Multiple sequence alignment - TraesCS5A01G401100

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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 TraesCS5A01G401100 chr5A 100.000 3645 0 0 1 3645 593759407 593763051 0.000000e+00 6732
1 TraesCS5A01G401100 chr5B 87.484 2357 179 59 681 2957 581711000 581708680 0.000000e+00 2612
2 TraesCS5A01G401100 chr5B 87.524 521 30 19 3138 3645 581708376 581707878 1.470000e-158 569
3 TraesCS5A01G401100 chr5D 87.488 2030 106 59 678 2609 474716788 474718767 0.000000e+00 2206
4 TraesCS5A01G401100 chr5D 83.317 1049 65 41 2673 3645 474718757 474719771 0.000000e+00 867
5 TraesCS5A01G401100 chr3A 91.910 581 44 2 1 579 40330474 40331053 0.000000e+00 809
6 TraesCS5A01G401100 chr3A 90.986 588 41 7 1 579 123293159 123292575 0.000000e+00 782
7 TraesCS5A01G401100 chr3A 90.186 591 45 9 3 581 600742783 600743372 0.000000e+00 758
8 TraesCS5A01G401100 chr4A 91.327 588 33 10 1 579 34673220 34673798 0.000000e+00 787
9 TraesCS5A01G401100 chr1A 90.878 592 38 8 1 579 532237813 532238401 0.000000e+00 780
10 TraesCS5A01G401100 chr1A 89.816 599 41 10 1 584 302940832 302941425 0.000000e+00 750
11 TraesCS5A01G401100 chr1A 89.626 588 49 9 1 582 567360915 567360334 0.000000e+00 737
12 TraesCS5A01G401100 chr1A 89.545 593 47 10 4 586 570927880 570927293 0.000000e+00 737
13 TraesCS5A01G401100 chrUn 89.848 591 47 11 1 587 11805291 11804710 0.000000e+00 747
14 TraesCS5A01G401100 chr1B 84.034 357 45 8 2260 2610 114601881 114601531 2.100000e-87 333
15 TraesCS5A01G401100 chr2B 81.765 340 52 6 2276 2610 473330777 473330443 3.590000e-70 276
16 TraesCS5A01G401100 chr2B 76.939 477 63 22 2286 2751 142541153 142540713 1.020000e-55 228


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 TraesCS5A01G401100 chr5A 593759407 593763051 3644 False 6732.0 6732 100.0000 1 3645 1 chr5A.!!$F1 3644
1 TraesCS5A01G401100 chr5B 581707878 581711000 3122 True 1590.5 2612 87.5040 681 3645 2 chr5B.!!$R1 2964
2 TraesCS5A01G401100 chr5D 474716788 474719771 2983 False 1536.5 2206 85.4025 678 3645 2 chr5D.!!$F1 2967
3 TraesCS5A01G401100 chr3A 40330474 40331053 579 False 809.0 809 91.9100 1 579 1 chr3A.!!$F1 578
4 TraesCS5A01G401100 chr3A 123292575 123293159 584 True 782.0 782 90.9860 1 579 1 chr3A.!!$R1 578
5 TraesCS5A01G401100 chr3A 600742783 600743372 589 False 758.0 758 90.1860 3 581 1 chr3A.!!$F2 578
6 TraesCS5A01G401100 chr4A 34673220 34673798 578 False 787.0 787 91.3270 1 579 1 chr4A.!!$F1 578
7 TraesCS5A01G401100 chr1A 532237813 532238401 588 False 780.0 780 90.8780 1 579 1 chr1A.!!$F2 578
8 TraesCS5A01G401100 chr1A 302940832 302941425 593 False 750.0 750 89.8160 1 584 1 chr1A.!!$F1 583
9 TraesCS5A01G401100 chr1A 567360334 567360915 581 True 737.0 737 89.6260 1 582 1 chr1A.!!$R1 581
10 TraesCS5A01G401100 chr1A 570927293 570927880 587 True 737.0 737 89.5450 4 586 1 chr1A.!!$R2 582
11 TraesCS5A01G401100 chrUn 11804710 11805291 581 True 747.0 747 89.8480 1 587 1 chrUn.!!$R1 586

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
685 735 0.032615 TCCTCTCCTCTCTGCCTTCC 60.033 60.0 0.0 0.0 0.0 3.46 F
1024 1087 0.033504 TATCCAAATCGCCGAGCCTC 59.966 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1956 0.682209 CACCCCTTTCCTCCTGCATG 60.682 60.0 0.0 0.0 0.0 4.06 R
2721 2915 0.614979 TCAGAAGGTTCGGGAGGGAG 60.615 60.0 0.0 0.0 0.0 4.30 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
463 505 3.360758 GCGCCGTATTTGACTTTTTCAAG 59.639 43.478 0.00 0.00 45.22 3.02
555 605 2.831526 GCAATTTTTAGCCCCTTCTGGA 59.168 45.455 0.00 0.00 35.39 3.86
591 641 4.020128 GCTCTAAGTAGCAGCCGC 57.980 61.111 0.00 0.00 42.30 6.53
592 642 1.946650 GCTCTAAGTAGCAGCCGCG 60.947 63.158 0.00 0.00 45.49 6.46
593 643 1.946650 CTCTAAGTAGCAGCCGCGC 60.947 63.158 0.00 0.00 45.49 6.86
594 644 2.202743 CTAAGTAGCAGCCGCGCA 60.203 61.111 8.75 0.00 45.49 6.09
595 645 2.202743 TAAGTAGCAGCCGCGCAG 60.203 61.111 8.75 0.00 45.49 5.18
616 666 3.648982 CGTCGCAGCAGCAACCAA 61.649 61.111 0.82 0.00 42.27 3.67
