Multiple sequence alignment - TraesCS5D01G363800

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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 TraesCS5D01G363800 chr5D 100.000 3185 0 0 1 3185 441393329 441390145 0.000000e+00 5882.0
1 TraesCS5D01G363800 chr5D 86.120 634 66 7 1 615 454024294 454024924 0.000000e+00 664.0
2 TraesCS5D01G363800 chr5D 81.029 622 99 12 1 607 360136416 360137033 7.990000e-131 477.0
3 TraesCS5D01G363800 chr5A 91.345 2253 132 36 873 3085 558165228 558162999 0.000000e+00 3022.0
4 TraesCS5D01G363800 chr5A 92.453 53 3 1 3132 3184 558162910 558162859 1.230000e-09 75.0
5 TraesCS5D01G363800 chr5A 80.392 102 10 8 2482 2579 403290739 403290644 5.700000e-08 69.4
6 TraesCS5D01G363800 chr5B 88.957 1476 125 22 1125 2591 537626738 537625292 0.000000e+00 1788.0
7 TraesCS5D01G363800 chr5B 92.424 198 15 0 905 1102 537626983 537626786 1.870000e-72 283.0
8 TraesCS5D01G363800 chr1A 87.956 631 60 6 1 615 494312848 494313478 0.000000e+00 730.0
9 TraesCS5D01G363800 chr7D 87.700 626 59 8 1 615 584608251 584608869 0.000000e+00 713.0
10 TraesCS5D01G363800 chr7D 86.473 621 61 8 1 600 59885284 59884666 0.000000e+00 660.0
11 TraesCS5D01G363800 chr7D 82.432 370 26 17 1146 1488 10835958 10835601 1.450000e-73 287.0
12 TraesCS5D01G363800 chr7D 93.243 148 10 0 1843 1990 10833114 10832967 5.350000e-53 219.0
13 TraesCS5D01G363800 chr7D 100.000 37 0 0 2484 2520 56403672 56403636 5.700000e-08 69.4
14 TraesCS5D01G363800 chr3B 86.888 633 63 6 1 615 764074015 764074645 0.000000e+00 691.0
15 TraesCS5D01G363800 chr3B 89.412 85 8 1 2485 2568 456554449 456554365 4.350000e-19 106.0
16 TraesCS5D01G363800 chr2D 86.709 632 59 8 1 613 485997577 485996952 0.000000e+00 678.0
17 TraesCS5D01G363800 chr2D 86.321 636 65 8 1 616 569683270 569683903 0.000000e+00 673.0
18 TraesCS5D01G363800 chr2D 85.331 634 72 6 1 615 480297873 480297242 1.250000e-178 636.0
19 TraesCS5D01G363800 chr2D 87.202 461 42 3 1 444 19510706 19511166 2.830000e-140 508.0
20 TraesCS5D01G363800 chr7A 86.364 638 66 6 1 618 49771064 49770428 0.000000e+00 676.0
21 TraesCS5D01G363800 chr7A 85.489 634 71 7 3 616 35175641 35176273 2.680000e-180 641.0
22 TraesCS5D01G363800 chr7A 82.967 364 29 14 1146 1488 10044233 10043882 6.680000e-77 298.0
23 TraesCS5D01G363800 chr7A 93.243 148 10 0 1843 1990 10041179 10041032 5.350000e-53 219.0
24 TraesCS5D01G363800 chr7A 78.082 219 22 12 2266 2468 10039703 10039495 7.220000e-22 115.0
25 TraesCS5D01G363800 chr7A 94.545 55 2 1 2093 2147 10039926 10039873 2.040000e-12 84.2
26 TraesCS5D01G363800 chr7A 95.745 47 2 0 1707 1753 10042641 10042595 3.410000e-10 76.8
27 TraesCS5D01G363800 chr4D 85.581 645 69 7 1 625 243355377 243354737 0.000000e+00 654.0
28 TraesCS5D01G363800 chr1B 85.537 643 69 6 1 625 118095310 118094674 0.000000e+00 651.0
29 TraesCS5D01G363800 chr1B 91.489 47 4 0 2484 2530 428723265 428723311 7.370000e-07 65.8
30 TraesCS5D01G363800 chr6B 85.692 629 61 9 19 629 92291490 92292107 1.250000e-178 636.0
31 TraesCS5D01G363800 chr6B 87.817 394 43 5 235 626 701457104 701456714 1.040000e-124 457.0
32 TraesCS5D01G363800 chr4A 85.150 633 75 5 1 615 97815376 97816007 5.800000e-177 630.0
33 TraesCS5D01G363800 chr4A 82.437 558 65 15 1 547 26979374 26979909 1.040000e-124 457.0
34 TraesCS5D01G363800 chr4A 84.890 364 22 11 1146 1488 727734373 727734724 1.420000e-88 337.0
35 TraesCS5D01G363800 chr4A 93.243 148 10 0 1843 1990 727737612 727737759 5.350000e-53 219.0
36 TraesCS5D01G363800 chr4A 77.725 211 22 9 2271 2466 727738939 727739139 4.350000e-19 106.0
37 TraesCS5D01G363800 chr4A 96.364 55 1 1 2093 2147 727738695 727738748 4.380000e-14 89.8
38 TraesCS5D01G363800 chr4A 97.727 44 1 0 1707 1750 727735934 727735977 3.410000e-10 76.8
39 TraesCS5D01G363800 chr4A 100.000 37 0 0 2484 2520 673073512 673073476 5.700000e-08 69.4
40 TraesCS5D01G363800 chr2B 84.567 635 75 8 1 615 751010225 751010856 2.720000e-170 608.0
41 TraesCS5D01G363800 chr7B 79.587 387 40 10 1 350 746806078 746805694 1.140000e-59 241.0
42 TraesCS5D01G363800 chrUn 93.243 148 10 0 1843 1990 480953700 480953553 5.350000e-53 219.0
43 TraesCS5D01G363800 chrUn 75.676 185 31 13 2739 2915 331154846 331155024 2.630000e-11 80.5
44 TraesCS5D01G363800 chr3A 82.723 191 22 3 1 181 634655422 634655611 3.290000e-35 159.0
45 TraesCS5D01G363800 chr3A 97.143 35 0 1 2482 2515 362548251 362548217 1.230000e-04 58.4
46 TraesCS5D01G363800 chr4B 75.500 200 35 13 2739 2930 648231396 648231203 5.660000e-13 86.1
47 TraesCS5D01G363800 chr4B 75.500 200 35 13 2739 2930 648257617 648257424 5.660000e-13 86.1
48 TraesCS5D01G363800 chr4B 75.000 200 36 13 2739 2930 648207900 648207707 2.630000e-11 80.5
49 TraesCS5D01G363800 chr1D 91.228 57 4 1 2484 2539 316619665 316619721 3.410000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G363800 chr5D 441390145 441393329 3184 True 5882.0 5882 100.0000 1 3185 1 chr5D.!!$R1 3184
1 TraesCS5D01G363800 chr5D 454024294 454024924 630 False 664.0 664 86.1200 1 615 1 chr5D.!!$F2 614
2 TraesCS5D01G363800 chr5D 360136416 360137033 617 False 477.0 477 81.0290 1 607 1 chr5D.!!$F1 606
