGAGCACCAGG 59.271 55.000 0.00 0.00 0.00 4.45
625 631 0.613260 AGTAAATGCGAGCACCAGGA 59.387 50.000 0.00 0.00 0.00 3.86
626 632 1.210478 AGTAAATGCGAGCACCAGGAT 59.790 47.619 0.00 0.00 0.00 3.24
627 633 2.017049 GTAAATGCGAGCACCAGGATT 58.983 47.619 0.00 0.00 0.00 3.01
628 634 1.549203 AAATGCGAGCACCAGGATTT 58.451 45.000 0.00 0.00 34.37 2.17
629 635 2.418368 AATGCGAGCACCAGGATTTA 57.582 45.000 0.00 0.00 0.00 1.40
630 636 2.418368 ATGCGAGCACCAGGATTTAA 57.582 45.000 0.00 0.00 0.00 1.52
631 637 2.192664 TGCGAGCACCAGGATTTAAA 57.807 45.000 0.00 0.00 0.00 1.52
632 638 1.810151 TGCGAGCACCAGGATTTAAAC 59.190 47.619 0.00 0.00 0.00 2.01
633 639 1.132453 GCGAGCACCAGGATTTAAACC 59.868 52.381 0.00 0.00 0.00 3.27
634 640 1.743394 CGAGCACCAGGATTTAAACCC 59.257 52.381 0.00 0.00 0.00 4.11
635 641 2.618045 CGAGCACCAGGATTTAAACCCT 60.618 50.000 0.00 0.00 0.00 4.34
651 657 3.569873 CCTGGTGGGTTGTGGATAC 57.430 57.895 0.00 0.00 0.00 2.24
652 658 0.034477 CCTGGTGGGTTGTGGATACC 60.034 60.000 0.00 0.00 34.82 2.73
653 659 0.695924 CTGGTGGGTTGTGGATACCA 59.304 55.000 0.00 0.00 38.98 3.25
665 671 3.769189 TGGATACCACAGTCCCTCTAA 57.231 47.619 0.00 0.00 33.45 2.10
666 672 3.371965 TGGATACCACAGTCCCTCTAAC 58.628 50.000 0.00 0.00 33.45 2.34
667 673 2.699321 GGATACCACAGTCCCTCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
668 674 3.371965 GATACCACAGTCCCTCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
669 675 2.344093 ACCACAGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
670 676 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
671 677 1.486726 CCACAGTCCCTCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
672 678 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
673 679 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
674 680 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
675 681 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
676 682 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
677 683 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
678 684 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
679 685 2.242196 CCCTCTAACCATCCAACCACAT 59.758 50.000 0.00 0.00 0.00 3.21
686 692 1.619827 CCATCCAACCACATTGTGCTT 59.380 47.619 11.41 1.23 36.47 3.91
765 803 2.010145 TGAGCTAATCCACTTCGTGC 57.990 50.000 0.00 0.00 31.34 5.34
770 808 2.935238 GCTAATCCACTTCGTGCCTTCA 60.935 50.000 0.00 0.00 31.34 3.02
776 814 1.455786 CACTTCGTGCCTTCAAGTACG 59.544 52.381 5.36 5.36 37.85 3.67
864 902 2.286772 CGCCATTACCGCCTAAAACATC 60.287 50.000 0.00 0.00 0.00 3.06
867 905 4.196193 CCATTACCGCCTAAAACATCTCA 58.804 43.478 0.00 0.00 0.00 3.27
887 925 3.855379 TCATTCGTACGATCAAAACCGAG 59.145 43.478 20.27 0.42 0.00 4.63
894 932 1.376609 GATCAAAACCGAGCGGCCAT 61.377 55.000 9.14 0.00 39.32 4.40
902 940 1.524621 CGAGCGGCCATGATTTCCT 60.525 57.895 2.24 0.00 0.00 3.36