617 667 2.050985 GTCGCAGCAGCAACCAAC 60.051 61.111 0.82 0.00 42.27 3.77
618 668 3.648982 TCGCAGCAGCAACCAACG 61.649 61.111 0.82 0.00 42.27 4.10
619 669 3.648982 CGCAGCAGCAACCAACGA 61.649 61.111 0.82 0.00 42.27 3.85
620 670 2.253452 GCAGCAGCAACCAACGAG 59.747 61.111 0.00 0.00 41.58 4.18
621 671 2.546494 GCAGCAGCAACCAACGAGT 61.546 57.895 0.00 0.00 41.58 4.18
622 672 1.227999 GCAGCAGCAACCAACGAGTA 61.228 55.000 0.00 0.00 41.58 2.59
623 673 1.442769 CAGCAGCAACCAACGAGTAT 58.557 50.000 0.00 0.00 0.00 2.12
624 674 1.394917 CAGCAGCAACCAACGAGTATC 59.605 52.381 0.00 0.00 0.00 2.24
625 675 1.001974 AGCAGCAACCAACGAGTATCA 59.998 47.619 0.00 0.00 33.17 2.15
626 676 1.128692 GCAGCAACCAACGAGTATCAC 59.871 52.381 0.00 0.00 33.17 3.06
627 677 1.732259 CAGCAACCAACGAGTATCACC 59.268 52.381 0.00 0.00 33.17 4.02
628 678 0.719465 GCAACCAACGAGTATCACCG 59.281 55.000 0.00 0.00 33.17 4.94
629 679 0.719465 CAACCAACGAGTATCACCGC 59.281 55.000 0.00 0.00 33.17 5.68
630 680 0.319083 AACCAACGAGTATCACCGCA 59.681 50.000 0.00 0.00 33.17 5.69
631 681 0.389426 ACCAACGAGTATCACCGCAC 60.389 55.000 0.00 0.00 33.17 5.34
632 682 1.082117 CCAACGAGTATCACCGCACC 61.082 60.000 0.00 0.00 33.17 5.01
633 683 1.153901 AACGAGTATCACCGCACCG 60.154 57.895 0.00 0.00 33.17 4.94
634 684 1.588824 AACGAGTATCACCGCACCGA 61.589 55.000 0.00 0.00 33.17 4.69
635 685 1.138036 CGAGTATCACCGCACCGAA 59.862 57.895 0.00 0.00 33.17 4.30
636 686 0.866061 CGAGTATCACCGCACCGAAG 60.866 60.000 0.00 0.00 33.17 3.79
637 687 1.146358 GAGTATCACCGCACCGAAGC 61.146 60.000 0.00 0.00 33.17 3.86
638 688 1.447140 GTATCACCGCACCGAAGCA 60.447 57.895 0.24 0.00 0.00 3.91
639 689 1.153647 TATCACCGCACCGAAGCAG 60.154 57.895 0.24 0.00 0.00 4.24
640 690 1.884075 TATCACCGCACCGAAGCAGT 61.884 55.000 0.24 0.00 0.00 4.40
641 691 3.716006 CACCGCACCGAAGCAGTG 61.716 66.667 1.92 1.92 36.68 3.66
642 692 4.235762 ACCGCACCGAAGCAGTGT 62.236 61.111 0.00 0.00 37.56 3.55
643 693 2.048597 CCGCACCGAAGCAGTGTA 60.049 61.111 0.00 0.00 37.56 2.90
644 694 2.094659 CCGCACCGAAGCAGTGTAG 61.095 63.158 0.00 0.00 37.56 2.74
645 695 2.094659 CGCACCGAAGCAGTGTAGG 61.095 63.158 0.00 0.00 37.56 3.18
646 696 2.391389 GCACCGAAGCAGTGTAGGC 61.391 63.158 0.00 0.00 37.56 3.93
647 697 1.005037 CACCGAAGCAGTGTAGGCA 60.005 57.895 0.00 0.00 0.00 4.75
648 698 1.016130 CACCGAAGCAGTGTAGGCAG 61.016 60.000 0.00 0.00 0.00 4.85
649 699 2.103042 CCGAAGCAGTGTAGGCAGC 61.103 63.158 0.00 0.00 0.00 5.25
650 700 2.103042 CGAAGCAGTGTAGGCAGCC 61.103 63.158 1.84 1.84 0.00 4.85
651 701 1.003355 GAAGCAGTGTAGGCAGCCA 60.003 57.895 15.80 0.00 0.00 4.75
652 702 1.301677 GAAGCAGTGTAGGCAGCCAC 61.302 60.000 15.80 10.54 0.00 5.01
653 703 2.032528 GCAGTGTAGGCAGCCACA 59.967 61.111 15.80 13.18 33.99 4.17
654 704 2.328099 GCAGTGTAGGCAGCCACAC 61.328 63.158 27.09 27.09 44.32 3.82
656 706 4.285851 GTGTAGGCAGCCACACTC 57.714 61.111 27.09 16.76 41.46 3.51
657 707 1.738099 GTGTAGGCAGCCACACTCG 60.738 63.158 27.09 0.00 41.46 4.18
658 708 2.815647 GTAGGCAGCCACACTCGC 60.816 66.667 15.80 0.00 0.00 5.03
659 709 2.997315 TAGGCAGCCACACTCGCT 60.997 61.111 15.80 0.00 36.91 4.93
660 710 3.006756 TAGGCAGCCACACTCGCTC 62.007 63.158 15.80 0.00 33.17 5.03
661 711 4.385405 GGCAGCCACACTCGCTCT 62.385 66.667 6.55 0.00 33.17 4.09
662 712 2.813042 GCAGCCACACTCGCTCTC 60.813 66.667 0.00 0.00 33.17 3.20
663 713 2.125753 CAGCCACACTCGCTCTCC 60.126 66.667 0.00 0.00 33.17 3.71
664 714 2.283532 AGCCACACTCGCTCTCCT 60.284 61.111 0.00 0.00 0.00 3.69
665 715 2.183046 GCCACACTCGCTCTCCTC 59.817 66.667 0.00 0.00 0.00 3.71
666 716 2.347322 GCCACACTCGCTCTCCTCT 61.347 63.158 0.00 0.00 0.00 3.69
667 717 1.806568 CCACACTCGCTCTCCTCTC 59.193 63.158 0.00 0.00 0.00 3.20
668 718 1.662438 CCACACTCGCTCTCCTCTCC 61.662 65.000 0.00 0.00 0.00 3.71
669 719 0.679640 CACACTCGCTCTCCTCTCCT 60.680 60.000 0.00 0.00 0.00 3.69
670 720 0.393808 ACACTCGCTCTCCTCTCCTC 60.394 60.000 0.00 0.00 0.00 3.71
671 721 0.107214 CACTCGCTCTCCTCTCCTCT 60.107 60.000 0.00 0.00 0.00 3.69