3 TraesCS5D01G363800 chr5A 558162859 558165228 2369 True 1548.5 3022 91.8990 873 3184 2 chr5A.!!$R2 2311
4 TraesCS5D01G363800 chr5B 537625292 537626983 1691 True 1035.5 1788 90.6905 905 2591 2 chr5B.!!$R1 1686
5 TraesCS5D01G363800 chr1A 494312848 494313478 630 False 730.0 730 87.9560 1 615 1 chr1A.!!$F1 614
6 TraesCS5D01G363800 chr7D 584608251 584608869 618 False 713.0 713 87.7000 1 615 1 chr7D.!!$F1 614
7 TraesCS5D01G363800 chr7D 59884666 59885284 618 True 660.0 660 86.4730 1 600 1 chr7D.!!$R2 599
8 TraesCS5D01G363800 chr7D 10832967 10835958 2991 True 253.0 287 87.8375 1146 1990 2 chr7D.!!$R3 844
9 TraesCS5D01G363800 chr3B 764074015 764074645 630 False 691.0 691 86.8880 1 615 1 chr3B.!!$F1 614
10 TraesCS5D01G363800 chr2D 485996952 485997577 625 True 678.0 678 86.7090 1 613 1 chr2D.!!$R2 612
11 TraesCS5D01G363800 chr2D 569683270 569683903 633 False 673.0 673 86.3210 1 616 1 chr2D.!!$F2 615
12 TraesCS5D01G363800 chr2D 480297242 480297873 631 True 636.0 636 85.3310 1 615 1 chr2D.!!$R1 614
13 TraesCS5D01G363800 chr7A 49770428 49771064 636 True 676.0 676 86.3640 1 618 1 chr7A.!!$R1 617
14 TraesCS5D01G363800 chr7A 35175641 35176273 632 False 641.0 641 85.4890 3 616 1 chr7A.!!$F1 613
15 TraesCS5D01G363800 chr4D 243354737 243355377 640 True 654.0 654 85.5810 1 625 1 chr4D.!!$R1 624
16 TraesCS5D01G363800 chr1B 118094674 118095310 636 True 651.0 651 85.5370 1 625 1 chr1B.!!$R1 624
17 TraesCS5D01G363800 chr6B 92291490 92292107 617 False 636.0 636 85.6920 19 629 1 chr6B.!!$F1 610
18 TraesCS5D01G363800 chr4A 97815376 97816007 631 False 630.0 630 85.1500 1 615 1 chr4A.!!$F2 614
19 TraesCS5D01G363800 chr4A 26979374 26979909 535 False 457.0 457 82.4370 1 547 1 chr4A.!!$F1 546
20 TraesCS5D01G363800 chr2B 751010225 751010856 631 False 608.0 608 84.5670 1 615 1 chr2B.!!$F1 614

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
456 486 0.620556 ACCAACCCCAGCACTATCAG 59.379 55.0 0.0 0.0 0.0 2.90 F
1500 2050 0.105039 ATTCGGTCTGCGATCCTTCC 59.895 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2832 0.107703 TAATGGCTCCTGTTCAGCGG 60.108 55.0 0.0 0.0 37.81 5.52 R
3025 5291 0.400594 CCGGGGTTTTTCCTCAGACT 59.599 55.0 0.0 0.0 36.19 3.24 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
47 50 5.184711 ACGTTGTTTTGGTAACTTCCAGTA 58.815 37.500 0.00 0.00 38.80 2.74
53 56 6.178324 GTTTTGGTAACTTCCAGTAGCCTAT 58.822 40.000 0.00 0.00 38.80 2.57
102 105 5.756347 CCACATGCCATTTGATGATAAAAGG 59.244 40.000 0.00 0.00 32.91 3.11
263 288 4.613944 CGCTGATTATGGCAATGAAATGT 58.386 39.130 0.00 0.00 0.00 2.71
264 289 4.678287 CGCTGATTATGGCAATGAAATGTC 59.322 41.667 0.00 0.00 0.00 3.06
316 342 2.036992 GCCATCATAGGAGAGAGTGGTG 59.963 54.545 0.00 0.00 0.00 4.17
364 390 1.202915 TGCAGCCACAAAATGAGGAGA 60.203 47.619 0.00 0.00 28.90 3.71
375 401 6.016360 CACAAAATGAGGAGACAACCATAACA 60.016 38.462 0.00 0.00 0.00 2.41
447 476 2.281484 CACACCGACCAACCCCAG 60.281 66.667 0.00 0.00 0.00 4.45
456 486 0.620556 ACCAACCCCAGCACTATCAG 59.379 55.000 0.00 0.00 0.00 2.90
607 647 2.203401 GTTGCAACGCACGGGTATATA 58.797 47.619 14.90 0.00 38.71 0.86
625 665 9.220767 GGGTATATATGCTAGTCTTTTCCAAAG 57.779 37.037 0.62 0.00 0.00 2.77
630 670 8.870075 ATATGCTAGTCTTTTCCAAAGTTTCT 57.130 30.769 0.00 0.00 0.00 2.52
631 671 7.588497 ATGCTAGTCTTTTCCAAAGTTTCTT 57.412 32.000 0.00 0.00 0.00 2.52
632 672 7.404671 TGCTAGTCTTTTCCAAAGTTTCTTT 57.595 32.000 0.00 0.00 0.00 2.52
633 673 7.257722 TGCTAGTCTTTTCCAAAGTTTCTTTG 58.742 34.615 13.28 13.28 0.00 2.77
634 674 7.122055 TGCTAGTCTTTTCCAAAGTTTCTTTGA 59.878 33.333 19.55 6.92 0.00 2.69
635 675 7.645735 GCTAGTCTTTTCCAAAGTTTCTTTGAG 59.354 37.037 19.55 11.17 0.00 3.02
636 676 7.703058 AGTCTTTTCCAAAGTTTCTTTGAGA 57.297 32.000 19.55 12.83 0.00 3.27
637 677 7.539436 AGTCTTTTCCAAAGTTTCTTTGAGAC 58.461 34.615 21.01 21.01 33.44 3.36
638 678 6.752351 GTCTTTTCCAAAGTTTCTTTGAGACC 59.248 38.462 19.55 8.49 30.11 3.85
639 679 6.663523 TCTTTTCCAAAGTTTCTTTGAGACCT 59.336 34.615 19.55 0.00 0.00 3.85
640 680 7.832187 TCTTTTCCAAAGTTTCTTTGAGACCTA 59.168 33.333 19.55 3.27 0.00 3.08
641 681 7.948034 TTTCCAAAGTTTCTTTGAGACCTAA 57.052 32.000 19.55 7.51 0.00 2.69
642 682 7.948034 TTCCAAAGTTTCTTTGAGACCTAAA 57.052 32.000 19.55 2.67 0.00 1.85
643 683 7.948034 TCCAAAGTTTCTTTGAGACCTAAAA 57.052 32.000 19.55 0.00 0.00 1.52
644 684 8.533569 TCCAAAGTTTCTTTGAGACCTAAAAT 57.466 30.769 19.55 0.00 0.00 1.82
645 685 8.977412 TCCAAAGTTTCTTTGAGACCTAAAATT 58.023 29.630 19.55 0.00 0.00 1.82
646 686 9.599866 CCAAAGTTTCTTTGAGACCTAAAATTT 57.400 29.630 19.55 0.00 30.24 1.82
654 694 9.621629 TCTTTGAGACCTAAAATTTGTTACTCA 57.378 29.630 0.00 1.84 0.00 3.41
676 716 9.522804 ACTCATTTTTCTTATAAGAGCTACTCG 57.477 33.333 14.63 6.55 36.22 4.18
677 717 9.737427 CTCATTTTTCTTATAAGAGCTACTCGA 57.263 33.333 14.63 6.98 36.22 4.04
681 721 9.871238 TTTTTCTTATAAGAGCTACTCGAATGT 57.129 29.630 14.63 0.00 36.22 2.71
682 722 9.871238 TTTTCTTATAAGAGCTACTCGAATGTT 57.129 29.630 14.63 0.00 36.22 2.71
683 723 9.517609 TTTCTTATAAGAGCTACTCGAATGTTC 57.482 33.333 14.63 0.00 36.22 3.18
