Multiple sequence alignment - TraesCS3D01G309900

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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 TraesCS3D01G309900 chr3D 100.000 5459 0 0 1 5459 424007746 424013204 0.000000e+00 10081
1 TraesCS3D01G309900 chr3B 93.787 4732 202 23 812 5459 552233418 552228695 0.000000e+00 7025
2 TraesCS3D01G309900 chr3B 84.553 615 40 15 2 592 552234212 552233629 4.780000e-155 558
3 TraesCS3D01G309900 chr3A 93.261 4719 217 30 813 5459 564946919 564942230 0.000000e+00 6859
4 TraesCS3D01G309900 chr3A 90.438 502 28 7 20 512 564947655 564947165 1.280000e-180 643


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 TraesCS3D01G309900 chr3D 424007746 424013204 5458 False 10081.0 10081 100.0000 1 5459 1 chr3D.!!$F1 5458
1 TraesCS3D01G309900 chr3B 552228695 552234212 5517 True 3791.5 7025 89.1700 2 5459 2 chr3B.!!$R1 5457
2 TraesCS3D01G309900 chr3A 564942230 564947655 5425 True 3751.0 6859 91.8495 20 5459 2 chr3A.!!$R1 5439

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
300 307 0.531090 CTCCTCATGCTGCTCTGCTC 60.531 60.0 0.0 0.0 0.0 4.26 F
650 775 0.535335 GGGACGATGCTTAGTGGACA 59.465 55.0 0.0 0.0 0.0 4.02 F
820 945 0.620556 TCCAGCATTCTCTTGGTCCC 59.379 55.0 0.0 0.0 0.0 4.46 F
910 1043 0.904865 ACCTGGCATTCGGTCTCTCA 60.905 55.0 0.0 0.0 0.0 3.27 F
2074 2243 1.017387 GTTCGGCAGATCATGTTCCC 58.983 55.0 0.0 0.0 0.0 3.97 F
3217 3391 0.477597 TCCCATCCCCAACCTTGACT 60.478 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 1419 0.462581 AATGCCGATGACAGTGCGAT 60.463 50.000 0.00 0.0 0.00 4.58 R
1480 1649 1.101049 CGCCCACAAGTTTCTGGTGT 61.101 55.000 3.99 0.0 33.83 4.16 R
2110 2279 2.545532 CGAGATGTCCTCTGCTTCCATC 60.546 54.545 0.00 0.0 39.78 3.51 R
2817 2988 2.562738 TCAGCAGGAGTTTCTGAATCGA 59.437 45.455 0.00 0.0 36.93 3.59 R
3772 3946 0.674895 CTTTCTCTGTTGGCCCTCCG 60.675 60.000 0.00 0.0 34.14 4.63 R
5081 5300 0.107017 CCAATGGAATGGCGGACTCT 60.107 55.000 0.00 0.0 32.78 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
29 36 1.671261 GCAGCAGTGAGTGACCACTAG 60.671 57.143 2.23 0.00 44.87 2.57
53 60 3.746492 CCAACTAAAACCAAGAGACGGAG 59.254 47.826 0.00 0.00 0.00 4.63
223 230 1.924629 GCTTTCGGTTTTGGCTCGTTC 60.925 52.381 0.00 0.00 0.00 3.95
286 293 3.118112 TCATCATTTTGCTCCTCCTCCTC 60.118 47.826 0.00 0.00 0.00 3.71
300 307 0.531090 CTCCTCATGCTGCTCTGCTC 60.531 60.000 0.00 0.00 0.00 4.26
344 362 1.227704 TTTTTGGCGTCTGCTCCGA 60.228 52.632 0.00 0.00 42.25 4.55
399 422 3.653344 CTGATTATCGGCTTGGATCGAA 58.347 45.455 0.00 0.00 38.92 3.71
431 454 6.308675 GTTCTACTAATTCTATCTCCGCTCG 58.691 44.000 0.00 0.00 0.00 5.03
448 471 1.200020 CTCGGCCTGTGATTTTGTTCC 59.800 52.381 0.00 0.00 0.00 3.62
482 505 5.215160 CGTGATTTGAGCTTAGTTTGCTTT 58.785 37.500 0.00 0.00 41.30 3.51
484 507 5.340667 GTGATTTGAGCTTAGTTTGCTTTCG 59.659 40.000 0.00 0.00 41.30 3.46
487 510 2.224426 TGAGCTTAGTTTGCTTTCGGGA 60.224 45.455 0.00 0.00 41.30 5.14
497 520 1.134220 TGCTTTCGGGACAGTGTCTTT 60.134 47.619 22.18 0.00 32.47 2.52
512 535 4.646492 AGTGTCTTTCAACTTGCAAGGAAT 59.354 37.500 29.18 13.04 0.00 3.01
518 541 6.545666 TCTTTCAACTTGCAAGGAATCAACTA 59.454 34.615 29.18 7.94 0.00 2.24
520 543 6.258230 TCAACTTGCAAGGAATCAACTATG 57.742 37.500 29.18 11.90 0.00 2.23
521 544 4.708726 ACTTGCAAGGAATCAACTATGC 57.291 40.909 29.18 0.00 0.00 3.14
522 545 4.338879 ACTTGCAAGGAATCAACTATGCT 58.661 39.130 29.18 0.93 34.97 3.79
524 547 5.945784 ACTTGCAAGGAATCAACTATGCTTA 59.054 36.000 29.18 0.00 34.97 3.09
525 548 5.818136 TGCAAGGAATCAACTATGCTTAC 57.182 39.130 0.00 0.00 34.97 2.34
532 559 5.652452 GGAATCAACTATGCTTACCCTGTTT 59.348 40.000 0.00 0.00 0.00 2.83
537 564 6.430000 TCAACTATGCTTACCCTGTTTCTTTC 59.570 38.462 0.00 0.00 0.00 2.62
538 565 5.254115 ACTATGCTTACCCTGTTTCTTTCC 58.746 41.667 0.00 0.00 0.00 3.13
541 568 5.313280 TGCTTACCCTGTTTCTTTCCTTA 57.687 39.130 0.00 0.00 0.00 2.69
546 573 7.415318 GCTTACCCTGTTTCTTTCCTTATTAGC 60.415 40.741 0.00 0.00 0.00 3.09
550 577 7.039714 ACCCTGTTTCTTTCCTTATTAGCTTTG 60.040 37.037 0.00 0.00 0.00 2.77
552 579 8.743714 CCTGTTTCTTTCCTTATTAGCTTTGAT 58.256 33.333 0.00 0.00 0.00 2.57
556 583 8.877864 TTCTTTCCTTATTAGCTTTGATTCCA 57.122 30.769 0.00 0.00 0.00 3.53
562 589 4.931661 ATTAGCTTTGATTCCATGGCTG 57.068 40.909 6.96 0.00 34.24 4.85
563 590 0.822164 AGCTTTGATTCCATGGCTGC 59.178 50.000 6.96 3.29 32.24 5.25
564 591 0.822164 GCTTTGATTCCATGGCTGCT 59.178 50.000 6.96 0.00 0.00 4.24
589 617 4.763073 TGCTTGATTCTGTACTCATCCTG 58.237 43.478 0.00 0.00 0.00 3.86
590 618 4.467438 TGCTTGATTCTGTACTCATCCTGA 59.533 41.667 0.00 0.00 0.00 3.86
591 619 5.129980 TGCTTGATTCTGTACTCATCCTGAT 59.870 40.000 0.00 0.00 0.00 2.90
592 620 5.466058 GCTTGATTCTGTACTCATCCTGATG 59.534 44.000 0.55 0.55 40.09 3.07
