Multiple sequence alignment - TraesCS5D01G192200

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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 TraesCS5D01G192200 chr5D 100.000 4705 0 0 1 4705 294955662 294950958 0.000000e+00 8689.0
1 TraesCS5D01G192200 chr5D 85.470 585 62 4 1 583 121485417 121485980 5.240000e-164 588.0
2 TraesCS5D01G192200 chr5D 84.783 598 60 8 1 597 121495427 121495994 5.280000e-159 571.0
3 TraesCS5D01G192200 chr5D 87.312 465 48 11 1 460 169781145 169780687 5.400000e-144 521.0
4 TraesCS5D01G192200 chr5D 83.110 598 74 11 1 594 321869200 321868626 1.940000e-143 520.0
5 TraesCS5D01G192200 chr5D 78.879 232 29 3 363 594 183347155 183347366 6.350000e-29 139.0
6 TraesCS5D01G192200 chr5D 90.667 75 6 1 597 670 58518259 58518333 1.080000e-16 99.0
7 TraesCS5D01G192200 chr5A 91.903 3878 200 56 885 4705 388636658 388632838 0.000000e+00 5317.0
8 TraesCS5D01G192200 chr5A 92.857 112 5 2 4594 4704 512841712 512841603 4.870000e-35 159.0
9 TraesCS5D01G192200 chr5B 93.336 3031 135 26 885 3873 336776399 336773394 0.000000e+00 4416.0
10 TraesCS5D01G192200 chr5B 88.056 854 69 17 3870 4705 336773315 336772477 0.000000e+00 981.0
11 TraesCS5D01G192200 chr5B 85.584 548 54 12 1 545 347925454 347924929 6.880000e-153 551.0
12 TraesCS5D01G192200 chr5B 94.118 51 1 1 3727 3775 689400247 689400197 5.050000e-10 76.8
13 TraesCS5D01G192200 chr5B 90.909 44 2 2 836 877 552914836 552914879 1.830000e-04 58.4
14 TraesCS5D01G192200 chr6B 85.077 583 64 6 1 583 393953852 393954411 1.470000e-159 573.0
15 TraesCS5D01G192200 chr6B 89.773 440 41 4 1 438 309085604 309086041 1.140000e-155 560.0
16 TraesCS5D01G192200 chr2D 84.281 598 66 10 1 594 276842798 276842225 4.110000e-155 558.0
17 TraesCS5D01G192200 chr2D 82.776 598 76 10 1 594 241996646 241997220 4.200000e-140 508.0
18 TraesCS5D01G192200 chr2D 95.349 43 2 0 841 883 208614015 208613973 8.450000e-08 69.4
19 TraesCS5D01G192200 chr2D 93.023 43 3 0 842 884 391719517 391719475 3.930000e-06 63.9
20 TraesCS5D01G192200 chr2D 97.297 37 1 0 841 877 634570656 634570620 3.930000e-06 63.9
21 TraesCS5D01G192200 chr2D 94.872 39 2 0 845 883 560854413 560854375 1.410000e-05 62.1
22 TraesCS5D01G192200 chr3D 84.007 594 70 7 3 594 272968963 272969533 8.900000e-152 547.0
23 TraesCS5D01G192200 chr7D 83.725 596 75 6 1 595 453125787 453126361 1.150000e-150 544.0
24 TraesCS5D01G192200 chr7D 82.857 595 63 12 1 594 104965928 104966484 9.090000e-137 497.0
25 TraesCS5D01G192200 chr7B 83.670 594 77 4 1 594 241188730 241188157 4.140000e-150 542.0
26 TraesCS5D01G192200 chr7B 83.333 114 11 7 4186 4293 39929632 39929743 1.080000e-16 99.0
27 TraesCS5D01G192200 chr6D 83.642 593 76 9 3 594 94049019 94048447 5.360000e-149 538.0
28 TraesCS5D01G192200 chr6D 94.286 70 4 0 597 666 452308610 452308679 1.790000e-19 108.0
29 TraesCS5D01G192200 chr1D 80.100 598 83 16 2 594 389124597 389124031 3.390000e-111 412.0
30 TraesCS5D01G192200 chr1D 89.286 112 12 0 486 597 264014513 264014402 1.770000e-29 141.0
31 TraesCS5D01G192200 chr1D 92.754 69 4 1 597 664 33843471 33843539 1.080000e-16 99.0
32 TraesCS5D01G192200 chrUn 81.530 536 65 11 60 594 212262053 212262555 1.220000e-110 411.0
33 TraesCS5D01G192200 chrUn 91.781 73 6 0 597 669 314591823 314591751 8.330000e-18 102.0
34 TraesCS5D01G192200 chrUn 96.000 50 0 1 3728 3775 338178541 338178590 3.900000e-11 80.5
35 TraesCS5D01G192200 chr1B 95.652 69 3 0 598 666 594063212 594063144 1.380000e-20 111.0
36 TraesCS5D01G192200 chr4B 91.667 72 5 1 593 664 592185454 592185384 1.080000e-16 99.0
37 TraesCS5D01G192200 chr4B 94.737 38 2 0 848 885 659691341 659691304 5.080000e-05 60.2
38 TraesCS5D01G192200 chr3B 92.647 68 5 0 597 664 790315762 790315695 1.080000e-16 99.0
39 TraesCS5D01G192200 chr3B 92.593 54 3 1 3722 3775 42628395 42628343 5.050000e-10 76.8
40 TraesCS5D01G192200 chr1A 90.541 74 7 0 597 670 301144318 301144245 1.080000e-16 99.0
41 TraesCS5D01G192200 chr4D 91.429 70 6 0 597 666 35486548 35486479 3.880000e-16 97.1
42 TraesCS5D01G192200 chr4D 80.870 115 15 6 4594 4705 493879941 493879831 3.020000e-12 84.2
43 TraesCS5D01G192200 chr4D 94.872 39 2 0 845 883 30415720 30415682 1.410000e-05 62.1
44 TraesCS5D01G192200 chr4A 96.000 50 0 1 3728 3775 622879706 622879755 3.900000e-11 80.5
45 TraesCS5D01G192200 chr4A 96.000 50 0 1 3728 3775 622898643 622898692 3.900000e-11 80.5
46 TraesCS5D01G192200 chr4A 90.164 61 2 3 3718 3775 622959167 622959226 5.050000e-10 76.8
47 TraesCS5D01G192200 chr2B 92.308 52 2 2 3724 3775 39154450 39154499 6.530000e-09 73.1
48 TraesCS5D01G192200 chr2B 95.000 40 1 1 839 877 61099397 61099358 1.410000e-05 62.1
49 TraesCS5D01G192200 chr7A 100.000 33 0 0 845 877 1447138 1447170 1.410000e-05 62.1


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 TraesCS5D01G192200 chr5D 294950958 294955662 4704 True 8689.0 8689 100.000 1 4705 1 chr5D.!!$R2 4704
1 TraesCS5D01G192200 chr5D 121485417 121485980 563 False 588.0 588 85.470 1 583 1 chr5D.!!$F2 582