684 724 8.221965 TCTTATAAGAGCTACTCGAATGTTCA 57.778 34.615 11.24 0.00 35.36 3.18
685 725 8.851145 TCTTATAAGAGCTACTCGAATGTTCAT 58.149 33.333 11.24 0.00 35.36 2.57
686 726 9.469807 CTTATAAGAGCTACTCGAATGTTCATT 57.530 33.333 6.64 0.00 35.36 2.57
687 727 7.938563 ATAAGAGCTACTCGAATGTTCATTC 57.061 36.000 13.56 13.56 35.36 2.67
688 728 5.330455 AGAGCTACTCGAATGTTCATTCA 57.670 39.130 20.57 10.21 35.36 2.57
689 729 5.105752 AGAGCTACTCGAATGTTCATTCAC 58.894 41.667 20.57 6.84 35.36 3.18
690 730 4.184629 AGCTACTCGAATGTTCATTCACC 58.815 43.478 20.57 6.30 0.00 4.02
691 731 3.932710 GCTACTCGAATGTTCATTCACCA 59.067 43.478 20.57 7.24 0.00 4.17
692 732 4.572389 GCTACTCGAATGTTCATTCACCAT 59.428 41.667 20.57 8.98 0.00 3.55
693 733 5.753438 GCTACTCGAATGTTCATTCACCATA 59.247 40.000 20.57 9.48 0.00 2.74
694 734 6.257849 GCTACTCGAATGTTCATTCACCATAA 59.742 38.462 20.57 4.97 0.00 1.90
695 735 7.201609 GCTACTCGAATGTTCATTCACCATAAA 60.202 37.037 20.57 3.80 0.00 1.40
696 736 7.447374 ACTCGAATGTTCATTCACCATAAAA 57.553 32.000 20.57 1.11 0.00 1.52
697 737 7.881142 ACTCGAATGTTCATTCACCATAAAAA 58.119 30.769 20.57 0.35 0.00 1.94
698 738 8.522830 ACTCGAATGTTCATTCACCATAAAAAT 58.477 29.630 20.57 0.00 0.00 1.82
699 739 9.357652 CTCGAATGTTCATTCACCATAAAAATT 57.642 29.630 20.57 0.00 0.00 1.82
700 740 9.703892 TCGAATGTTCATTCACCATAAAAATTT 57.296 25.926 20.57 0.00 0.00 1.82
701 741 9.743937 CGAATGTTCATTCACCATAAAAATTTG 57.256 29.630 20.57 1.47 0.00 2.32
702 742 9.545611 GAATGTTCATTCACCATAAAAATTTGC 57.454 29.630 17.31 0.00 0.00 3.68
703 743 8.618702 ATGTTCATTCACCATAAAAATTTGCA 57.381 26.923 0.00 0.00 0.00 4.08
704 744 8.618702 TGTTCATTCACCATAAAAATTTGCAT 57.381 26.923 0.00 0.00 0.00 3.96
705 745 8.719648 TGTTCATTCACCATAAAAATTTGCATC 58.280 29.630 0.00 0.00 0.00 3.91
706 746 7.846644 TCATTCACCATAAAAATTTGCATCC 57.153 32.000 0.00 0.00 0.00 3.51
707 747 7.392418 TCATTCACCATAAAAATTTGCATCCA 58.608 30.769 0.00 0.00 0.00 3.41
708 748 7.333921 TCATTCACCATAAAAATTTGCATCCAC 59.666 33.333 0.00 0.00 0.00 4.02
709 749 5.486526 TCACCATAAAAATTTGCATCCACC 58.513 37.500 0.00 0.00 0.00 4.61
710 750 5.248020 TCACCATAAAAATTTGCATCCACCT 59.752 36.000 0.00 0.00 0.00 4.00
711 751 6.438741 TCACCATAAAAATTTGCATCCACCTA 59.561 34.615 0.00 0.00 0.00 3.08
712 752 7.038729 TCACCATAAAAATTTGCATCCACCTAA 60.039 33.333 0.00 0.00 0.00 2.69
713 753 7.605691 CACCATAAAAATTTGCATCCACCTAAA 59.394 33.333 0.00 0.00 0.00 1.85
714 754 7.823799 ACCATAAAAATTTGCATCCACCTAAAG 59.176 33.333 0.00 0.00 0.00 1.85
715 755 7.823799 CCATAAAAATTTGCATCCACCTAAAGT 59.176 33.333 0.00 0.00 0.00 2.66
716 756 9.868277 CATAAAAATTTGCATCCACCTAAAGTA 57.132 29.630 0.00 0.00 0.00 2.24
719 759 9.435688 AAAAATTTGCATCCACCTAAAGTATTC 57.564 29.630 0.00 0.00 0.00 1.75
720 760 7.961326 AATTTGCATCCACCTAAAGTATTCT 57.039 32.000 0.00 0.00 0.00 2.40
721 761 6.757897 TTTGCATCCACCTAAAGTATTCTG 57.242 37.500 0.00 0.00 0.00 3.02
722 762 5.692115 TGCATCCACCTAAAGTATTCTGA 57.308 39.130 0.00 0.00 0.00 3.27
723 763 6.252599 TGCATCCACCTAAAGTATTCTGAT 57.747 37.500 0.00 0.00 0.00 2.90
724 764 6.662755 TGCATCCACCTAAAGTATTCTGATT 58.337 36.000 0.00 0.00 0.00 2.57
725 765 7.118723 TGCATCCACCTAAAGTATTCTGATTT 58.881 34.615 0.00 0.00 0.00 2.17
726 766 7.615365 TGCATCCACCTAAAGTATTCTGATTTT 59.385 33.333 0.00 0.00 0.00 1.82
727 767 8.470002 GCATCCACCTAAAGTATTCTGATTTTT 58.530 33.333 0.00 0.00 0.00 1.94
763 803 8.880878 TGAATTTACTAGTATTCGCTAATGCA 57.119 30.769 2.79 1.66 39.64 3.96
764 804 8.978539 TGAATTTACTAGTATTCGCTAATGCAG 58.021 33.333 2.79 0.88 39.64 4.41
765 805 9.193133 GAATTTACTAGTATTCGCTAATGCAGA 57.807 33.333 2.79 0.00 39.64 4.26
766 806 9.712305 AATTTACTAGTATTCGCTAATGCAGAT 57.288 29.630 2.79 0.00 39.64 2.90
767 807 8.520835 TTTACTAGTATTCGCTAATGCAGATG 57.479 34.615 2.79 0.00 39.64 2.90
768 808 6.332735 ACTAGTATTCGCTAATGCAGATGA 57.667 37.500 0.00 0.00 39.64 2.92
769 809 6.385843 ACTAGTATTCGCTAATGCAGATGAG 58.614 40.000 0.00 0.00 39.64 2.90
770 810 5.207110 AGTATTCGCTAATGCAGATGAGT 57.793 39.130 2.07 0.00 39.64 3.41
771 811 5.226396 AGTATTCGCTAATGCAGATGAGTC 58.774 41.667 2.07 0.00 39.64 3.36
772 812 3.808466 TTCGCTAATGCAGATGAGTCT 57.192 42.857 0.00 0.00 39.64 3.24
787 827 4.975490 TCTGGGCTCAGACCTGAA 57.025 55.556 13.72 0.00 44.39 3.02
788 828 3.406442 TCTGGGCTCAGACCTGAAT 57.594 52.632 13.72 0.00 44.39 2.57
789 829 1.661463 TCTGGGCTCAGACCTGAATT 58.339 50.000 13.72 0.00 44.39 2.17
790 830 2.832838 TCTGGGCTCAGACCTGAATTA 58.167 47.619 13.72 0.00 44.39 1.40
791 831 2.501723 TCTGGGCTCAGACCTGAATTAC 59.498 50.000 13.72 0.00 44.39 1.89
792 832 2.237143 CTGGGCTCAGACCTGAATTACA 59.763 50.000 8.28 0.00 43.49 2.41
793 833 2.237143 TGGGCTCAGACCTGAATTACAG 59.763 50.000 0.00 0.00 45.36 2.74
807 847 7.552458 CTGAATTACAGGTATATTGTGTGCA 57.448 36.000 3.79 0.00 42.39 4.57
808 848 7.929941 TGAATTACAGGTATATTGTGTGCAA 57.070 32.000 0.00 0.00 39.16 4.08
809 849 8.518430 TGAATTACAGGTATATTGTGTGCAAT 57.482 30.769 0.00 0.00 46.14 3.56
810 850 8.620416 TGAATTACAGGTATATTGTGTGCAATC 58.380 33.333 0.00 0.00 43.61 2.67
811 851 8.752005 AATTACAGGTATATTGTGTGCAATCT 57.248 30.769 0.00 0.00 43.61 2.40
