Multiple sequence alignment - TraesCS5A01G365800

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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 TraesCS5A01G365800 chr5A 100.000 3787 0 0 1 3787 565685319 565681533 0.000000e+00 6994.0
1 TraesCS5A01G365800 chr5A 80.986 426 41 22 466 858 690786192 690785774 6.150000e-78 302.0
2 TraesCS5A01G365800 chr5B 91.763 2173 138 16 903 3047 546705976 546703817 0.000000e+00 2983.0
3 TraesCS5A01G365800 chr5B 91.529 543 28 11 1 530 546706511 546705974 0.000000e+00 732.0
4 TraesCS5A01G365800 chr5B 86.335 161 17 3 300 459 670065516 670065672 1.810000e-38 171.0
5 TraesCS5A01G365800 chr5D 93.486 1182 66 9 1947 3127 447777416 447776245 0.000000e+00 1746.0
6 TraesCS5A01G365800 chr5D 93.010 1030 50 11 856 1866 447778499 447777473 0.000000e+00 1483.0
7 TraesCS5A01G365800 chr5D 90.924 628 43 13 3139 3757 447774532 447773910 0.000000e+00 832.0
8 TraesCS5A01G365800 chr5D 85.345 232 27 4 1 225 447819644 447819413 2.270000e-57 233.0
9 TraesCS5A01G365800 chr5D 88.462 182 12 6 467 646 370108985 370108811 1.070000e-50 211.0
10 TraesCS5A01G365800 chr4D 81.230 618 92 18 3139 3745 328329069 328329673 9.520000e-131 477.0
11 TraesCS5A01G365800 chr2A 78.906 640 105 23 3139 3765 152603316 152602694 1.270000e-109 407.0
12 TraesCS5A01G365800 chr3D 81.087 423 44 14 466 858 591661076 591660660 4.750000e-79 305.0
13 TraesCS5A01G365800 chr3D 79.717 424 48 21 466 858 470722469 470722053 4.820000e-69 272.0
14 TraesCS5A01G365800 chr3D 79.193 322 47 13 3431 3746 614341218 614341525 4.960000e-49 206.0
15 TraesCS5A01G365800 chr2D 80.706 425 45 27 466 859 648171053 648170635 2.860000e-76 296.0
16 TraesCS5A01G365800 chr7D 80.332 422 45 16 466 858 264985080 264984668 6.190000e-73 285.0
17 TraesCS5A01G365800 chr6B 80.328 427 41 23 466 858 143197013 143197430 2.230000e-72 283.0
18 TraesCS5A01G365800 chr1B 79.907 428 48 23 462 858 605472933 605473353 2.880000e-71 279.0
19 TraesCS5A01G365800 chr3B 80.000 425 46 23 466 858 690108612 690109029 1.040000e-70 278.0
20 TraesCS5A01G365800 chr6D 79.157 427 47 28 466 858 347446627 347446209 1.350000e-64 257.0
21 TraesCS5A01G365800 chr4B 88.426 216 21 4 648 861 427518943 427518730 1.350000e-64 257.0
22 TraesCS5A01G365800 chr7A 79.012 405 46 17 463 838 677870714 677871108 1.360000e-59 241.0
23 TraesCS5A01G365800 chr6A 87.500 208 20 5 649 855 603107196 603107398 6.320000e-58 235.0
24 TraesCS5A01G365800 chr6A 92.593 54 4 0 3431 3484 539978928 539978875 1.130000e-10 78.7
25 TraesCS5A01G365800 chr2B 79.937 319 51 9 3368 3681 195920635 195920945 4.920000e-54 222.0
26 TraesCS5A01G365800 chr4A 87.912 182 17 3 466 646 609563193 609563016 3.830000e-50 209.0
27 TraesCS5A01G365800 chr1D 85.326 184 18 7 466 647 7824907 7824731 8.360000e-42 182.0
28 TraesCS5A01G365800 chr3A 92.593 54 4 0 3431 3484 7213937 7213884 1.130000e-10 78.7


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 TraesCS5A01G365800 chr5A 565681533 565685319 3786 True 6994.000000 6994 100.000000 1 3787 1 chr5A.!!$R1 3786
1 TraesCS5A01G365800 chr5B 546703817 546706511 2694 True 1857.500000 2983 91.646000 1 3047 2 chr5B.!!$R1 3046
2 TraesCS5A01G365800 chr5D 447773910 447778499 4589 True 1353.666667 1746 92.473333 856 3757 3 chr5D.!!$R3 2901
3 TraesCS5A01G365800 chr4D 328329069 328329673 604 False 477.000000 477 81.230000 3139 3745 1 chr4D.!!$F1 606
4 TraesCS5A01G365800 chr2A 152602694 152603316 622 True 407.000000 407 78.906000 3139 3765 1 chr2A.!!$R1 626

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
843 856 0.400213 TTTCAATGCACCCGTCCTCT 59.600 50.0 0.00 0.00 0.00 3.69 F
1172 1191 0.456312 GACACTGACCCGATGACGTC 60.456 60.0 9.11 9.11 37.88 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1958 0.863956 ATTTCAAACCCTGGACCCCA 59.136 50.000 0.00 0.0 0.0 4.96 R
3127 3202 1.007271 CAGGTGAGCGGCGTATAGG 60.007 63.158 9.37 0.0 0.0 2.57 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
101 103 3.693578 TCAGTCTGCACAAACATGACAAA 59.306 39.130 0.00 0.00 0.00 2.83
122 124 9.118236 GACAAAACTTAGCAGTATTGACAATTC 57.882 33.333 5.89 0.96 30.68 2.17
213 215 3.963428 GGCGACCTATTCACCAGATAT 57.037 47.619 0.00 0.00 0.00 1.63
216 218 4.489810 GCGACCTATTCACCAGATATCTG 58.510 47.826 23.53 23.53 43.40 2.90