593 621 6.684865 GCTTGATTCTGTACTCATCCTGATGA 60.685 42.308 9.35 9.35 44.83 2.92
594 622 6.990908 TGATTCTGTACTCATCCTGATGAT 57.009 37.500 10.10 4.38 45.74 2.45
595 623 7.370905 TGATTCTGTACTCATCCTGATGATT 57.629 36.000 10.10 7.62 45.74 2.57
597 625 7.930325 TGATTCTGTACTCATCCTGATGATTTC 59.070 37.037 10.10 4.19 45.74 2.17
598 626 7.429374 TTCTGTACTCATCCTGATGATTTCT 57.571 36.000 10.10 0.00 45.74 2.52
600 628 7.270779 TCTGTACTCATCCTGATGATTTCTTG 58.729 38.462 10.10 1.12 45.74 3.02
602 630 4.789807 ACTCATCCTGATGATTTCTTGGG 58.210 43.478 10.10 0.00 45.74 4.12
603 631 4.142790 CTCATCCTGATGATTTCTTGGGG 58.857 47.826 10.10 0.00 45.74 4.96
606 634 5.612261 TCATCCTGATGATTTCTTGGGGATA 59.388 40.000 5.74 0.00 42.42 2.59
607 635 5.310409 TCCTGATGATTTCTTGGGGATAC 57.690 43.478 0.00 0.00 0.00 2.24
608 636 4.067896 CCTGATGATTTCTTGGGGATACG 58.932 47.826 0.00 0.00 37.60 3.06
609 637 4.067896 CTGATGATTTCTTGGGGATACGG 58.932 47.826 0.00 0.00 37.60 4.02
610 638 3.458118 TGATGATTTCTTGGGGATACGGT 59.542 43.478 0.00 0.00 37.60 4.83
611 639 3.275617 TGATTTCTTGGGGATACGGTG 57.724 47.619 0.00 0.00 37.60 4.94
612 640 1.947456 GATTTCTTGGGGATACGGTGC 59.053 52.381 0.00 0.00 37.60 5.01
613 641 0.988832 TTTCTTGGGGATACGGTGCT 59.011 50.000 0.00 0.00 37.60 4.40
614 642 1.868713 TTCTTGGGGATACGGTGCTA 58.131 50.000 0.00 0.00 37.60 3.49
615 643 1.868713 TCTTGGGGATACGGTGCTAA 58.131 50.000 0.00 0.00 37.60 3.09
623 651 4.020485 GGGGATACGGTGCTAATTCTATGT 60.020 45.833 0.00 0.00 37.60 2.29
626 654 5.279306 GGATACGGTGCTAATTCTATGTGGA 60.279 44.000 0.00 0.00 0.00 4.02
635 663 6.321181 TGCTAATTCTATGTGGAATTTGGGAC 59.679 38.462 9.19 0.00 41.42 4.46
636 664 5.835113 AATTCTATGTGGAATTTGGGACG 57.165 39.130 0.00 0.00 41.42 4.79
637 665 4.561500 TTCTATGTGGAATTTGGGACGA 57.438 40.909 0.00 0.00 0.00 4.20
638 666 4.771114 TCTATGTGGAATTTGGGACGAT 57.229 40.909 0.00 0.00 0.00 3.73
639 667 4.450976 TCTATGTGGAATTTGGGACGATG 58.549 43.478 0.00 0.00 0.00 3.84
640 668 1.173043 TGTGGAATTTGGGACGATGC 58.827 50.000 0.00 0.00 0.00 3.91
641 669 1.271871 TGTGGAATTTGGGACGATGCT 60.272 47.619 0.00 0.00 0.00 3.79
642 670 1.818674 GTGGAATTTGGGACGATGCTT 59.181 47.619 0.00 0.00 0.00 3.91
643 671 3.013921 GTGGAATTTGGGACGATGCTTA 58.986 45.455 0.00 0.00 0.00 3.09
650 775 0.535335 GGGACGATGCTTAGTGGACA 59.465 55.000 0.00 0.00 0.00 4.02
655 780 3.458189 ACGATGCTTAGTGGACATTAGC 58.542 45.455 0.00 0.00 0.00 3.09
660 785 3.274288 GCTTAGTGGACATTAGCTGCTT 58.726 45.455 7.79 0.00 0.00 3.91
667 792 3.129871 GGACATTAGCTGCTTAGCTCTG 58.870 50.000 7.79 7.49 45.00 3.35
672 797 2.383368 AGCTGCTTAGCTCTGAACAG 57.617 50.000 5.60 0.00 42.12 3.16
678 803 2.413453 GCTTAGCTCTGAACAGGTTTCG 59.587 50.000 0.00 0.00 0.00 3.46
682 807 1.884235 CTCTGAACAGGTTTCGGCTT 58.116 50.000 1.93 0.00 0.00 4.35
686 811 2.737252 CTGAACAGGTTTCGGCTTACTC 59.263 50.000 0.00 0.00 0.00 2.59
687 812 2.367567 TGAACAGGTTTCGGCTTACTCT 59.632 45.455 0.00 0.00 0.00 3.24
688 813 2.457366 ACAGGTTTCGGCTTACTCTG 57.543 50.000 0.00 0.00 0.00 3.35
716 841 7.392673 GGATCATCTGTCCTGCATAATTTATGT 59.607 37.037 15.88 0.00 34.48 2.29
717 842 7.734924 TCATCTGTCCTGCATAATTTATGTC 57.265 36.000 15.88 9.89 38.43 3.06
718 843 6.712095 TCATCTGTCCTGCATAATTTATGTCC 59.288 38.462 15.88 3.45 38.43 4.02
719 844 5.056480 TCTGTCCTGCATAATTTATGTCCG 58.944 41.667 15.88 6.73 38.43 4.79
720 845 4.776349 TGTCCTGCATAATTTATGTCCGT 58.224 39.130 15.88 0.00 38.43 4.69
721 846 4.574421 TGTCCTGCATAATTTATGTCCGTG 59.426 41.667 15.88 3.78 38.43 4.94
722 847 3.563808 TCCTGCATAATTTATGTCCGTGC 59.436 43.478 15.88 4.77 38.43 5.34
723 848 3.565482 CCTGCATAATTTATGTCCGTGCT 59.435 43.478 15.88 0.00 38.43 4.40
724 849 4.036734 CCTGCATAATTTATGTCCGTGCTT 59.963 41.667 15.88 0.00 38.43 3.91
725 850 5.168526 TGCATAATTTATGTCCGTGCTTC 57.831 39.130 15.88 0.00 38.43 3.86
726 851 4.881273 TGCATAATTTATGTCCGTGCTTCT 59.119 37.500 15.88 0.00 38.43 2.85
727 852 5.007626 TGCATAATTTATGTCCGTGCTTCTC 59.992 40.000 15.88 0.00 38.43 2.87
728 853 5.560953 GCATAATTTATGTCCGTGCTTCTCC 60.561 44.000 15.88 0.00 38.43 3.71
729 854 3.627395 ATTTATGTCCGTGCTTCTCCA 57.373 42.857 0.00 0.00 0.00 3.86
730 855 2.672961 TTATGTCCGTGCTTCTCCAG 57.327 50.000 0.00 0.00 0.00 3.86
744 869 6.552859 GCTTCTCCAGCTATTATTTTCCTC 57.447 41.667 0.00 0.00 46.27 3.71
745 870 5.471797 GCTTCTCCAGCTATTATTTTCCTCC 59.528 44.000 0.00 0.00 46.27 4.30
746 871 5.215252 TCTCCAGCTATTATTTTCCTCCG 57.785 43.478 0.00 0.00 0.00 4.63
747 872 4.899457 TCTCCAGCTATTATTTTCCTCCGA 59.101 41.667 0.00 0.00 0.00 4.55
748 873 5.365605 TCTCCAGCTATTATTTTCCTCCGAA 59.634 40.000 0.00 0.00 0.00 4.30
749 874 5.996644 TCCAGCTATTATTTTCCTCCGAAA 58.003 37.500 0.00 0.00 36.18 3.46
774 899 9.952030 AAAAACCTTTTCTTTTATTCCTGTTCA 57.048 25.926 0.00 0.00 0.00 3.18