812 852 9.845740 AATTACAGGTATATTGTGTGCAATCTA 57.154 29.630 0.00 0.00 43.61 1.98
813 853 9.845740 ATTACAGGTATATTGTGTGCAATCTAA 57.154 29.630 0.00 0.00 43.61 2.10
814 854 7.792374 ACAGGTATATTGTGTGCAATCTAAG 57.208 36.000 0.00 0.00 43.61 2.18
815 855 6.767902 ACAGGTATATTGTGTGCAATCTAAGG 59.232 38.462 0.00 0.00 43.61 2.69
816 856 6.992123 CAGGTATATTGTGTGCAATCTAAGGA 59.008 38.462 0.00 0.00 43.61 3.36
817 857 7.172190 CAGGTATATTGTGTGCAATCTAAGGAG 59.828 40.741 0.00 0.00 43.61 3.69
818 858 6.992715 GGTATATTGTGTGCAATCTAAGGAGT 59.007 38.462 0.00 0.00 43.61 3.85
819 859 6.932356 ATATTGTGTGCAATCTAAGGAGTG 57.068 37.500 0.00 0.00 43.61 3.51
827 867 4.972514 CAATCTAAGGAGTGCTTTTCCC 57.027 45.455 0.90 0.00 35.20 3.97
828 868 3.653835 ATCTAAGGAGTGCTTTTCCCC 57.346 47.619 0.90 0.00 35.20 4.81
829 869 2.632537 TCTAAGGAGTGCTTTTCCCCT 58.367 47.619 0.90 0.00 35.20 4.79
830 870 3.798515 TCTAAGGAGTGCTTTTCCCCTA 58.201 45.455 0.90 0.00 35.20 3.53
831 871 4.172807 TCTAAGGAGTGCTTTTCCCCTAA 58.827 43.478 0.90 0.00 35.20 2.69
832 872 3.895704 AAGGAGTGCTTTTCCCCTAAA 57.104 42.857 0.00 0.00 35.20 1.85
833 873 3.895704 AGGAGTGCTTTTCCCCTAAAA 57.104 42.857 0.00 0.00 35.20 1.52
834 874 4.193240 AGGAGTGCTTTTCCCCTAAAAA 57.807 40.909 0.00 0.00 36.64 1.94
861 901 9.533831 AATAAAAATTCTAAGGAGAGCTTTGGA 57.466 29.630 0.00 0.00 31.77 3.53
862 902 6.825944 AAAATTCTAAGGAGAGCTTTGGAC 57.174 37.500 0.00 0.00 31.77 4.02
863 903 3.983044 TTCTAAGGAGAGCTTTGGACC 57.017 47.619 0.00 0.00 31.77 4.46
864 904 2.902608 TCTAAGGAGAGCTTTGGACCA 58.097 47.619 0.00 0.00 0.00 4.02
865 905 3.248024 TCTAAGGAGAGCTTTGGACCAA 58.752 45.455 1.69 1.69 0.00 3.67
866 906 3.650942 TCTAAGGAGAGCTTTGGACCAAA 59.349 43.478 18.59 18.59 0.00 3.28
867 907 3.532641 AAGGAGAGCTTTGGACCAAAT 57.467 42.857 19.87 6.44 32.70 2.32
868 908 4.657814 AAGGAGAGCTTTGGACCAAATA 57.342 40.909 19.87 0.00 32.70 1.40
869 909 3.956744 AGGAGAGCTTTGGACCAAATAC 58.043 45.455 19.87 14.69 32.70 1.89
870 910 3.330701 AGGAGAGCTTTGGACCAAATACA 59.669 43.478 19.87 0.00 32.70 2.29
871 911 3.440522 GGAGAGCTTTGGACCAAATACAC 59.559 47.826 19.87 13.24 32.70 2.90
878 918 3.603965 TGGACCAAATACACCCTTGTT 57.396 42.857 0.00 0.00 37.15 2.83
893 933 3.154710 CCTTGTTTTCTAACCACCCCTC 58.845 50.000 0.00 0.00 33.15 4.30
894 934 3.435890 CCTTGTTTTCTAACCACCCCTCA 60.436 47.826 0.00 0.00 33.15 3.86
895 935 3.955524 TGTTTTCTAACCACCCCTCAA 57.044 42.857 0.00 0.00 33.15 3.02
1064 1104 2.673523 GGCCTGTCTCCTGTGCAT 59.326 61.111 0.00 0.00 0.00 3.96
1102 1142 4.021925 ACCTGCTTGACCCGCTCC 62.022 66.667 0.00 0.00 0.00 4.70
1104 1144 2.125350 CTGCTTGACCCGCTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
1106 1146 4.821589 GCTTGACCCGCTCCTCCG 62.822 72.222 0.00 0.00 0.00 4.63
1123 1163 4.357947 GCGCGGTCTGTGTCCTGA 62.358 66.667 8.83 0.00 0.00 3.86
1166 1231 4.471904 TGTCGATGAGGAGTTGCTATTT 57.528 40.909 0.00 0.00 0.00 1.40
1345 1431 0.383231 CTCATCCAAATCCAAGCGCC 59.617 55.000 2.29 0.00 0.00 6.53
1464 1556 1.006102 CAAGAACCTCGCCGACTGT 60.006 57.895 0.00 0.00 0.00 3.55
1500 2050 0.105039 ATTCGGTCTGCGATCCTTCC 59.895 55.000 0.00 0.00 0.00 3.46
1622 2172 4.216902 TGCAAGAGATGAGTTGTTTGATGG 59.783 41.667 0.00 0.00 0.00 3.51
1675 2679 3.006967 TGGAACTGCAACCTCTTCTACTC 59.993 47.826 5.96 0.00 0.00 2.59
1676 2680 3.591023 GAACTGCAACCTCTTCTACTCC 58.409 50.000 0.00 0.00 0.00 3.85
1684 2688 3.508426 ACCTCTTCTACTCCGAAAAGGT 58.492 45.455 0.00 0.00 39.05 3.50
1694 2698 2.037251 CTCCGAAAAGGTCACAGGAGAA 59.963 50.000 3.40 0.00 45.88 2.87
1697 2701 2.037251 CGAAAAGGTCACAGGAGAAGGA 59.963 50.000 0.00 0.00 0.00 3.36
1698 2702 3.494398 CGAAAAGGTCACAGGAGAAGGAA 60.494 47.826 0.00 0.00 0.00 3.36
1700 2704 3.493767 AAGGTCACAGGAGAAGGAAAC 57.506 47.619 0.00 0.00 0.00 2.78
1701 2705 2.408565 AGGTCACAGGAGAAGGAAACA 58.591 47.619 0.00 0.00 0.00 2.83
1702 2706 2.370189 AGGTCACAGGAGAAGGAAACAG 59.630 50.000 0.00 0.00 0.00 3.16
1705 2709 2.368875 TCACAGGAGAAGGAAACAGGAC 59.631 50.000 0.00 0.00 0.00 3.85
1770 3907 5.356190 TCATCTGTCCTGCATTCTTGAATTC 59.644 40.000 0.00 0.00 0.00 2.17
1836 3973 1.737355 TAATAAGGCGACCGGACGGG 61.737 60.000 26.63 6.67 43.62 5.28
1870 4103 1.740296 CTACGCGAGGGTTTGGGTG 60.740 63.158 15.93 0.00 35.63 4.61
2013 4246 2.541556 GATCTCTGGCGTGTTAGGAAC 58.458 52.381 0.00 0.00 0.00 3.62
2025 4258 4.986034 CGTGTTAGGAACGATAATATGGCA 59.014 41.667 0.00 0.00 43.68 4.92
2049 4282 4.207165 ACTTGTGCAAGAAAGCTAAGGAA 58.793 39.130 17.62 0.00 40.79 3.36
2056 4289 4.614764 GCAAGAAAGCTAAGGAACTCAAGC 60.615 45.833 0.00 0.00 44.56 4.01
2355 4588 2.210013 TGGTTGCGAGCTGGAGTCT 61.210 57.895 0.00 0.00 0.00 3.24
2607 4873 4.765273 TGCCTCGCAATTTATCTGTCTTA 58.235 39.130 0.00 0.00 34.76 2.10
2673 4939 7.454260 AATTTAACCTCTAAGAGTGCCTTTG 57.546 36.000 0.00 0.00 36.34 2.77
2841 5107 9.874205 CCATCAACTCAAACCATTGTTATAATT 57.126 29.630 0.00 0.00 37.79 1.40
2875 5141 8.682936 TCTTTCTATGCTTTCAGAACTTTTCT 57.317 30.769 0.00 0.00 41.70 2.52
2938 5204 8.494433 AGAGGATTTGGCACTCTAATTATACAA 58.506 33.333 3.73 0.00 39.65 2.41
3023 5289 6.432936 GGTTACGAAGGAACCAAGTTAAAAG 58.567 40.000 9.17 0.00 44.92 2.27