2 TraesCS5D01G192200 chr5D 121495427 121495994 567 False 571.0 571 84.783 1 597 1 chr5D.!!$F3 596
3 TraesCS5D01G192200 chr5D 321868626 321869200 574 True 520.0 520 83.110 1 594 1 chr5D.!!$R3 593
4 TraesCS5D01G192200 chr5A 388632838 388636658 3820 True 5317.0 5317 91.903 885 4705 1 chr5A.!!$R1 3820
5 TraesCS5D01G192200 chr5B 336772477 336776399 3922 True 2698.5 4416 90.696 885 4705 2 chr5B.!!$R3 3820
6 TraesCS5D01G192200 chr5B 347924929 347925454 525 True 551.0 551 85.584 1 545 1 chr5B.!!$R1 544
7 TraesCS5D01G192200 chr6B 393953852 393954411 559 False 573.0 573 85.077 1 583 1 chr6B.!!$F2 582
8 TraesCS5D01G192200 chr2D 276842225 276842798 573 True 558.0 558 84.281 1 594 1 chr2D.!!$R2 593
9 TraesCS5D01G192200 chr2D 241996646 241997220 574 False 508.0 508 82.776 1 594 1 chr2D.!!$F1 593
10 TraesCS5D01G192200 chr3D 272968963 272969533 570 False 547.0 547 84.007 3 594 1 chr3D.!!$F1 591
11 TraesCS5D01G192200 chr7D 453125787 453126361 574 False 544.0 544 83.725 1 595 1 chr7D.!!$F2 594
12 TraesCS5D01G192200 chr7D 104965928 104966484 556 False 497.0 497 82.857 1 594 1 chr7D.!!$F1 593
13 TraesCS5D01G192200 chr7B 241188157 241188730 573 True 542.0 542 83.670 1 594 1 chr7B.!!$R1 593
14 TraesCS5D01G192200 chr6D 94048447 94049019 572 True 538.0 538 83.642 3 594 1 chr6D.!!$R1 591
15 TraesCS5D01G192200 chr1D 389124031 389124597 566 True 412.0 412 80.100 2 594 1 chr1D.!!$R2 592
16 TraesCS5D01G192200 chrUn 212262053 212262555 502 False 411.0 411 81.530 60 594 1 chrUn.!!$F1 534

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
717 768 0.107410 TGTTTCGGTGAGCTGTTGGT 60.107 50.0 0.00 0.0 0.00 3.67 F
719 770 0.179234 TTTCGGTGAGCTGTTGGTGA 59.821 50.0 0.00 0.0 0.00 4.02 F
1729 1786 0.312102 GGGTGTCTGTTTGCTTCTGC 59.688 55.0 0.00 0.0 40.20 4.26 F
2604 2691 0.459237 GCAGCTGCTCACATCGTACT 60.459 55.0 31.33 0.0 38.21 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1940 0.469917 GGCTCCAGATTCGAATCCCA 59.530 55.000 29.82 15.6 36.04 4.37 R
2148 2206 3.005791 GCAGTGGTAAAAGAATGCTGGTT 59.994 43.478 0.00 0.0 0.00 3.67 R
3672 3762 0.523546 CGACCAGTCCTCGATTCACG 60.524 60.000 0.00 0.0 44.09 4.35 R
3811 3903 0.105224 CCCCCAAAACCAAAACGTCC 59.895 55.000 0.00 0.0 0.00 4.79 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
130 135 1.070134 CCTGACGAAAGGTGGTCTTCA 59.930 52.381 0.00 0.00 33.86 3.02
147 152 0.473755 TCACCTGCAAAGCTTCTGGA 59.526 50.000 15.34 9.46 0.00 3.86
187 192 1.141881 GCGATGACATCCGTCCTGT 59.858 57.895 9.87 0.00 41.85 4.00
218 223 2.288666 GTCTTGGTCTTGTTGCACTGA 58.711 47.619 0.00 0.00 0.00 3.41
223 228 3.286353 TGGTCTTGTTGCACTGAAATGA 58.714 40.909 0.00 0.00 0.00 2.57
246 252 2.467880 ACCTTTAGCAGATTCCTCGGA 58.532 47.619 0.00 0.00 0.00 4.55
270 277 4.020617 CGCCTGTCCTTGCTCCCA 62.021 66.667 0.00 0.00 0.00 4.37
336 352 2.422519 GCCTGACCTTGGTCATCATGAT 60.423 50.000 21.09 1.18 32.39 2.45
362 380 2.362397 GTCATCGGAACCTCATGAGCTA 59.638 50.000 17.76 0.00 0.00 3.32
406 424 0.260230 CCTCAGGAGTCAGCCTAGGA 59.740 60.000 14.75 0.00 36.22 2.94
463 512 4.410400 CGAGGCTTGACCCCACCC 62.410 72.222 0.00 0.00 40.58 4.61
464 513 4.048470 GAGGCTTGACCCCACCCC 62.048 72.222 0.00 0.00 40.58 4.95
467 516 4.678743 GCTTGACCCCACCCCCAC 62.679 72.222 0.00 0.00 0.00 4.61
468 517 3.979497 CTTGACCCCACCCCCACC 61.979 72.222 0.00 0.00 0.00 4.61
497 546 2.006772 CGCGCAAGGGTATTGTCTC 58.993 57.895 8.75 0.00 46.48 3.36
504 553 3.873910 CAAGGGTATTGTCTCGATGGTT 58.126 45.455 0.00 0.00 0.00 3.67
584 635 1.836166 GTCTAGGTACCTTGGTTCCCC 59.164 57.143 22.11 3.86 0.00 4.81
587 638 0.908180 AGGTACCTTGGTTCCCCGAG 60.908 60.000 9.21 0.00 41.44 4.63
607 658 2.106332 CCGATACGGGCAGTGACC 59.894 66.667 4.30 4.30 44.15 4.02
631 682 2.742372 CCTGCCCGGACGTTTGAG 60.742 66.667 0.73 0.00 33.16 3.02
632 683 2.342279 CTGCCCGGACGTTTGAGA 59.658 61.111 0.73 0.00 0.00 3.27
633 684 2.027625 CTGCCCGGACGTTTGAGAC 61.028 63.158 0.73 0.00 0.00 3.36
646 697 3.718815 GTTTGAGACGAGTTTGAGAGGT 58.281 45.455 0.00 0.00 0.00 3.85
647 698 3.644884 TTGAGACGAGTTTGAGAGGTC 57.355 47.619 0.00 0.00 0.00 3.85
648 699 1.887198 TGAGACGAGTTTGAGAGGTCC 59.113 52.381 0.00 0.00 0.00 4.46
649 700 0.882474 AGACGAGTTTGAGAGGTCCG 59.118 55.000 0.00 0.00 0.00 4.79
650 701 0.109226 GACGAGTTTGAGAGGTCCGG 60.109 60.000 0.00 0.00 0.00 5.14
651 702 0.826672 ACGAGTTTGAGAGGTCCGGT 60.827 55.000 0.00 0.00 0.00 5.28
652 703 0.317479 CGAGTTTGAGAGGTCCGGTT 59.683 55.000 0.00 0.00 0.00 4.44
653 704 1.797025 GAGTTTGAGAGGTCCGGTTG 58.203 55.000 0.00 0.00 0.00 3.77
654 705 1.070289 GAGTTTGAGAGGTCCGGTTGT 59.930 52.381 0.00 0.00 0.00 3.32
655 706 2.298163 GAGTTTGAGAGGTCCGGTTGTA 59.702 50.000 0.00 0.00 0.00 2.41
656 707 2.299297 AGTTTGAGAGGTCCGGTTGTAG 59.701 50.000 0.00 0.00 0.00 2.74
657 708 2.297698 TTGAGAGGTCCGGTTGTAGA 57.702 50.000 0.00 0.00 0.00 2.59
658 709 2.526888 TGAGAGGTCCGGTTGTAGAT 57.473 50.000 0.00 0.00 0.00 1.98
659 710 2.100197 TGAGAGGTCCGGTTGTAGATG 58.900 52.381 0.00 0.00 0.00 2.90