225 227 9.994432 CTATTCACCAGATATCTGAAAACAAAC 57.006 33.333 30.40 0.00 46.59 2.93
230 232 6.998074 ACCAGATATCTGAAAACAAACACTCA 59.002 34.615 30.40 0.00 46.59 3.41
232 234 7.173907 CCAGATATCTGAAAACAAACACTCAGT 59.826 37.037 30.40 0.00 46.59 3.41
266 268 1.733389 GCATGATGTTTTGCGTCCCAG 60.733 52.381 0.00 0.00 32.20 4.45
269 271 2.212900 GATGTTTTGCGTCCCAGGCC 62.213 60.000 0.00 0.00 0.00 5.19
278 280 3.857038 TCCCAGGCCGCCGATTAC 61.857 66.667 3.05 0.00 0.00 1.89
360 370 4.854784 GCGTGGCTGCTCGATCGA 62.855 66.667 18.32 18.32 0.00 3.59
362 372 1.589993 CGTGGCTGCTCGATCGATT 60.590 57.895 19.78 0.00 0.00 3.34
366 376 0.579156 GGCTGCTCGATCGATTGTTC 59.421 55.000 19.78 7.08 0.00 3.18
368 378 1.550065 CTGCTCGATCGATTGTTCGT 58.450 50.000 19.78 0.00 45.65 3.85
369 379 1.920574 CTGCTCGATCGATTGTTCGTT 59.079 47.619 19.78 0.00 45.65 3.85
370 380 1.653609 TGCTCGATCGATTGTTCGTTG 59.346 47.619 19.78 4.51 45.65 4.10
371 381 1.917955 GCTCGATCGATTGTTCGTTGA 59.082 47.619 19.78 0.00 45.65 3.18
392 402 7.008447 CGTTGACTGTAGCTAGAAAACACTATC 59.992 40.741 0.00 0.00 0.00 2.08
416 426 4.928601 TGACACTGTTCAGTACTGTACAC 58.071 43.478 25.97 18.24 36.24 2.90
461 473 3.119291 CCAAGCTAGCTATGAACTGACG 58.881 50.000 19.70 0.00 0.00 4.35
462 474 3.429547 CCAAGCTAGCTATGAACTGACGT 60.430 47.826 19.70 0.00 0.00 4.34
464 476 2.099921 AGCTAGCTATGAACTGACGTGG 59.900 50.000 17.69 0.00 0.00 4.94
476 488 1.269448 CTGACGTGGGTGGATTTTTGG 59.731 52.381 0.00 0.00 0.00 3.28
482 494 0.981183 GGGTGGATTTTTGGAACCCC 59.019 55.000 0.00 0.00 44.05 4.95
535 548 9.883142 ACTTTAAAAATCACATTTGAAGTTCCA 57.117 25.926 0.00 0.00 41.16 3.53
563 576 9.729281 AAAAATCCAAAAAGAATGCTACATGAT 57.271 25.926 0.00 0.00 0.00 2.45
564 577 8.937634 AAATCCAAAAAGAATGCTACATGATC 57.062 30.769 0.00 0.00 0.00 2.92
565 578 7.649533 ATCCAAAAAGAATGCTACATGATCA 57.350 32.000 0.00 0.00 0.00 2.92
566 579 7.649533 TCCAAAAAGAATGCTACATGATCAT 57.350 32.000 1.18 1.18 0.00 2.45
567 580 8.750515 TCCAAAAAGAATGCTACATGATCATA 57.249 30.769 8.15 0.00 0.00 2.15
568 581 9.358406 TCCAAAAAGAATGCTACATGATCATAT 57.642 29.630 8.15 0.00 0.00 1.78
569 582 9.406828 CCAAAAAGAATGCTACATGATCATATG 57.593 33.333 8.15 0.73 0.00 1.78
570 583 9.406828 CAAAAAGAATGCTACATGATCATATGG 57.593 33.333 8.15 0.00 32.32 2.74
571 584 8.929260 AAAAGAATGCTACATGATCATATGGA 57.071 30.769 8.15 3.31 32.32 3.41
572 585 9.529823 AAAAGAATGCTACATGATCATATGGAT 57.470 29.630 8.15 5.53 39.53 3.41
573 586 8.507524 AAGAATGCTACATGATCATATGGATG 57.492 34.615 8.15 0.00 36.00 3.51
574 587 7.631007 AGAATGCTACATGATCATATGGATGT 58.369 34.615 8.15 15.66 36.00 3.06
575 588 8.765517 AGAATGCTACATGATCATATGGATGTA 58.234 33.333 8.15 16.04 36.00 2.29
576 589 9.557061 GAATGCTACATGATCATATGGATGTAT 57.443 33.333 8.15 7.94 36.00 2.29
578 591 9.993454 ATGCTACATGATCATATGGATGTATAC 57.007 33.333 8.15 13.94 36.00 1.47
579 592 9.205513 TGCTACATGATCATATGGATGTATACT 57.794 33.333 8.15 0.00 36.00 2.12
603 616 9.132521 ACTACATACGTATGTGTAAAGTTTGTC 57.867 33.333 38.87 0.00 45.77 3.18
604 617 7.041187 ACATACGTATGTGTAAAGTTTGTCG 57.959 36.000 34.29 8.37 44.66 4.35
605 618 6.862608 ACATACGTATGTGTAAAGTTTGTCGA 59.137 34.615 34.29 0.00 44.66 4.20
606 619 7.543172 ACATACGTATGTGTAAAGTTTGTCGAT 59.457 33.333 34.29 8.67 44.66 3.59
607 620 6.148270 ACGTATGTGTAAAGTTTGTCGATG 57.852 37.500 0.00 0.00 0.00 3.84
608 621 5.921976 ACGTATGTGTAAAGTTTGTCGATGA 59.078 36.000 0.00 0.00 0.00 2.92
609 622 6.421501 ACGTATGTGTAAAGTTTGTCGATGAA 59.578 34.615 0.00 0.00 0.00 2.57
610 623 7.042590 ACGTATGTGTAAAGTTTGTCGATGAAA 60.043 33.333 0.00 0.00 0.00 2.69
611 624 7.955324 CGTATGTGTAAAGTTTGTCGATGAAAT 59.045 33.333 0.00 0.00 0.00 2.17
614 627 9.825972 ATGTGTAAAGTTTGTCGATGAAATAAG 57.174 29.630 0.00 0.00 0.00 1.73
615 628 8.832521 TGTGTAAAGTTTGTCGATGAAATAAGT 58.167 29.630 0.00 0.00 0.00 2.24
622 635 9.825972 AGTTTGTCGATGAAATAAGTAAACATG 57.174 29.630 0.00 0.00 0.00 3.21
623 636 9.607285 GTTTGTCGATGAAATAAGTAAACATGT 57.393 29.630 0.00 0.00 0.00 3.21
627 640 9.422196 GTCGATGAAATAAGTAAACATGTAAGC 57.578 33.333 0.00 0.00 0.00 3.09
628 641 9.378551 TCGATGAAATAAGTAAACATGTAAGCT 57.621 29.630 0.00 0.00 0.00 3.74
668 681 9.783081 AAAAAGCACTATTCATCTTTCCAAAAT 57.217 25.926 0.00 0.00 0.00 1.82
669 682 8.992835 AAAGCACTATTCATCTTTCCAAAATC 57.007 30.769 0.00 0.00 0.00 2.17