3024 5290 4.563337 ACGAAGGAACCAAGTTAAAAGC 57.437 40.909 0.00 0.00 0.00 3.51
3025 5291 3.949113 ACGAAGGAACCAAGTTAAAAGCA 59.051 39.130 0.00 0.00 0.00 3.91
3026 5292 4.036380 ACGAAGGAACCAAGTTAAAAGCAG 59.964 41.667 0.00 0.00 0.00 4.24
3027 5293 4.036380 CGAAGGAACCAAGTTAAAAGCAGT 59.964 41.667 0.00 0.00 0.00 4.40
3028 5294 5.515797 AAGGAACCAAGTTAAAAGCAGTC 57.484 39.130 0.00 0.00 0.00 3.51
3041 5310 2.278332 AGCAGTCTGAGGAAAAACCC 57.722 50.000 3.32 0.00 40.05 4.11
3042 5311 1.202940 AGCAGTCTGAGGAAAAACCCC 60.203 52.381 3.32 0.00 40.05 4.95
3064 5333 1.636340 GACTCGTGTGTGTGTGTGC 59.364 57.895 0.00 0.00 0.00 4.57
3066 5335 3.491508 CTCGTGTGTGTGTGTGCGC 62.492 63.158 0.00 0.00 0.00 6.09
3088 5361 3.319904 GCGTGTGCGTGAGTTCTT 58.680 55.556 0.00 0.00 40.81 2.52
3090 5363 0.654472 GCGTGTGCGTGAGTTCTTTG 60.654 55.000 0.00 0.00 40.81 2.77
3091 5364 0.654472 CGTGTGCGTGAGTTCTTTGC 60.654 55.000 0.00 0.00 0.00 3.68
3092 5365 0.317020 GTGTGCGTGAGTTCTTTGCC 60.317 55.000 0.00 0.00 0.00 4.52
3093 5366 0.463654 TGTGCGTGAGTTCTTTGCCT 60.464 50.000 0.00 0.00 0.00 4.75
3094 5367 1.202592 TGTGCGTGAGTTCTTTGCCTA 60.203 47.619 0.00 0.00 0.00 3.93
3095 5368 1.194772 GTGCGTGAGTTCTTTGCCTAC 59.805 52.381 0.00 0.00 0.00 3.18
3096 5369 1.070134 TGCGTGAGTTCTTTGCCTACT 59.930 47.619 0.00 0.00 0.00 2.57
3097 5370 2.297880 TGCGTGAGTTCTTTGCCTACTA 59.702 45.455 0.00 0.00 0.00 1.82
3098 5371 3.243941 TGCGTGAGTTCTTTGCCTACTAA 60.244 43.478 0.00 0.00 0.00 2.24
3099 5372 3.123116 GCGTGAGTTCTTTGCCTACTAAC 59.877 47.826 0.00 0.00 0.00 2.34
3100 5373 3.678548 CGTGAGTTCTTTGCCTACTAACC 59.321 47.826 0.00 0.00 0.00 2.85
3101 5374 4.638304 GTGAGTTCTTTGCCTACTAACCA 58.362 43.478 0.00 0.00 0.00 3.67
3102 5375 5.246307 GTGAGTTCTTTGCCTACTAACCAT 58.754 41.667 0.00 0.00 0.00 3.55
3103 5376 5.122396 GTGAGTTCTTTGCCTACTAACCATG 59.878 44.000 0.00 0.00 0.00 3.66
3106 5379 5.705905 AGTTCTTTGCCTACTAACCATGAAC 59.294 40.000 0.00 0.00 0.00 3.18
3107 5380 5.499004 TCTTTGCCTACTAACCATGAACT 57.501 39.130 0.00 0.00 0.00 3.01
3108 5381 5.488341 TCTTTGCCTACTAACCATGAACTC 58.512 41.667 0.00 0.00 0.00 3.01
3109 5382 3.520290 TGCCTACTAACCATGAACTCG 57.480 47.619 0.00 0.00 0.00 4.18
3111 5384 3.119245 TGCCTACTAACCATGAACTCGAC 60.119 47.826 0.00 0.00 0.00 4.20
3112 5385 3.737355 GCCTACTAACCATGAACTCGACC 60.737 52.174 0.00 0.00 0.00 4.79
3115 5388 4.189639 ACTAACCATGAACTCGACCTTC 57.810 45.455 0.00 0.00 0.00 3.46
3116 5389 2.474410 AACCATGAACTCGACCTTCC 57.526 50.000 0.00 0.00 0.00 3.46
3118 5391 1.978580 ACCATGAACTCGACCTTCCTT 59.021 47.619 0.00 0.00 0.00 3.36
3119 5392 2.372172 ACCATGAACTCGACCTTCCTTT 59.628 45.455 0.00 0.00 0.00 3.11
3120 5393 3.181443 ACCATGAACTCGACCTTCCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
3122 5395 4.083271 CCATGAACTCGACCTTCCTTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
3124 5397 4.377897 TGAACTCGACCTTCCTTTTTCTC 58.622 43.478 0.00 0.00 0.00 2.87
3125 5398 3.027974 ACTCGACCTTCCTTTTTCTCG 57.972 47.619 0.00 0.00 0.00 4.04
3127 5400 3.246619 CTCGACCTTCCTTTTTCTCGAG 58.753 50.000 5.93 5.93 40.65 4.04
3130 5403 4.056050 CGACCTTCCTTTTTCTCGAGAAA 58.944 43.478 31.62 31.62 41.77 2.52
3131 5404 7.448278 CTCGACCTTCCTTTTTCTCGAGAAAA 61.448 42.308 37.30 37.30 46.41 2.29
3166 5476 7.976826 TGTTACCAAGTTATAGCCAAATAACG 58.023 34.615 7.96 0.00 43.87 3.18
3169 5479 9.664332 TTACCAAGTTATAGCCAAATAACGTAA 57.336 29.630 0.00 7.94 43.87 3.18
3184 5494 0.451783 CGTAATTGAGCCCACCAAGC 59.548 55.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 1.478837 CGTCTGGGATAGGCTACTGGA 60.479 57.143 0.00 0.00 0.00 3.86
47 50 1.115930 ATTCGCGTCTGGGATAGGCT 61.116 55.000 5.77 0.00 36.87 4.58
53 56 0.250124 ACAACAATTCGCGTCTGGGA 60.250 50.000 5.77 0.00 34.90 4.37
102 105 8.860088 ACAATTTCTAGCCAACCAATATATTCC 58.140 33.333 0.00 0.00 0.00 3.01
263 288 7.054124 GGATGGGTTACTAATTCAGTGAATGA 58.946 38.462 18.94 10.87 38.24 2.57
264 289 6.017934 CGGATGGGTTACTAATTCAGTGAATG 60.018 42.308 18.94 10.03 38.24 2.67
282 308 0.110295 TGATGGCATAACCGGATGGG 59.890 55.000 9.46 0.00 43.94 4.00
364 390 4.382685 CCTCCGTGTCTATGTTATGGTTGT 60.383 45.833 0.00 0.00 0.00 3.32
375 401 2.125961 GGTCCGCCTCCGTGTCTAT 61.126 63.158 0.00 0.00 0.00 1.98
447 476 0.387878 CCGCGAGATCCTGATAGTGC 60.388 60.000 8.23 0.00 0.00 4.40
456 486 0.462047 ATGTTTGACCCGCGAGATCC 60.462 55.000 8.23 0.00 0.00 3.36
607 647 7.588497 AAGAAACTTTGGAAAAGACTAGCAT 57.412 32.000 6.73 0.00 0.00 3.79
628 668 9.621629 TGAGTAACAAATTTTAGGTCTCAAAGA 57.378 29.630 0.00 0.00 0.00 2.52
650 690 9.522804 CGAGTAGCTCTTATAAGAAAAATGAGT 57.477 33.333 15.85 2.53 34.03 3.41
651 691 9.737427 TCGAGTAGCTCTTATAAGAAAAATGAG 57.263 33.333 15.85 4.28 34.03 2.90
655 695 9.871238 ACATTCGAGTAGCTCTTATAAGAAAAA 57.129 29.630 15.85 2.03 34.03 1.94
656 696 9.871238 AACATTCGAGTAGCTCTTATAAGAAAA 57.129 29.630 15.85 2.36 34.03 2.29
657 697 9.517609 GAACATTCGAGTAGCTCTTATAAGAAA 57.482 33.333 15.85 5.68 34.03 2.52
658 698 8.683615 TGAACATTCGAGTAGCTCTTATAAGAA 58.316 33.333 15.85 0.00 34.03 2.52
659 699 8.221965 TGAACATTCGAGTAGCTCTTATAAGA 57.778 34.615 14.42 14.42 0.00 2.10
660 700 9.469807 AATGAACATTCGAGTAGCTCTTATAAG 57.530 33.333 6.11 6.11 0.00 1.73