776 901 9.546428 AAACCTTTTCTTTTATTCCTGTTCATG 57.454 29.630 0.00 0.00 0.00 3.07
777 902 8.250143 ACCTTTTCTTTTATTCCTGTTCATGT 57.750 30.769 0.00 0.00 0.00 3.21
778 903 8.143835 ACCTTTTCTTTTATTCCTGTTCATGTG 58.856 33.333 0.00 0.00 0.00 3.21
779 904 8.359642 CCTTTTCTTTTATTCCTGTTCATGTGA 58.640 33.333 0.00 0.00 0.00 3.58
780 905 9.403110 CTTTTCTTTTATTCCTGTTCATGTGAG 57.597 33.333 0.00 0.00 0.00 3.51
781 906 8.690203 TTTCTTTTATTCCTGTTCATGTGAGA 57.310 30.769 0.00 0.00 0.00 3.27
782 907 8.868522 TTCTTTTATTCCTGTTCATGTGAGAT 57.131 30.769 0.00 0.00 0.00 2.75
783 908 8.272545 TCTTTTATTCCTGTTCATGTGAGATG 57.727 34.615 0.00 0.00 0.00 2.90
784 909 7.337689 TCTTTTATTCCTGTTCATGTGAGATGG 59.662 37.037 0.00 0.00 0.00 3.51
785 910 2.408271 TCCTGTTCATGTGAGATGGC 57.592 50.000 0.00 0.00 0.00 4.40
786 911 1.911357 TCCTGTTCATGTGAGATGGCT 59.089 47.619 0.00 0.00 0.00 4.75
787 912 2.306805 TCCTGTTCATGTGAGATGGCTT 59.693 45.455 0.00 0.00 0.00 4.35
788 913 3.087031 CCTGTTCATGTGAGATGGCTTT 58.913 45.455 0.00 0.00 0.00 3.51
789 914 4.019411 TCCTGTTCATGTGAGATGGCTTTA 60.019 41.667 0.00 0.00 0.00 1.85
790 915 4.334759 CCTGTTCATGTGAGATGGCTTTAG 59.665 45.833 0.00 0.00 0.00 1.85
791 916 4.264253 TGTTCATGTGAGATGGCTTTAGG 58.736 43.478 0.00 0.00 0.00 2.69
792 917 2.923121 TCATGTGAGATGGCTTTAGGC 58.077 47.619 0.00 0.00 41.50 3.93
793 918 2.507058 TCATGTGAGATGGCTTTAGGCT 59.493 45.455 4.87 0.00 41.69 4.58
794 919 3.711190 TCATGTGAGATGGCTTTAGGCTA 59.289 43.478 4.87 0.00 41.69 3.93
795 920 4.164030 TCATGTGAGATGGCTTTAGGCTAA 59.836 41.667 2.04 2.04 41.69 3.09
796 921 4.568072 TGTGAGATGGCTTTAGGCTAAA 57.432 40.909 18.11 18.11 41.69 1.85
797 922 4.917385 TGTGAGATGGCTTTAGGCTAAAA 58.083 39.130 19.46 6.73 41.69 1.52
798 923 5.509498 TGTGAGATGGCTTTAGGCTAAAAT 58.491 37.500 19.46 11.07 41.69 1.82
799 924 5.590259 TGTGAGATGGCTTTAGGCTAAAATC 59.410 40.000 19.46 18.00 41.69 2.17
800 925 5.825151 GTGAGATGGCTTTAGGCTAAAATCT 59.175 40.000 23.18 23.18 41.69 2.40
801 926 6.319911 GTGAGATGGCTTTAGGCTAAAATCTT 59.680 38.462 23.55 15.57 41.69 2.40
802 927 6.543831 TGAGATGGCTTTAGGCTAAAATCTTC 59.456 38.462 23.55 20.39 41.69 2.87
803 928 5.830457 AGATGGCTTTAGGCTAAAATCTTCC 59.170 40.000 19.74 15.51 41.69 3.46
804 929 4.929479 TGGCTTTAGGCTAAAATCTTCCA 58.071 39.130 19.46 16.68 41.69 3.53
805 930 4.949856 TGGCTTTAGGCTAAAATCTTCCAG 59.050 41.667 19.46 7.43 41.69 3.86
806 931 4.202060 GGCTTTAGGCTAAAATCTTCCAGC 60.202 45.833 19.46 15.72 41.46 4.85
807 932 4.399303 GCTTTAGGCTAAAATCTTCCAGCA 59.601 41.667 19.46 0.00 35.69 4.41
808 933 5.068329 GCTTTAGGCTAAAATCTTCCAGCAT 59.932 40.000 19.46 0.00 35.69 3.79
809 934 6.406288 GCTTTAGGCTAAAATCTTCCAGCATT 60.406 38.462 19.46 0.00 35.69 3.56
810 935 6.699575 TTAGGCTAAAATCTTCCAGCATTC 57.300 37.500 4.06 0.00 35.69 2.67
811 936 4.864726 AGGCTAAAATCTTCCAGCATTCT 58.135 39.130 0.00 0.00 35.69 2.40
819 944 2.026822 TCTTCCAGCATTCTCTTGGTCC 60.027 50.000 0.00 0.00 0.00 4.46
820 945 0.620556 TCCAGCATTCTCTTGGTCCC 59.379 55.000 0.00 0.00 0.00 4.46
910 1043 0.904865 ACCTGGCATTCGGTCTCTCA 60.905 55.000 0.00 0.00 0.00 3.27
978 1125 3.426695 GCTGCAATGACACTACCATTCAC 60.427 47.826 0.00 0.00 32.40 3.18
992 1139 7.440556 CACTACCATTCACCTTCTCAATGATAG 59.559 40.741 0.00 0.00 31.99 2.08
995 1142 6.102321 ACCATTCACCTTCTCAATGATAGGAT 59.898 38.462 15.64 0.41 30.31 3.24
1018 1165 5.729974 AAAGGCTTTAATCGTACCGAATC 57.270 39.130 11.52 0.00 39.99 2.52
1032 1179 2.625790 ACCGAATCCTGATGTCTCTAGC 59.374 50.000 0.00 0.00 0.00 3.42
1033 1180 2.029470 CCGAATCCTGATGTCTCTAGCC 60.029 54.545 0.00 0.00 0.00 3.93
1049 1203 3.935993 GCCTACAGCTCCAGTGAAA 57.064 52.632 0.00 0.00 38.99 2.69
1058 1212 5.376625 ACAGCTCCAGTGAAATCTTGTTAA 58.623 37.500 0.00 0.00 0.00 2.01
1061 1215 7.025963 CAGCTCCAGTGAAATCTTGTTAATTC 58.974 38.462 0.00 0.00 0.00 2.17
1073 1227 8.814038 AATCTTGTTAATTCTATCACCAAGCT 57.186 30.769 0.00 0.00 0.00 3.74
1076 1230 8.049117 TCTTGTTAATTCTATCACCAAGCTGAT 58.951 33.333 0.00 0.00 35.05 2.90
1086 1240 6.992063 ATCACCAAGCTGATTAACTGTAAG 57.008 37.500 0.00 0.00 42.29 2.34
1127 1296 8.500753 TTAACTTTGCTTTGACTTCTTGTAGA 57.499 30.769 0.00 0.00 0.00 2.59
1129 1298 5.529060 ACTTTGCTTTGACTTCTTGTAGAGG 59.471 40.000 0.00 0.00 0.00 3.69
1240 1409 4.442038 AGGATGACAGTCCTGCGA 57.558 55.556 0.00 0.00 46.76 5.10
1250 1419 3.700970 TCCTGCGACGATTGCCCA 61.701 61.111 0.00 0.00 0.00 5.36
1427 1596 2.789409 ACCATGCTTCTACAGGGAAC 57.211 50.000 1.77 0.00 44.28 3.62
1462 1631 2.495270 TCACAAGTCAGAGCTCTCATCC 59.505 50.000 14.96 1.67 0.00 3.51
1513 1682 2.403586 GGCGCGGAAAGTATGTGC 59.596 61.111 8.83 0.00 38.36 4.57
1606 1775 3.490933 CCGTGGATGTCGATGTACTCAAT 60.491 47.826 0.00 0.00 0.00 2.57
1607 1776 4.261447 CCGTGGATGTCGATGTACTCAATA 60.261 45.833 0.00 0.00 0.00 1.90