954 992 0.991920 CCAGGAAGGAACCCTAGCAA 59.008 55.000 0.00 0.00 41.22 3.91
961 999 2.530916 AACCCTAGCAACCCCCGT 60.531 61.111 0.00 0.00 0.00 5.28
1010 1048 1.619363 CTCCCACCCCCATCCTCAA 60.619 63.158 0.00 0.00 0.00 3.02
1013 1051 0.995675 CCCACCCCCATCCTCAATCT 60.996 60.000 0.00 0.00 0.00 2.40
1076 1114 1.003233 GGTCAGTTTCCCGATCCAGTT 59.997 52.381 0.00 0.00 0.00 3.16
1093 1131 4.599241 TCCAGTTCCCTTCTCTTTTCAGAT 59.401 41.667 0.00 0.00 0.00 2.90
1099 1137 3.120060 CCCTTCTCTTTTCAGATGCGTTG 60.120 47.826 0.00 0.00 0.00 4.10
1110 1148 2.603135 GATGCGTTGTCCATGGCTGC 62.603 60.000 6.96 6.71 0.00 5.25
1159 1197 4.023963 GTCTCAGTTTCTGTTTAGTTGCCC 60.024 45.833 0.00 0.00 32.61 5.36
1232 1270 2.742589 CCGTTTCTACTTTGAAGGGCTC 59.257 50.000 0.00 0.00 0.00 4.70
1308 1346 2.582202 TAGCGCAATTGCAAGCTCGC 62.582 55.000 28.67 24.81 42.21 5.03
1330 1368 3.951775 ATACCGAATCATCTCTGCTCC 57.048 47.619 0.00 0.00 0.00 4.70
1336 1374 3.555139 CGAATCATCTCTGCTCCTTGTTC 59.445 47.826 0.00 0.00 0.00 3.18
1396 1434 3.170791 AGGATGCACAGATTACAGTCG 57.829 47.619 0.00 0.00 0.00 4.18
1424 1462 6.756542 TGGAATATTTATATGTCGCTCCATCG 59.243 38.462 0.00 0.00 0.00 3.84
1476 1516 4.233789 CGAGATCTAGTTATGGCTTCTGC 58.766 47.826 0.00 0.00 38.76 4.26
1537 1577 7.879160 ACCATCTTTTTACTGTTAACCGTCATA 59.121 33.333 5.89 0.00 0.00 2.15
1549 1589 9.256477 CTGTTAACCGTCATAGCATCTTATTAA 57.744 33.333 2.48 0.00 0.00 1.40
1576 1617 3.489047 TCTTTTTACCGTTTACCGTCACG 59.511 43.478 0.00 0.00 36.12 4.35
1618 1659 8.932945 TGATCTATCAGTTTATGTCACTTGTC 57.067 34.615 0.00 0.00 32.11 3.18
1636 1677 2.577563 TGTCCACATGATGATTCCCTGT 59.422 45.455 0.00 0.00 0.00 4.00
1644 1685 2.835156 TGATGATTCCCTGTGTCCGTTA 59.165 45.455 0.00 0.00 0.00 3.18
1656 1697 7.550196 TCCCTGTGTCCGTTAGTTTTAATAATC 59.450 37.037 0.00 0.00 0.00 1.75
2220 2264 6.321181 AGGCCATGTAACCATATTACTTTGTG 59.679 38.462 5.01 0.00 0.00 3.33
3515 4201 2.570302 GGAGACCTTTGCTACTTACCCA 59.430 50.000 0.00 0.00 0.00 4.51
3765 4459 8.832521 TGTCATTTGAGTACTGTCGTTAATTTT 58.167 29.630 0.00 0.00 0.00 1.82
3879 4590 3.297134 TCTCTTTGAAGCCTTTGGTGT 57.703 42.857 0.00 0.00 0.00 4.16
3881 4592 3.632145 TCTCTTTGAAGCCTTTGGTGTTC 59.368 43.478 0.00 0.00 0.00 3.18
3924 4635 5.182760 AGGTTGTTTTCATTCTCAGATCTGC 59.817 40.000 18.36 0.39 0.00 4.26
4007 4718 0.704076 TTGGGGCTTGCTTGGATAGT 59.296 50.000 0.00 0.00 0.00 2.12
4008 4719 1.590591 TGGGGCTTGCTTGGATAGTA 58.409 50.000 0.00 0.00 0.00 1.82
4009 4720 1.211949 TGGGGCTTGCTTGGATAGTAC 59.788 52.381 0.00 0.00 0.00 2.73
4021 4732 8.004087 TGCTTGGATAGTACTAACTACGAAAT 57.996 34.615 6.70 0.00 40.98 2.17
4068 4780 6.449698 TGATCTGTTTTCAAGCCAAAAGATC 58.550 36.000 5.46 5.46 32.58 2.75
4106 4828 5.940192 TGCAGTTCGTTACAATCAAATCT 57.060 34.783 0.00 0.00 0.00 2.40
4126 4848 8.810427 CAAATCTGAACTAATGCGCAAATAAAT 58.190 29.630 17.11 0.00 0.00 1.40