661 701 9.464714 GAATGAACATTCGAGTAGCTCTTATAA 57.535 33.333 10.98 0.00 37.97 0.98
663 703 7.938563 GAATGAACATTCGAGTAGCTCTTAT 57.061 36.000 10.98 0.00 37.97 1.73
676 716 9.545611 GCAAATTTTTATGGTGAATGAACATTC 57.454 29.630 17.35 17.35 45.55 2.67
677 717 9.064706 TGCAAATTTTTATGGTGAATGAACATT 57.935 25.926 0.00 0.00 0.00 2.71
678 718 8.618702 TGCAAATTTTTATGGTGAATGAACAT 57.381 26.923 0.00 0.00 0.00 2.71
679 719 8.618702 ATGCAAATTTTTATGGTGAATGAACA 57.381 26.923 0.00 0.00 0.00 3.18
680 720 8.177013 GGATGCAAATTTTTATGGTGAATGAAC 58.823 33.333 0.00 0.00 0.00 3.18
681 721 7.881751 TGGATGCAAATTTTTATGGTGAATGAA 59.118 29.630 0.00 0.00 0.00 2.57
682 722 7.333921 GTGGATGCAAATTTTTATGGTGAATGA 59.666 33.333 0.00 0.00 0.00 2.57
683 723 7.414319 GGTGGATGCAAATTTTTATGGTGAATG 60.414 37.037 0.00 0.00 0.00 2.67
684 724 6.598850 GGTGGATGCAAATTTTTATGGTGAAT 59.401 34.615 0.00 0.00 0.00 2.57
685 725 5.936956 GGTGGATGCAAATTTTTATGGTGAA 59.063 36.000 0.00 0.00 0.00 3.18
686 726 5.248020 AGGTGGATGCAAATTTTTATGGTGA 59.752 36.000 0.00 0.00 0.00 4.02
687 727 5.490159 AGGTGGATGCAAATTTTTATGGTG 58.510 37.500 0.00 0.00 0.00 4.17
688 728 5.760484 AGGTGGATGCAAATTTTTATGGT 57.240 34.783 0.00 0.00 0.00 3.55
689 729 7.823799 ACTTTAGGTGGATGCAAATTTTTATGG 59.176 33.333 0.00 0.00 0.00 2.74
690 730 8.776376 ACTTTAGGTGGATGCAAATTTTTATG 57.224 30.769 0.00 0.00 0.00 1.90
693 733 9.435688 GAATACTTTAGGTGGATGCAAATTTTT 57.564 29.630 0.00 0.00 0.00 1.94
694 734 8.815912 AGAATACTTTAGGTGGATGCAAATTTT 58.184 29.630 0.00 0.00 0.00 1.82
695 735 8.253113 CAGAATACTTTAGGTGGATGCAAATTT 58.747 33.333 0.00 0.00 0.00 1.82
696 736 7.615365 TCAGAATACTTTAGGTGGATGCAAATT 59.385 33.333 0.00 0.00 0.00 1.82
697 737 7.118723 TCAGAATACTTTAGGTGGATGCAAAT 58.881 34.615 0.00 0.00 0.00 2.32
698 738 6.480763 TCAGAATACTTTAGGTGGATGCAAA 58.519 36.000 0.00 0.00 0.00 3.68
699 739 6.061022 TCAGAATACTTTAGGTGGATGCAA 57.939 37.500 0.00 0.00 0.00 4.08
700 740 5.692115 TCAGAATACTTTAGGTGGATGCA 57.308 39.130 0.00 0.00 0.00 3.96
701 741 7.573968 AAATCAGAATACTTTAGGTGGATGC 57.426 36.000 0.00 0.00 0.00 3.91
737 777 9.320352 TGCATTAGCGAATACTAGTAAATTCAA 57.680 29.630 15.44 5.92 46.23 2.69
738 778 8.880878 TGCATTAGCGAATACTAGTAAATTCA 57.119 30.769 15.44 5.48 46.23 2.57
739 779 9.193133 TCTGCATTAGCGAATACTAGTAAATTC 57.807 33.333 6.70 7.44 46.23 2.17
740 780 9.712305 ATCTGCATTAGCGAATACTAGTAAATT 57.288 29.630 6.70 0.00 46.23 1.82
741 781 9.144747 CATCTGCATTAGCGAATACTAGTAAAT 57.855 33.333 6.70 0.00 46.23 1.40
742 782 8.357402 TCATCTGCATTAGCGAATACTAGTAAA 58.643 33.333 6.70 0.00 46.23 2.01
743 783 7.882179 TCATCTGCATTAGCGAATACTAGTAA 58.118 34.615 6.70 0.00 46.23 2.24
744 784 7.175119 ACTCATCTGCATTAGCGAATACTAGTA 59.825 37.037 4.77 4.77 46.23 1.82
745 785 6.015856 ACTCATCTGCATTAGCGAATACTAGT 60.016 38.462 0.00 0.00 46.23 2.57
746 786 6.385843 ACTCATCTGCATTAGCGAATACTAG 58.614 40.000 0.00 0.00 46.23 2.57
747 787 6.207614 AGACTCATCTGCATTAGCGAATACTA 59.792 38.462 0.00 0.00 46.23 1.82
748 788 5.010516 AGACTCATCTGCATTAGCGAATACT 59.989 40.000 0.00 0.00 46.23 2.12
749 789 5.118357 CAGACTCATCTGCATTAGCGAATAC 59.882 44.000 0.00 0.00 45.83 1.89
750 790 5.225642 CAGACTCATCTGCATTAGCGAATA 58.774 41.667 0.00 0.00 45.83 1.75
751 791 4.056740 CAGACTCATCTGCATTAGCGAAT 58.943 43.478 0.00 0.00 45.83 3.34
752 792 3.451526 CAGACTCATCTGCATTAGCGAA 58.548 45.455 0.00 0.00 45.83 4.70
753 793 3.089573 CAGACTCATCTGCATTAGCGA 57.910 47.619 0.00 0.00 45.83 4.93
770 810 1.661463 AATTCAGGTCTGAGCCCAGA 58.339 50.000 2.76 0.00 46.48 3.86
771 811 2.237143 TGTAATTCAGGTCTGAGCCCAG 59.763 50.000 2.76 0.00 41.13 4.45
772 812 2.237143 CTGTAATTCAGGTCTGAGCCCA 59.763 50.000 2.76 0.00 41.13 5.36
773 813 2.911484 CTGTAATTCAGGTCTGAGCCC 58.089 52.381 2.76 0.00 41.13 5.19
783 823 7.552458 TGCACACAATATACCTGTAATTCAG 57.448 36.000 0.00 0.00 43.27 3.02
784 824 7.929941 TTGCACACAATATACCTGTAATTCA 57.070 32.000 0.00 0.00 0.00 2.57
785 825 8.840321 AGATTGCACACAATATACCTGTAATTC 58.160 33.333 0.00 0.00 46.59 2.17
786 826 8.752005 AGATTGCACACAATATACCTGTAATT 57.248 30.769 0.00 0.00 46.59 1.40
787 827 9.845740 TTAGATTGCACACAATATACCTGTAAT 57.154 29.630 0.00 0.00 46.59 1.89
788 828 9.325198 CTTAGATTGCACACAATATACCTGTAA 57.675 33.333 0.00 0.00 46.59 2.41
789 829 7.931407 CCTTAGATTGCACACAATATACCTGTA 59.069 37.037 0.00 0.00 46.59 2.74
790 830 6.767902 CCTTAGATTGCACACAATATACCTGT 59.232 38.462 0.00 0.00 46.59 4.00
791 831 6.992123 TCCTTAGATTGCACACAATATACCTG 59.008 38.462 0.00 0.00 46.59 4.00
792 832 7.136822 TCCTTAGATTGCACACAATATACCT 57.863 36.000 0.00 0.00 46.59 3.08
793 833 6.992715 ACTCCTTAGATTGCACACAATATACC 59.007 38.462 0.00 0.00 46.59 2.73
794 834 7.519008 GCACTCCTTAGATTGCACACAATATAC 60.519 40.741 0.00 0.00 46.59 1.47
795 835 6.483307 GCACTCCTTAGATTGCACACAATATA 59.517 38.462 0.00 0.00 46.59 0.86
796 836 5.297776 GCACTCCTTAGATTGCACACAATAT 59.702 40.000 0.00 0.00 46.59 1.28
797 837 4.635765 GCACTCCTTAGATTGCACACAATA 59.364 41.667 0.00 0.00 46.59 1.90
799 839 2.813754 GCACTCCTTAGATTGCACACAA 59.186 45.455 0.00 0.00 45.44 3.33
800 840 2.426522 GCACTCCTTAGATTGCACACA 58.573 47.619 0.00 0.00 45.44 3.72