1608 1777 4.675565 CGTGGATGTCGATGTACTCAATAC 59.324 45.833 0.00 0.00 0.00 1.89
1648 1817 7.239763 TGATGTGTTACATTCTCCTCTTACA 57.760 36.000 0.00 0.00 39.27 2.41
1690 1859 3.242712 CACAACATTTTGAACAACGGAGC 59.757 43.478 0.00 0.00 36.48 4.70
1908 2077 3.666274 CTGATGATGGCAGAGATTCTCC 58.334 50.000 10.09 0.00 35.39 3.71
2074 2243 1.017387 GTTCGGCAGATCATGTTCCC 58.983 55.000 0.00 0.00 0.00 3.97
2110 2279 1.556911 AGTGTGATTAGTGGGAGCCAG 59.443 52.381 0.00 0.00 32.34 4.85
2247 2417 8.485976 TTCCACTATTTCCACTTTTGTTTTTG 57.514 30.769 0.00 0.00 0.00 2.44
2315 2485 1.337118 TCCCCAAATTCCAGTTGCAC 58.663 50.000 0.00 0.00 0.00 4.57
2381 2551 1.202348 AGAGGACGAATGACAGCATCG 60.202 52.381 0.00 6.55 32.35 3.84
2642 2813 6.371548 GCTAATGATCCAGTTACAAGTGAACA 59.628 38.462 0.00 0.00 0.00 3.18
2679 2850 7.615403 ACTATCACTATGTTGCTTCAGAAGAA 58.385 34.615 14.86 0.00 0.00 2.52
2732 2903 3.849911 TCTTTCTCCACTGTAGCATTCG 58.150 45.455 0.00 0.00 0.00 3.34
2813 2984 2.483014 TATCCCCGTTTCACAGGTTG 57.517 50.000 0.00 0.00 0.00 3.77
2817 2988 0.750182 CCCGTTTCACAGGTTGGTGT 60.750 55.000 0.00 0.00 39.76 4.16
2832 3003 3.040147 TGGTGTCGATTCAGAAACTCC 57.960 47.619 0.00 0.00 0.00 3.85
2936 3107 4.746611 CCAGTTCAACTTCCAAAGATTTGC 59.253 41.667 0.00 0.00 36.86 3.68
2937 3108 4.746611 CAGTTCAACTTCCAAAGATTTGCC 59.253 41.667 0.00 0.00 36.86 4.52
2953 3124 3.895232 TTGCCAGCAAAAGGTTTGTTA 57.105 38.095 1.81 0.00 32.44 2.41
2956 3127 3.181480 TGCCAGCAAAAGGTTTGTTAGTC 60.181 43.478 2.92 0.00 0.00 2.59
3029 3200 4.346734 TTTTGATCAGATGCGAAAGAGC 57.653 40.909 0.00 0.00 37.71 4.09
3037 3208 4.524328 TCAGATGCGAAAGAGCCTCATATA 59.476 41.667 0.00 0.00 34.82 0.86
3051 3222 2.874701 CTCATATACCACCAGTTGCTGC 59.125 50.000 0.00 0.00 0.00 5.25
3123 3294 2.286563 CCCAAACAATTGAAACGGTTGC 59.713 45.455 13.59 0.00 38.94 4.17
3217 3391 0.477597 TCCCATCCCCAACCTTGACT 60.478 55.000 0.00 0.00 0.00 3.41
3235 3409 6.016024 CCTTGACTGATGTGATTCTTGGAAAA 60.016 38.462 0.00 0.00 0.00 2.29
3265 3439 4.951715 TCGGCTAGTGTAAATGGAGAACTA 59.048 41.667 0.00 0.00 0.00 2.24
3277 3451 3.173965 TGGAGAACTAAGGCTACTGCTT 58.826 45.455 0.00 0.00 39.59 3.91
3424 3598 5.634118 AGAAATGTTTCTGGTCTGGAATCA 58.366 37.500 7.18 0.00 45.27 2.57
3440 3614 3.531538 GAATCACTGGACGGAAGCATTA 58.468 45.455 0.00 0.00 0.00 1.90
3442 3616 3.179443 TCACTGGACGGAAGCATTATC 57.821 47.619 0.00 0.00 0.00 1.75
3448 3622 2.201732 GACGGAAGCATTATCAGCGAA 58.798 47.619 0.00 0.00 37.01 4.70
3628 3802 1.804598 TGCAATGCAGATGGAAGCG 59.195 52.632 2.72 0.00 33.32 4.68
3772 3946 1.294780 CTGGACACAGTCTGGAGGC 59.705 63.158 4.53 0.00 39.92 4.70
3954 4128 9.730705 TTTATCAAATTCAGATGCTATAGAGGG 57.269 33.333 3.21 0.00 0.00 4.30
4060 4258 2.047002 AGACTCTAGAAGGAGACCGC 57.953 55.000 0.00 0.00 37.13 5.68
4111 4309 1.909700 AGAATGGAAAAGAAGGCGCA 58.090 45.000 10.83 0.00 0.00 6.09
4287 4485 8.817100 CAAAAGGAAAGAAATTGTTGTTAGGTC 58.183 33.333 0.00 0.00 0.00 3.85
4302 4500 5.138276 TGTTAGGTCGCTACATCTAGGAAT 58.862 41.667 0.00 0.00 0.00 3.01
4408 4607 3.393800 ACGAGTCAGTTTGTCTTGGATG 58.606 45.455 0.00 0.00 0.00 3.51
4411 4610 4.380531 GAGTCAGTTTGTCTTGGATGTGA 58.619 43.478 0.00 0.00 0.00 3.58
4419 4618 7.387673 CAGTTTGTCTTGGATGTGAACATAGTA 59.612 37.037 0.00 0.00 36.57 1.82
4448 4647 4.316025 AACAACATACCAAGTGGCCTAT 57.684 40.909 3.32 0.00 39.32 2.57
4449 4648 5.444744 AACAACATACCAAGTGGCCTATA 57.555 39.130 3.32 0.00 39.32 1.31
4486 4686 4.499183 CAAGTGATCAGTACTTGGGACTC 58.501 47.826 13.99 0.00 46.97 3.36
4498 4698 0.108585 TGGGACTCAACAGGAAGTGC 59.891 55.000 0.00 0.00 0.00 4.40
4503 4703 1.411246 ACTCAACAGGAAGTGCGTGTA 59.589 47.619 0.00 0.00 44.25 2.90
4512 4712 0.586319 AAGTGCGTGTATGTGTGTGC 59.414 50.000 0.00 0.00 0.00 4.57
4514 4714 2.202171 GCGTGTATGTGTGTGCGC 60.202 61.111 0.00 0.00 38.15 6.09
4516 4716 2.202171 GTGTATGTGTGTGCGCGC 60.202 61.111 27.26 27.26 0.00 6.86
4606 4806 2.274542 TCCTGGCATCCTACCAAAGAA 58.725 47.619 0.00 0.00 36.56 2.52
4613 4813 3.869912 GCATCCTACCAAAGAAGTGCAGA 60.870 47.826 0.00 0.00 31.25 4.26
4684 4884 1.802337 GCGACAAAACCCCAGGTTCC 61.802 60.000 0.00 0.00 46.20 3.62
4688 4888 2.703536 GACAAAACCCCAGGTTCCATTT 59.296 45.455 0.00 0.00 46.20 2.32
4738 4938 6.024552 ACAGAACAAAGCAAAACAGAGAAA 57.975 33.333 0.00 0.00 0.00 2.52
4743 4943 6.036577 ACAAAGCAAAACAGAGAAAAAGGA 57.963 33.333 0.00 0.00 0.00 3.36
4764 4964 7.856145 AGGAAAGAAACATATAAGCACTCTG 57.144 36.000 0.00 0.00 0.00 3.35
4769 4969 7.840342 AGAAACATATAAGCACTCTGACAAG 57.160 36.000 0.00 0.00 0.00 3.16
4778 4978 4.392940 AGCACTCTGACAAGCAGTTAATT 58.607 39.130 0.00 0.00 45.14 1.40
4784 4984 6.870965 ACTCTGACAAGCAGTTAATTGACTAG 59.129 38.462 2.09 0.00 45.14 2.57
4864 5076 3.307379 GTTGAGCGAACCTTGGACT 57.693 52.632 0.00 0.00 0.00 3.85