672 722 0.180406 ACTCGCTCTCCTCTCCTCTC 59.820 60.000 0.00 0.00 0.00 3.20
673 723 0.535102 CTCGCTCTCCTCTCCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
674 724 0.986019 TCGCTCTCCTCTCCTCTCCT 60.986 60.000 0.00 0.00 0.00 3.69
675 725 0.535102 CGCTCTCCTCTCCTCTCCTC 60.535 65.000 0.00 0.00 0.00 3.71
676 726 0.846693 GCTCTCCTCTCCTCTCCTCT 59.153 60.000 0.00 0.00 0.00 3.69
677 727 1.202818 GCTCTCCTCTCCTCTCCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
678 728 2.412591 CTCTCCTCTCCTCTCCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
679 729 2.105477 CTCTCCTCTCCTCTCCTCTCTG 59.895 59.091 0.00 0.00 0.00 3.35
680 730 0.550914 TCCTCTCCTCTCCTCTCTGC 59.449 60.000 0.00 0.00 0.00 4.26
681 731 0.468029 CCTCTCCTCTCCTCTCTGCC 60.468 65.000 0.00 0.00 0.00 4.85
682 732 0.552848 CTCTCCTCTCCTCTCTGCCT 59.447 60.000 0.00 0.00 0.00 4.75
683 733 1.006813 TCTCCTCTCCTCTCTGCCTT 58.993 55.000 0.00 0.00 0.00 4.35
684 734 1.064017 TCTCCTCTCCTCTCTGCCTTC 60.064 57.143 0.00 0.00 0.00 3.46
685 735 0.032615 TCCTCTCCTCTCTGCCTTCC 60.033 60.000 0.00 0.00 0.00 3.46
686 736 0.325110 CCTCTCCTCTCTGCCTTCCA 60.325 60.000 0.00 0.00 0.00 3.53
687 737 0.823460 CTCTCCTCTCTGCCTTCCAC 59.177 60.000 0.00 0.00 0.00 4.02
688 738 0.616111 TCTCCTCTCTGCCTTCCACC 60.616 60.000 0.00 0.00 0.00 4.61
689 739 0.617249 CTCCTCTCTGCCTTCCACCT 60.617 60.000 0.00 0.00 0.00 4.00
690 740 0.616111 TCCTCTCTGCCTTCCACCTC 60.616 60.000 0.00 0.00 0.00 3.85
691 741 1.515020 CTCTCTGCCTTCCACCTCG 59.485 63.158 0.00 0.00 0.00 4.63
703 753 3.118454 ACCTCGCGTCGCCAATTG 61.118 61.111 12.44 0.00 0.00 2.32
742 792 4.244802 GAGTCGCTCCGAGCTCCG 62.245 72.222 18.14 5.92 39.60 4.63
754 804 3.490890 GCTCCGCAGCCTTTACTG 58.509 61.111 0.00 0.00 40.14 2.74
765 815 5.146010 CAGCCTTTACTGCCCAATTAAAA 57.854 39.130 0.00 0.00 0.00 1.52
771 821 5.476091 TTACTGCCCAATTAAAACCCTTG 57.524 39.130 0.00 0.00 0.00 3.61
781 831 5.638530 ATTAAAACCCTTGGCTTCCAAAA 57.361 34.783 0.00 0.00 43.44 2.44
803 854 2.691409 TTTAAGATGCGCTAGTGGCT 57.309 45.000 9.73 0.00 39.13 4.75
811 862 2.034607 CGCTAGTGGCTACTCCTCC 58.965 63.158 5.78 0.00 38.36 4.30
837 888 3.582743 GGCCGTACCGATTCCTAAG 57.417 57.895 0.00 0.00 0.00 2.18
839 890 0.103572 GCCGTACCGATTCCTAAGCA 59.896 55.000 0.00 0.00 0.00 3.91
840 891 1.270147 GCCGTACCGATTCCTAAGCAT 60.270 52.381 0.00 0.00 0.00 3.79
841 892 2.805657 GCCGTACCGATTCCTAAGCATT 60.806 50.000 0.00 0.00 0.00 3.56
842 893 3.463944 CCGTACCGATTCCTAAGCATTT 58.536 45.455 0.00 0.00 0.00 2.32
847 898 5.757850 ACCGATTCCTAAGCATTTCATTC 57.242 39.130 0.00 0.00 0.00 2.67
848 899 4.580580 ACCGATTCCTAAGCATTTCATTCC 59.419 41.667 0.00 0.00 0.00 3.01
849 900 4.580167 CCGATTCCTAAGCATTTCATTCCA 59.420 41.667 0.00 0.00 0.00 3.53
850 901 5.278169 CCGATTCCTAAGCATTTCATTCCAG 60.278 44.000 0.00 0.00 0.00 3.86
851 902 5.297776 CGATTCCTAAGCATTTCATTCCAGT 59.702 40.000 0.00 0.00 0.00 4.00
852 903 5.902613 TTCCTAAGCATTTCATTCCAGTG 57.097 39.130 0.00 0.00 0.00 3.66
853 904 3.696051 TCCTAAGCATTTCATTCCAGTGC 59.304 43.478 0.00 0.00 36.11 4.40
854 905 2.642139 AAGCATTTCATTCCAGTGCG 57.358 45.000 0.00 0.00 40.54 5.34
855 906 1.538047 AGCATTTCATTCCAGTGCGT 58.462 45.000 0.00 0.00 40.54 5.24
856 907 1.200716 AGCATTTCATTCCAGTGCGTG 59.799 47.619 0.00 0.00 40.54 5.34
876 927 3.687102 CGCACTGGGTGGGTCGTA 61.687 66.667 6.57 0.00 40.76 3.43
941 1001 0.179100 CCGGCTCTCACGTGATTCAT 60.179 55.000 20.40 0.00 0.00 2.57
1011 1074 3.630769 CCGCCGTCTAGCTATATATCCAA 59.369 47.826 0.00 0.00 0.00 3.53
1012 1075 4.097437 CCGCCGTCTAGCTATATATCCAAA 59.903 45.833 0.00 0.00 0.00 3.28
1013 1076 5.221263 CCGCCGTCTAGCTATATATCCAAAT 60.221 44.000 0.00 0.00 0.00 2.32
1014 1077 5.915758 CGCCGTCTAGCTATATATCCAAATC 59.084 44.000 0.00 0.00 0.00 2.17
1016 1079 5.915758 CCGTCTAGCTATATATCCAAATCGC 59.084 44.000 0.00 0.00 0.00 4.58
1018 1081 5.915758 GTCTAGCTATATATCCAAATCGCCG 59.084 44.000 0.00 0.00 0.00 6.46
1020 1083 4.938080 AGCTATATATCCAAATCGCCGAG 58.062 43.478 0.00 0.00 0.00 4.63