4245 5007 2.528134 GGCTCCATGTACAGGCCTA 58.472 57.895 3.98 0.00 39.68 3.93
4260 5351 1.004277 GGCCTACTGGTGAAATGTGGA 59.996 52.381 0.00 0.00 35.27 4.02
4292 5383 3.365265 GCACCAAGCCGGAACCAG 61.365 66.667 5.05 0.00 38.63 4.00
4293 5384 3.365265 CACCAAGCCGGAACCAGC 61.365 66.667 5.05 0.00 38.63 4.85
4294 5385 4.660938 ACCAAGCCGGAACCAGCC 62.661 66.667 5.05 0.00 38.63 4.85
4295 5386 4.659172 CCAAGCCGGAACCAGCCA 62.659 66.667 5.05 0.00 36.56 4.75
4296 5387 3.058160 CAAGCCGGAACCAGCCAG 61.058 66.667 5.05 0.00 0.00 4.85
4333 5424 2.093764 CACCTTGGTGCCAAAGTTTTGA 60.094 45.455 6.88 0.00 40.55 2.69
4334 5425 2.569404 ACCTTGGTGCCAAAGTTTTGAA 59.431 40.909 5.10 0.00 40.55 2.69
4340 5431 3.063861 GGTGCCAAAGTTTTGAAAAGCTG 59.936 43.478 6.18 0.00 40.55 4.24
4341 5432 3.932089 GTGCCAAAGTTTTGAAAAGCTGA 59.068 39.130 6.18 0.00 40.55 4.26
4342 5433 4.571984 GTGCCAAAGTTTTGAAAAGCTGAT 59.428 37.500 6.18 0.00 40.55 2.90
4343 5434 4.571580 TGCCAAAGTTTTGAAAAGCTGATG 59.428 37.500 6.18 0.00 40.55 3.07
4344 5435 4.571984 GCCAAAGTTTTGAAAAGCTGATGT 59.428 37.500 6.18 0.00 40.55 3.06
4345 5436 5.752955 GCCAAAGTTTTGAAAAGCTGATGTA 59.247 36.000 6.18 0.00 40.55 2.29
4346 5437 6.424812 GCCAAAGTTTTGAAAAGCTGATGTAT 59.575 34.615 6.18 0.00 40.55 2.29
4347 5438 7.598493 GCCAAAGTTTTGAAAAGCTGATGTATA 59.402 33.333 6.18 0.00 40.55 1.47
4348 5439 9.132521 CCAAAGTTTTGAAAAGCTGATGTATAG 57.867 33.333 6.18 0.00 40.55 1.31
4349 5440 9.683069 CAAAGTTTTGAAAAGCTGATGTATAGT 57.317 29.630 0.00 0.00 40.55 2.12
4352 5443 8.947115 AGTTTTGAAAAGCTGATGTATAGTACC 58.053 33.333 0.00 0.00 0.00 3.34
4353 5444 7.859325 TTTGAAAAGCTGATGTATAGTACCC 57.141 36.000 0.00 0.00 0.00 3.69
4354 5445 5.925509 TGAAAAGCTGATGTATAGTACCCC 58.074 41.667 0.00 0.00 0.00 4.95
4355 5446 5.665812 TGAAAAGCTGATGTATAGTACCCCT 59.334 40.000 0.00 0.00 0.00 4.79
4356 5447 5.810080 AAAGCTGATGTATAGTACCCCTC 57.190 43.478 0.00 0.00 0.00 4.30
4357 5448 4.750833 AGCTGATGTATAGTACCCCTCT 57.249 45.455 0.00 0.00 0.00 3.69
4358 5449 4.411927 AGCTGATGTATAGTACCCCTCTG 58.588 47.826 0.00 0.00 0.00 3.35
4359 5450 4.140900 AGCTGATGTATAGTACCCCTCTGT 60.141 45.833 0.00 0.00 0.00 3.41
4360 5451 5.074652 AGCTGATGTATAGTACCCCTCTGTA 59.925 44.000 0.00 0.00 0.00 2.74
4361 5452 5.773680 GCTGATGTATAGTACCCCTCTGTAA 59.226 44.000 0.00 0.00 0.00 2.41
4362 5453 6.267014 GCTGATGTATAGTACCCCTCTGTAAA 59.733 42.308 0.00 0.00 0.00 2.01
4363 5454 7.201974 GCTGATGTATAGTACCCCTCTGTAAAA 60.202 40.741 0.00 0.00 0.00 1.52
4364 5455 8.612486 TGATGTATAGTACCCCTCTGTAAAAA 57.388 34.615 0.00 0.00 0.00 1.94
4442 5540 2.829023 TGGAGGGAATAAGACCGTTCT 58.171 47.619 0.00 0.00 0.00 3.01
4450 5548 5.579904 GGGAATAAGACCGTTCTAAAGTGTC 59.420 44.000 0.00 0.00 0.00 3.67
4534 5633 6.342338 TCTAGTCTTTGTCTTTAGGTCACC 57.658 41.667 0.00 0.00 0.00 4.02