5012 5231 0.252696 TGTAGTCCCCCATCTGCTGT 60.253 55.000 0.00 0.00 0.00 4.40
5237 5456 2.048222 TCTGCGAAGTTGCCTCCG 60.048 61.111 0.00 0.00 0.00 4.63
5286 5505 4.534103 GGTATTCATGGATAGGAGGCTCTT 59.466 45.833 15.23 9.77 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.543802 ACTCACTGCTGCTGAGTAGAC 59.456 52.381 19.31 0.00 45.35 2.59
17 18 5.464030 TTTAGTTGGTCTAGTGGTCACTC 57.536 43.478 6.91 0.00 42.54 3.51
29 36 3.497262 CCGTCTCTTGGTTTTAGTTGGTC 59.503 47.826 0.00 0.00 0.00 4.02
53 60 3.050275 GTGCGGTGGTTGAGCTCC 61.050 66.667 12.15 0.00 0.00 4.70
130 137 4.491409 GGGAGAAAGCCGGCCTCC 62.491 72.222 31.37 31.37 44.32 4.30
131 138 2.485780 AAAGGGAGAAAGCCGGCCTC 62.486 60.000 26.15 22.17 0.00 4.70
132 139 2.485780 GAAAGGGAGAAAGCCGGCCT 62.486 60.000 26.15 14.08 0.00 5.19
133 140 2.035783 AAAGGGAGAAAGCCGGCC 59.964 61.111 26.15 8.19 0.00 6.13
134 141 2.399356 CGAAAGGGAGAAAGCCGGC 61.399 63.158 21.89 21.89 0.00 6.13
135 142 3.890674 CGAAAGGGAGAAAGCCGG 58.109 61.111 0.00 0.00 0.00 6.13
223 230 1.189524 TATATTCTCCCCACCGCCGG 61.190 60.000 0.00 0.00 0.00 6.13
399 422 6.778559 AGATAGAATTAGTAGAACCTCGCCTT 59.221 38.462 0.00 0.00 0.00 4.35
413 436 2.416162 GGCCGAGCGGAGATAGAATTAG 60.416 54.545 13.94 0.00 37.50 1.73
431 454 0.958822 ACGGAACAAAATCACAGGCC 59.041 50.000 0.00 0.00 0.00 5.19
448 471 1.671054 AAATCACGGGTCAGCCACG 60.671 57.895 0.00 0.00 36.17 4.94
482 505 1.760613 AGTTGAAAGACACTGTCCCGA 59.239 47.619 5.51 0.00 32.18 5.14
484 507 2.033424 GCAAGTTGAAAGACACTGTCCC 59.967 50.000 7.16 0.00 32.18 4.46
487 510 3.129287 CCTTGCAAGTTGAAAGACACTGT 59.871 43.478 23.16 0.00 34.90 3.55
497 520 5.335897 GCATAGTTGATTCCTTGCAAGTTGA 60.336 40.000 24.35 13.01 0.00 3.18
512 535 5.499004 AGAAACAGGGTAAGCATAGTTGA 57.501 39.130 0.00 0.00 0.00 3.18
518 541 4.388577 AGGAAAGAAACAGGGTAAGCAT 57.611 40.909 0.00 0.00 0.00 3.79
520 543 6.835819 AATAAGGAAAGAAACAGGGTAAGC 57.164 37.500 0.00 0.00 0.00 3.09
521 544 7.829706 AGCTAATAAGGAAAGAAACAGGGTAAG 59.170 37.037 0.00 0.00 0.00 2.34
522 545 7.696017 AGCTAATAAGGAAAGAAACAGGGTAA 58.304 34.615 0.00 0.00 0.00 2.85
524 547 6.140968 AGCTAATAAGGAAAGAAACAGGGT 57.859 37.500 0.00 0.00 0.00 4.34
525 548 7.176690 TCAAAGCTAATAAGGAAAGAAACAGGG 59.823 37.037 0.00 0.00 0.00 4.45
532 559 8.906867 CATGGAATCAAAGCTAATAAGGAAAGA 58.093 33.333 0.00 0.00 0.00 2.52
537 564 5.537674 AGCCATGGAATCAAAGCTAATAAGG 59.462 40.000 18.40 0.00 34.76 2.69
538 565 6.444633 CAGCCATGGAATCAAAGCTAATAAG 58.555 40.000 18.40 0.00 34.76 1.73
541 568 3.069158 GCAGCCATGGAATCAAAGCTAAT 59.931 43.478 18.40 0.00 34.76 1.73
546 573 3.604875 AAAGCAGCCATGGAATCAAAG 57.395 42.857 18.40 0.00 0.00 2.77
550 577 1.206371 AGCAAAAGCAGCCATGGAATC 59.794 47.619 18.40 2.37 0.00 2.52
552 579 1.050204 AAGCAAAAGCAGCCATGGAA 58.950 45.000 18.40 0.00 0.00 3.53
553 580 0.319083 CAAGCAAAAGCAGCCATGGA 59.681 50.000 18.40 0.00 0.00 3.41
554 581 0.319083 TCAAGCAAAAGCAGCCATGG 59.681 50.000 7.63 7.63 0.00 3.66
556 583 2.565834 AGAATCAAGCAAAAGCAGCCAT 59.434 40.909 0.00 0.00 0.00 4.40
562 589 5.362556 TGAGTACAGAATCAAGCAAAAGC 57.637 39.130 0.00 0.00 0.00 3.51
563 590 6.373774 AGGATGAGTACAGAATCAAGCAAAAG 59.626 38.462 0.00 0.00 0.00 2.27
564 591 6.149973 CAGGATGAGTACAGAATCAAGCAAAA 59.850 38.462 0.00 0.00 39.69 2.44
589 617 3.815401 CACCGTATCCCCAAGAAATCATC 59.185 47.826 0.00 0.00 0.00 2.92
590 618 3.820557 CACCGTATCCCCAAGAAATCAT 58.179 45.455 0.00 0.00 0.00 2.45
591 619 2.682563 GCACCGTATCCCCAAGAAATCA 60.683 50.000 0.00 0.00 0.00 2.57
592 620 1.947456 GCACCGTATCCCCAAGAAATC 59.053 52.381 0.00 0.00 0.00 2.17
593 621 1.564348 AGCACCGTATCCCCAAGAAAT 59.436 47.619 0.00 0.00 0.00 2.17
594 622 0.988832 AGCACCGTATCCCCAAGAAA 59.011 50.000 0.00 0.00 0.00 2.52
595 623 1.868713 TAGCACCGTATCCCCAAGAA 58.131 50.000 0.00 0.00 0.00 2.52
597 625 2.930826 ATTAGCACCGTATCCCCAAG 57.069 50.000 0.00 0.00 0.00 3.61
598 626 2.775384 AGAATTAGCACCGTATCCCCAA 59.225 45.455 0.00 0.00 0.00 4.12
600 628 4.020485 ACATAGAATTAGCACCGTATCCCC 60.020 45.833 0.00 0.00 0.00 4.81
602 630 4.929808 CCACATAGAATTAGCACCGTATCC 59.070 45.833 0.00 0.00 0.00 2.59
603 631 5.779922 TCCACATAGAATTAGCACCGTATC 58.220 41.667 0.00 0.00 0.00 2.24
606 634 4.481368 TTCCACATAGAATTAGCACCGT 57.519 40.909 0.00 0.00 0.00 4.83
607 635 6.201517 CAAATTCCACATAGAATTAGCACCG 58.798 40.000 0.29 0.00 43.90 4.94
608 636 6.461509 CCCAAATTCCACATAGAATTAGCACC 60.462 42.308 0.29 0.00 43.90 5.01
609 637 6.321181 TCCCAAATTCCACATAGAATTAGCAC 59.679 38.462 0.29 0.00 43.90 4.40
610 638 6.321181 GTCCCAAATTCCACATAGAATTAGCA 59.679 38.462 0.29 0.00 43.90 3.49
611 639 6.513393 CGTCCCAAATTCCACATAGAATTAGC 60.513 42.308 0.29 0.00 43.90 3.09
612 640 6.765989 TCGTCCCAAATTCCACATAGAATTAG 59.234 38.462 0.29 0.00 43.90 1.73