1021 1084 3.491267 GCTATATATCCAAATCGCCGAGC 59.509 47.826 0.00 0.00 0.00 5.03
1023 1086 0.687354 ATATCCAAATCGCCGAGCCT 59.313 50.000 0.00 0.00 0.00 4.58
1024 1087 0.033504 TATCCAAATCGCCGAGCCTC 59.966 55.000 0.00 0.00 0.00 4.70
1025 1088 2.666596 ATCCAAATCGCCGAGCCTCC 62.667 60.000 0.00 0.00 0.00 4.30
1026 1089 2.125147 CAAATCGCCGAGCCTCCA 60.125 61.111 0.00 0.00 0.00 3.86
1035 1112 4.741239 GAGCCTCCACCCCCTCCA 62.741 72.222 0.00 0.00 0.00 3.86
1040 1117 1.768077 CTCCACCCCCTCCATCTCC 60.768 68.421 0.00 0.00 0.00 3.71
1048 1125 0.755686 CCCTCCATCTCCCTTTCTCG 59.244 60.000 0.00 0.00 0.00 4.04
1052 1129 0.249238 CCATCTCCCTTTCTCGCGAG 60.249 60.000 30.03 30.03 0.00 5.03
1054 1131 1.040339 ATCTCCCTTTCTCGCGAGCT 61.040 55.000 30.97 4.00 0.00 4.09
1055 1132 1.226831 CTCCCTTTCTCGCGAGCTC 60.227 63.158 30.97 2.73 0.00 4.09
1062 1139 4.462417 CTCGCGAGCTCGTCCGTT 62.462 66.667 34.46 0.00 42.22 4.44
1070 1155 2.357517 CTCGTCCGTTTGCCTGCT 60.358 61.111 0.00 0.00 0.00 4.24
1078 1163 0.392998 CGTTTGCCTGCTACCCATCT 60.393 55.000 0.00 0.00 0.00 2.90
1105 1190 4.095410 CTGCTTACAGTCAGAGAGTGAG 57.905 50.000 8.71 0.00 39.22 3.51
1106 1191 3.491342 TGCTTACAGTCAGAGAGTGAGT 58.509 45.455 8.71 0.00 39.67 3.41
1114 1199 2.095263 GTCAGAGAGTGAGTGAGTGAGC 60.095 54.545 0.00 0.00 35.13 4.26
1378 1533 1.403972 GCTGCGTTCTCCGTTCGTAG 61.404 60.000 0.00 0.00 39.48 3.51
1407 1563 1.269723 CGTTTTGCCTTTTCCTCCTCC 59.730 52.381 0.00 0.00 0.00 4.30
1417 1573 4.398358 CCTTTTCCTCCTCCCGTTTAATTC 59.602 45.833 0.00 0.00 0.00 2.17
1698 1864 8.683550 ACGTGTATAATATAACACCATCATCG 57.316 34.615 9.21 0.00 42.39 3.84
1721 1887 5.172053 CGTCAAGAAAGAAACATGCAACTTC 59.828 40.000 0.00 0.00 0.00 3.01
1723 1889 4.228912 AGAAAGAAACATGCAACTTCCG 57.771 40.909 0.00 0.00 0.00 4.30
1725 1891 3.626028 AAGAAACATGCAACTTCCGAC 57.374 42.857 0.00 0.00 0.00 4.79
1738 1904 2.824341 ACTTCCGACTATCGAACCAGTT 59.176 45.455 0.00 0.00 43.74 3.16
1740 1906 3.498927 TCCGACTATCGAACCAGTTTC 57.501 47.619 0.00 0.00 43.74 2.78
1754 1947 3.502211 ACCAGTTTCTAACTTGGAATGCG 59.498 43.478 12.06 0.00 40.46 4.73
1759 1952 3.627395 TCTAACTTGGAATGCGATGGT 57.373 42.857 0.00 0.00 0.00 3.55
1760 1953 3.270027 TCTAACTTGGAATGCGATGGTG 58.730 45.455 0.00 0.00 0.00 4.17
1761 1954 0.527565 AACTTGGAATGCGATGGTGC 59.472 50.000 0.00 0.00 0.00 5.01
2148 2341 4.415783 GGGGACGTTGAGGCATTT 57.584 55.556 0.00 0.00 0.00 2.32
2223 2416 4.415332 TTCCGTCTCGAGGTGCGC 62.415 66.667 13.56 0.00 40.61 6.09
2635 2828 7.173907 CCAGAGAGTTTTAGCTTCATTTTCAGA 59.826 37.037 0.00 0.00 0.00 3.27
2659 2852 9.282569 AGATTTTCTGAATTAGATCATGTAGGC 57.717 33.333 0.00 0.00 34.80 3.93
2712 2906 1.071987 CTTCCAGAGCACTGTGCCA 59.928 57.895 27.74 5.60 46.52 4.92
2721 2915 2.987547 ACTGTGCCATGCCAGTGC 60.988 61.111 9.32 0.00 38.15 4.40
2769 2963 2.160813 GGACGCGGTACATCACATTTTT 59.839 45.455 12.47 0.00 0.00 1.94
2987 3253 4.229876 GCTTCGTAGATTTGCTGCTTTTT 58.770 39.130 0.00 0.00 35.04 1.94
3001 3267 4.481195 TTTTTGCGCTCTGCCTCT 57.519 50.000 9.73 0.00 45.60 3.69
3002 3268 1.951510 TTTTTGCGCTCTGCCTCTG 59.048 52.632 9.73 0.00 45.60 3.35
3003 3269 2.133742 TTTTTGCGCTCTGCCTCTGC 62.134 55.000 9.73 0.00 45.60 4.26
3051 3320 1.888512 TCAGATCCTGCTTTTGTTGGC 59.111 47.619 0.00 0.00 0.00 4.52
3056 3325 0.040067 CCTGCTTTTGTTGGCTCGAC 60.040 55.000 0.00 0.00 0.00 4.20
3068 3337 3.209812 CTCGACGATGAGCCCGGA 61.210 66.667 0.73 0.00 0.00 5.14
3069 3338 3.471244 CTCGACGATGAGCCCGGAC 62.471 68.421 0.73 0.00 0.00 4.79
3070 3339 3.518998 CGACGATGAGCCCGGACT 61.519 66.667 0.73 0.00 0.00 3.85
3071 3340 2.893398 GACGATGAGCCCGGACTT 59.107 61.111 0.73 0.00 0.00 3.01
3074 3343 0.968901 ACGATGAGCCCGGACTTGTA 60.969 55.000 0.73 0.00 0.00 2.41
3075 3344 0.174845 CGATGAGCCCGGACTTGTAA 59.825 55.000 0.73 0.00 0.00 2.41
3076 3345 1.404986 CGATGAGCCCGGACTTGTAAA 60.405 52.381 0.73 0.00 0.00 2.01
3077 3346 2.741878 CGATGAGCCCGGACTTGTAAAT 60.742 50.000 0.73 0.00 0.00 1.40
3078 3347 2.107950 TGAGCCCGGACTTGTAAATG 57.892 50.000 0.73 0.00 0.00 2.32