4675 5774 8.655970 AGTTACAAAAATGTTTTCTTCTTGCAC 58.344 29.630 0.00 0.00 0.00 4.57
4681 5780 2.687935 TGTTTTCTTCTTGCACCTGACC 59.312 45.455 0.00 0.00 0.00 4.02
4746 5845 1.535462 CAAGCCAACTCGGTCGAAAAT 59.465 47.619 0.00 0.00 36.97 1.82
4793 5892 1.135083 AGTTGCTTGACCGGAGTATCG 60.135 52.381 9.46 0.00 34.37 2.92
4893 5992 3.206150 TCAACACAAAGGTCTTGAGAGC 58.794 45.455 2.07 2.07 42.47 4.09
5025 6146 5.283717 GTGTGTATACAAAGAAAATGCAGCG 59.716 40.000 7.25 0.00 38.82 5.18
5072 6193 0.250684 TCTTTTGAGCGGTGATGCCA 60.251 50.000 0.00 0.00 36.97 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 142 4.212716 ACTTTCTTCGGGCCTTTTTACTT 58.787 39.130 0.84 0.00 0.00 2.24
172 175 7.999679 TGGATGGAATATTGTTTAGAGCTTTG 58.000 34.615 0.00 0.00 0.00 2.77
215 218 4.460948 AGGTCCATTTGTTGATGCAATC 57.539 40.909 0.00 0.00 45.83 2.67
379 384 3.827876 TCTCATGCCAACAATGTGAACAT 59.172 39.130 0.00 0.00 38.41 2.71
481 487 2.603110 CGTGCTTGCGTCTATATTGTGT 59.397 45.455 0.00 0.00 0.00 3.72
482 488 2.033747 CCGTGCTTGCGTCTATATTGTG 60.034 50.000 0.00 0.00 0.00 3.33
484 490 1.070577 GCCGTGCTTGCGTCTATATTG 60.071 52.381 0.00 0.00 0.00 1.90
487 493 0.104120 ATGCCGTGCTTGCGTCTATA 59.896 50.000 0.00 0.00 0.00 1.31
488 494 0.104120 TATGCCGTGCTTGCGTCTAT 59.896 50.000 0.00 0.00 0.00 1.98
492 498 0.815213 ATGATATGCCGTGCTTGCGT 60.815 50.000 0.00 0.00 0.00 5.24
493 499 0.110509 GATGATATGCCGTGCTTGCG 60.111 55.000 0.00 0.00 0.00 4.85
494 500 1.233019 AGATGATATGCCGTGCTTGC 58.767 50.000 0.00 0.00 0.00 4.01
495 501 2.874086 TCAAGATGATATGCCGTGCTTG 59.126 45.455 0.00 0.00 34.23 4.01
496 502 3.198409 TCAAGATGATATGCCGTGCTT 57.802 42.857 0.00 0.00 0.00 3.91
497 503 2.916702 TCAAGATGATATGCCGTGCT 57.083 45.000 0.00 0.00 0.00 4.40
498 504 3.969117 TTTCAAGATGATATGCCGTGC 57.031 42.857 0.00 0.00 0.00 5.34
499 505 6.574832 CGTAAATTTCAAGATGATATGCCGTG 59.425 38.462 0.00 0.00 0.00 4.94
500 506 6.481976 TCGTAAATTTCAAGATGATATGCCGT 59.518 34.615 0.00 0.00 0.00 5.68
501 507 6.887368 TCGTAAATTTCAAGATGATATGCCG 58.113 36.000 0.00 0.00 0.00 5.69
502 508 8.345565 ACTTCGTAAATTTCAAGATGATATGCC 58.654 33.333 0.00 0.00 0.00 4.40
503 509 9.374960 GACTTCGTAAATTTCAAGATGATATGC 57.625 33.333 0.00 0.00 0.00 3.14
506 512 8.879759 GGTGACTTCGTAAATTTCAAGATGATA 58.120 33.333 0.00 0.00 0.00 2.15
507 513 7.413000 CGGTGACTTCGTAAATTTCAAGATGAT 60.413 37.037 0.00 0.00 0.00 2.45
508 514 6.128661 CGGTGACTTCGTAAATTTCAAGATGA 60.129 38.462 0.00 0.00 0.00 2.92
509 515 6.015504 CGGTGACTTCGTAAATTTCAAGATG 58.984 40.000 0.00 0.00 0.00 2.90
510 516 5.699458 ACGGTGACTTCGTAAATTTCAAGAT 59.301 36.000 0.00 0.00 39.22 2.40
511 517 5.051816 ACGGTGACTTCGTAAATTTCAAGA 58.948 37.500 0.00 0.00 39.22 3.02
512 518 5.338614 ACGGTGACTTCGTAAATTTCAAG 57.661 39.130 0.00 0.00 39.22 3.02
513 519 5.406175 CCTACGGTGACTTCGTAAATTTCAA 59.594 40.000 0.00 0.00 41.62 2.69