670 683 7.707624 AGCACTATTCATCTTTCCAAAATCA 57.292 32.000 0.00 0.00 0.00 2.57
671 684 7.769220 AGCACTATTCATCTTTCCAAAATCAG 58.231 34.615 0.00 0.00 0.00 2.90
672 685 6.976925 GCACTATTCATCTTTCCAAAATCAGG 59.023 38.462 0.00 0.00 0.00 3.86
673 686 7.148018 GCACTATTCATCTTTCCAAAATCAGGA 60.148 37.037 0.00 0.00 0.00 3.86
674 687 8.910944 CACTATTCATCTTTCCAAAATCAGGAT 58.089 33.333 0.00 0.00 34.56 3.24
675 688 9.484806 ACTATTCATCTTTCCAAAATCAGGATT 57.515 29.630 0.00 0.00 34.56 3.01
679 692 8.884124 TCATCTTTCCAAAATCAGGATTTAGT 57.116 30.769 7.62 0.00 39.88 2.24
680 693 8.960591 TCATCTTTCCAAAATCAGGATTTAGTC 58.039 33.333 7.62 0.00 39.88 2.59
681 694 8.742777 CATCTTTCCAAAATCAGGATTTAGTCA 58.257 33.333 7.62 0.00 39.88 3.41
682 695 8.884124 TCTTTCCAAAATCAGGATTTAGTCAT 57.116 30.769 7.62 0.00 39.88 3.06
683 696 9.312904 TCTTTCCAAAATCAGGATTTAGTCATT 57.687 29.630 7.62 0.00 39.88 2.57
684 697 9.933723 CTTTCCAAAATCAGGATTTAGTCATTT 57.066 29.630 7.62 0.00 39.88 2.32
713 726 7.812648 TGTAACTCACATGGTTACTTATTTGC 58.187 34.615 18.35 0.00 45.19 3.68
714 727 6.892658 AACTCACATGGTTACTTATTTGCA 57.107 33.333 0.00 0.00 0.00 4.08
715 728 6.254281 ACTCACATGGTTACTTATTTGCAC 57.746 37.500 0.00 0.00 0.00 4.57
716 729 5.767665 ACTCACATGGTTACTTATTTGCACA 59.232 36.000 0.00 0.00 0.00 4.57
717 730 6.434028 ACTCACATGGTTACTTATTTGCACAT 59.566 34.615 0.00 0.00 0.00 3.21
718 731 6.851609 TCACATGGTTACTTATTTGCACATC 58.148 36.000 0.00 0.00 0.00 3.06
719 732 6.432472 TCACATGGTTACTTATTTGCACATCA 59.568 34.615 0.00 0.00 0.00 3.07
720 733 7.040132 TCACATGGTTACTTATTTGCACATCAA 60.040 33.333 0.00 0.00 0.00 2.57
722 735 8.147058 ACATGGTTACTTATTTGCACATCAAAA 58.853 29.630 0.00 0.00 46.60 2.44
723 736 9.153721 CATGGTTACTTATTTGCACATCAAAAT 57.846 29.630 0.00 0.00 46.60 1.82
724 737 9.723601 ATGGTTACTTATTTGCACATCAAAATT 57.276 25.926 0.00 0.00 46.60 1.82
725 738 9.553064 TGGTTACTTATTTGCACATCAAAATTT 57.447 25.926 0.00 0.00 46.60 1.82
726 739 9.810231 GGTTACTTATTTGCACATCAAAATTTG 57.190 29.630 0.00 0.00 46.60 2.32
727 740 9.316859 GTTACTTATTTGCACATCAAAATTTGC 57.683 29.630 0.00 0.00 46.60 3.68
728 741 7.493743 ACTTATTTGCACATCAAAATTTGCA 57.506 28.000 0.00 0.00 46.60 4.08
729 742 7.354257 ACTTATTTGCACATCAAAATTTGCAC 58.646 30.769 0.00 0.00 45.65 4.57
730 743 5.752892 ATTTGCACATCAAAATTTGCACA 57.247 30.435 0.00 0.00 45.65 4.57
731 744 5.752892 TTTGCACATCAAAATTTGCACAT 57.247 30.435 0.00 0.00 45.65 3.21
732 745 4.733972 TGCACATCAAAATTTGCACATG 57.266 36.364 0.00 2.90 42.21 3.21
733 746 4.127907 TGCACATCAAAATTTGCACATGT 58.872 34.783 0.00 3.52 42.21 3.21
734 747 4.575236 TGCACATCAAAATTTGCACATGTT 59.425 33.333 8.28 0.00 42.21 2.71
735 748 5.066117 TGCACATCAAAATTTGCACATGTTT 59.934 32.000 8.28 0.00 42.21 2.83
736 749 6.259387 TGCACATCAAAATTTGCACATGTTTA 59.741 30.769 8.28 0.71 42.21 2.01
737 750 7.130917 GCACATCAAAATTTGCACATGTTTAA 58.869 30.769 8.28 0.00 38.26 1.52
738 751 7.804129 GCACATCAAAATTTGCACATGTTTAAT 59.196 29.630 8.28 0.00 38.26 1.40
837 850 5.964958 AATATAGGATTTCAATGCACCCG 57.035 39.130 0.00 0.00 0.00 5.28
838 851 2.799126 TAGGATTTCAATGCACCCGT 57.201 45.000 0.00 0.00 0.00 5.28
839 852 1.463674 AGGATTTCAATGCACCCGTC 58.536 50.000 0.00 0.00 0.00 4.79
840 853 0.455815 GGATTTCAATGCACCCGTCC 59.544 55.000 0.00 0.00 0.00 4.79
841 854 1.463674 GATTTCAATGCACCCGTCCT 58.536 50.000 0.00 0.00 0.00 3.85
842 855 1.401905 GATTTCAATGCACCCGTCCTC 59.598 52.381 0.00 0.00 0.00 3.71
843 856 0.400213 TTTCAATGCACCCGTCCTCT 59.600 50.000 0.00 0.00 0.00 3.69
844 857 1.271856 TTCAATGCACCCGTCCTCTA 58.728 50.000 0.00 0.00 0.00 2.43
845 858 1.271856 TCAATGCACCCGTCCTCTAA 58.728 50.000 0.00 0.00 0.00 2.10
846 859 1.626321 TCAATGCACCCGTCCTCTAAA 59.374 47.619 0.00 0.00 0.00 1.85
847 860 2.039216 TCAATGCACCCGTCCTCTAAAA 59.961 45.455 0.00 0.00 0.00 1.52
848 861 3.016736 CAATGCACCCGTCCTCTAAAAT 58.983 45.455 0.00 0.00 0.00 1.82
849 862 2.107950 TGCACCCGTCCTCTAAAATG 57.892 50.000 0.00 0.00 0.00 2.32
850 863 1.626321 TGCACCCGTCCTCTAAAATGA 59.374 47.619 0.00 0.00 0.00 2.57
851 864 2.007608 GCACCCGTCCTCTAAAATGAC 58.992 52.381 0.00 0.00 0.00 3.06
852 865 2.354805 GCACCCGTCCTCTAAAATGACT 60.355 50.000 0.00 0.00 0.00 3.41
853 866 3.868754 GCACCCGTCCTCTAAAATGACTT 60.869 47.826 0.00 0.00 0.00 3.01
854 867 4.324267 CACCCGTCCTCTAAAATGACTTT 58.676 43.478 0.00 0.00 0.00 2.66