3080 3349 0.988832 AGCCCGGACTTGTAAATGGA 59.011 50.000 0.73 0.00 0.00 3.41
3081 3350 1.564348 AGCCCGGACTTGTAAATGGAT 59.436 47.619 0.73 0.00 0.00 3.41
3082 3351 1.676006 GCCCGGACTTGTAAATGGATG 59.324 52.381 0.73 0.00 0.00 3.51
3164 3571 1.740296 CGACCGTGGGGATTCACAC 60.740 63.158 0.00 0.00 37.50 3.82
3196 3603 2.868583 CCGACAACAGAGCAGGATAATG 59.131 50.000 0.00 0.00 0.00 1.90
3203 3610 0.767375 GAGCAGGATAATGGAGCCCA 59.233 55.000 0.00 0.00 38.19 5.36
3214 3621 2.054453 GGAGCCCAGGACATTTGCC 61.054 63.158 0.00 0.00 0.00 4.52
3237 3644 3.632145 AGTGGGGTGAAATTCGATAATGC 59.368 43.478 0.00 0.00 0.00 3.56
3267 3674 9.286946 CACTTTATGTCTTTTAGTACTCCGTAG 57.713 37.037 0.00 0.00 0.00 3.51
3273 3680 9.796180 ATGTCTTTTAGTACTCCGTAGATAGAT 57.204 33.333 0.00 0.00 0.00 1.98
3283 3690 4.825422 TCCGTAGATAGATAGTACCGGTG 58.175 47.826 19.93 0.00 0.00 4.94
3347 3766 2.281484 TGTCTGGCTCGGTTTGGC 60.281 61.111 0.00 0.00 0.00 4.52
3385 3804 2.675317 GCTAGAATCAGCAACGTCCAGT 60.675 50.000 0.00 0.00 41.40 4.00
3387 3806 1.079503 GAATCAGCAACGTCCAGTCC 58.920 55.000 0.00 0.00 0.00 3.85
3388 3807 0.396435 AATCAGCAACGTCCAGTCCA 59.604 50.000 0.00 0.00 0.00 4.02
3390 3809 1.112916 TCAGCAACGTCCAGTCCAGA 61.113 55.000 0.00 0.00 0.00 3.86
3411 3830 3.784338 ACTGGTCTGTTCGTTCGTAAAA 58.216 40.909 0.00 0.00 0.00 1.52
3418 3837 3.668100 TGTTCGTTCGTAAAACCAAACG 58.332 40.909 0.00 0.00 44.25 3.60
3420 3839 1.004079 TCGTTCGTAAAACCAAACGGC 60.004 47.619 6.64 0.00 43.37 5.68
3452 3871 0.475044 TAATGATTGGCCCCGTACCC 59.525 55.000 0.00 0.00 0.00 3.69
3464 3883 0.390603 CCGTACCCTGCAATCGACAA 60.391 55.000 0.00 0.00 0.00 3.18
3465 3884 1.434555 CGTACCCTGCAATCGACAAA 58.565 50.000 0.00 0.00 0.00 2.83
3468 3887 0.591170 ACCCTGCAATCGACAAAACG 59.409 50.000 0.00 0.00 0.00 3.60
3487 3906 1.445716 GGAGAGTGATGCATGCTGGC 61.446 60.000 20.33 8.58 0.00 4.85
3516 3936 2.173669 CGGGCGGCTGATACTGTTG 61.174 63.158 13.52 0.00 0.00 3.33
3547 3967 2.490903 AGATTTGCAGGTGTCATTGCTC 59.509 45.455 11.93 3.93 40.87 4.26
3563 3989 1.864711 TGCTCGTACTGCAACAAACTC 59.135 47.619 7.76 0.00 37.51 3.01
3575 4001 0.535102 ACAAACTCAACTCCCTGGCG 60.535 55.000 0.00 0.00 0.00 5.69
3576 4002 1.073199 AAACTCAACTCCCTGGCGG 59.927 57.895 0.00 0.00 0.00 6.13
3577 4003 1.705997 AAACTCAACTCCCTGGCGGT 61.706 55.000 0.00 0.00 0.00 5.68
3578 4004 0.834687 AACTCAACTCCCTGGCGGTA 60.835 55.000 0.00 0.00 0.00 4.02
3579 4005 0.617820 ACTCAACTCCCTGGCGGTAT 60.618 55.000 0.00 0.00 0.00 2.73
3589 4015 1.270305 CCTGGCGGTATGTATGTCCAG 60.270 57.143 0.00 0.00 40.43 3.86
3634 4060 0.994995 CGAATTGACTCCACAGAGCG 59.005 55.000 0.00 0.00 44.65 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 194 4.559063 CTGCTGCATCCCTCCCCG 62.559 72.222 1.31 0.00 0.00 5.73
228 247 0.023103 GTAGTCGTCGTCGTCGTCTC 59.977 60.000 13.60 5.87 38.33 3.36
229 248 0.664466 TGTAGTCGTCGTCGTCGTCT 60.664 55.000 14.42 14.42 38.33 4.18
240 268 0.166814 GTAGAACCGCGTGTAGTCGT 59.833 55.000 4.92 0.00 0.00 4.34
409 450 6.457799 GGCTCAAATTTATCGTAAACATCGGT 60.458 38.462 0.00 0.00 0.00 4.69
463 505 0.725784 CAGTCGCGGTGCATGTTTTC 60.726 55.000 6.13 0.00 0.00 2.29
523 571 4.466370 GGCTAAAAATTGCTCTTTAGGGGT 59.534 41.667 8.66 0.00 36.20 4.95
528 577 6.016555 AGAAGGGGCTAAAAATTGCTCTTTA 58.983 36.000 0.00 0.00 29.03 1.85
601 651 3.648982 CGTTGGTTGCTGCTGCGA 61.649 61.111 11.21 6.22 43.34 5.10
602 652 3.584250 CTCGTTGGTTGCTGCTGCG 62.584 63.158 11.21 0.00 43.34 5.18
603 653 1.227999 TACTCGTTGGTTGCTGCTGC 61.228 55.000 8.89 8.89 40.20 5.25
604 654 1.394917 GATACTCGTTGGTTGCTGCTG 59.605 52.381 0.00 0.00 0.00 4.41
605 655 1.001974 TGATACTCGTTGGTTGCTGCT 59.998 47.619 0.00 0.00 0.00 4.24
606 656 1.128692 GTGATACTCGTTGGTTGCTGC 59.871 52.381 0.00 0.00 0.00 5.25
607 657 1.732259 GGTGATACTCGTTGGTTGCTG 59.268 52.381 0.00 0.00 0.00 4.41
608 658 1.671850 CGGTGATACTCGTTGGTTGCT 60.672 52.381 0.00 0.00 0.00 3.91
609 659 0.719465 CGGTGATACTCGTTGGTTGC 59.281 55.000 0.00 0.00 0.00 4.17