514 520 4.925054 CCTACGGTGACTTCGTAAATTTCA 59.075 41.667 0.00 0.00 41.62 2.69
515 521 4.201656 GCCTACGGTGACTTCGTAAATTTC 60.202 45.833 0.00 0.00 41.62 2.17
516 522 3.681417 GCCTACGGTGACTTCGTAAATTT 59.319 43.478 0.00 0.00 41.62 1.82
517 523 3.256558 GCCTACGGTGACTTCGTAAATT 58.743 45.455 0.00 0.00 41.62 1.82
518 524 2.231964 TGCCTACGGTGACTTCGTAAAT 59.768 45.455 0.00 0.00 41.62 1.40
519 525 1.612950 TGCCTACGGTGACTTCGTAAA 59.387 47.619 0.00 0.00 41.62 2.01
520 526 1.068333 GTGCCTACGGTGACTTCGTAA 60.068 52.381 0.00 0.00 41.62 3.18
521 527 0.523072 GTGCCTACGGTGACTTCGTA 59.477 55.000 0.00 0.00 41.38 3.43
522 528 1.177256 AGTGCCTACGGTGACTTCGT 61.177 55.000 0.00 0.00 43.64 3.85
523 529 0.038526 AAGTGCCTACGGTGACTTCG 60.039 55.000 0.00 0.00 0.00 3.79
524 530 1.711206 GAAGTGCCTACGGTGACTTC 58.289 55.000 0.00 0.00 37.25 3.01
525 531 0.038526 CGAAGTGCCTACGGTGACTT 60.039 55.000 0.00 0.00 32.76 3.01
526 532 1.177256 ACGAAGTGCCTACGGTGACT 61.177 55.000 0.00 0.00 42.51 3.41
527 533 1.288127 ACGAAGTGCCTACGGTGAC 59.712 57.895 0.00 0.00 42.51 3.67
528 534 3.767816 ACGAAGTGCCTACGGTGA 58.232 55.556 0.00 0.00 42.51 4.02
555 561 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
556 562 1.276421 CATTCAGTGGGAGGAGACGTT 59.724 52.381 0.00 0.00 0.00 3.99
557 563 0.898320 CATTCAGTGGGAGGAGACGT 59.102 55.000 0.00 0.00 0.00 4.34
558 564 0.460987 GCATTCAGTGGGAGGAGACG 60.461 60.000 0.00 0.00 0.00 4.18
559 565 0.460987 CGCATTCAGTGGGAGGAGAC 60.461 60.000 0.00 0.00 43.02 3.36
560 566 1.900351 CGCATTCAGTGGGAGGAGA 59.100 57.895 0.00 0.00 43.02 3.71
561 567 1.817099 GCGCATTCAGTGGGAGGAG 60.817 63.158 0.30 0.00 43.02 3.69
562 568 1.913951 ATGCGCATTCAGTGGGAGGA 61.914 55.000 19.28 0.00 43.02 3.71
563 569 1.442526 GATGCGCATTCAGTGGGAGG 61.443 60.000 26.12 0.00 43.02 4.30
564 570 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
565 571 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
566 572 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
577 583 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
578 584 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
579 585 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
580 586 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
581 587 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
582 588 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
583 589 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
584 590 5.594317 ACTGGATTTATTTCAGGATTTCCGG 59.406 40.000 0.00 0.00 42.08 5.14
585 591 6.699575 ACTGGATTTATTTCAGGATTTCCG 57.300 37.500 0.00 0.00 42.08 4.30
588 594 9.822185 GCATTTACTGGATTTATTTCAGGATTT 57.178 29.630 0.00 0.00 33.19 2.17
589 595 8.137437 CGCATTTACTGGATTTATTTCAGGATT 58.863 33.333 0.00 0.00 33.19 3.01
590 596 7.502226 TCGCATTTACTGGATTTATTTCAGGAT 59.498 33.333 0.00 0.00 33.19 3.24
591 597 6.826231 TCGCATTTACTGGATTTATTTCAGGA 59.174 34.615 0.00 0.00 33.19 3.86