660 711 0.824759 AGAGGTCCGGTTGTAGATGC 59.175 55.000 0.00 0.00 0.00 3.91
661 712 0.824759 GAGGTCCGGTTGTAGATGCT 59.175 55.000 0.00 0.00 0.00 3.79
662 713 0.824759 AGGTCCGGTTGTAGATGCTC 59.175 55.000 0.00 0.00 0.00 4.26
663 714 0.824759 GGTCCGGTTGTAGATGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
664 715 2.029623 GGTCCGGTTGTAGATGCTCTA 58.970 52.381 0.00 0.00 0.00 2.43
665 716 2.429610 GGTCCGGTTGTAGATGCTCTAA 59.570 50.000 0.00 0.00 29.58 2.10
666 717 3.445857 GTCCGGTTGTAGATGCTCTAAC 58.554 50.000 0.00 0.00 29.58 2.34
667 718 3.130693 GTCCGGTTGTAGATGCTCTAACT 59.869 47.826 0.00 0.00 29.58 2.24
668 719 3.130516 TCCGGTTGTAGATGCTCTAACTG 59.869 47.826 0.00 0.00 29.58 3.16
669 720 2.860735 CGGTTGTAGATGCTCTAACTGC 59.139 50.000 0.00 0.00 29.58 4.40
670 721 3.429547 CGGTTGTAGATGCTCTAACTGCT 60.430 47.826 0.00 0.00 29.58 4.24
671 722 3.868077 GGTTGTAGATGCTCTAACTGCTG 59.132 47.826 0.00 0.00 29.58 4.41
672 723 4.382040 GGTTGTAGATGCTCTAACTGCTGA 60.382 45.833 0.00 0.00 29.58 4.26
673 724 4.645762 TGTAGATGCTCTAACTGCTGAG 57.354 45.455 0.00 0.00 29.58 3.35
683 734 6.734104 CTCTAACTGCTGAGCAACTAAATT 57.266 37.500 9.07 0.00 38.41 1.82
684 735 7.138692 CTCTAACTGCTGAGCAACTAAATTT 57.861 36.000 9.07 0.00 38.41 1.82
685 736 6.902341 TCTAACTGCTGAGCAACTAAATTTG 58.098 36.000 9.07 0.00 38.41 2.32
686 737 4.510038 ACTGCTGAGCAACTAAATTTGG 57.490 40.909 9.07 0.00 38.41 3.28
687 738 4.144297 ACTGCTGAGCAACTAAATTTGGA 58.856 39.130 9.07 0.00 38.41 3.53
688 739 4.768968 ACTGCTGAGCAACTAAATTTGGAT 59.231 37.500 9.07 0.00 38.41 3.41
689 740 5.105997 ACTGCTGAGCAACTAAATTTGGATC 60.106 40.000 9.07 1.05 38.41 3.36
690 741 4.142622 TGCTGAGCAACTAAATTTGGATCG 60.143 41.667 3.81 0.00 34.76 3.69
691 742 4.094887 GCTGAGCAACTAAATTTGGATCGA 59.905 41.667 8.72 0.00 0.00 3.59
692 743 5.220931 GCTGAGCAACTAAATTTGGATCGAT 60.221 40.000 8.72 0.00 0.00 3.59
693 744 6.363577 TGAGCAACTAAATTTGGATCGATC 57.636 37.500 17.36 17.36 0.00 3.69
705 756 1.933853 GGATCGATCCACTTGTTTCGG 59.066 52.381 34.65 0.00 46.38 4.30
706 757 2.618053 GATCGATCCACTTGTTTCGGT 58.382 47.619 14.76 0.00 32.67 4.69
707 758 1.790755 TCGATCCACTTGTTTCGGTG 58.209 50.000 0.00 0.00 32.67 4.94
708 759 1.341852 TCGATCCACTTGTTTCGGTGA 59.658 47.619 0.00 0.00 35.69 4.02
709 760 1.726791 CGATCCACTTGTTTCGGTGAG 59.273 52.381 0.00 0.00 35.69 3.51
710 761 1.464997 GATCCACTTGTTTCGGTGAGC 59.535 52.381 0.00 0.00 35.69 4.26
711 762 0.468226 TCCACTTGTTTCGGTGAGCT 59.532 50.000 0.00 0.00 35.69 4.09
712 763 0.588252 CCACTTGTTTCGGTGAGCTG 59.412 55.000 0.00 0.00 35.69 4.24
713 764 1.299541 CACTTGTTTCGGTGAGCTGT 58.700 50.000 0.00 0.00 35.69 4.40
714 765 1.670811 CACTTGTTTCGGTGAGCTGTT 59.329 47.619 0.00 0.00 35.69 3.16
715 766 1.670811 ACTTGTTTCGGTGAGCTGTTG 59.329 47.619 0.00 0.00 0.00 3.33
716 767 1.002468 CTTGTTTCGGTGAGCTGTTGG 60.002 52.381 0.00 0.00 0.00 3.77
717 768 0.107410 TGTTTCGGTGAGCTGTTGGT 60.107 50.000 0.00 0.00 0.00 3.67
718 769 0.307760 GTTTCGGTGAGCTGTTGGTG 59.692 55.000 0.00 0.00 0.00 4.17
719 770 0.179234 TTTCGGTGAGCTGTTGGTGA 59.821 50.000 0.00 0.00 0.00 4.02
720 771 0.531974 TTCGGTGAGCTGTTGGTGAC 60.532 55.000 0.00 0.00 0.00 3.67
721 772 1.961277 CGGTGAGCTGTTGGTGACC 60.961 63.158 0.00 0.00 43.02 4.02
722 773 1.961277 GGTGAGCTGTTGGTGACCG 60.961 63.158 0.00 0.00 38.11 4.79
723 774 1.961277 GTGAGCTGTTGGTGACCGG 60.961 63.158 0.00 0.00 0.00 5.28
724 775 3.050275 GAGCTGTTGGTGACCGGC 61.050 66.667 0.00 0.00 0.00 6.13
725 776 3.537206 GAGCTGTTGGTGACCGGCT 62.537 63.158 0.00 10.07 38.45 5.52
726 777 3.050275 GCTGTTGGTGACCGGCTC 61.050 66.667 0.00 0.00 0.00 4.70
727 778 2.358737 CTGTTGGTGACCGGCTCC 60.359 66.667 0.00 5.66 0.00 4.70
728 779 3.901797 CTGTTGGTGACCGGCTCCC 62.902 68.421 0.00 0.00 0.00 4.30
729 780 4.717313 GTTGGTGACCGGCTCCCC 62.717 72.222 0.00 0.00 0.00 4.81
730 781 4.974438 TTGGTGACCGGCTCCCCT 62.974 66.667 0.00 0.00 0.00 4.79
739 790 4.079961 GGCTCCCCTGGCCCAATT 62.080 66.667 0.00 0.00 43.49 2.32
740 791 2.039462 GCTCCCCTGGCCCAATTT 59.961 61.111 0.00 0.00 0.00 1.82
741 792 1.613332 GCTCCCCTGGCCCAATTTT 60.613 57.895 0.00 0.00 0.00 1.82
742 793 1.200760 GCTCCCCTGGCCCAATTTTT 61.201 55.000 0.00 0.00 0.00 1.94
763 814 6.723298 TTTTCATGAAGCCAACCTAAAAGA 57.277 33.333 8.41 0.00 0.00 2.52
764 815 5.705609 TTCATGAAGCCAACCTAAAAGAC 57.294 39.130 3.38 0.00 0.00 3.01
765 816 4.079253 TCATGAAGCCAACCTAAAAGACC 58.921 43.478 0.00 0.00 0.00 3.85
766 817 2.871453 TGAAGCCAACCTAAAAGACCC 58.129 47.619 0.00 0.00 0.00 4.46
767 818 2.175931 TGAAGCCAACCTAAAAGACCCA 59.824 45.455 0.00 0.00 0.00 4.51
768 819 3.181423 TGAAGCCAACCTAAAAGACCCAT 60.181 43.478 0.00 0.00 0.00 4.00
769 820 4.043561 TGAAGCCAACCTAAAAGACCCATA 59.956 41.667 0.00 0.00 0.00 2.74
770 821 4.236527 AGCCAACCTAAAAGACCCATAG 57.763 45.455 0.00 0.00 0.00 2.23
771 822 3.850173 AGCCAACCTAAAAGACCCATAGA 59.150 43.478 0.00 0.00 0.00 1.98
772 823 3.945921 GCCAACCTAAAAGACCCATAGAC 59.054 47.826 0.00 0.00 0.00 2.59