863 876 6.038825 TCCTCTAAAATGACTTTTTGACGCAA 59.961 34.615 8.83 0.00 38.03 4.85
866 879 7.921787 TCTAAAATGACTTTTTGACGCAAGTA 58.078 30.769 8.83 0.00 44.10 2.24
883 898 6.084277 CGCAAGTAAAATTTTCAGGTACCTC 58.916 40.000 12.84 0.00 0.00 3.85
884 899 6.293735 CGCAAGTAAAATTTTCAGGTACCTCA 60.294 38.462 12.84 0.00 0.00 3.86
896 911 5.815581 TCAGGTACCTCATGTTTAGCAAAT 58.184 37.500 12.84 0.00 0.00 2.32
930 946 2.126463 ACTCGATGACCGCACACG 60.126 61.111 0.00 0.00 38.37 4.49
960 976 3.554129 CGACTGACATTCTTGTACCCACA 60.554 47.826 0.00 0.00 35.79 4.17
968 984 5.009610 ACATTCTTGTACCCACACATCAAAC 59.990 40.000 0.00 0.00 33.30 2.93
1022 1041 4.670896 TGGATCGTTCATCAGATAAGCA 57.329 40.909 0.00 0.00 32.33 3.91
1040 1059 1.134946 GCAGCCACCAACCATTCATAC 59.865 52.381 0.00 0.00 0.00 2.39
1041 1060 1.401552 CAGCCACCAACCATTCATACG 59.598 52.381 0.00 0.00 0.00 3.06
1076 1095 1.283029 CATGGCTTCCTCCTTCTCCAA 59.717 52.381 0.00 0.00 0.00 3.53
1112 1131 2.685380 CCTCCTCCTGGCCGTCTT 60.685 66.667 0.00 0.00 0.00 3.01
1125 1144 1.227089 CGTCTTCCTCCATGGCTCG 60.227 63.158 6.96 0.00 35.26 5.03
1126 1145 1.901085 GTCTTCCTCCATGGCTCGT 59.099 57.895 6.96 0.00 35.26 4.18
1130 1149 4.227134 CCTCCATGGCTCGTCCGG 62.227 72.222 6.96 0.00 37.80 5.14
1171 1190 1.585006 GACACTGACCCGATGACGT 59.415 57.895 0.00 0.00 37.88 4.34
1172 1191 0.456312 GACACTGACCCGATGACGTC 60.456 60.000 9.11 9.11 37.88 4.34
1531 1553 2.733218 CGAGCGTTGACTGGCGAA 60.733 61.111 0.00 0.00 0.00 4.70
1655 1682 4.599041 TCCCTTGGTCTCCAATTATTGTG 58.401 43.478 4.15 0.00 43.07 3.33
1656 1683 4.044065 TCCCTTGGTCTCCAATTATTGTGT 59.956 41.667 4.15 0.00 43.07 3.72
1686 1713 1.879380 TGTAAACACATGGCTGTCTGC 59.121 47.619 0.00 0.00 41.94 4.26
1687 1714 1.135972 GTAAACACATGGCTGTCTGCG 60.136 52.381 0.00 0.00 44.05 5.18
1716 1743 2.543687 CTTGCATGTGCTCCTGCTGC 62.544 60.000 15.43 0.00 42.66 5.25
1718 1745 2.045242 CATGTGCTCCTGCTGCCT 60.045 61.111 0.00 0.00 40.48 4.75
1746 1785 5.312079 AGCTGCTTCATCATTAGGGATTAC 58.688 41.667 0.00 0.00 0.00 1.89
1770 1809 8.615878 ACACAATTGCTTACTTAACTGTCATA 57.384 30.769 5.05 0.00 0.00 2.15
1791 1830 7.798516 GTCATACACACTGTTAATTGTCAACTG 59.201 37.037 0.00 0.00 0.00 3.16
1889 1958 2.568623 AGAAGCATTTCCTTGTCGGT 57.431 45.000 0.00 0.00 33.64 4.69
1890 1959 2.154462 AGAAGCATTTCCTTGTCGGTG 58.846 47.619 0.00 0.00 33.64 4.94
1912 1981 2.969262 GGGTCCAGGGTTTGAAATTTCA 59.031 45.455 16.91 16.91 34.92 2.69
1961 2030 5.972382 TCGAACTGACCGGTTTTTATTTTTG 59.028 36.000 9.42 0.00 0.00 2.44
1962 2031 5.744819 CGAACTGACCGGTTTTTATTTTTGT 59.255 36.000 9.42 0.00 0.00 2.83
1963 2032 6.253942 CGAACTGACCGGTTTTTATTTTTGTT 59.746 34.615 9.42 2.22 0.00 2.83
1964 2033 6.895607 ACTGACCGGTTTTTATTTTTGTTG 57.104 33.333 9.42 0.00 0.00 3.33
1970 2039 7.698628 ACCGGTTTTTATTTTTGTTGGAAATG 58.301 30.769 0.00 0.00 0.00 2.32
1986 2055 7.967854 TGTTGGAAATGATTCGAATAACATCAC 59.032 33.333 11.38 8.60 35.99 3.06
1999 2068 9.062524 TCGAATAACATCACCATATTTTAAGGG 57.937 33.333 0.00 0.00 0.00 3.95
2123 2198 4.898320 TGGTCGATCATATGATTTGAGGG 58.102 43.478 19.11 5.78 34.37 4.30
2136 2211 5.063204 TGATTTGAGGGACAATATAAGCGG 58.937 41.667 0.00 0.00 38.36 5.52
2142 2217 3.838317 AGGGACAATATAAGCGGCTATCA 59.162 43.478 1.35 0.00 0.00 2.15
2154 2229 6.942532 AAGCGGCTATCAAATTTTATCTCA 57.057 33.333 1.35 0.00 0.00 3.27
2172 2247 9.990360 TTTATCTCATAGTTCTTGTGTGTGTTA 57.010 29.630 0.00 0.00 0.00 2.41
2393 2468 3.835395 CCTCCCAGGAAGACTATCCATAC 59.165 52.174 0.00 0.00 42.27 2.39
2506 2581 3.103875 GTTGACAAACGCGGTGGT 58.896 55.556 2.29 2.29 0.00 4.16
2675 2750 4.523173 AGTTACTGGATCGTGAAGAACTCA 59.477 41.667 0.00 0.00 0.00 3.41
2693 2768 1.930656 ATGGGGTGAGAAGTGGGGG 60.931 63.158 0.00 0.00 0.00 5.40
2756 2831 2.512896 GAGGGGATCTGCGGCATT 59.487 61.111 1.75 0.00 0.00 3.56
2806 2881 1.894881 TGTGATCATGTGTGGTGTGG 58.105 50.000 0.00 0.00 0.00 4.17
2808 2883 1.536766 GTGATCATGTGTGGTGTGGTG 59.463 52.381 0.00 0.00 0.00 4.17
2833 2908 3.955471 TCATTGTTCTTTCCCTAGCAGG 58.045 45.455 0.00 0.00 34.30 4.85
2847 2922 2.714991 GCAGGGGCCAAAGCTTAGC 61.715 63.158 4.39 11.94 39.73 3.09
2978 3053 4.341806 TGTTCATGTGGATTCAGCACTTTT 59.658 37.500 0.00 0.00 0.00 2.27
3009 3084 8.816640 TTTTCTATGAGCTTTTAGGCTTTTTG 57.183 30.769 0.00 0.00 43.20 2.44
3020 3095 2.407562 AGGCTTTTTGGTGGATTTGGT 58.592 42.857 0.00 0.00 0.00 3.67