592 598 7.026631 TCGCATTTACTGGATTTATTTCAGG 57.973 36.000 0.00 0.00 33.19 3.86
593 599 6.634436 GCTCGCATTTACTGGATTTATTTCAG 59.366 38.462 0.00 0.00 34.91 3.02
594 600 6.094742 TGCTCGCATTTACTGGATTTATTTCA 59.905 34.615 0.00 0.00 0.00 2.69
595 601 6.414987 GTGCTCGCATTTACTGGATTTATTTC 59.585 38.462 0.00 0.00 0.00 2.17
596 602 6.265577 GTGCTCGCATTTACTGGATTTATTT 58.734 36.000 0.00 0.00 0.00 1.40
597 603 5.221048 GGTGCTCGCATTTACTGGATTTATT 60.221 40.000 0.00 0.00 0.00 1.40
598 604 4.275936 GGTGCTCGCATTTACTGGATTTAT 59.724 41.667 0.00 0.00 0.00 1.40
599 605 3.625764 GGTGCTCGCATTTACTGGATTTA 59.374 43.478 0.00 0.00 0.00 1.40
600 606 2.423538 GGTGCTCGCATTTACTGGATTT 59.576 45.455 0.00 0.00 0.00 2.17
601 607 2.017049 GGTGCTCGCATTTACTGGATT 58.983 47.619 0.00 0.00 0.00 3.01
602 608 1.065491 TGGTGCTCGCATTTACTGGAT 60.065 47.619 0.00 0.00 0.00 3.41
603 609 0.323302 TGGTGCTCGCATTTACTGGA 59.677 50.000 0.00 0.00 0.00 3.86
604 610 0.729116 CTGGTGCTCGCATTTACTGG 59.271 55.000 0.00 0.00 0.00 4.00
605 611 0.729116 CCTGGTGCTCGCATTTACTG 59.271 55.000 0.00 0.00 0.00 2.74
606 612 0.613260 TCCTGGTGCTCGCATTTACT 59.387 50.000 0.00 0.00 0.00 2.24
607 613 1.668419 ATCCTGGTGCTCGCATTTAC 58.332 50.000 0.00 0.00 0.00 2.01
608 614 2.418368 AATCCTGGTGCTCGCATTTA 57.582 45.000 0.00 0.00 0.00 1.40
609 615 1.549203 AAATCCTGGTGCTCGCATTT 58.451 45.000 0.00 0.00 0.00 2.32
610 616 2.418368 TAAATCCTGGTGCTCGCATT 57.582 45.000 0.00 0.00 0.00 3.56
611 617 2.418368 TTAAATCCTGGTGCTCGCAT 57.582 45.000 0.00 0.00 0.00 4.73
612 618 1.810151 GTTTAAATCCTGGTGCTCGCA 59.190 47.619 0.00 0.00 0.00 5.10
613 619 1.132453 GGTTTAAATCCTGGTGCTCGC 59.868 52.381 0.00 0.00 0.00 5.03
614 620 1.743394 GGGTTTAAATCCTGGTGCTCG 59.257 52.381 10.45 0.00 0.00 5.03
615 621 3.087370 AGGGTTTAAATCCTGGTGCTC 57.913 47.619 19.53 0.00 38.36 4.26
633 639 0.034477 GGTATCCACAACCCACCAGG 60.034 60.000 0.00 0.00 43.78 4.45
634 640 0.695924 TGGTATCCACAACCCACCAG 59.304 55.000 0.00 0.00 34.40 4.00
635 641 2.869940 TGGTATCCACAACCCACCA 58.130 52.632 0.00 0.00 36.94 4.17
645 651 3.371965 GTTAGAGGGACTGTGGTATCCA 58.628 50.000 0.00 0.00 41.55 3.41
646 652 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
647 653 3.371965 TGGTTAGAGGGACTGTGGTATC 58.628 50.000 0.00 0.00 41.55 2.24
648 654 3.484953 TGGTTAGAGGGACTGTGGTAT 57.515 47.619 0.00 0.00 41.55 2.73
649 655 3.371965 GATGGTTAGAGGGACTGTGGTA 58.628 50.000 0.00 0.00 41.55 3.25
650 656 2.188817 GATGGTTAGAGGGACTGTGGT 58.811 52.381 0.00 0.00 41.55 4.16
651 657 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
652 658 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
653 659 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
654 660 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
656 662 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