773 824 4.524053 CCAACCTAAAAGACCCATAGACC 58.476 47.826 0.00 0.00 0.00 3.85
774 825 4.227527 CCAACCTAAAAGACCCATAGACCT 59.772 45.833 0.00 0.00 0.00 3.85
775 826 5.281037 CCAACCTAAAAGACCCATAGACCTT 60.281 44.000 0.00 0.00 0.00 3.50
776 827 5.437191 ACCTAAAAGACCCATAGACCTTG 57.563 43.478 0.00 0.00 0.00 3.61
777 828 5.098663 ACCTAAAAGACCCATAGACCTTGA 58.901 41.667 0.00 0.00 0.00 3.02
778 829 5.550403 ACCTAAAAGACCCATAGACCTTGAA 59.450 40.000 0.00 0.00 0.00 2.69
779 830 6.045106 ACCTAAAAGACCCATAGACCTTGAAA 59.955 38.462 0.00 0.00 0.00 2.69
780 831 7.119387 CCTAAAAGACCCATAGACCTTGAAAT 58.881 38.462 0.00 0.00 0.00 2.17
781 832 7.615757 CCTAAAAGACCCATAGACCTTGAAATT 59.384 37.037 0.00 0.00 0.00 1.82
782 833 9.681062 CTAAAAGACCCATAGACCTTGAAATTA 57.319 33.333 0.00 0.00 0.00 1.40
784 835 8.525290 AAAGACCCATAGACCTTGAAATTATG 57.475 34.615 0.00 0.00 0.00 1.90
785 836 6.605119 AGACCCATAGACCTTGAAATTATGG 58.395 40.000 2.58 2.58 40.15 2.74
787 838 5.712152 CCATAGACCTTGAAATTATGGGC 57.288 43.478 1.75 0.00 37.94 5.36
788 839 5.388654 CCATAGACCTTGAAATTATGGGCT 58.611 41.667 0.00 0.00 41.48 5.19
789 840 5.242393 CCATAGACCTTGAAATTATGGGCTG 59.758 44.000 0.00 0.00 38.58 4.85
790 841 3.635591 AGACCTTGAAATTATGGGCTGG 58.364 45.455 0.00 0.00 36.43 4.85
791 842 3.269381 AGACCTTGAAATTATGGGCTGGA 59.731 43.478 0.00 0.00 36.43 3.86
792 843 3.365472 ACCTTGAAATTATGGGCTGGAC 58.635 45.455 0.00 0.00 0.00 4.02
793 844 3.245586 ACCTTGAAATTATGGGCTGGACA 60.246 43.478 0.00 0.00 0.00 4.02
794 845 3.962718 CCTTGAAATTATGGGCTGGACAT 59.037 43.478 0.00 0.00 0.00 3.06
795 846 4.202182 CCTTGAAATTATGGGCTGGACATG 60.202 45.833 0.00 0.00 0.00 3.21
796 847 4.248174 TGAAATTATGGGCTGGACATGA 57.752 40.909 0.00 0.00 0.00 3.07
797 848 3.953612 TGAAATTATGGGCTGGACATGAC 59.046 43.478 0.00 0.00 0.00 3.06
798 849 3.668141 AATTATGGGCTGGACATGACA 57.332 42.857 0.00 0.00 0.00 3.58
799 850 3.889859 ATTATGGGCTGGACATGACAT 57.110 42.857 0.00 0.00 0.00 3.06
800 851 2.643995 TATGGGCTGGACATGACATG 57.356 50.000 14.02 14.02 0.00 3.21
883 934 9.968870 ATAAAAGCGTTTAAATCACTGGTTTAA 57.031 25.926 8.90 3.48 32.98 1.52
912 963 3.302347 CTCGTTCCCCGCAGCTTCT 62.302 63.158 0.00 0.00 36.19 2.85
960 1014 2.734591 GCAGTGACTCCGTCCACA 59.265 61.111 0.00 0.00 0.00 4.17
1195 1249 1.408822 GGGTAATCTGGAACTGCCCTG 60.409 57.143 0.00 0.00 34.97 4.45
1200 1254 4.666253 TGGAACTGCCCTGCCAGC 62.666 66.667 0.00 0.00 36.29 4.85
1282 1338 2.031919 TCCGTCCATGGTGTGTGC 59.968 61.111 12.58 0.00 0.00 4.57
1284 1340 2.034879 CCGTCCATGGTGTGTGCTC 61.035 63.158 12.58 0.00 0.00 4.26
1373 1429 2.865308 CTCGGTGAGTCGCGTGTA 59.135 61.111 5.77 0.00 0.00 2.90
1437 1493 2.009774 CCTGGTCTCGTGCAAAATAGG 58.990 52.381 0.00 0.00 0.00 2.57
1569 1625 5.007039 TGCTGCATCTTGAATTCTCGATTAC 59.993 40.000 7.05 4.32 0.00 1.89
1570 1626 5.007039 GCTGCATCTTGAATTCTCGATTACA 59.993 40.000 7.05 7.97 0.00 2.41
1571 1627 6.293298 GCTGCATCTTGAATTCTCGATTACAT 60.293 38.462 7.05 0.00 0.00 2.29
1572 1628 7.095481 GCTGCATCTTGAATTCTCGATTACATA 60.095 37.037 7.05 0.00 0.00 2.29
1573 1629 8.837788 TGCATCTTGAATTCTCGATTACATAT 57.162 30.769 7.05 0.00 0.00 1.78
1574 1630 9.276590 TGCATCTTGAATTCTCGATTACATATT 57.723 29.630 7.05 0.00 0.00 1.28
1609 1666 7.437862 TGTTCATTCTTTATTTGTCCTTGTTGC 59.562 33.333 0.00 0.00 0.00 4.17
1618 1675 1.896660 TCCTTGTTGCGGGACTTGC 60.897 57.895 0.00 0.00 0.00 4.01
1729 1786 0.312102 GGGTGTCTGTTTGCTTCTGC 59.688 55.000 0.00 0.00 40.20 4.26
1882 1940 2.421424 GCTTCGCTCAATCAGTGGATTT 59.579 45.455 0.00 0.00 41.78 2.17
2102 2160 2.989422 AAGTGAACCTTAATGCGTGC 57.011 45.000 0.00 0.00 0.00 5.34
2103 2161 1.890876 AGTGAACCTTAATGCGTGCA 58.109 45.000 0.00 0.00 0.00 4.57
2148 2206 8.333235 ACAAACTACATTGGTCCATTTATCCTA 58.667 33.333 0.00 0.00 34.56 2.94
2249 2307 7.973388 CAGATGTGGTAAGTTTGAAGTTTTTCA 59.027 33.333 0.00 0.00 41.44 2.69
2604 2691 0.459237 GCAGCTGCTCACATCGTACT 60.459 55.000 31.33 0.00 38.21 2.73
2628 2715 4.846940 ACCATTCTAACAGTTTCCCTCTCT 59.153 41.667 0.00 0.00 0.00 3.10
2631 2718 3.442076 TCTAACAGTTTCCCTCTCTCCC 58.558 50.000 0.00 0.00 0.00 4.30
2632 2719 2.424684 AACAGTTTCCCTCTCTCCCT 57.575 50.000 0.00 0.00 0.00 4.20
2806 2893 7.234187 TGTATGCTTCTTGCTTTAGTATTCG 57.766 36.000 0.00 0.00 43.37 3.34
2821 2908 2.609427 ATTCGCTTCATGCAGCTCTA 57.391 45.000 15.41 1.00 43.06 2.43
2838 2925 8.424133 TGCAGCTCTAATCTACAAAATCTATCA 58.576 33.333 0.00 0.00 0.00 2.15
2902 2989 8.466798 TCTCATATGAACTTCATCGACAACTTA 58.533 33.333 7.57 0.00 38.26 2.24
2941 3029 5.255687 TCTCTGTCATGTATGTGCCATTTT 58.744 37.500 0.00 0.00 0.00 1.82
2968 3056 2.685897 TGTCTTGTGTTTTTCCCTTCCG 59.314 45.455 0.00 0.00 0.00 4.30
3083 3171 2.622942 TGTCTGACCCAAATGTCAAAGC 59.377 45.455 5.17 0.00 44.19 3.51
3133 3221 8.809468 AGTTCTGTTCTCTTTTCCTTTTTACT 57.191 30.769 0.00 0.00 0.00 2.24
3199 3287 3.282885 TCATCTCTCTGTCGTGCTATGT 58.717 45.455 0.00 0.00 0.00 2.29
3214 3302 5.677567 GTGCTATGTTACCTTAAGCCCTTA 58.322 41.667 0.00 0.00 0.00 2.69
3217 3305 7.935210 GTGCTATGTTACCTTAAGCCCTTATAA 59.065 37.037 0.00 0.00 0.00 0.98