613 641 6.654959 TCGTCCCAAATTCCACATAGAATTA 58.345 36.000 0.29 0.00 43.90 1.40
614 642 5.505780 TCGTCCCAAATTCCACATAGAATT 58.494 37.500 0.00 0.00 46.04 2.17
615 643 5.110814 TCGTCCCAAATTCCACATAGAAT 57.889 39.130 0.00 0.00 38.11 2.40
623 651 2.214376 AAGCATCGTCCCAAATTCCA 57.786 45.000 0.00 0.00 0.00 3.53
626 654 3.016736 CCACTAAGCATCGTCCCAAATT 58.983 45.455 0.00 0.00 0.00 1.82
635 663 3.492383 CAGCTAATGTCCACTAAGCATCG 59.508 47.826 0.00 0.00 35.63 3.84
636 664 3.249559 GCAGCTAATGTCCACTAAGCATC 59.750 47.826 0.00 0.00 35.63 3.91
637 665 3.118112 AGCAGCTAATGTCCACTAAGCAT 60.118 43.478 0.00 0.00 35.63 3.79
638 666 2.237143 AGCAGCTAATGTCCACTAAGCA 59.763 45.455 0.00 0.00 35.63 3.91
639 667 2.911484 AGCAGCTAATGTCCACTAAGC 58.089 47.619 0.00 0.00 0.00 3.09
640 668 4.509600 GCTAAGCAGCTAATGTCCACTAAG 59.490 45.833 0.00 0.00 44.93 2.18
641 669 4.442706 GCTAAGCAGCTAATGTCCACTAA 58.557 43.478 0.00 0.00 44.93 2.24
642 670 4.060038 GCTAAGCAGCTAATGTCCACTA 57.940 45.455 0.00 0.00 44.93 2.74
643 671 2.911484 GCTAAGCAGCTAATGTCCACT 58.089 47.619 0.00 0.00 44.93 4.00
655 780 2.758736 ACCTGTTCAGAGCTAAGCAG 57.241 50.000 1.00 0.00 0.00 4.24
660 785 1.337823 GCCGAAACCTGTTCAGAGCTA 60.338 52.381 1.00 0.00 0.00 3.32
667 792 2.737252 CAGAGTAAGCCGAAACCTGTTC 59.263 50.000 0.00 0.00 0.00 3.18
672 797 0.392595 CCCCAGAGTAAGCCGAAACC 60.393 60.000 0.00 0.00 0.00 3.27
678 803 2.038295 CAGATGATCCCCAGAGTAAGCC 59.962 54.545 0.00 0.00 0.00 4.35
682 807 2.520120 AGGACAGATGATCCCCAGAGTA 59.480 50.000 0.00 0.00 36.86 2.59
686 811 0.108207 GCAGGACAGATGATCCCCAG 59.892 60.000 0.00 0.00 36.86 4.45
687 812 0.621280 TGCAGGACAGATGATCCCCA 60.621 55.000 0.00 0.00 36.86 4.96
688 813 0.769873 ATGCAGGACAGATGATCCCC 59.230 55.000 0.00 0.00 36.86 4.81
722 847 5.698545 CGGAGGAAAATAATAGCTGGAGAAG 59.301 44.000 0.00 0.00 0.00 2.85
723 848 5.365605 TCGGAGGAAAATAATAGCTGGAGAA 59.634 40.000 0.00 0.00 0.00 2.87
724 849 4.899457 TCGGAGGAAAATAATAGCTGGAGA 59.101 41.667 0.00 0.00 0.00 3.71
725 850 5.215252 TCGGAGGAAAATAATAGCTGGAG 57.785 43.478 0.00 0.00 0.00 3.86
726 851 5.623956 TTCGGAGGAAAATAATAGCTGGA 57.376 39.130 0.00 0.00 0.00 3.86
727 852 6.693315 TTTTCGGAGGAAAATAATAGCTGG 57.307 37.500 0.00 0.00 44.86 4.85
748 873 9.952030 TGAACAGGAATAAAAGAAAAGGTTTTT 57.048 25.926 0.00 0.00 0.00 1.94
750 875 9.546428 CATGAACAGGAATAAAAGAAAAGGTTT 57.454 29.630 0.00 0.00 0.00 3.27
751 876 8.704668 ACATGAACAGGAATAAAAGAAAAGGTT 58.295 29.630 0.00 0.00 0.00 3.50
752 877 8.143835 CACATGAACAGGAATAAAAGAAAAGGT 58.856 33.333 0.00 0.00 0.00 3.50
753 878 8.359642 TCACATGAACAGGAATAAAAGAAAAGG 58.640 33.333 0.00 0.00 0.00 3.11
754 879 9.403110 CTCACATGAACAGGAATAAAAGAAAAG 57.597 33.333 0.00 0.00 0.00 2.27
755 880 9.130661 TCTCACATGAACAGGAATAAAAGAAAA 57.869 29.630 0.00 0.00 0.00 2.29
756 881 8.690203 TCTCACATGAACAGGAATAAAAGAAA 57.310 30.769 0.00 0.00 0.00 2.52
757 882 8.733458 CATCTCACATGAACAGGAATAAAAGAA 58.267 33.333 0.00 0.00 0.00 2.52
758 883 7.337689 CCATCTCACATGAACAGGAATAAAAGA 59.662 37.037 0.00 0.00 0.00 2.52
759 884 7.478322 CCATCTCACATGAACAGGAATAAAAG 58.522 38.462 0.00 0.00 0.00 2.27
760 885 6.127647 GCCATCTCACATGAACAGGAATAAAA 60.128 38.462 0.00 0.00 0.00 1.52
761 886 5.357878 GCCATCTCACATGAACAGGAATAAA 59.642 40.000 0.00 0.00 0.00 1.40
762 887 4.883585 GCCATCTCACATGAACAGGAATAA 59.116 41.667 0.00 0.00 0.00 1.40
763 888 4.164796 AGCCATCTCACATGAACAGGAATA 59.835 41.667 0.00 0.00 0.00 1.75
764 889 3.053842 AGCCATCTCACATGAACAGGAAT 60.054 43.478 0.00 0.00 0.00 3.01
765 890 2.306805 AGCCATCTCACATGAACAGGAA 59.693 45.455 0.00 0.00 0.00 3.36
766 891 1.911357 AGCCATCTCACATGAACAGGA 59.089 47.619 0.00 0.00 0.00 3.86
767 892 2.414994 AGCCATCTCACATGAACAGG 57.585 50.000 0.00 0.00 0.00 4.00
768 893 4.334759 CCTAAAGCCATCTCACATGAACAG 59.665 45.833 0.00 0.00 0.00 3.16
769 894 4.264253 CCTAAAGCCATCTCACATGAACA 58.736 43.478 0.00 0.00 0.00 3.18
770 895 3.065925 GCCTAAAGCCATCTCACATGAAC 59.934 47.826 0.00 0.00 34.35 3.18
771 896 3.054139 AGCCTAAAGCCATCTCACATGAA 60.054 43.478 0.00 0.00 45.47 2.57
772 897 2.507058 AGCCTAAAGCCATCTCACATGA 59.493 45.455 0.00 0.00 45.47 3.07
773 898 2.928334 AGCCTAAAGCCATCTCACATG 58.072 47.619 0.00 0.00 45.47 3.21
774 899 4.778213 TTAGCCTAAAGCCATCTCACAT 57.222 40.909 0.00 0.00 45.47 3.21
775 900 4.568072 TTTAGCCTAAAGCCATCTCACA 57.432 40.909 0.00 0.00 45.47 3.58
776 901 5.825151 AGATTTTAGCCTAAAGCCATCTCAC 59.175 40.000 4.70 0.00 45.47 3.51
777 902 6.006275 AGATTTTAGCCTAAAGCCATCTCA 57.994 37.500 4.70 0.00 45.47 3.27
778 903 6.016693 GGAAGATTTTAGCCTAAAGCCATCTC 60.017 42.308 9.30 5.17 45.47 2.75
779 904 5.830457 GGAAGATTTTAGCCTAAAGCCATCT 59.170 40.000 4.70 4.70 45.47 2.90
780 905 5.594317 TGGAAGATTTTAGCCTAAAGCCATC 59.406 40.000 0.00 0.00 45.47 3.51