657 663 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
658 664 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
659 665 3.652057 ATGTGGTTGGATGGTTAGAGG 57.348 47.619 0.00 0.00 0.00 3.69
660 666 4.156556 CACAATGTGGTTGGATGGTTAGAG 59.843 45.833 5.29 0.00 42.28 2.43
661 667 4.078537 CACAATGTGGTTGGATGGTTAGA 58.921 43.478 5.29 0.00 42.28 2.10
662 668 3.367292 GCACAATGTGGTTGGATGGTTAG 60.367 47.826 15.78 0.00 42.28 2.34
663 669 2.560542 GCACAATGTGGTTGGATGGTTA 59.439 45.455 15.78 0.00 42.28 2.85
664 670 1.344114 GCACAATGTGGTTGGATGGTT 59.656 47.619 15.78 0.00 42.28 3.67
665 671 0.968405 GCACAATGTGGTTGGATGGT 59.032 50.000 15.78 0.00 42.28 3.55
666 672 1.259609 AGCACAATGTGGTTGGATGG 58.740 50.000 12.76 0.00 41.72 3.51
740 777 6.161855 ACGAAGTGGATTAGCTCATTCATA 57.838 37.500 0.00 0.00 42.51 2.15
765 803 3.022607 ACCGACTTTCGTACTTGAAGG 57.977 47.619 0.00 0.00 38.40 3.46
864 902 3.855379 TCGGTTTTGATCGTACGAATGAG 59.145 43.478 23.56 8.56 0.00 2.90
867 905 2.601763 GCTCGGTTTTGATCGTACGAAT 59.398 45.455 23.56 10.88 0.00 3.34
887 925 1.947597 TTGCAGGAAATCATGGCCGC 61.948 55.000 0.00 0.00 0.00 6.53
894 932 0.874390 GCTGTCGTTGCAGGAAATCA 59.126 50.000 0.00 0.00 37.00 2.57
902 940 0.950555 GTCTGATGGCTGTCGTTGCA 60.951 55.000 0.00 0.00 0.00 4.08
954 992 2.242708 TCTTTATATTGGCAACGGGGGT 59.757 45.455 0.00 0.00 42.51 4.95
961 999 3.436470 GCCTCCCCTCTTTATATTGGCAA 60.436 47.826 0.68 0.68 37.91 4.52
1003 1041 1.124477 GGCGGGAGGAGATTGAGGAT 61.124 60.000 0.00 0.00 0.00 3.24
1037 1075 3.903360 ACCTCGAAGAAGAAGAACGAAG 58.097 45.455 0.00 0.00 34.09 3.79
1076 1114 2.303022 ACGCATCTGAAAAGAGAAGGGA 59.697 45.455 0.00 0.00 30.54 4.20
1093 1131 3.364441 GCAGCCATGGACAACGCA 61.364 61.111 18.40 0.00 0.00 5.24
1099 1137 1.817099 CTTCTCGGCAGCCATGGAC 60.817 63.158 18.40 7.03 0.00 4.02
1110 1148 2.158841 GCGTAGATCTAGAGCTTCTCGG 59.841 54.545 16.99 0.00 35.36 4.63
1217 1255 1.740718 GCGGAGAGCCCTTCAAAGTAG 60.741 57.143 0.00 0.00 40.81 2.57
1232 1270 2.604046 AGGCAACAGTATTAGCGGAG 57.396 50.000 0.00 0.00 41.41 4.63
1308 1346 3.993081 GGAGCAGAGATGATTCGGTATTG 59.007 47.826 0.00 0.00 0.00 1.90
1330 1368 7.148639 CCATGGACCGATAAATATACGAACAAG 60.149 40.741 5.56 0.00 0.00 3.16
1336 1374 4.796830 CGTCCATGGACCGATAAATATACG 59.203 45.833 34.05 17.53 41.76 3.06
1396 1434 6.649141 TGGAGCGACATATAAATATTCCACAC 59.351 38.462 0.00 0.00 0.00 3.82
1440 1480 2.469465 ATCTCGGCAACACCACCAGG 62.469 60.000 0.00 0.00 39.03 4.45
1476 1516 6.936335 TGTTATTACACCTCCAGCATATCATG 59.064 38.462 0.00 0.00 0.00 3.07
1549 1589 5.361135 CGGTAAACGGTAAAAAGATGGTT 57.639 39.130 0.00 0.00 39.42 3.67
1563 1604 1.339711 CTAACCCGTGACGGTAAACG 58.660 55.000 23.73 9.52 46.80 3.60
1567 1608 1.745087 CTTAGCTAACCCGTGACGGTA 59.255 52.381 23.73 8.73 46.80 4.02
1618 1659 2.947652 GACACAGGGAATCATCATGTGG 59.052 50.000 12.31 0.00 43.61 4.17