610 660 0.719465 GCGGTGATACTCGTTGGTTG 59.281 55.000 0.00 0.00 0.00 3.77
611 661 0.319083 TGCGGTGATACTCGTTGGTT 59.681 50.000 0.00 0.00 0.00 3.67
612 662 0.389426 GTGCGGTGATACTCGTTGGT 60.389 55.000 0.00 0.00 0.00 3.67
613 663 1.082117 GGTGCGGTGATACTCGTTGG 61.082 60.000 0.00 0.00 0.00 3.77
614 664 1.410737 CGGTGCGGTGATACTCGTTG 61.411 60.000 0.00 0.00 0.00 4.10
615 665 1.153901 CGGTGCGGTGATACTCGTT 60.154 57.895 0.00 0.00 0.00 3.85
616 666 1.588824 TTCGGTGCGGTGATACTCGT 61.589 55.000 0.00 0.00 0.00 4.18
617 667 0.866061 CTTCGGTGCGGTGATACTCG 60.866 60.000 0.00 0.00 0.00 4.18
618 668 1.146358 GCTTCGGTGCGGTGATACTC 61.146 60.000 0.00 0.00 0.00 2.59
619 669 1.153628 GCTTCGGTGCGGTGATACT 60.154 57.895 0.00 0.00 0.00 2.12
620 670 1.421410 CTGCTTCGGTGCGGTGATAC 61.421 60.000 2.02 0.00 34.82 2.24
621 671 1.153647 CTGCTTCGGTGCGGTGATA 60.154 57.895 2.02 0.00 34.82 2.15
622 672 2.434884 CTGCTTCGGTGCGGTGAT 60.435 61.111 2.02 0.00 34.82 3.06
626 676 2.048597 TACACTGCTTCGGTGCGG 60.049 61.111 5.75 7.63 43.84 5.69
627 677 2.094659 CCTACACTGCTTCGGTGCG 61.095 63.158 5.75 0.00 43.84 5.34
628 678 2.391389 GCCTACACTGCTTCGGTGC 61.391 63.158 5.75 0.00 43.84 5.01
629 679 1.005037 TGCCTACACTGCTTCGGTG 60.005 57.895 4.38 4.38 45.33 4.94
630 680 1.293498 CTGCCTACACTGCTTCGGT 59.707 57.895 0.00 0.00 0.00 4.69
631 681 2.103042 GCTGCCTACACTGCTTCGG 61.103 63.158 0.00 0.00 0.00 4.30
632 682 2.103042 GGCTGCCTACACTGCTTCG 61.103 63.158 12.43 0.00 35.11 3.79
633 683 1.003355 TGGCTGCCTACACTGCTTC 60.003 57.895 21.03 0.00 35.11 3.86
634 684 1.302832 GTGGCTGCCTACACTGCTT 60.303 57.895 21.03 0.00 34.84 3.91
635 685 2.348998 GTGGCTGCCTACACTGCT 59.651 61.111 21.03 0.00 34.84 4.24
636 686 2.032528 TGTGGCTGCCTACACTGC 59.967 61.111 21.03 2.21 38.39 4.40
637 687 3.972227 GTGTGGCTGCCTACACTG 58.028 61.111 30.12 0.00 42.86 3.66
639 689 1.738099 CGAGTGTGGCTGCCTACAC 60.738 63.158 30.20 30.20 45.68 2.90
640 690 2.656646 CGAGTGTGGCTGCCTACA 59.343 61.111 21.03 18.36 0.00 2.74
641 691 2.815647 GCGAGTGTGGCTGCCTAC 60.816 66.667 21.03 17.92 0.00 3.18
642 692 2.997315 AGCGAGTGTGGCTGCCTA 60.997 61.111 21.03 6.16 39.77 3.93
643 693 4.385405 GAGCGAGTGTGGCTGCCT 62.385 66.667 21.03 0.00 41.72 4.75
644 694 4.385405 AGAGCGAGTGTGGCTGCC 62.385 66.667 12.87 12.87 41.72 4.85
645 695 2.813042 GAGAGCGAGTGTGGCTGC 60.813 66.667 0.00 0.00 41.72 5.25
646 696 2.125753 GGAGAGCGAGTGTGGCTG 60.126 66.667 0.00 0.00 41.72 4.85
647 697 2.283532 AGGAGAGCGAGTGTGGCT 60.284 61.111 0.00 0.00 45.00 4.75
648 698 2.183046 GAGGAGAGCGAGTGTGGC 59.817 66.667 0.00 0.00 0.00 5.01
649 699 1.662438 GGAGAGGAGAGCGAGTGTGG 61.662 65.000 0.00 0.00 0.00 4.17
650 700 0.679640 AGGAGAGGAGAGCGAGTGTG 60.680 60.000 0.00 0.00 0.00 3.82
651 701 0.393808 GAGGAGAGGAGAGCGAGTGT 60.394 60.000 0.00 0.00 0.00 3.55
652 702 0.107214 AGAGGAGAGGAGAGCGAGTG 60.107 60.000 0.00 0.00 0.00 3.51
653 703 0.180406 GAGAGGAGAGGAGAGCGAGT 59.820 60.000 0.00 0.00 0.00 4.18
654 704 0.535102 GGAGAGGAGAGGAGAGCGAG 60.535 65.000 0.00 0.00 0.00 5.03
655 705 0.986019 AGGAGAGGAGAGGAGAGCGA 60.986 60.000 0.00 0.00 0.00 4.93
656 706 0.535102 GAGGAGAGGAGAGGAGAGCG 60.535 65.000 0.00 0.00 0.00 5.03
657 707 0.846693 AGAGGAGAGGAGAGGAGAGC 59.153 60.000 0.00 0.00 0.00 4.09
658 708 2.105477 CAGAGAGGAGAGGAGAGGAGAG 59.895 59.091 0.00 0.00 0.00 3.20
659 709 2.126882 CAGAGAGGAGAGGAGAGGAGA 58.873 57.143 0.00 0.00 0.00 3.71
660 710 1.477558 GCAGAGAGGAGAGGAGAGGAG 60.478 61.905 0.00 0.00 0.00 3.69
661 711 0.550914 GCAGAGAGGAGAGGAGAGGA 59.449 60.000 0.00 0.00 0.00 3.71
662 712 0.468029 GGCAGAGAGGAGAGGAGAGG 60.468 65.000 0.00 0.00 0.00 3.69
663 713 0.552848 AGGCAGAGAGGAGAGGAGAG 59.447 60.000 0.00 0.00 0.00 3.20
664 714 1.006813 AAGGCAGAGAGGAGAGGAGA 58.993 55.000 0.00 0.00 0.00 3.71
665 715 1.402787 GAAGGCAGAGAGGAGAGGAG 58.597 60.000 0.00 0.00 0.00 3.69
666 716 0.032615 GGAAGGCAGAGAGGAGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
667 717 0.325110 TGGAAGGCAGAGAGGAGAGG 60.325 60.000 0.00 0.00 0.00 3.69