781 906 5.518865 TGGAAGATTTTAGCCTAAAGCCAT 58.481 37.500 0.00 0.00 45.47 4.40
782 907 4.929479 TGGAAGATTTTAGCCTAAAGCCA 58.071 39.130 0.00 0.21 45.47 4.75
783 908 4.202060 GCTGGAAGATTTTAGCCTAAAGCC 60.202 45.833 0.00 0.00 38.40 4.35
784 909 4.399303 TGCTGGAAGATTTTAGCCTAAAGC 59.601 41.667 0.00 0.00 37.93 3.51
785 910 6.705863 ATGCTGGAAGATTTTAGCCTAAAG 57.294 37.500 0.00 0.00 34.07 1.85
786 911 6.891908 AGAATGCTGGAAGATTTTAGCCTAAA 59.108 34.615 0.00 0.00 34.07 1.85
787 912 6.426587 AGAATGCTGGAAGATTTTAGCCTAA 58.573 36.000 0.00 0.00 34.07 2.69
788 913 6.006275 AGAATGCTGGAAGATTTTAGCCTA 57.994 37.500 0.00 0.00 34.07 3.93
789 914 4.864726 AGAATGCTGGAAGATTTTAGCCT 58.135 39.130 0.00 0.00 34.07 4.58
790 915 4.886489 AGAGAATGCTGGAAGATTTTAGCC 59.114 41.667 0.00 0.00 34.07 3.93
791 916 6.264088 CAAGAGAATGCTGGAAGATTTTAGC 58.736 40.000 0.00 0.00 34.07 3.09
792 917 6.376581 ACCAAGAGAATGCTGGAAGATTTTAG 59.623 38.462 0.00 0.00 34.07 1.85
793 918 6.248433 ACCAAGAGAATGCTGGAAGATTTTA 58.752 36.000 0.00 0.00 34.07 1.52
794 919 5.082425 ACCAAGAGAATGCTGGAAGATTTT 58.918 37.500 0.00 0.00 34.07 1.82
795 920 4.670765 ACCAAGAGAATGCTGGAAGATTT 58.329 39.130 0.00 0.00 34.07 2.17
796 921 4.268359 GACCAAGAGAATGCTGGAAGATT 58.732 43.478 0.00 0.00 34.07 2.40
797 922 3.371380 GGACCAAGAGAATGCTGGAAGAT 60.371 47.826 0.00 0.00 34.07 2.40
798 923 2.026822 GGACCAAGAGAATGCTGGAAGA 60.027 50.000 0.00 0.00 34.07 2.87
799 924 2.363683 GGACCAAGAGAATGCTGGAAG 58.636 52.381 0.00 0.00 0.00 3.46
800 925 1.004745 GGGACCAAGAGAATGCTGGAA 59.995 52.381 0.00 0.00 0.00 3.53
801 926 0.620556 GGGACCAAGAGAATGCTGGA 59.379 55.000 0.00 0.00 0.00 3.86
802 927 0.745845 CGGGACCAAGAGAATGCTGG 60.746 60.000 0.00 0.00 0.00 4.85
803 928 0.036010 ACGGGACCAAGAGAATGCTG 60.036 55.000 0.00 0.00 0.00 4.41
804 929 0.036010 CACGGGACCAAGAGAATGCT 60.036 55.000 0.00 0.00 0.00 3.79
805 930 0.321653 ACACGGGACCAAGAGAATGC 60.322 55.000 0.00 0.00 0.00 3.56
806 931 3.133003 AGATACACGGGACCAAGAGAATG 59.867 47.826 0.00 0.00 0.00 2.67
807 932 3.133003 CAGATACACGGGACCAAGAGAAT 59.867 47.826 0.00 0.00 0.00 2.40
808 933 2.496070 CAGATACACGGGACCAAGAGAA 59.504 50.000 0.00 0.00 0.00 2.87
809 934 2.100197 CAGATACACGGGACCAAGAGA 58.900 52.381 0.00 0.00 0.00 3.10
810 935 1.471676 GCAGATACACGGGACCAAGAG 60.472 57.143 0.00 0.00 0.00 2.85
811 936 0.535335 GCAGATACACGGGACCAAGA 59.465 55.000 0.00 0.00 0.00 3.02
819 944 0.809636 TGGCAATCGCAGATACACGG 60.810 55.000 0.00 0.00 45.12 4.94
820 945 1.006086 TTGGCAATCGCAGATACACG 58.994 50.000 0.00 0.00 45.12 4.49
978 1125 6.777782 AGCCTTTATCCTATCATTGAGAAGG 58.222 40.000 10.32 10.32 33.88 3.46
1018 1165 2.295909 GCTGTAGGCTAGAGACATCAGG 59.704 54.545 21.74 0.00 38.06 3.86
1032 1179 3.902881 AGATTTCACTGGAGCTGTAGG 57.097 47.619 0.00 0.00 0.00 3.18
1033 1180 4.573900 ACAAGATTTCACTGGAGCTGTAG 58.426 43.478 0.00 0.00 0.00 2.74
1041 1195 9.994432 GTGATAGAATTAACAAGATTTCACTGG 57.006 33.333 0.00 0.00 0.00 4.00
1049 1203 8.049117 TCAGCTTGGTGATAGAATTAACAAGAT 58.951 33.333 12.18 4.41 36.79 2.40
1058 1212 7.341805 ACAGTTAATCAGCTTGGTGATAGAAT 58.658 34.615 14.50 4.64 36.07 2.40
1061 1215 7.981789 TCTTACAGTTAATCAGCTTGGTGATAG 59.018 37.037 14.50 7.05 36.07 2.08
1073 1227 6.989759 TCAGCAAAGTGTCTTACAGTTAATCA 59.010 34.615 0.80 0.00 40.60 2.57
1076 1230 7.801716 AATCAGCAAAGTGTCTTACAGTTAA 57.198 32.000 0.80 0.00 40.60 2.01
1086 1240 7.809806 AGCAAAGTTAATAATCAGCAAAGTGTC 59.190 33.333 0.00 0.00 0.00 3.67
1127 1296 0.550914 TTGGTGTTGAAGCAGGACCT 59.449 50.000 0.00 0.00 37.63 3.85
1129 1298 0.668535 GGTTGGTGTTGAAGCAGGAC 59.331 55.000 0.00 0.00 37.63 3.85
1250 1419 0.462581 AATGCCGATGACAGTGCGAT 60.463 50.000 0.00 0.00 0.00 4.58
1261 1430 1.522355 CCACTCGAGCAATGCCGAT 60.522 57.895 13.61 7.06 32.86 4.18
1411 1580 4.036518 AGATCAGTTCCCTGTAGAAGCAT 58.963 43.478 0.00 0.00 39.82 3.79
1427 1596 4.274214 TGACTTGTGAGTTTTGCAGATCAG 59.726 41.667 0.00 0.00 35.88 2.90
1480 1649 1.101049 CGCCCACAAGTTTCTGGTGT 61.101 55.000 3.99 0.00 33.83 4.16
1513 1682 2.232750 GCTACTGCTGCATCCATCG 58.767 57.895 1.31 0.00 36.03 3.84
1551 1720 6.219473 TCTGTGTTGTCATTGTTGTTTTGTT 58.781 32.000 0.00 0.00 0.00 2.83
1554 1723 6.629128 TCATCTGTGTTGTCATTGTTGTTTT 58.371 32.000 0.00 0.00 0.00 2.43
1626 1795 7.907389 TCTTGTAAGAGGAGAATGTAACACAT 58.093 34.615 0.00 0.00 41.31 3.21
1648 1817 5.417811 TGTGCACAACATGAACAAATTCTT 58.582 33.333 19.28 0.00 44.58 2.52
1690 1859 3.064134 TCTTCTGAGAGAACAGCGATACG 59.936 47.826 0.00 0.00 37.75 3.06
1702 1871 4.628471 TGGATCTCTCCACTCTTCTGAGAG 60.628 50.000 9.00 9.00 46.95 3.20
1721 1890 6.662755 TCTTTGGTGACTTAGCATATTGGAT 58.337 36.000 0.00 0.00 36.53 3.41
1908 2077 4.384978 CCATATCATAGGCTTCATGAGGGG 60.385 50.000 6.99 3.99 35.93 4.79
2074 2243 4.578871 TCACACTGTCAGGGTCATAATTG 58.421 43.478 4.25 0.00 21.60 2.32