3533 3623 7.093354 CAGCTCTGAGTTTTAGTTCTGTATCA 58.907 38.462 6.53 0.00 0.00 2.15
3656 3746 2.859273 CTTCAGCGTTGCTCCGGGAT 62.859 60.000 0.00 0.00 36.40 3.85
3672 3762 0.032815 GGATCTGCGGCTTAGAGACC 59.967 60.000 0.00 1.59 0.00 3.85
3690 3780 0.179134 CCGTGAATCGAGGACTGGTC 60.179 60.000 0.00 0.00 42.86 4.02
3794 3884 0.246086 GCATCTCTAGCAGATCCCCG 59.754 60.000 0.00 0.00 40.20 5.73
3811 3903 2.487265 CCCCGAAGTCATATTTGAGGGG 60.487 54.545 11.32 11.32 43.61 4.79
3812 3904 2.487265 CCCGAAGTCATATTTGAGGGGG 60.487 54.545 1.55 0.25 32.45 5.40
3813 3905 2.438021 CCGAAGTCATATTTGAGGGGGA 59.562 50.000 0.00 0.00 30.85 4.81
3814 3906 3.467803 CGAAGTCATATTTGAGGGGGAC 58.532 50.000 0.00 0.00 30.85 4.46
3815 3907 3.467803 GAAGTCATATTTGAGGGGGACG 58.532 50.000 0.00 0.00 30.85 4.79
3830 3928 0.105224 GGACGTTTTGGTTTTGGGGG 59.895 55.000 0.00 0.00 0.00 5.40
3898 4077 5.768164 GGGATTAAGACACTTCTTGGAAACA 59.232 40.000 0.00 0.00 42.41 2.83
3937 4116 3.118920 TGATTTCTCTCCGCGATACCAAA 60.119 43.478 8.23 0.86 0.00 3.28
3965 4145 3.244078 GGCCTCCGTTTTCCTTTGAAATT 60.244 43.478 0.00 0.00 40.08 1.82
3988 4168 0.525242 CGCCCCGCAAAACATACATG 60.525 55.000 0.00 0.00 0.00 3.21
3993 4194 1.466950 CCGCAAAACATACATGTCGGT 59.533 47.619 0.00 0.00 40.80 4.69
4002 4203 0.455464 TACATGTCGGTTCGCTCACG 60.455 55.000 0.00 0.00 42.01 4.35
4066 4270 1.511768 GACGGTTCTTCCTCTCCCG 59.488 63.158 0.00 0.00 44.06 5.14
4068 4272 1.982938 CGGTTCTTCCTCTCCCGGT 60.983 63.158 0.00 0.00 35.11 5.28
4085 4289 1.162800 GGTTCGCCATCATCTCTGCC 61.163 60.000 0.00 0.00 37.19 4.85
4107 4311 1.961277 CGTTTCCTGCTCGGTGCTT 60.961 57.895 3.53 0.00 43.37 3.91
4170 4374 1.141254 AGCCTGCATCTCAAGATCTGG 59.859 52.381 0.00 0.00 31.21 3.86
4200 4404 1.828768 GAGCACATCTCCCTCCCAG 59.171 63.158 0.00 0.00 35.77 4.45
4255 4460 2.956132 TGCCTCCTTTGTTGAATTCCA 58.044 42.857 2.27 0.00 0.00 3.53
4384 4594 1.148310 CAAACGGAGCGTGAATGTCT 58.852 50.000 0.00 0.00 39.99 3.41
4448 4663 6.250819 CCTTGAATCAATCGACACATTGTAC 58.749 40.000 0.00 0.00 35.56 2.90
4457 4672 7.604545 TCAATCGACACATTGTACCTTTTGATA 59.395 33.333 0.00 0.00 35.56 2.15
4530 4745 4.261489 GCTCATATTGGGTGCTTCTTCATG 60.261 45.833 0.00 0.00 0.00 3.07
4613 4836 5.664665 TCATTGGGATATCCTCCTCATGTA 58.335 41.667 21.18 0.00 44.28 2.29
4616 4839 3.406152 TGGGATATCCTCCTCATGTAGGT 59.594 47.826 21.18 3.09 46.62 3.08
4651 4874 7.707624 TGATCATTTGAAGACTTTTAGGCAT 57.292 32.000 0.00 0.00 0.00 4.40
4665 4888 1.304381 GGCATCCCAAAGAGGTGCA 60.304 57.895 0.00 0.00 36.35 4.57
4666 4889 0.899717 GGCATCCCAAAGAGGTGCAA 60.900 55.000 0.00 0.00 36.35 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.184579 GAAAGAGGACCGAGGCCG 59.815 66.667 0.00 0.00 0.00 6.13
130 135 0.886490 CGTCCAGAAGCTTTGCAGGT 60.886 55.000 0.00 0.00 0.00 4.00
147 152 1.079127 GCCCACTGCTACATCACGT 60.079 57.895 0.00 0.00 36.87 4.49
218 223 7.544804 AGGAATCTGCTAAAGGTTTTCATTT 57.455 32.000 0.00 0.00 37.55 2.32
223 228 4.010349 CCGAGGAATCTGCTAAAGGTTTT 58.990 43.478 0.00 0.00 0.00 2.43
246 252 1.528309 CAAGGACAGGCGTGGGTTT 60.528 57.895 11.67 0.00 0.00 3.27
270 277 4.074970 CACAGTTTCCTCTTTGGTGCTAT 58.925 43.478 0.00 0.00 37.07 2.97
320 336 2.424601 CGCAAATCATGATGACCAAGGT 59.575 45.455 9.46 0.00 0.00 3.50
336 352 0.034198 TGAGGTTCCGATGACGCAAA 59.966 50.000 0.00 0.00 38.29 3.68
362 380 4.740934 GCGAAGATTTCTATGCAGGTACCT 60.741 45.833 9.21 9.21 0.00 3.08
422 453 0.038892 GTGAACGACGCCAAGACCTA 60.039 55.000 0.00 0.00 0.00 3.08
478 527 1.429148 GAGACAATACCCTTGCGCGG 61.429 60.000 8.83 0.00 0.00 6.46
479 528 1.752501 CGAGACAATACCCTTGCGCG 61.753 60.000 0.00 0.00 0.00 6.86
480 529 0.459585 TCGAGACAATACCCTTGCGC 60.460 55.000 0.00 0.00 0.00 6.09
497 546 1.676006 GGCCCATCTACAAAACCATCG 59.324 52.381 0.00 0.00 0.00 3.84
504 553 1.208535 CTGGTACGGCCCATCTACAAA 59.791 52.381 0.00 0.00 36.04 2.83
559 608 1.549170 ACCAAGGTACCTAGACTTGCG 59.451 52.381 16.67 6.21 40.08 4.85
614 665 2.742372 CTCAAACGTCCGGGCAGG 60.742 66.667 6.96 0.00 42.97 4.85
615 666 2.027625 GTCTCAAACGTCCGGGCAG 61.028 63.158 6.96 0.77 0.00 4.85
616 667 2.029964 GTCTCAAACGTCCGGGCA 59.970 61.111 6.96 0.00 0.00 5.36
617 668 3.110178 CGTCTCAAACGTCCGGGC 61.110 66.667 0.00 0.00 46.42 6.13
625 676 3.718815 ACCTCTCAAACTCGTCTCAAAC 58.281 45.455 0.00 0.00 0.00 2.93
626 677 3.243771 GGACCTCTCAAACTCGTCTCAAA 60.244 47.826 0.00 0.00 0.00 2.69
627 678 2.296471 GGACCTCTCAAACTCGTCTCAA 59.704 50.000 0.00 0.00 0.00 3.02
628 679 1.887198 GGACCTCTCAAACTCGTCTCA 59.113 52.381 0.00 0.00 0.00 3.27
629 680 1.135632 CGGACCTCTCAAACTCGTCTC 60.136 57.143 0.00 0.00 0.00 3.36
630 681 0.882474 CGGACCTCTCAAACTCGTCT 59.118 55.000 0.00 0.00 0.00 4.18
631 682 0.109226 CCGGACCTCTCAAACTCGTC 60.109 60.000 0.00 0.00 0.00 4.20
632 683 0.826672 ACCGGACCTCTCAAACTCGT 60.827 55.000 9.46 0.00 0.00 4.18
633 684 0.317479 AACCGGACCTCTCAAACTCG 59.683 55.000 9.46 0.00 0.00 4.18
634 685 1.070289 ACAACCGGACCTCTCAAACTC 59.930 52.381 9.46 0.00 0.00 3.01