805 845 3.129462 GGGAAAAGCACTCCTTAGATTGC 59.871 47.826 0.00 0.00 46.23 3.56
806 846 3.696548 GGGGAAAAGCACTCCTTAGATTG 59.303 47.826 0.00 0.00 32.20 2.67
807 847 3.593780 AGGGGAAAAGCACTCCTTAGATT 59.406 43.478 0.00 0.00 32.20 2.40
808 848 3.193782 AGGGGAAAAGCACTCCTTAGAT 58.806 45.455 0.00 0.00 32.20 1.98
809 849 2.632537 AGGGGAAAAGCACTCCTTAGA 58.367 47.619 0.00 0.00 32.20 2.10
810 850 4.569719 TTAGGGGAAAAGCACTCCTTAG 57.430 45.455 0.00 0.00 32.20 2.18
811 851 5.327737 TTTTAGGGGAAAAGCACTCCTTA 57.672 39.130 0.00 0.00 31.90 2.69
812 852 3.895704 TTTAGGGGAAAAGCACTCCTT 57.104 42.857 0.00 0.00 33.11 3.36
813 853 3.895704 TTTTAGGGGAAAAGCACTCCT 57.104 42.857 0.00 0.00 31.90 3.69
835 875 9.533831 TCCAAAGCTCTCCTTAGAATTTTTATT 57.466 29.630 0.00 0.00 32.20 1.40
836 876 8.961634 GTCCAAAGCTCTCCTTAGAATTTTTAT 58.038 33.333 0.00 0.00 32.20 1.40
837 877 7.393515 GGTCCAAAGCTCTCCTTAGAATTTTTA 59.606 37.037 0.00 0.00 32.20 1.52
838 878 6.209589 GGTCCAAAGCTCTCCTTAGAATTTTT 59.790 38.462 0.00 0.00 32.20 1.94
839 879 5.712446 GGTCCAAAGCTCTCCTTAGAATTTT 59.288 40.000 0.00 0.00 32.20 1.82
840 880 5.222130 TGGTCCAAAGCTCTCCTTAGAATTT 60.222 40.000 0.00 0.00 32.20 1.82
841 881 4.289672 TGGTCCAAAGCTCTCCTTAGAATT 59.710 41.667 0.00 0.00 32.20 2.17
842 882 3.846588 TGGTCCAAAGCTCTCCTTAGAAT 59.153 43.478 0.00 0.00 32.20 2.40
843 883 3.248024 TGGTCCAAAGCTCTCCTTAGAA 58.752 45.455 0.00 0.00 32.20 2.10
844 884 2.902608 TGGTCCAAAGCTCTCCTTAGA 58.097 47.619 0.00 0.00 32.20 2.10
845 885 3.703001 TTGGTCCAAAGCTCTCCTTAG 57.297 47.619 0.40 0.00 32.20 2.18
846 886 4.657814 ATTTGGTCCAAAGCTCTCCTTA 57.342 40.909 21.31 0.00 36.76 2.69
847 887 3.532641 ATTTGGTCCAAAGCTCTCCTT 57.467 42.857 21.31 0.33 36.76 3.36
848 888 3.330701 TGTATTTGGTCCAAAGCTCTCCT 59.669 43.478 21.31 6.42 36.76 3.69
849 889 3.440522 GTGTATTTGGTCCAAAGCTCTCC 59.559 47.826 21.31 6.89 36.76 3.71
850 890 3.440522 GGTGTATTTGGTCCAAAGCTCTC 59.559 47.826 21.31 13.65 36.76 3.20
851 891 3.421844 GGTGTATTTGGTCCAAAGCTCT 58.578 45.455 21.31 8.13 36.76 4.09
852 892 2.492088 GGGTGTATTTGGTCCAAAGCTC 59.508 50.000 21.31 15.84 36.76 4.09
853 893 2.110011 AGGGTGTATTTGGTCCAAAGCT 59.890 45.455 21.31 9.16 36.76 3.74
854 894 2.525368 AGGGTGTATTTGGTCCAAAGC 58.475 47.619 21.31 16.33 36.76 3.51
855 895 3.895041 ACAAGGGTGTATTTGGTCCAAAG 59.105 43.478 21.31 7.83 36.76 2.77
856 896 3.917300 ACAAGGGTGTATTTGGTCCAAA 58.083 40.909 19.29 19.29 35.72 3.28
857 897 3.603965 ACAAGGGTGTATTTGGTCCAA 57.396 42.857 0.00 0.00 35.72 3.53
858 898 3.603965 AACAAGGGTGTATTTGGTCCA 57.396 42.857 0.00 0.00 36.80 4.02
859 899 4.587262 AGAAAACAAGGGTGTATTTGGTCC 59.413 41.667 0.00 0.00 36.80 4.46
860 900 5.784578 AGAAAACAAGGGTGTATTTGGTC 57.215 39.130 0.00 0.00 36.80 4.02
861 901 6.041182 GGTTAGAAAACAAGGGTGTATTTGGT 59.959 38.462 0.00 0.00 36.80 3.67
862 902 6.041069 TGGTTAGAAAACAAGGGTGTATTTGG 59.959 38.462 0.00 0.00 36.80 3.28
863 903 6.921307 GTGGTTAGAAAACAAGGGTGTATTTG 59.079 38.462 0.00 0.00 36.80 2.32
864 904 6.041182 GGTGGTTAGAAAACAAGGGTGTATTT 59.959 38.462 0.00 0.00 36.80 1.40
865 905 5.537295 GGTGGTTAGAAAACAAGGGTGTATT 59.463 40.000 0.00 0.00 36.80 1.89
866 906 5.074804 GGTGGTTAGAAAACAAGGGTGTAT 58.925 41.667 0.00 0.00 36.80 2.29
867 907 4.463070 GGTGGTTAGAAAACAAGGGTGTA 58.537 43.478 0.00 0.00 36.80 2.90
868 908 3.293337 GGTGGTTAGAAAACAAGGGTGT 58.707 45.455 0.00 0.00 40.75 4.16
869 909 2.626266 GGGTGGTTAGAAAACAAGGGTG 59.374 50.000 0.00 0.00 37.34 4.61
870 910 2.425247 GGGGTGGTTAGAAAACAAGGGT 60.425 50.000 0.00 0.00 37.34 4.34
871 911 2.158370 AGGGGTGGTTAGAAAACAAGGG 60.158 50.000 0.00 0.00 37.34 3.95
1000 1040 2.687200 TACTGGGCGTGAGGGCAT 60.687 61.111 0.21 0.00 44.56 4.40
1047 1087 1.748122 CATGCACAGGAGACAGGCC 60.748 63.158 0.00 0.00 0.00 5.19
1106 1146 3.858868 TTCAGGACACAGACCGCGC 62.859 63.158 0.00 0.00 0.00 6.86
1108 1148 2.022129 CGTTCAGGACACAGACCGC 61.022 63.158 0.00 0.00 0.00 5.68
1109 1149 0.663568 GTCGTTCAGGACACAGACCG 60.664 60.000 0.00 0.00 36.91 4.79
1110 1150 0.663568 CGTCGTTCAGGACACAGACC 60.664 60.000 0.94 0.00 36.73 3.85
1111 1151 1.276145 GCGTCGTTCAGGACACAGAC 61.276 60.000 0.00 0.00 36.73 3.51
1112 1152 1.007734 GCGTCGTTCAGGACACAGA 60.008 57.895 0.00 0.00 36.73 3.41
1114 1154 2.028484 GGCGTCGTTCAGGACACA 59.972 61.111 0.00 0.00 36.73 3.72
1116 1156 2.915659 AGGGCGTCGTTCAGGACA 60.916 61.111 0.00 0.00 36.73 4.02
1117 1157 2.126031 GAGGGCGTCGTTCAGGAC 60.126 66.667 0.00 0.00 0.00 3.85
1118 1158 1.469335 AAAGAGGGCGTCGTTCAGGA 61.469 55.000 2.53 0.00 0.00 3.86
1122 1162 1.206831 GCAAAAGAGGGCGTCGTTC 59.793 57.895 8.72 0.00 0.00 3.95
1123 1163 1.227853 AGCAAAAGAGGGCGTCGTT 60.228 52.632 2.53 2.53 34.54 3.85
1166 1231 3.073062 CCCACAGAGGAAAGGAGAAGAAA 59.927 47.826 0.00 0.00 41.22 2.52
1286 1372 2.269978 GCAAGGCCAAGAGCAATGA 58.730 52.632 5.01 0.00 46.50 2.57
1305 1391 0.172352 AGGAAGAGAAGAAGCGCTCG 59.828 55.000 12.06 0.00 36.29 5.03
1345 1431 1.937546 GCGGCAGATTTCTTGGTGGG 61.938 60.000 0.00 0.00 0.00 4.61
1429 1521 1.854743 CTTGTAGATGCCGATGACGTG 59.145 52.381 0.00 0.00 37.88 4.49