2110 2279 2.545532 CGAGATGTCCTCTGCTTCCATC 60.546 54.545 0.00 0.00 39.78 3.51
2247 2417 6.925610 TGCAATTATAGGATCTGTCAACAC 57.074 37.500 0.00 0.00 0.00 3.32
2381 2551 7.814587 TGTGAATTGAGATGTATATGGATCGAC 59.185 37.037 0.00 0.00 0.00 4.20
2642 2813 6.203072 ACATAGTGATAGTCCTTGGGTACTT 58.797 40.000 0.00 0.00 0.00 2.24
2679 2850 8.631480 AAACTAAGAAACCTTTCGGATATGTT 57.369 30.769 0.00 0.00 41.92 2.71
2707 2878 2.828520 TGCTACAGTGGAGAAAGAGAGG 59.171 50.000 6.53 0.00 0.00 3.69
2732 2903 7.757624 CCCGAGATTCAGTTAAGATAGATAAGC 59.242 40.741 0.00 0.00 0.00 3.09
2734 2905 8.935614 TCCCGAGATTCAGTTAAGATAGATAA 57.064 34.615 0.00 0.00 0.00 1.75
2813 2984 2.996621 CAGGAGTTTCTGAATCGACACC 59.003 50.000 0.00 0.00 36.93 4.16
2817 2988 2.562738 TCAGCAGGAGTTTCTGAATCGA 59.437 45.455 0.00 0.00 36.93 3.59
2832 3003 8.498054 TTTAGGATTATCTTCAACTTCAGCAG 57.502 34.615 0.00 0.00 0.00 4.24
2888 3059 4.165565 AGGATCATGTGATGTCAGTCCATT 59.834 41.667 0.00 0.00 34.37 3.16
2936 3107 4.097892 ACAGACTAACAAACCTTTTGCTGG 59.902 41.667 0.00 0.00 0.00 4.85
2937 3108 5.248870 ACAGACTAACAAACCTTTTGCTG 57.751 39.130 0.00 0.00 0.00 4.41
2953 3124 1.834263 GCTGGATGGAAGGTACAGACT 59.166 52.381 0.00 0.00 0.00 3.24
2956 3127 1.278985 TGTGCTGGATGGAAGGTACAG 59.721 52.381 0.00 0.00 0.00 2.74
3029 3200 3.470709 CAGCAACTGGTGGTATATGAGG 58.529 50.000 0.00 0.00 39.67 3.86
3037 3208 2.072874 ATCTGGCAGCAACTGGTGGT 62.073 55.000 10.34 0.00 43.24 4.16
3051 3222 5.163269 TGAGATACCTCACCATTTGATCTGG 60.163 44.000 0.00 0.00 44.01 3.86
3123 3294 4.161189 TGCTAAGAGATGGTCTCCTTTCAG 59.839 45.833 3.47 0.00 44.42 3.02
3217 3391 4.410099 AGCCTTTTCCAAGAATCACATCA 58.590 39.130 0.00 0.00 30.57 3.07
3235 3409 1.848652 TTACACTAGCCGAAGAGCCT 58.151 50.000 0.00 0.00 0.00 4.58
3265 3439 3.142174 GAGTTGTGAAAGCAGTAGCCTT 58.858 45.455 0.00 0.00 43.56 4.35
3277 3451 0.756294 TGGAAGCCGAGAGTTGTGAA 59.244 50.000 0.00 0.00 0.00 3.18
3341 3515 0.836606 TCATCACCACGCCCATATGT 59.163 50.000 1.24 0.00 0.00 2.29
3343 3517 2.886523 CAAATCATCACCACGCCCATAT 59.113 45.455 0.00 0.00 0.00 1.78
3424 3598 2.743183 GCTGATAATGCTTCCGTCCAGT 60.743 50.000 0.00 0.00 0.00 4.00
3440 3614 2.237143 TCTCACCTTCCATTTCGCTGAT 59.763 45.455 0.00 0.00 0.00 2.90
3442 3616 2.005451 CTCTCACCTTCCATTTCGCTG 58.995 52.381 0.00 0.00 0.00 5.18
3628 3802 4.590647 TCCATCATCCTCTGGTAATGAGAC 59.409 45.833 0.00 0.00 33.24 3.36
3700 3874 7.663081 TGTATTTGATCTTCTCTTTGAGCAAGT 59.337 33.333 0.00 0.00 39.28 3.16
3755 3929 2.574018 CGCCTCCAGACTGTGTCCA 61.574 63.158 0.93 0.00 32.18 4.02
3772 3946 0.674895 CTTTCTCTGTTGGCCCTCCG 60.675 60.000 0.00 0.00 34.14 4.63
4111 4309 5.627503 GCAGGCAATTTCCCTTATGAATTGT 60.628 40.000 9.07 0.00 40.88 2.71
4287 4485 7.273381 CCAAAAACAAAATTCCTAGATGTAGCG 59.727 37.037 0.00 0.00 0.00 4.26
4302 4500 5.600484 TCTCCCTCAATAGCCAAAAACAAAA 59.400 36.000 0.00 0.00 0.00 2.44
4408 4607 6.707161 TGTTGTTACCCACTTACTATGTTCAC 59.293 38.462 0.00 0.00 0.00 3.18
4411 4610 7.825761 GGTATGTTGTTACCCACTTACTATGTT 59.174 37.037 7.35 0.00 36.42 2.71
4419 4618 4.825085 CACTTGGTATGTTGTTACCCACTT 59.175 41.667 0.00 0.00 40.87 3.16
4486 4686 2.096268 CACATACACGCACTTCCTGTTG 60.096 50.000 0.00 0.00 0.00 3.33
4498 4698 2.093799 CGCGCACACACATACACG 59.906 61.111 8.75 0.00 0.00 4.49
4522 4722 0.108186 TCTCAACCAGGCTACATGCG 60.108 55.000 0.00 0.00 44.05 4.73
4524 4724 3.005554 CAAGTCTCAACCAGGCTACATG 58.994 50.000 0.00 0.00 35.26 3.21
4525 4725 2.639839 ACAAGTCTCAACCAGGCTACAT 59.360 45.455 0.00 0.00 35.26 2.29
4530 4730 1.202698 AGTCACAAGTCTCAACCAGGC 60.203 52.381 0.00 0.00 0.00 4.85
4613 4813 4.530710 AAGTGATGTGATTTTGCAGCAT 57.469 36.364 0.00 0.00 33.50 3.79
4684 4884 7.696755 TGTTATATGACTGCAGCTAACAAATG 58.303 34.615 15.27 0.00 34.54 2.32
4688 4888 5.977635 ACTGTTATATGACTGCAGCTAACA 58.022 37.500 15.27 16.97 35.40 2.41
4738 4938 8.734386 CAGAGTGCTTATATGTTTCTTTCCTTT 58.266 33.333 0.00 0.00 0.00 3.11
4743 4943 8.621532 TTGTCAGAGTGCTTATATGTTTCTTT 57.378 30.769 0.00 0.00 0.00 2.52
4764 4964 7.054855 CAGTCTAGTCAATTAACTGCTTGTC 57.945 40.000 0.00 0.00 31.87 3.18
4778 4978 5.270893 TGTAAAGTGTTGCAGTCTAGTCA 57.729 39.130 0.00 0.00 0.00 3.41
4784 4984 8.122952 GGATACATTATGTAAAGTGTTGCAGTC 58.877 37.037 9.24 0.00 36.31 3.51
4864 5076 1.968704 TGTAACCGAACATGGTGCAA 58.031 45.000 0.00 0.00 42.89 4.08
5012 5231 2.438763 TCCTGGAGTTAACGGGTTTTCA 59.561 45.455 0.00 0.00 35.79 2.69
5081 5300 0.107017 CCAATGGAATGGCGGACTCT 60.107 55.000 0.00 0.00 32.78 3.24
5237 5456 0.975887 TTGGCTTGCCATTTTCTCCC 59.024 50.000 15.58 0.00 0.00 4.30
5286 5505 2.241160 ACAAAGCAATGTGAGCATGGA 58.759 42.857 0.00 0.00 35.15 3.41


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

AutoCloner maintained by Alex Coulton.