3046 3121 6.039270 TGTCCAATAGGTCAAGTCACTTTTTG 59.961 38.462 0.00 0.00 35.89 2.44
3055 3130 1.111277 GTCACTTTTTGTGTGGGCCT 58.889 50.000 4.53 0.00 46.27 5.19
3070 3145 1.109323 GGCCTGACTGGTGCAAACTT 61.109 55.000 0.00 0.00 38.35 2.66
3072 3147 1.953686 GCCTGACTGGTGCAAACTTTA 59.046 47.619 0.00 0.00 38.35 1.85
3094 3169 9.941664 CTTTATGGAATTTAGAAGCTACATGTG 57.058 33.333 9.11 0.00 0.00 3.21
3101 3176 3.252974 AGAAGCTACATGTGGTACAGC 57.747 47.619 9.11 9.13 41.80 4.40
3127 3202 3.544698 TGAGATGACTATAGGGACCCC 57.455 52.381 7.00 1.17 0.00 4.95
3128 3203 2.111972 TGAGATGACTATAGGGACCCCC 59.888 54.545 7.00 0.00 45.90 5.40
3137 3212 3.308705 GGGACCCCCTATACGCCG 61.309 72.222 0.00 0.00 41.34 6.46
3185 4961 4.692475 GGGGTGGCACGCGTTAGT 62.692 66.667 25.62 0.00 41.51 2.24
3240 5016 0.391597 ACTGGGAATCGAACACACGT 59.608 50.000 0.00 0.00 34.70 4.49
3245 5021 0.438830 GAATCGAACACACGTCCTGC 59.561 55.000 0.00 0.00 34.70 4.85
3250 5026 1.860676 GAACACACGTCCTGCAAGTA 58.139 50.000 0.00 0.00 0.00 2.24
3280 5057 2.158959 CGCACCGTGCTAGCACTAC 61.159 63.158 37.42 24.59 44.16 2.73
3372 5153 2.480073 CCGCAGCACAAATTCCCATAAG 60.480 50.000 0.00 0.00 0.00 1.73
3600 5383 5.578727 CGAACTTTTCATGAAACCCAAACAA 59.421 36.000 20.35 2.75 0.00 2.83
3747 5539 7.537715 TCACGAACAAATTTATCAAGATGCAT 58.462 30.769 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.973973 ACCATAGAGGGCAACTATAGCAA 59.026 43.478 0.00 0.00 43.89 3.91
79 81 2.916640 TGTCATGTTTGTGCAGACTGA 58.083 42.857 6.65 0.00 0.00 3.41
84 86 5.051508 GCTAAGTTTTGTCATGTTTGTGCAG 60.052 40.000 0.00 0.00 0.00 4.41
101 103 7.986085 ACTGAATTGTCAATACTGCTAAGTT 57.014 32.000 0.00 0.00 33.71 2.66
122 124 4.631813 AGATTTTTGCCGAACTAGCTACTG 59.368 41.667 0.00 0.00 0.00 2.74
165 167 4.944619 TTCACAAGTGAGATCAGTGAGT 57.055 40.909 0.00 0.00 41.13 3.41
199 201 9.994432 GTTTGTTTTCAGATATCTGGTGAATAG 57.006 33.333 28.30 4.67 43.91 1.73
213 215 7.214467 AAGAAACTGAGTGTTTGTTTTCAGA 57.786 32.000 7.29 0.00 45.84 3.27
225 227 3.605692 GCGCAAGAAGAAGAAACTGAGTG 60.606 47.826 0.30 0.00 43.02 3.51
230 232 3.141398 TCATGCGCAAGAAGAAGAAACT 58.859 40.909 17.11 0.00 43.02 2.66
232 234 3.503363 ACATCATGCGCAAGAAGAAGAAA 59.497 39.130 22.75 0.00 43.02 2.52
278 280 4.169696 TGGTAATCCGGCTGGCGG 62.170 66.667 33.86 33.86 36.30 6.13
330 340 4.517815 CACGCCCAATGCCATGGC 62.518 66.667 30.54 30.54 39.26 4.40
359 369 5.399858 TCTAGCTACAGTCAACGAACAATC 58.600 41.667 0.00 0.00 0.00 2.67
360 370 5.386958 TCTAGCTACAGTCAACGAACAAT 57.613 39.130 0.00 0.00 0.00 2.71
362 372 4.841443 TTCTAGCTACAGTCAACGAACA 57.159 40.909 0.00 0.00 0.00 3.18
366 376 4.982916 AGTGTTTTCTAGCTACAGTCAACG 59.017 41.667 0.00 0.00 0.00 4.10
368 378 8.123639 AGATAGTGTTTTCTAGCTACAGTCAA 57.876 34.615 0.00 0.00 35.32 3.18
369 379 7.704578 AGATAGTGTTTTCTAGCTACAGTCA 57.295 36.000 0.00 0.00 35.32 3.41
370 380 8.244802 TCAAGATAGTGTTTTCTAGCTACAGTC 58.755 37.037 0.00 0.00 35.92 3.51
371 381 8.030106 GTCAAGATAGTGTTTTCTAGCTACAGT 58.970 37.037 0.00 0.00 35.92 3.55
392 402 5.459107 GTGTACAGTACTGAACAGTGTCAAG 59.541 44.000 29.30 0.00 42.52 3.02
461 473 1.346395 GGGTTCCAAAAATCCACCCAC 59.654 52.381 0.54 0.00 45.82 4.61
462 474 1.723288 GGGTTCCAAAAATCCACCCA 58.277 50.000 0.54 0.00 45.82 4.51
464 476 0.606096 CGGGGTTCCAAAAATCCACC 59.394 55.000 0.00 0.00 0.00 4.61
476 488 0.906775 TCCTCCAATACACGGGGTTC 59.093 55.000 0.00 0.00 0.00 3.62
537 550 9.729281 ATCATGTAGCATTCTTTTTGGATTTTT 57.271 25.926 0.00 0.00 0.00 1.94
538 551 9.374838 GATCATGTAGCATTCTTTTTGGATTTT 57.625 29.630 0.00 0.00 0.00 1.82
539 552 8.533657 TGATCATGTAGCATTCTTTTTGGATTT 58.466 29.630 0.00 0.00 0.00 2.17
540 553 8.070034 TGATCATGTAGCATTCTTTTTGGATT 57.930 30.769 0.00 0.00 0.00 3.01
541 554 7.649533 TGATCATGTAGCATTCTTTTTGGAT 57.350 32.000 0.00 0.00 0.00 3.41
542 555 7.649533 ATGATCATGTAGCATTCTTTTTGGA 57.350 32.000 7.59 0.00 26.62 3.53
543 556 9.406828 CATATGATCATGTAGCATTCTTTTTGG 57.593 33.333 18.72 0.00 35.38 3.28
544 557 9.406828 CCATATGATCATGTAGCATTCTTTTTG 57.593 33.333 18.72 0.00 35.38 2.44
545 558 9.358406 TCCATATGATCATGTAGCATTCTTTTT 57.642 29.630 18.72 0.00 35.38 1.94
546 559 8.929260 TCCATATGATCATGTAGCATTCTTTT 57.071 30.769 18.72 0.00 35.38 2.27
547 560 8.957466 CATCCATATGATCATGTAGCATTCTTT 58.043 33.333 18.72 0.00 35.38 2.52