668 718 0.823460 GTGGAAGGCAGAGAGGAGAG 59.177 60.000 0.00 0.00 0.00 3.20
669 719 0.616111 GGTGGAAGGCAGAGAGGAGA 60.616 60.000 0.00 0.00 0.00 3.71
670 720 0.617249 AGGTGGAAGGCAGAGAGGAG 60.617 60.000 0.00 0.00 0.00 3.69
671 721 0.616111 GAGGTGGAAGGCAGAGAGGA 60.616 60.000 0.00 0.00 0.00 3.71
672 722 1.904032 GAGGTGGAAGGCAGAGAGG 59.096 63.158 0.00 0.00 0.00 3.69
673 723 1.515020 CGAGGTGGAAGGCAGAGAG 59.485 63.158 0.00 0.00 0.00 3.20
674 724 2.650116 GCGAGGTGGAAGGCAGAGA 61.650 63.158 0.00 0.00 0.00 3.10
675 725 2.125350 GCGAGGTGGAAGGCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
676 726 4.069232 CGCGAGGTGGAAGGCAGA 62.069 66.667 0.00 0.00 0.00 4.26
677 727 4.379243 ACGCGAGGTGGAAGGCAG 62.379 66.667 15.93 0.00 0.00 4.85
678 728 4.373116 GACGCGAGGTGGAAGGCA 62.373 66.667 15.93 0.00 0.00 4.75
685 735 3.118454 AATTGGCGACGCGAGGTG 61.118 61.111 15.93 0.00 0.00 4.00
686 736 3.118454 CAATTGGCGACGCGAGGT 61.118 61.111 15.93 0.00 0.00 3.85
687 737 1.906994 TTTCAATTGGCGACGCGAGG 61.907 55.000 15.93 4.68 0.00 4.63
688 738 0.110419 TTTTCAATTGGCGACGCGAG 60.110 50.000 15.93 7.68 0.00 5.03
689 739 0.110419 CTTTTCAATTGGCGACGCGA 60.110 50.000 15.93 7.20 0.00 5.87
690 740 1.664643 GCTTTTCAATTGGCGACGCG 61.665 55.000 14.61 3.53 0.00 6.01
691 741 1.344226 GGCTTTTCAATTGGCGACGC 61.344 55.000 12.43 12.43 0.00 5.19
752 802 2.615240 GCCAAGGGTTTTAATTGGGCAG 60.615 50.000 6.86 0.00 43.06 4.85
754 804 1.628340 AGCCAAGGGTTTTAATTGGGC 59.372 47.619 6.86 0.00 43.06 5.36
765 815 2.174685 AAGTTTTGGAAGCCAAGGGT 57.825 45.000 0.00 0.00 44.84 4.34
771 821 4.385748 CGCATCTTAAAAGTTTTGGAAGCC 59.614 41.667 11.18 3.28 0.00 4.35
781 831 2.678336 GCCACTAGCGCATCTTAAAAGT 59.322 45.455 11.47 0.00 0.00 2.66
803 854 4.593033 CCGATTCGGGGAGGAGTA 57.407 61.111 17.53 0.00 44.15 2.59
837 888 1.621107 CACGCACTGGAATGAAATGC 58.379 50.000 0.00 0.00 0.00 3.56
839 890 1.176527 CCCACGCACTGGAATGAAAT 58.823 50.000 0.00 0.00 43.95 2.17
840 891 1.523154 GCCCACGCACTGGAATGAAA 61.523 55.000 0.00 0.00 43.95 2.69
841 892 1.971167 GCCCACGCACTGGAATGAA 60.971 57.895 0.00 0.00 43.95 2.57
842 893 2.359850 GCCCACGCACTGGAATGA 60.360 61.111 0.00 0.00 43.95 2.57
859 910 3.642778 CTACGACCCACCCAGTGCG 62.643 68.421 0.00 0.00 31.34 5.34
860 911 1.252904 TACTACGACCCACCCAGTGC 61.253 60.000 0.00 0.00 31.34 4.40
863 914 1.203994 CAGTTACTACGACCCACCCAG 59.796 57.143 0.00 0.00 0.00 4.45
866 917 2.163211 GTCTCAGTTACTACGACCCACC 59.837 54.545 0.00 0.00 0.00 4.61
870 921 1.202121 GCCGTCTCAGTTACTACGACC 60.202 57.143 7.62 0.00 37.53 4.79
876 927 2.214181 CTGCCGCCGTCTCAGTTACT 62.214 60.000 0.00 0.00 0.00 2.24
902 961 0.461163 GAAGGAGGAGGCGCTCTTTC 60.461 60.000 7.64 5.37 0.00 2.62
916 975 3.068691 CGTGAGAGCCGGGAAGGA 61.069 66.667 2.18 0.00 45.00 3.36
924 983 2.474816 GGTATGAATCACGTGAGAGCC 58.525 52.381 24.41 14.83 0.00 4.70
1011 1074 4.162690 GGTGGAGGCTCGGCGATT 62.163 66.667 11.27 0.00 0.00 3.34
1018 1081 4.741239 TGGAGGGGGTGGAGGCTC 62.741 72.222 5.78 5.78 0.00 4.70
1020 1083 3.493303 GATGGAGGGGGTGGAGGC 61.493 72.222 0.00 0.00 0.00 4.70
1021 1084 1.768077 GAGATGGAGGGGGTGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
1023 1086 2.372688 GGAGATGGAGGGGGTGGA 59.627 66.667 0.00 0.00 0.00 4.02
1024 1087 2.774351 GGGAGATGGAGGGGGTGG 60.774 72.222 0.00 0.00 0.00 4.61
1025 1088 0.921256 AAAGGGAGATGGAGGGGGTG 60.921 60.000 0.00 0.00 0.00 4.61
1026 1089 0.624795 GAAAGGGAGATGGAGGGGGT 60.625 60.000 0.00 0.00 0.00 4.95
1029 1106 0.755686 CGAGAAAGGGAGATGGAGGG 59.244 60.000 0.00 0.00 0.00 4.30
1030 1107 0.105778 GCGAGAAAGGGAGATGGAGG 59.894 60.000 0.00 0.00 0.00 4.30
1033 1110 1.816537 TCGCGAGAAAGGGAGATGG 59.183 57.895 3.71 0.00 37.03 3.51
1040 1117 1.870016 GACGAGCTCGCGAGAAAGG 60.870 63.158 38.74 24.26 44.43 3.11
1048 1125 4.135493 GCAAACGGACGAGCTCGC 62.135 66.667 34.83 25.65 44.43 5.03
1052 1129 4.090057 GCAGGCAAACGGACGAGC 62.090 66.667 0.00 0.00 0.00 5.03
1054 1131 1.373748 GTAGCAGGCAAACGGACGA 60.374 57.895 0.00 0.00 0.00 4.20
1055 1132 2.388232 GGTAGCAGGCAAACGGACG 61.388 63.158 0.00 0.00 0.00 4.79