635 686 1.129058 ACAACCGGACCTCTCAAACT 58.871 50.000 9.46 0.00 0.00 2.66
636 687 2.298163 TCTACAACCGGACCTCTCAAAC 59.702 50.000 9.46 0.00 0.00 2.93
637 688 2.600790 TCTACAACCGGACCTCTCAAA 58.399 47.619 9.46 0.00 0.00 2.69
638 689 2.297698 TCTACAACCGGACCTCTCAA 57.702 50.000 9.46 0.00 0.00 3.02
639 690 2.100197 CATCTACAACCGGACCTCTCA 58.900 52.381 9.46 0.00 0.00 3.27
640 691 1.202428 GCATCTACAACCGGACCTCTC 60.202 57.143 9.46 0.00 0.00 3.20
641 692 0.824759 GCATCTACAACCGGACCTCT 59.175 55.000 9.46 0.00 0.00 3.69
642 693 0.824759 AGCATCTACAACCGGACCTC 59.175 55.000 9.46 0.00 0.00 3.85
643 694 0.824759 GAGCATCTACAACCGGACCT 59.175 55.000 9.46 0.00 0.00 3.85
644 695 3.364277 GAGCATCTACAACCGGACC 57.636 57.895 9.46 0.00 0.00 4.46
660 711 6.734104 AATTTAGTTGCTCAGCAGTTAGAG 57.266 37.500 0.00 0.00 40.61 2.43
661 712 6.072508 CCAAATTTAGTTGCTCAGCAGTTAGA 60.073 38.462 0.00 0.00 40.61 2.10
662 713 6.072508 TCCAAATTTAGTTGCTCAGCAGTTAG 60.073 38.462 0.00 0.00 40.61 2.34
663 714 5.767665 TCCAAATTTAGTTGCTCAGCAGTTA 59.232 36.000 0.00 0.00 40.61 2.24
664 715 4.584325 TCCAAATTTAGTTGCTCAGCAGTT 59.416 37.500 0.00 0.00 40.61 3.16
665 716 4.144297 TCCAAATTTAGTTGCTCAGCAGT 58.856 39.130 0.00 0.00 40.61 4.40
666 717 4.771590 TCCAAATTTAGTTGCTCAGCAG 57.228 40.909 0.00 0.00 40.61 4.24
667 718 4.142622 CGATCCAAATTTAGTTGCTCAGCA 60.143 41.667 0.00 0.00 36.47 4.41
668 719 4.094887 TCGATCCAAATTTAGTTGCTCAGC 59.905 41.667 0.00 0.00 0.00 4.26
669 720 5.801350 TCGATCCAAATTTAGTTGCTCAG 57.199 39.130 0.00 0.00 0.00 3.35
670 721 5.296780 GGATCGATCCAAATTTAGTTGCTCA 59.703 40.000 34.65 0.00 46.38 4.26
671 722 5.752712 GGATCGATCCAAATTTAGTTGCTC 58.247 41.667 34.65 5.58 46.38 4.26
672 723 5.757850 GGATCGATCCAAATTTAGTTGCT 57.242 39.130 34.65 0.00 46.38 3.91
686 737 2.348666 CACCGAAACAAGTGGATCGATC 59.651 50.000 17.36 17.36 37.48 3.69
687 738 2.028476 TCACCGAAACAAGTGGATCGAT 60.028 45.455 0.00 0.00 37.48 3.59
688 739 1.341852 TCACCGAAACAAGTGGATCGA 59.658 47.619 8.89 0.00 37.48 3.59
689 740 1.726791 CTCACCGAAACAAGTGGATCG 59.273 52.381 0.00 2.20 34.67 3.69
690 741 1.464997 GCTCACCGAAACAAGTGGATC 59.535 52.381 0.00 0.00 34.67 3.36
691 742 1.072331 AGCTCACCGAAACAAGTGGAT 59.928 47.619 0.00 0.00 34.67 3.41
692 743 0.468226 AGCTCACCGAAACAAGTGGA 59.532 50.000 0.00 0.00 34.67 4.02
693 744 0.588252 CAGCTCACCGAAACAAGTGG 59.412 55.000 0.00 0.00 34.67 4.00
694 745 1.299541 ACAGCTCACCGAAACAAGTG 58.700 50.000 0.00 0.00 35.24 3.16
695 746 1.670811 CAACAGCTCACCGAAACAAGT 59.329 47.619 0.00 0.00 0.00 3.16
696 747 1.002468 CCAACAGCTCACCGAAACAAG 60.002 52.381 0.00 0.00 0.00 3.16
697 748 1.021202 CCAACAGCTCACCGAAACAA 58.979 50.000 0.00 0.00 0.00 2.83
698 749 0.107410 ACCAACAGCTCACCGAAACA 60.107 50.000 0.00 0.00 0.00 2.83
699 750 0.307760 CACCAACAGCTCACCGAAAC 59.692 55.000 0.00 0.00 0.00 2.78
700 751 0.179234 TCACCAACAGCTCACCGAAA 59.821 50.000 0.00 0.00 0.00 3.46
701 752 0.531974 GTCACCAACAGCTCACCGAA 60.532 55.000 0.00 0.00 0.00 4.30
702 753 1.069090 GTCACCAACAGCTCACCGA 59.931 57.895 0.00 0.00 0.00 4.69
703 754 1.961277 GGTCACCAACAGCTCACCG 60.961 63.158 0.00 0.00 0.00 4.94
704 755 1.961277 CGGTCACCAACAGCTCACC 60.961 63.158 0.00 0.00 0.00 4.02
705 756 1.961277 CCGGTCACCAACAGCTCAC 60.961 63.158 0.00 0.00 0.00 3.51
706 757 2.425592 CCGGTCACCAACAGCTCA 59.574 61.111 0.00 0.00 0.00 4.26
707 758 3.050275 GCCGGTCACCAACAGCTC 61.050 66.667 1.90 0.00 0.00 4.09
708 759 3.537206 GAGCCGGTCACCAACAGCT 62.537 63.158 1.90 0.00 40.57 4.24
709 760 3.050275 GAGCCGGTCACCAACAGC 61.050 66.667 1.90 0.00 0.00 4.40
710 761 2.358737 GGAGCCGGTCACCAACAG 60.359 66.667 1.90 0.00 0.00 3.16
711 762 3.948719 GGGAGCCGGTCACCAACA 61.949 66.667 1.90 0.00 0.00 3.33
723 774 1.200760 AAAAATTGGGCCAGGGGAGC 61.201 55.000 6.23 0.00 0.00 4.70
724 775 3.087343 AAAAATTGGGCCAGGGGAG 57.913 52.632 6.23 0.00 0.00 4.30
739 790 6.983890 GTCTTTTAGGTTGGCTTCATGAAAAA 59.016 34.615 9.88 1.80 0.00 1.94
740 791 6.462347 GGTCTTTTAGGTTGGCTTCATGAAAA 60.462 38.462 9.88 0.00 0.00 2.29
741 792 5.010617 GGTCTTTTAGGTTGGCTTCATGAAA 59.989 40.000 9.88 0.00 0.00 2.69
742 793 4.522789 GGTCTTTTAGGTTGGCTTCATGAA 59.477 41.667 8.12 8.12 0.00 2.57
743 794 4.079253 GGTCTTTTAGGTTGGCTTCATGA 58.921 43.478 0.00 0.00 0.00 3.07
744 795 3.193479 GGGTCTTTTAGGTTGGCTTCATG 59.807 47.826 0.00 0.00 0.00 3.07
745 796 3.181423 TGGGTCTTTTAGGTTGGCTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
746 797 2.175931 TGGGTCTTTTAGGTTGGCTTCA 59.824 45.455 0.00 0.00 0.00 3.02
747 798 2.871453 TGGGTCTTTTAGGTTGGCTTC 58.129 47.619 0.00 0.00 0.00 3.86
748 799 3.542969 ATGGGTCTTTTAGGTTGGCTT 57.457 42.857 0.00 0.00 0.00 4.35
749 800 3.850173 TCTATGGGTCTTTTAGGTTGGCT 59.150 43.478 0.00 0.00 0.00 4.75
750 801 3.945921 GTCTATGGGTCTTTTAGGTTGGC 59.054 47.826 0.00 0.00 0.00 4.52
751 802 4.227527 AGGTCTATGGGTCTTTTAGGTTGG 59.772 45.833 0.00 0.00 0.00 3.77
752 803 5.437191 AGGTCTATGGGTCTTTTAGGTTG 57.563 43.478 0.00 0.00 0.00 3.77