548 561 8.107729 ACATCCATATGATCATGTAGCATTCTT 58.892 33.333 18.72 0.00 35.38 2.52
549 562 7.631007 ACATCCATATGATCATGTAGCATTCT 58.369 34.615 18.72 0.00 35.38 2.40
550 563 7.860918 ACATCCATATGATCATGTAGCATTC 57.139 36.000 18.72 0.00 35.38 2.67
552 565 9.993454 GTATACATCCATATGATCATGTAGCAT 57.007 33.333 18.72 0.00 35.67 3.79
553 566 9.205513 AGTATACATCCATATGATCATGTAGCA 57.794 33.333 18.72 0.00 35.67 3.49
577 590 9.132521 GACAAACTTTACACATACGTATGTAGT 57.867 33.333 34.24 31.32 44.57 2.73
578 591 8.309019 CGACAAACTTTACACATACGTATGTAG 58.691 37.037 34.24 28.92 44.57 2.74
579 592 8.020244 TCGACAAACTTTACACATACGTATGTA 58.980 33.333 34.24 21.09 44.57 2.29
581 594 7.268186 TCGACAAACTTTACACATACGTATG 57.732 36.000 29.48 29.48 39.55 2.39
582 595 7.756272 TCATCGACAAACTTTACACATACGTAT 59.244 33.333 1.14 1.14 0.00 3.06
583 596 7.083230 TCATCGACAAACTTTACACATACGTA 58.917 34.615 0.00 0.00 0.00 3.57
584 597 5.921976 TCATCGACAAACTTTACACATACGT 59.078 36.000 0.00 0.00 0.00 3.57
585 598 6.384178 TCATCGACAAACTTTACACATACG 57.616 37.500 0.00 0.00 0.00 3.06
588 601 9.825972 CTTATTTCATCGACAAACTTTACACAT 57.174 29.630 0.00 0.00 0.00 3.21
589 602 8.832521 ACTTATTTCATCGACAAACTTTACACA 58.167 29.630 0.00 0.00 0.00 3.72
596 609 9.825972 CATGTTTACTTATTTCATCGACAAACT 57.174 29.630 0.00 0.00 0.00 2.66
597 610 9.607285 ACATGTTTACTTATTTCATCGACAAAC 57.393 29.630 0.00 0.00 0.00 2.93
601 614 9.422196 GCTTACATGTTTACTTATTTCATCGAC 57.578 33.333 2.30 0.00 0.00 4.20
602 615 9.378551 AGCTTACATGTTTACTTATTTCATCGA 57.621 29.630 2.30 0.00 0.00 3.59
642 655 9.783081 ATTTTGGAAAGATGAATAGTGCTTTTT 57.217 25.926 0.00 0.00 31.30 1.94
643 656 9.428097 GATTTTGGAAAGATGAATAGTGCTTTT 57.572 29.630 0.00 0.00 31.30 2.27
644 657 8.587608 TGATTTTGGAAAGATGAATAGTGCTTT 58.412 29.630 0.00 0.00 33.62 3.51
645 658 8.125978 TGATTTTGGAAAGATGAATAGTGCTT 57.874 30.769 0.00 0.00 0.00 3.91
646 659 7.147949 CCTGATTTTGGAAAGATGAATAGTGCT 60.148 37.037 0.00 0.00 0.00 4.40
647 660 6.976925 CCTGATTTTGGAAAGATGAATAGTGC 59.023 38.462 0.00 0.00 0.00 4.40
648 661 8.284945 TCCTGATTTTGGAAAGATGAATAGTG 57.715 34.615 0.00 0.00 0.00 2.74
649 662 9.484806 AATCCTGATTTTGGAAAGATGAATAGT 57.515 29.630 0.00 0.00 37.13 2.12
653 666 9.312904 ACTAAATCCTGATTTTGGAAAGATGAA 57.687 29.630 10.15 0.00 40.99 2.57
654 667 8.884124 ACTAAATCCTGATTTTGGAAAGATGA 57.116 30.769 10.15 0.00 40.99 2.92
655 668 8.742777 TGACTAAATCCTGATTTTGGAAAGATG 58.257 33.333 10.15 0.00 40.99 2.90
656 669 8.884124 TGACTAAATCCTGATTTTGGAAAGAT 57.116 30.769 10.15 0.00 40.99 2.40
657 670 8.884124 ATGACTAAATCCTGATTTTGGAAAGA 57.116 30.769 10.15 0.00 40.99 2.52
658 671 9.933723 AAATGACTAAATCCTGATTTTGGAAAG 57.066 29.630 10.15 4.57 40.99 2.62
689 702 7.749126 GTGCAAATAAGTAACCATGTGAGTTAC 59.251 37.037 12.83 12.83 46.45 2.50
690 703 7.445707 TGTGCAAATAAGTAACCATGTGAGTTA 59.554 33.333 0.00 0.00 0.00 2.24
691 704 6.264292 TGTGCAAATAAGTAACCATGTGAGTT 59.736 34.615 0.00 0.00 0.00 3.01
692 705 5.767665 TGTGCAAATAAGTAACCATGTGAGT 59.232 36.000 0.00 0.00 0.00 3.41
693 706 6.252967 TGTGCAAATAAGTAACCATGTGAG 57.747 37.500 0.00 0.00 0.00 3.51
694 707 6.432472 TGATGTGCAAATAAGTAACCATGTGA 59.568 34.615 0.00 0.00 0.00 3.58
695 708 6.619744 TGATGTGCAAATAAGTAACCATGTG 58.380 36.000 0.00 0.00 0.00 3.21
696 709 6.832520 TGATGTGCAAATAAGTAACCATGT 57.167 33.333 0.00 0.00 0.00 3.21
697 710 8.531622 TTTTGATGTGCAAATAAGTAACCATG 57.468 30.769 0.00 0.00 45.30 3.66
698 711 9.723601 AATTTTGATGTGCAAATAAGTAACCAT 57.276 25.926 0.00 0.00 45.30 3.55
699 712 9.553064 AAATTTTGATGTGCAAATAAGTAACCA 57.447 25.926 0.00 0.00 45.30 3.67
700 713 9.810231 CAAATTTTGATGTGCAAATAAGTAACC 57.190 29.630 2.88 0.00 45.30 2.85
701 714 9.316859 GCAAATTTTGATGTGCAAATAAGTAAC 57.683 29.630 13.26 0.00 45.30 2.50
702 715 9.049523 TGCAAATTTTGATGTGCAAATAAGTAA 57.950 25.926 13.26 0.00 45.30 2.24
703 716 8.599055 TGCAAATTTTGATGTGCAAATAAGTA 57.401 26.923 13.26 0.00 45.30 2.24
704 717 7.493743 TGCAAATTTTGATGTGCAAATAAGT 57.506 28.000 13.26 0.00 45.30 2.24
711 724 4.127907 ACATGTGCAAATTTTGATGTGCA 58.872 34.783 13.26 0.00 44.36 4.57
712 725 4.735662 ACATGTGCAAATTTTGATGTGC 57.264 36.364 13.26 0.00 37.51 4.57
811 824 8.356657 CGGGTGCATTGAAATCCTATATTTTTA 58.643 33.333 0.00 0.00 0.00 1.52
812 825 7.147742 ACGGGTGCATTGAAATCCTATATTTTT 60.148 33.333 0.00 0.00 0.00 1.94