1464 1556 2.481568 CGAATTGCTGACTTGAGCTTGA 59.518 45.455 0.00 0.00 39.90 3.02
1675 2679 2.417719 CTTCTCCTGTGACCTTTTCGG 58.582 52.381 0.00 0.00 39.35 4.30
1676 2680 2.037251 TCCTTCTCCTGTGACCTTTTCG 59.963 50.000 0.00 0.00 0.00 3.46
1684 2688 2.368875 GTCCTGTTTCCTTCTCCTGTGA 59.631 50.000 0.00 0.00 0.00 3.58
1694 2698 0.329596 GGGATGCTGTCCTGTTTCCT 59.670 55.000 8.33 0.00 46.91 3.36
1697 2701 2.242043 CTTTGGGATGCTGTCCTGTTT 58.758 47.619 8.33 0.00 46.91 2.83
1698 2702 1.915141 CTTTGGGATGCTGTCCTGTT 58.085 50.000 8.33 0.00 46.91 3.16
1700 2704 1.318158 GGCTTTGGGATGCTGTCCTG 61.318 60.000 8.33 0.25 46.91 3.86
1701 2705 1.000396 GGCTTTGGGATGCTGTCCT 60.000 57.895 8.33 0.00 46.91 3.85
1705 2709 2.753043 AGCGGCTTTGGGATGCTG 60.753 61.111 0.00 0.00 38.49 4.41
1718 2832 0.107703 TAATGGCTCCTGTTCAGCGG 60.108 55.000 0.00 0.00 37.81 5.52
1770 3907 1.213537 CCCTTTGCAAGCACCATCG 59.786 57.895 0.00 0.00 0.00 3.84
1836 3973 1.546834 GTAGTTGAGCGATCACGGAC 58.453 55.000 1.08 0.00 40.15 4.79
2013 4246 3.809279 TGCACAAGTCTGCCATATTATCG 59.191 43.478 0.00 0.00 36.21 2.92
2025 4258 3.817647 CCTTAGCTTTCTTGCACAAGTCT 59.182 43.478 10.05 6.43 39.38 3.24
2049 4282 3.134458 CTGAAGAAACTTCCGCTTGAGT 58.866 45.455 8.67 0.00 0.00 3.41
2056 4289 6.494842 TGATTTGAAACTGAAGAAACTTCCG 58.505 36.000 8.67 5.46 0.00 4.30
2058 4291 7.759433 TGGTTGATTTGAAACTGAAGAAACTTC 59.241 33.333 0.00 0.00 0.00 3.01
2355 4588 6.936900 GCTTGCACTTCTTATCCCAATATCTA 59.063 38.462 0.00 0.00 0.00 1.98
2477 4714 6.051179 AGTTTACAGAGGGAGTACCAAATC 57.949 41.667 0.00 0.00 43.89 2.17
2601 4867 4.751060 ACTCTGAACAACGTTGTAAGACA 58.249 39.130 32.47 25.11 41.31 3.41
2607 4873 0.928229 GCGACTCTGAACAACGTTGT 59.072 50.000 27.70 27.70 44.72 3.32
2652 4918 5.818678 TCAAAGGCACTCTTAGAGGTTAA 57.181 39.130 14.24 0.00 38.49 2.01
2653 4919 6.013725 TGAATCAAAGGCACTCTTAGAGGTTA 60.014 38.462 14.24 0.00 38.49 2.85
2656 4922 4.836825 TGAATCAAAGGCACTCTTAGAGG 58.163 43.478 14.24 3.97 38.49 3.69
2841 5107 8.849168 TCTGAAAGCATAGAAAGAAACAAATGA 58.151 29.630 0.00 0.00 0.00 2.57
2905 5171 3.359950 AGTGCCAAATCCTCTTGAATCC 58.640 45.455 0.00 0.00 0.00 3.01
2940 5206 9.541143 AAAATTCTCAAACGTGTAAATTGGAAT 57.459 25.926 0.00 0.00 31.41 3.01
3023 5289 1.248486 GGGGTTTTTCCTCAGACTGC 58.752 55.000 0.00 0.00 36.51 4.40
3024 5290 1.523758 CGGGGTTTTTCCTCAGACTG 58.476 55.000 0.00 0.00 36.19 3.51
3025 5291 0.400594 CCGGGGTTTTTCCTCAGACT 59.599 55.000 0.00 0.00 36.19 3.24
3026 5292 1.241990 GCCGGGGTTTTTCCTCAGAC 61.242 60.000 2.18 0.00 36.19 3.51
3027 5293 1.074248 GCCGGGGTTTTTCCTCAGA 59.926 57.895 2.18 0.00 36.19 3.27
3028 5294 2.332654 CGCCGGGGTTTTTCCTCAG 61.333 63.158 11.01 0.00 36.19 3.35
3041 5310 4.640855 ACACACACGAGTCGCCGG 62.641 66.667 13.59 0.00 0.00 6.13
3042 5311 3.394874 CACACACACGAGTCGCCG 61.395 66.667 13.59 6.74 0.00 6.46
3066 5335 4.339809 CTCACGCACACGCACACG 62.340 66.667 0.00 0.00 45.53 4.49
3078 5351 3.678548 GGTTAGTAGGCAAAGAACTCACG 59.321 47.826 0.00 0.00 0.00 4.35
3082 5355 5.499004 TCATGGTTAGTAGGCAAAGAACT 57.501 39.130 0.00 0.00 0.00 3.01
3085 5358 5.488341 GAGTTCATGGTTAGTAGGCAAAGA 58.512 41.667 0.00 0.00 0.00 2.52
3086 5359 4.330074 CGAGTTCATGGTTAGTAGGCAAAG 59.670 45.833 0.00 0.00 0.00 2.77
3087 5360 4.020928 TCGAGTTCATGGTTAGTAGGCAAA 60.021 41.667 0.00 0.00 0.00 3.68
3088 5361 3.512329 TCGAGTTCATGGTTAGTAGGCAA 59.488 43.478 0.00 0.00 0.00 4.52
3090 5363 3.445857 GTCGAGTTCATGGTTAGTAGGC 58.554 50.000 0.00 0.00 0.00 3.93
3091 5364 3.700038 AGGTCGAGTTCATGGTTAGTAGG 59.300 47.826 0.00 0.00 0.00 3.18
3092 5365 4.985538 AGGTCGAGTTCATGGTTAGTAG 57.014 45.455 0.00 0.00 0.00 2.57
3093 5366 4.159135 GGAAGGTCGAGTTCATGGTTAGTA 59.841 45.833 9.16 0.00 0.00 1.82
3094 5367 3.056035 GGAAGGTCGAGTTCATGGTTAGT 60.056 47.826 9.16 0.00 0.00 2.24
3095 5368 3.195825 AGGAAGGTCGAGTTCATGGTTAG 59.804 47.826 9.16 0.00 0.00 2.34
3096 5369 3.170717 AGGAAGGTCGAGTTCATGGTTA 58.829 45.455 9.16 0.00 0.00 2.85
3097 5370 1.978580 AGGAAGGTCGAGTTCATGGTT 59.021 47.619 9.16 0.00 0.00 3.67
3098 5371 1.645710 AGGAAGGTCGAGTTCATGGT 58.354 50.000 9.16 0.00 0.00 3.55
3099 5372 2.770164 AAGGAAGGTCGAGTTCATGG 57.230 50.000 9.16 0.00 0.00 3.66
3100 5373 4.757149 AGAAAAAGGAAGGTCGAGTTCATG 59.243 41.667 9.16 0.00 0.00 3.07
3101 5374 4.974399 AGAAAAAGGAAGGTCGAGTTCAT 58.026 39.130 9.16 0.09 0.00 2.57
3102 5375 4.377897 GAGAAAAAGGAAGGTCGAGTTCA 58.622 43.478 9.16 0.00 0.00 3.18
3103 5376 3.429207 CGAGAAAAAGGAAGGTCGAGTTC 59.571 47.826 0.00 0.00 0.00 3.01
3106 5379 3.246619 CTCGAGAAAAAGGAAGGTCGAG 58.753 50.000 6.58 5.28 45.06 4.04
3107 5380 2.889045 TCTCGAGAAAAAGGAAGGTCGA 59.111 45.455 14.01 0.00 35.33 4.20
3108 5381 3.299340 TCTCGAGAAAAAGGAAGGTCG 57.701 47.619 14.01 0.00 0.00 4.79
3119 5392 5.012768 ACAATCTACCCCTTTTCTCGAGAAA 59.987 40.000 31.62 31.62 41.77 2.52
3120 5393 4.530946 ACAATCTACCCCTTTTCTCGAGAA 59.469 41.667 23.74 23.74 0.00 2.87
3122 5395 4.473477 ACAATCTACCCCTTTTCTCGAG 57.527 45.455 5.93 5.93 0.00 4.04
3124 5397 4.874396 GGTAACAATCTACCCCTTTTCTCG 59.126 45.833 0.00 0.00 36.13 4.04


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

AutoCloner maintained by Alex Coulton.