753 804 5.550403 TCAAGGTCTATGGGTCTTTTAGGTT 59.450 40.000 0.00 0.00 0.00 3.50
754 805 5.098663 TCAAGGTCTATGGGTCTTTTAGGT 58.901 41.667 0.00 0.00 0.00 3.08
755 806 5.693769 TCAAGGTCTATGGGTCTTTTAGG 57.306 43.478 0.00 0.00 0.00 2.69
756 807 8.581253 AATTTCAAGGTCTATGGGTCTTTTAG 57.419 34.615 0.00 0.00 0.00 1.85
758 809 8.971073 CATAATTTCAAGGTCTATGGGTCTTTT 58.029 33.333 0.00 0.00 0.00 2.27
759 810 7.561356 CCATAATTTCAAGGTCTATGGGTCTTT 59.439 37.037 0.00 0.00 36.76 2.52
760 811 7.062957 CCATAATTTCAAGGTCTATGGGTCTT 58.937 38.462 0.00 0.00 36.76 3.01
761 812 6.605119 CCATAATTTCAAGGTCTATGGGTCT 58.395 40.000 0.00 0.00 36.76 3.85
762 813 6.884280 CCATAATTTCAAGGTCTATGGGTC 57.116 41.667 0.00 0.00 36.76 4.46
765 816 5.242393 CAGCCCATAATTTCAAGGTCTATGG 59.758 44.000 0.00 0.00 39.07 2.74
766 817 5.242393 CCAGCCCATAATTTCAAGGTCTATG 59.758 44.000 0.00 0.00 0.00 2.23
767 818 5.134339 TCCAGCCCATAATTTCAAGGTCTAT 59.866 40.000 0.00 0.00 0.00 1.98
768 819 4.476846 TCCAGCCCATAATTTCAAGGTCTA 59.523 41.667 0.00 0.00 0.00 2.59
769 820 3.269381 TCCAGCCCATAATTTCAAGGTCT 59.731 43.478 0.00 0.00 0.00 3.85
770 821 3.381590 GTCCAGCCCATAATTTCAAGGTC 59.618 47.826 0.00 0.00 0.00 3.85
771 822 3.245586 TGTCCAGCCCATAATTTCAAGGT 60.246 43.478 0.00 0.00 0.00 3.50
772 823 3.364549 TGTCCAGCCCATAATTTCAAGG 58.635 45.455 0.00 0.00 0.00 3.61
773 824 4.646040 TCATGTCCAGCCCATAATTTCAAG 59.354 41.667 0.00 0.00 0.00 3.02
774 825 4.402155 GTCATGTCCAGCCCATAATTTCAA 59.598 41.667 0.00 0.00 0.00 2.69
775 826 3.953612 GTCATGTCCAGCCCATAATTTCA 59.046 43.478 0.00 0.00 0.00 2.69
776 827 3.953612 TGTCATGTCCAGCCCATAATTTC 59.046 43.478 0.00 0.00 0.00 2.17
777 828 3.979911 TGTCATGTCCAGCCCATAATTT 58.020 40.909 0.00 0.00 0.00 1.82
778 829 3.668141 TGTCATGTCCAGCCCATAATT 57.332 42.857 0.00 0.00 0.00 1.40
779 830 3.117398 ACATGTCATGTCCAGCCCATAAT 60.117 43.478 12.87 0.00 39.92 1.28
780 831 2.241941 ACATGTCATGTCCAGCCCATAA 59.758 45.455 12.87 0.00 39.92 1.90
781 832 1.845791 ACATGTCATGTCCAGCCCATA 59.154 47.619 12.87 0.00 39.92 2.74
782 833 0.627451 ACATGTCATGTCCAGCCCAT 59.373 50.000 12.87 0.00 39.92 4.00
783 834 2.077579 ACATGTCATGTCCAGCCCA 58.922 52.632 12.87 0.00 39.92 5.36
857 908 9.968870 TTAAACCAGTGATTTAAACGCTTTTAT 57.031 25.926 0.00 0.00 30.47 1.40
858 909 9.798994 TTTAAACCAGTGATTTAAACGCTTTTA 57.201 25.926 10.57 0.00 36.86 1.52
859 910 8.705048 TTTAAACCAGTGATTTAAACGCTTTT 57.295 26.923 10.57 0.00 36.86 2.27
860 911 7.977293 ACTTTAAACCAGTGATTTAAACGCTTT 59.023 29.630 10.57 0.00 36.86 3.51
861 912 7.485810 ACTTTAAACCAGTGATTTAAACGCTT 58.514 30.769 10.57 0.00 36.86 4.68
862 913 7.034685 ACTTTAAACCAGTGATTTAAACGCT 57.965 32.000 10.57 0.00 36.86 5.07
863 914 7.688478 AACTTTAAACCAGTGATTTAAACGC 57.312 32.000 10.57 0.00 36.86 4.84
864 915 8.053653 GCAAACTTTAAACCAGTGATTTAAACG 58.946 33.333 10.57 9.60 36.86 3.60
865 916 8.332464 GGCAAACTTTAAACCAGTGATTTAAAC 58.668 33.333 10.57 2.22 36.86 2.01
866 917 8.041323 TGGCAAACTTTAAACCAGTGATTTAAA 58.959 29.630 13.40 13.40 38.53 1.52
867 918 7.556844 TGGCAAACTTTAAACCAGTGATTTAA 58.443 30.769 0.00 0.00 31.30 1.52
868 919 7.113658 TGGCAAACTTTAAACCAGTGATTTA 57.886 32.000 0.00 0.00 0.00 1.40
869 920 5.983540 TGGCAAACTTTAAACCAGTGATTT 58.016 33.333 0.00 0.00 0.00 2.17
870 921 5.606348 TGGCAAACTTTAAACCAGTGATT 57.394 34.783 0.00 0.00 0.00 2.57
871 922 5.128663 AGTTGGCAAACTTTAAACCAGTGAT 59.871 36.000 0.00 0.00 44.47 3.06
872 923 4.464597 AGTTGGCAAACTTTAAACCAGTGA 59.535 37.500 0.00 0.00 44.47 3.41
873 924 4.754322 AGTTGGCAAACTTTAAACCAGTG 58.246 39.130 0.00 0.00 44.47 3.66
874 925 4.439563 CGAGTTGGCAAACTTTAAACCAGT 60.440 41.667 8.18 0.00 46.84 4.00
875 926 4.041723 CGAGTTGGCAAACTTTAAACCAG 58.958 43.478 8.18 0.00 46.84 4.00
876 927 3.444388 ACGAGTTGGCAAACTTTAAACCA 59.556 39.130 8.18 0.00 46.84 3.67
877 928 4.036567 ACGAGTTGGCAAACTTTAAACC 57.963 40.909 8.18 0.00 46.84 3.27
878 929 4.501559 GGAACGAGTTGGCAAACTTTAAAC 59.498 41.667 8.18 0.00 46.84 2.01
879 930 4.440387 GGGAACGAGTTGGCAAACTTTAAA 60.440 41.667 8.18 0.00 46.84 1.52
880 931 3.067040 GGGAACGAGTTGGCAAACTTTAA 59.933 43.478 8.18 0.00 46.84 1.52
881 932 2.619646 GGGAACGAGTTGGCAAACTTTA 59.380 45.455 8.18 0.00 46.84 1.85
882 933 1.407618 GGGAACGAGTTGGCAAACTTT 59.592 47.619 8.18 0.00 46.84 2.66
883 934 1.029681 GGGAACGAGTTGGCAAACTT 58.970 50.000 8.18 0.00 46.84 2.66
912 963 0.178068 GAACGGCTGGATCCTTGCTA 59.822 55.000 22.88 0.00 0.00 3.49
1026 1080 2.743928 CAGAACTGGGGCGAGCAC 60.744 66.667 0.00 0.00 0.00 4.40
1200 1254 3.454375 ACGATAAAATAGGCAGACACGG 58.546 45.455 0.00 0.00 0.00 4.94
1373 1429 2.088763 CGCACGAGCACGACAAGAT 61.089 57.895 11.40 0.00 42.27 2.40
1494 1550 6.753279 GTGGTGAATAATGACATGAAACATGG 59.247 38.462 14.70 0.00 0.00 3.66
1542 1598 3.560481 CGAGAATTCAAGATGCAGCAGAT 59.440 43.478 4.07 0.00 0.00 2.90
1576 1632 9.643693 GGACAAATAAAGAATGAACATGAATGT 57.356 29.630 0.00 0.00 44.20 2.71
1609 1666 2.753966 CCGCTGAATGCAAGTCCCG 61.754 63.158 0.00 0.00 43.06 5.14
1618 1675 3.996150 ATCATTTTAGGCCGCTGAATG 57.004 42.857 14.22 14.22 0.00 2.67