813 826 6.323739 ACGGGTGCATTGAAATCCTATATTTT 59.676 34.615 0.00 0.00 0.00 1.82
814 827 5.833131 ACGGGTGCATTGAAATCCTATATTT 59.167 36.000 0.00 0.00 0.00 1.40
815 828 5.385198 ACGGGTGCATTGAAATCCTATATT 58.615 37.500 0.00 0.00 0.00 1.28
816 829 4.985538 ACGGGTGCATTGAAATCCTATAT 58.014 39.130 0.00 0.00 0.00 0.86
817 830 4.385825 GACGGGTGCATTGAAATCCTATA 58.614 43.478 0.00 0.00 0.00 1.31
818 831 3.214328 GACGGGTGCATTGAAATCCTAT 58.786 45.455 0.00 0.00 0.00 2.57
819 832 2.639065 GACGGGTGCATTGAAATCCTA 58.361 47.619 0.00 0.00 0.00 2.94
820 833 1.463674 GACGGGTGCATTGAAATCCT 58.536 50.000 0.00 0.00 0.00 3.24
821 834 0.455815 GGACGGGTGCATTGAAATCC 59.544 55.000 0.00 0.00 0.00 3.01
822 835 1.401905 GAGGACGGGTGCATTGAAATC 59.598 52.381 0.00 0.00 0.00 2.17
823 836 1.004745 AGAGGACGGGTGCATTGAAAT 59.995 47.619 0.00 0.00 0.00 2.17
824 837 0.400213 AGAGGACGGGTGCATTGAAA 59.600 50.000 0.00 0.00 0.00 2.69
825 838 1.271856 TAGAGGACGGGTGCATTGAA 58.728 50.000 0.00 0.00 0.00 2.69
826 839 1.271856 TTAGAGGACGGGTGCATTGA 58.728 50.000 0.00 0.00 0.00 2.57
827 840 2.107950 TTTAGAGGACGGGTGCATTG 57.892 50.000 0.00 0.00 0.00 2.82
828 841 2.871096 TTTTAGAGGACGGGTGCATT 57.129 45.000 0.00 0.00 0.00 3.56
829 842 2.238646 TCATTTTAGAGGACGGGTGCAT 59.761 45.455 0.00 0.00 0.00 3.96
830 843 1.626321 TCATTTTAGAGGACGGGTGCA 59.374 47.619 0.00 0.00 0.00 4.57
831 844 2.007608 GTCATTTTAGAGGACGGGTGC 58.992 52.381 0.00 0.00 0.00 5.01
832 845 3.611766 AGTCATTTTAGAGGACGGGTG 57.388 47.619 0.00 0.00 36.68 4.61
833 846 4.635699 AAAGTCATTTTAGAGGACGGGT 57.364 40.909 0.00 0.00 36.68 5.28
834 847 5.472137 TCAAAAAGTCATTTTAGAGGACGGG 59.528 40.000 0.00 0.00 39.20 5.28
835 848 6.371389 GTCAAAAAGTCATTTTAGAGGACGG 58.629 40.000 0.00 0.00 39.20 4.79
836 849 6.071463 CGTCAAAAAGTCATTTTAGAGGACG 58.929 40.000 8.50 8.50 39.20 4.79
837 850 5.851703 GCGTCAAAAAGTCATTTTAGAGGAC 59.148 40.000 0.00 0.00 39.20 3.85
838 851 5.529430 TGCGTCAAAAAGTCATTTTAGAGGA 59.471 36.000 0.00 0.00 39.20 3.71
839 852 5.757886 TGCGTCAAAAAGTCATTTTAGAGG 58.242 37.500 0.00 0.00 39.20 3.69
840 853 6.912591 ACTTGCGTCAAAAAGTCATTTTAGAG 59.087 34.615 0.00 0.00 39.20 2.43
841 854 6.791303 ACTTGCGTCAAAAAGTCATTTTAGA 58.209 32.000 0.00 0.00 39.20 2.10
842 855 8.555166 TTACTTGCGTCAAAAAGTCATTTTAG 57.445 30.769 0.00 0.00 39.20 1.85
843 856 8.912787 TTTACTTGCGTCAAAAAGTCATTTTA 57.087 26.923 0.00 0.00 39.20 1.52
844 857 7.820044 TTTACTTGCGTCAAAAAGTCATTTT 57.180 28.000 0.00 0.00 41.93 1.82
845 858 7.820044 TTTTACTTGCGTCAAAAAGTCATTT 57.180 28.000 0.00 0.00 37.74 2.32
846 859 8.419076 AATTTTACTTGCGTCAAAAAGTCATT 57.581 26.923 0.00 0.00 37.74 2.57
847 860 8.419076 AAATTTTACTTGCGTCAAAAAGTCAT 57.581 26.923 0.00 0.00 37.74 3.06
848 861 7.820044 AAATTTTACTTGCGTCAAAAAGTCA 57.180 28.000 0.00 0.00 37.74 3.41
849 862 8.376942 TGAAAATTTTACTTGCGTCAAAAAGTC 58.623 29.630 2.75 0.00 37.74 3.01
850 863 8.245701 TGAAAATTTTACTTGCGTCAAAAAGT 57.754 26.923 2.75 0.00 39.82 2.66
851 864 7.845622 CCTGAAAATTTTACTTGCGTCAAAAAG 59.154 33.333 2.75 0.00 0.00 2.27
852 865 7.332182 ACCTGAAAATTTTACTTGCGTCAAAAA 59.668 29.630 2.75 0.00 0.00 1.94
853 866 6.814146 ACCTGAAAATTTTACTTGCGTCAAAA 59.186 30.769 2.75 0.00 0.00 2.44
854 867 6.334202 ACCTGAAAATTTTACTTGCGTCAAA 58.666 32.000 2.75 0.00 0.00 2.69
863 876 8.706322 AACATGAGGTACCTGAAAATTTTACT 57.294 30.769 22.10 0.00 0.00 2.24
866 879 8.088365 GCTAAACATGAGGTACCTGAAAATTTT 58.912 33.333 22.10 12.62 0.00 1.82
870 883 5.626142 TGCTAAACATGAGGTACCTGAAAA 58.374 37.500 22.10 2.06 0.00 2.29
876 889 4.672409 GCATTTGCTAAACATGAGGTACC 58.328 43.478 2.73 2.73 38.21 3.34
883 898 5.573296 TTTTCACGCATTTGCTAAACATG 57.427 34.783 0.51 0.00 39.32 3.21
918 934 2.048222 CCAGTCGTGTGCGGTCAT 60.048 61.111 0.00 0.00 38.89 3.06
930 946 1.071605 GAATGTCAGTCGTGCCAGTC 58.928 55.000 0.00 0.00 0.00 3.51
960 976 1.282570 CTGCGCAACGGTTTGATGT 59.717 52.632 13.05 0.00 34.24 3.06
968 984 1.897398 GAGGTACAACTGCGCAACGG 61.897 60.000 13.05 5.87 0.00 4.44
1022 1041 1.681780 CCGTATGAATGGTTGGTGGCT 60.682 52.381 0.00 0.00 0.00 4.75
1076 1095 1.383248 AGGAGGCATAGGGAGCGTT 60.383 57.895 0.00 0.00 0.00 4.84
1112 1131 3.147595 CGGACGAGCCATGGAGGA 61.148 66.667 18.40 0.00 41.22 3.71
1178 1197 2.305853 CGGAATCGCTGCTCCATCG 61.306 63.158 7.14 0.00 0.00 3.84