2220 2264 4.315803 ACCACACAAGTAGCAACATCTAC 58.684 43.478 0.00 0.00 39.28 2.59
2539 2922 6.932947 AGTTACAGGAGTACAGGATAACAAC 58.067 40.000 0.00 0.00 0.00 3.32
2602 3022 3.961480 ATCAACTAGCACAGCAGTACA 57.039 42.857 0.00 0.00 0.00 2.90
3765 4459 1.487976 TCCATGTTTTGCCAAAAGCCA 59.512 42.857 2.15 0.00 42.71 4.75
3879 4590 6.170506 ACCTGCTATTATCACGACAAAAGAA 58.829 36.000 0.00 0.00 0.00 2.52
3881 4592 6.128282 ACAACCTGCTATTATCACGACAAAAG 60.128 38.462 0.00 0.00 0.00 2.27
3966 4677 6.096705 CCAACATTTTGGTCATGCCTCTATTA 59.903 38.462 2.21 0.00 46.63 0.98
4007 4718 9.798994 TTTTTGCCAAAAATTTCGTAGTTAGTA 57.201 25.926 11.16 0.00 35.57 1.82
4008 4719 8.705048 TTTTTGCCAAAAATTTCGTAGTTAGT 57.295 26.923 11.16 0.00 35.57 2.24
4021 4732 6.769822 TCAAAGCCTATGATTTTTGCCAAAAA 59.230 30.769 16.94 16.94 43.76 1.94
4068 4780 4.970662 ACTGCATTTTACTACATGGCTG 57.029 40.909 0.00 0.00 0.00 4.85
4106 4828 5.804473 CACCATTTATTTGCGCATTAGTTCA 59.196 36.000 12.75 0.00 0.00 3.18
4126 4848 6.406400 GGGTGTATGCTAATTATTTTGCACCA 60.406 38.462 20.27 10.50 44.33 4.17
4245 5007 1.238439 CGCTTCCACATTTCACCAGT 58.762 50.000 0.00 0.00 0.00 4.00
4293 5384 4.910585 GGATGTACCGCCGGCTGG 62.911 72.222 28.27 28.27 38.77 4.85
4294 5385 3.792053 GAGGATGTACCGCCGGCTG 62.792 68.421 26.68 21.87 44.74 4.85
4295 5386 3.537874 GAGGATGTACCGCCGGCT 61.538 66.667 26.68 9.55 44.74 5.52
4296 5387 3.845259 TGAGGATGTACCGCCGGC 61.845 66.667 19.07 19.07 44.74 6.13
4297 5388 2.106332 GTGAGGATGTACCGCCGG 59.894 66.667 0.00 0.00 44.74 6.13
4298 5389 1.956629 AAGGTGAGGATGTACCGCCG 61.957 60.000 0.00 0.00 44.74 6.46
4299 5390 0.462047 CAAGGTGAGGATGTACCGCC 60.462 60.000 0.00 0.00 44.74 6.13
4300 5391 0.462047 CCAAGGTGAGGATGTACCGC 60.462 60.000 0.00 0.00 44.74 5.68
4333 5424 5.905913 AGAGGGGTACTATACATCAGCTTTT 59.094 40.000 0.00 0.00 0.00 2.27
4334 5425 5.305644 CAGAGGGGTACTATACATCAGCTTT 59.694 44.000 0.00 0.00 0.00 3.51
4422 5513 2.829023 AGAACGGTCTTATTCCCTCCA 58.171 47.619 0.00 0.00 0.00 3.86
4423 5514 5.105023 ACTTTAGAACGGTCTTATTCCCTCC 60.105 44.000 9.04 0.00 35.12 4.30
4442 5540 5.534407 TGCTAAACTCGACATGACACTTTA 58.466 37.500 0.00 0.00 0.00 1.85
4450 5548 4.327357 ACTCGAATTGCTAAACTCGACATG 59.673 41.667 0.00 0.00 35.52 3.21
4534 5633 5.601662 ACAAGATACACCATGTCCTATTCG 58.398 41.667 0.00 0.00 0.00 3.34
4541 5640 8.887036 TTGATGTATACAAGATACACCATGTC 57.113 34.615 10.14 0.00 37.33 3.06
4675 5774 6.793505 AACTTAGAATGGTACTAGGTCAGG 57.206 41.667 0.00 0.00 30.89 3.86
4681 5780 7.108841 TGTGGCTAACTTAGAATGGTACTAG 57.891 40.000 0.00 0.00 0.00 2.57
4746 5845 2.566913 TGCTGCTCGACCTGTTTAAAA 58.433 42.857 0.00 0.00 0.00 1.52
4793 5892 2.217112 GCACATGCCGATAGACGAC 58.783 57.895 0.00 0.00 45.77 4.34
4893 5992 3.155167 GGCCTAGGGACGTGGAGG 61.155 72.222 11.72 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.