1729 1786 3.550233 GCAGCAGTGATGATAATGGCAAG 60.550 47.826 13.68 0.00 0.00 4.01
1761 1818 4.435651 CGAATTTCTTTAGCGGTCTGGTTC 60.436 45.833 0.00 0.00 0.00 3.62
1882 1940 0.469917 GGCTCCAGATTCGAATCCCA 59.530 55.000 29.82 15.60 36.04 4.37
2056 2114 8.052141 AGAGAATTGGCTAGATAAAAGAAAGCT 58.948 33.333 0.00 0.00 33.67 3.74
2102 2160 3.811497 TGTCTGCATCACTCTGAAAGTTG 59.189 43.478 0.00 0.00 35.45 3.16
2103 2161 4.077300 TGTCTGCATCACTCTGAAAGTT 57.923 40.909 0.00 0.00 35.45 2.66
2148 2206 3.005791 GCAGTGGTAAAAGAATGCTGGTT 59.994 43.478 0.00 0.00 0.00 3.67
2261 2319 5.464030 AAAGTTCATACAGTCGGTGTACT 57.536 39.130 0.00 0.00 44.65 2.73
2286 2344 4.588899 ACAATAGTTCAACATAGGCTGCA 58.411 39.130 0.50 0.00 0.00 4.41
2287 2345 5.335127 CAACAATAGTTCAACATAGGCTGC 58.665 41.667 0.00 0.00 35.28 5.25
2592 2679 6.792326 TGTTAGAATGGTAGTACGATGTGAG 58.208 40.000 0.00 0.00 0.00 3.51
2604 2691 6.023603 AGAGAGGGAAACTGTTAGAATGGTA 58.976 40.000 0.00 0.00 0.00 3.25
2628 2715 5.762179 ATCAAAGAGAATGTGTACAGGGA 57.238 39.130 0.00 0.00 0.00 4.20
2631 2718 7.952101 CGTGTTAATCAAAGAGAATGTGTACAG 59.048 37.037 0.00 0.00 0.00 2.74
2632 2719 7.439955 ACGTGTTAATCAAAGAGAATGTGTACA 59.560 33.333 0.00 0.00 0.00 2.90
2806 2893 4.375272 TGTAGATTAGAGCTGCATGAAGC 58.625 43.478 18.84 18.84 43.88 3.86
2838 2925 4.015084 CTGCAATGGGAGAAAATGAGACT 58.985 43.478 0.00 0.00 33.71 3.24
2902 2989 5.954752 TGACAGAGATACCAGAAGAGATGTT 59.045 40.000 0.00 0.00 0.00 2.71
2941 3029 4.165372 AGGGAAAAACACAAGACAGGACTA 59.835 41.667 0.00 0.00 0.00 2.59
2968 3056 8.175069 TCAAATACGACTGCATGAAGAATAAAC 58.825 33.333 8.02 0.00 0.00 2.01
3083 3171 6.458210 ACAGAAGAACATAATTTTGCAAGGG 58.542 36.000 0.00 0.00 0.00 3.95
3133 3221 8.143193 TGTACCAAAGATAACTAACGAGTTTCA 58.857 33.333 0.00 0.00 43.70 2.69
3487 3576 4.855531 TGGTACTGAATGTCGATACATCG 58.144 43.478 5.25 5.25 45.79 3.84
3533 3623 1.366319 ACTTCCCAGATGCTTCCTGT 58.634 50.000 0.00 0.00 0.00 4.00
3656 3746 3.197614 CGGTCTCTAAGCCGCAGA 58.802 61.111 0.00 0.00 41.53 4.26
3672 3762 0.523546 CGACCAGTCCTCGATTCACG 60.524 60.000 0.00 0.00 44.09 4.35
3690 3780 4.854399 TGTCAAATTTACAAGCTGGTTCG 58.146 39.130 0.00 0.00 0.00 3.95
3794 3884 3.118371 ACGTCCCCCTCAAATATGACTTC 60.118 47.826 0.00 0.00 0.00 3.01
3811 3903 0.105224 CCCCCAAAACCAAAACGTCC 59.895 55.000 0.00 0.00 0.00 4.79
3812 3904 1.112950 TCCCCCAAAACCAAAACGTC 58.887 50.000 0.00 0.00 0.00 4.34
3813 3905 1.796017 ATCCCCCAAAACCAAAACGT 58.204 45.000 0.00 0.00 0.00 3.99
3814 3906 2.920724 AATCCCCCAAAACCAAAACG 57.079 45.000 0.00 0.00 0.00 3.60
3815 3907 4.069304 GCTTAATCCCCCAAAACCAAAAC 58.931 43.478 0.00 0.00 0.00 2.43
3830 3928 7.489239 AGGATCTGTTAGATAGGGCTTAATC 57.511 40.000 0.00 0.00 34.53 1.75
3876 4055 7.730364 TCTGTTTCCAAGAAGTGTCTTAATC 57.270 36.000 0.00 0.00 42.45 1.75
3890 4069 5.800296 TCTCGGTATTGAATCTGTTTCCAA 58.200 37.500 0.00 0.00 33.04 3.53
3898 4077 7.069331 AGAGAAATCACTCTCGGTATTGAATCT 59.931 37.037 0.00 0.00 45.53 2.40
3927 4106 1.095807 GGCCTGGAGTTTGGTATCGC 61.096 60.000 0.00 0.00 0.00 4.58
3937 4116 1.375326 GAAAACGGAGGCCTGGAGT 59.625 57.895 12.00 3.82 0.00 3.85
3988 4168 3.103911 CACCGTGAGCGAACCGAC 61.104 66.667 0.00 0.00 41.33 4.79
3993 4194 1.942677 TCTTTTTCACCGTGAGCGAA 58.057 45.000 0.64 0.00 41.33 4.70
4002 4203 3.379057 TCCCTTGTCGTTTCTTTTTCACC 59.621 43.478 0.00 0.00 0.00 4.02
4066 4270 1.162800 GGCAGAGATGATGGCGAACC 61.163 60.000 0.00 0.00 33.23 3.62
4068 4272 1.146930 GGGCAGAGATGATGGCGAA 59.853 57.895 0.00 0.00 43.74 4.70
4085 4289 2.125512 CCGAGCAGGAAACGAGGG 60.126 66.667 0.00 0.00 45.00 4.30
4114 4318 4.787280 CGGGAGAGGAGGGGCAGT 62.787 72.222 0.00 0.00 0.00 4.40
4148 4352 0.945813 GATCTTGAGATGCAGGCTGC 59.054 55.000 31.91 31.91 45.29 5.25
4150 4354 1.141254 CCAGATCTTGAGATGCAGGCT 59.859 52.381 0.00 0.00 34.37 4.58
4158 4362 2.735772 GGGGCGCCAGATCTTGAGA 61.736 63.158 30.85 0.00 0.00 3.27
4200 4404 5.830912 TGTTTGGATGTTCTGTTGATGAAC 58.169 37.500 0.00 0.00 42.77 3.18
4255 4460 3.132925 GTTGCACATGAAATTGCTGGTT 58.867 40.909 0.00 0.00 39.62 3.67
4259 4464 3.472283 TTGGTTGCACATGAAATTGCT 57.528 38.095 0.00 0.00 39.62 3.91
4308 4513 2.369203 TCCAATACCAGTGTTGTTCCGA 59.631 45.455 6.54 0.00 30.94 4.55
4339 4549 8.142551 GGACGTATGTATTGAGAACCTCTAAAT 58.857 37.037 0.00 0.00 32.44 1.40
4342 4552 6.124340 TGGACGTATGTATTGAGAACCTCTA 58.876 40.000 0.00 0.00 0.00 2.43
4362 4572 0.165944 CATTCACGCTCCGTTTGGAC 59.834 55.000 0.00 0.00 40.17 4.02
4384 4594 4.321899 GGCCAAAACACTCAGATATGCAAA 60.322 41.667 0.00 0.00 0.00 3.68
4448 4663 5.580691 TGTCAATCACTAGCGTATCAAAAGG 59.419 40.000 0.00 0.00 0.00 3.11
4483 4698 1.529010 CACAAGGGCAGGTGCTTGA 60.529 57.895 10.07 0.00 41.70 3.02
4504 4719 3.907221 AGAAGCACCCAATATGAGCAAT 58.093 40.909 0.00 0.00 0.00 3.56
4613 4836 5.045359 TCAAATGATCATCTCCTCACAACCT 60.045 40.000 9.06 0.00 0.00 3.50
4616 4839 6.596888 GTCTTCAAATGATCATCTCCTCACAA 59.403 38.462 9.06 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.