1270 1289 1.256376 CTCGATGTAGCGCATGTTGTC 59.744 52.381 11.47 0.00 38.06 3.18
1276 1295 2.029666 GGCCTCGATGTAGCGCAT 59.970 61.111 11.47 0.00 41.24 4.73
1423 1445 2.224378 GGGTGGTGATCATCATCATCGT 60.224 50.000 20.66 0.00 39.47 3.73
1531 1553 4.421479 CGTGACGGCGCCTCTCTT 62.421 66.667 26.68 2.59 0.00 2.85
1655 1682 1.975680 TGTGTTTACAGGGAGGAGGAC 59.024 52.381 0.00 0.00 31.91 3.85
1656 1683 2.409064 TGTGTTTACAGGGAGGAGGA 57.591 50.000 0.00 0.00 31.91 3.71
1686 1713 3.544615 CATGCAAGCATGTGGATCG 57.455 52.632 23.25 0.00 46.20 3.69
1746 1785 8.503196 TGTATGACAGTTAAGTAAGCAATTGTG 58.497 33.333 7.40 0.00 0.00 3.33
1770 1809 5.220854 GCTCAGTTGACAATTAACAGTGTGT 60.221 40.000 0.00 0.00 29.18 3.72
1791 1830 7.332182 GGCCAACTGTCTAATACTATAATGCTC 59.668 40.741 0.00 0.00 0.00 4.26
1882 1951 3.246112 CCTGGACCCCACCGACAA 61.246 66.667 0.00 0.00 0.00 3.18
1885 1954 4.585216 AACCCTGGACCCCACCGA 62.585 66.667 0.00 0.00 0.00 4.69
1886 1955 3.576259 AAACCCTGGACCCCACCG 61.576 66.667 0.00 0.00 0.00 4.94
1887 1956 2.014033 TTCAAACCCTGGACCCCACC 62.014 60.000 0.00 0.00 0.00 4.61
1889 1958 0.863956 ATTTCAAACCCTGGACCCCA 59.136 50.000 0.00 0.00 0.00 4.96
1890 1959 2.024176 AATTTCAAACCCTGGACCCC 57.976 50.000 0.00 0.00 0.00 4.95
1923 1992 6.183360 CGGTCAGTTCGATAAGGTCTAAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
1929 1998 1.749634 CCGGTCAGTTCGATAAGGTCT 59.250 52.381 0.00 0.00 0.00 3.85
1937 2006 5.754543 AAAATAAAAACCGGTCAGTTCGA 57.245 34.783 8.04 0.00 0.00 3.71
1961 2030 7.432252 GGTGATGTTATTCGAATCATTTCCAAC 59.568 37.037 15.25 11.81 33.19 3.77
1962 2031 7.121907 TGGTGATGTTATTCGAATCATTTCCAA 59.878 33.333 15.25 0.00 33.19 3.53
1963 2032 6.601217 TGGTGATGTTATTCGAATCATTTCCA 59.399 34.615 15.25 18.62 33.19 3.53
1964 2033 7.026631 TGGTGATGTTATTCGAATCATTTCC 57.973 36.000 15.25 16.72 33.19 3.13
2085 2160 2.878406 CGACCATCACAAGGTTCAAACT 59.122 45.455 0.00 0.00 40.09 2.66
2086 2161 2.875933 TCGACCATCACAAGGTTCAAAC 59.124 45.455 0.00 0.00 40.09 2.93
2097 2172 6.091849 CCTCAAATCATATGATCGACCATCAC 59.908 42.308 18.44 0.00 44.70 3.06
2133 2208 8.034058 ACTATGAGATAAAATTTGATAGCCGC 57.966 34.615 0.00 0.00 0.00 6.53
2393 2468 1.157870 AAGTGTCGTCCTTTGCCGTG 61.158 55.000 0.00 0.00 0.00 4.94
2675 2750 1.930656 CCCCCACTTCTCACCCCAT 60.931 63.158 0.00 0.00 0.00 4.00
2693 2768 4.223953 TCATTCTGAGGTACCCACTATCC 58.776 47.826 8.74 0.00 0.00 2.59
2762 2837 2.045340 AACGGGAAAGATGGCCGG 60.045 61.111 0.00 0.00 0.00 6.13
2806 2881 3.230976 AGGGAAAGAACAATGAACCCAC 58.769 45.455 0.00 0.00 38.42 4.61
2808 2883 3.444034 GCTAGGGAAAGAACAATGAACCC 59.556 47.826 0.00 0.00 36.47 4.11
2868 2943 8.962111 GCACGTATTAACTACCTTACAAGTATC 58.038 37.037 0.00 0.00 0.00 2.24
2978 3053 9.632638 AGCCTAAAAGCTCATAGAAAAATCATA 57.367 29.630 7.19 0.00 39.48 2.15
3020 3095 4.974645 AGTGACTTGACCTATTGGACAA 57.025 40.909 10.18 10.18 43.54 3.18
3046 3121 2.281761 CACCAGTCAGGCCCACAC 60.282 66.667 0.00 0.00 43.14 3.82
3055 3130 3.826524 TCCATAAAGTTTGCACCAGTCA 58.173 40.909 0.00 0.00 0.00 3.41
3070 3145 8.052748 ACCACATGTAGCTTCTAAATTCCATAA 58.947 33.333 0.00 0.00 0.00 1.90
3072 3147 6.426587 ACCACATGTAGCTTCTAAATTCCAT 58.573 36.000 0.00 0.00 0.00 3.41
3094 3169 3.067461 AGTCATCTCAATCTCGCTGTACC 59.933 47.826 0.00 0.00 0.00 3.34
3101 3176 5.124776 GGTCCCTATAGTCATCTCAATCTCG 59.875 48.000 0.00 0.00 0.00 4.04
3127 3202 1.007271 CAGGTGAGCGGCGTATAGG 60.007 63.158 9.37 0.00 0.00 2.57
3128 3203 1.007271 CCAGGTGAGCGGCGTATAG 60.007 63.158 9.37 0.00 0.00 1.31
3129 3204 2.495409 CCCAGGTGAGCGGCGTATA 61.495 63.158 9.37 0.00 0.00 1.47
3130 3205 3.849951 CCCAGGTGAGCGGCGTAT 61.850 66.667 9.37 0.00 0.00 3.06
3152 4928 2.267351 CCCGTGCACTGCAAATGGA 61.267 57.895 16.19 0.00 41.47 3.41
3185 4961 8.215926 TCCTTTTTCTTCTTTTTATCACGTCA 57.784 30.769 0.00 0.00 0.00 4.35
3240 5016 1.079127 GCTTCCGCTACTTGCAGGA 60.079 57.895 1.40 0.00 43.06 3.86
3280 5057 7.772332 ATCTAATACTAAAACTTGCCTCACG 57.228 36.000 0.00 0.00 0.00 4.35
3385 5166 0.179108 GACCTCGGTTCAATCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
3577 5360 6.976636 TTGTTTGGGTTTCATGAAAAGTTC 57.023 33.333 22.07 9.89 31.33 3.01
3706 5495 7.462109 TGTTCGTGATTTGAAAAGGAAATTG 57.538 32.000 0.00 0.00 0.00 2.32
3708 5497 8.661352 ATTTGTTCGTGATTTGAAAAGGAAAT 57.339 26.923 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.