1062 1139 1.838112 CAAAGATGGGTAGCAGGCAA 58.162 50.000 0.00 0.00 0.00 4.52
1070 1155 2.584835 AAGCAGTGCAAAGATGGGTA 57.415 45.000 19.20 0.00 0.00 3.69
1098 1183 1.164411 CTCGCTCACTCACTCACTCT 58.836 55.000 0.00 0.00 0.00 3.24
1099 1184 0.455972 GCTCGCTCACTCACTCACTC 60.456 60.000 0.00 0.00 0.00 3.51
1100 1185 0.893270 AGCTCGCTCACTCACTCACT 60.893 55.000 0.00 0.00 0.00 3.41
1101 1186 0.455972 GAGCTCGCTCACTCACTCAC 60.456 60.000 13.69 0.00 42.31 3.51
1102 1187 1.879480 GAGCTCGCTCACTCACTCA 59.121 57.895 13.69 0.00 42.31 3.41
1103 1188 1.226267 CGAGCTCGCTCACTCACTC 60.226 63.158 25.07 0.00 42.86 3.51
1104 1189 1.029408 ATCGAGCTCGCTCACTCACT 61.029 55.000 30.97 4.00 42.86 3.41
1105 1190 0.591236 GATCGAGCTCGCTCACTCAC 60.591 60.000 29.52 6.70 42.86 3.51
1106 1191 1.724467 GATCGAGCTCGCTCACTCA 59.276 57.895 29.52 13.79 42.86 3.41
1107 1192 1.368731 CGATCGAGCTCGCTCACTC 60.369 63.158 32.04 20.57 42.86 3.51
1108 1193 2.712539 CGATCGAGCTCGCTCACT 59.287 61.111 32.04 15.43 42.86 3.41
1109 1194 2.352915 CCGATCGAGCTCGCTCAC 60.353 66.667 32.04 20.65 42.86 3.51
1110 1195 2.824489 ACCGATCGAGCTCGCTCA 60.824 61.111 32.04 18.03 42.86 4.26
1131 1216 1.303561 GCCACTGCCTCAACCATGA 60.304 57.895 0.00 0.00 0.00 3.07
1164 1264 3.740397 CGTCGTACTCCCGCACCA 61.740 66.667 0.00 0.00 0.00 4.17
1378 1533 5.124936 AGGAAAAGGCAAAACGGATATACAC 59.875 40.000 0.00 0.00 0.00 2.90
1407 1563 1.734163 AGCGACAGGGAATTAAACGG 58.266 50.000 0.00 0.00 0.00 4.44
1451 1607 7.322699 ACATGCGTTTCGAGTTAATTAGTTTTG 59.677 33.333 0.00 0.00 0.00 2.44
1600 1766 2.035783 GGGGTCCTTGTCCTTGGC 59.964 66.667 0.00 0.00 0.00 4.52
1602 1768 0.995024 AGATGGGGTCCTTGTCCTTG 59.005 55.000 0.00 0.00 0.00 3.61
1603 1769 2.197465 GTAGATGGGGTCCTTGTCCTT 58.803 52.381 0.00 0.00 0.00 3.36
1604 1770 1.080498 TGTAGATGGGGTCCTTGTCCT 59.920 52.381 0.00 0.00 0.00 3.85
1605 1771 1.209747 GTGTAGATGGGGTCCTTGTCC 59.790 57.143 0.00 0.00 0.00 4.02
1606 1772 1.209747 GGTGTAGATGGGGTCCTTGTC 59.790 57.143 0.00 0.00 0.00 3.18
1607 1773 1.286248 GGTGTAGATGGGGTCCTTGT 58.714 55.000 0.00 0.00 0.00 3.16
1687 1853 4.271696 TCTTTCTTGACGATGATGGTGT 57.728 40.909 0.00 0.00 0.00 4.16
1698 1864 5.460091 GGAAGTTGCATGTTTCTTTCTTGAC 59.540 40.000 0.00 0.00 0.00 3.18
1721 1887 3.505464 AGAAACTGGTTCGATAGTCGG 57.495 47.619 0.00 0.00 41.52 4.79
1723 1889 6.310711 CCAAGTTAGAAACTGGTTCGATAGTC 59.689 42.308 0.00 0.00 41.91 2.59
1725 1891 6.395629 TCCAAGTTAGAAACTGGTTCGATAG 58.604 40.000 0.00 0.00 41.91 2.08
1738 1904 3.689161 CACCATCGCATTCCAAGTTAGAA 59.311 43.478 0.00 0.00 0.00 2.10
1740 1906 2.223340 GCACCATCGCATTCCAAGTTAG 60.223 50.000 0.00 0.00 0.00 2.34
1754 1947 2.825387 TCCTGCATGCGCACCATC 60.825 61.111 14.90 2.20 45.36 3.51
1760 1953 2.768492 CCTTTCCTCCTGCATGCGC 61.768 63.158 14.09 0.00 39.24 6.09
1761 1954 2.117156 CCCTTTCCTCCTGCATGCG 61.117 63.158 14.09 7.87 0.00 4.73
1763 1956 0.682209 CACCCCTTTCCTCCTGCATG 60.682 60.000 0.00 0.00 0.00 4.06
1764 1957 1.693640 CACCCCTTTCCTCCTGCAT 59.306 57.895 0.00 0.00 0.00 3.96
1765 1958 2.538141 CCACCCCTTTCCTCCTGCA 61.538 63.158 0.00 0.00 0.00 4.41
2635 2828 9.638176 AAGCCTACATGATCTAATTCAGAAAAT 57.362 29.630 0.00 0.00 36.67 1.82
2712 2906 3.415087 GGGAGGGAGCACTGGCAT 61.415 66.667 0.00 0.00 44.61 4.40
2721 2915 0.614979 TCAGAAGGTTCGGGAGGGAG 60.615 60.000 0.00 0.00 0.00 4.30
2783 2977 3.118905 AGTTGAAACAGAGAGCACTCC 57.881 47.619 7.60 0.00 43.53 3.85
2867 3082 3.179443 ACTCAGCTCTGTCGACAAAAA 57.821 42.857 20.49 7.21 0.00 1.94
2868 3083 2.890808 ACTCAGCTCTGTCGACAAAA 57.109 45.000 20.49 9.80 0.00 2.44
2869 3084 2.351835 GCTACTCAGCTCTGTCGACAAA 60.352 50.000 20.49 5.35 44.93 2.83
3003 3269 2.106683 GGAAGGGGATGCGTCAACG 61.107 63.158 8.47 0.00 43.27 4.10
3004 3270 1.749258 GGGAAGGGGATGCGTCAAC 60.749 63.158 8.47 0.00 0.00 3.18
3005 3271 2.674754 GGGAAGGGGATGCGTCAA 59.325 61.111 8.47 0.00 0.00 3.18
3006 3272 3.407967 GGGGAAGGGGATGCGTCA 61.408 66.667 8.47 0.00 0.00 4.35
3051 3320 3.209812 TCCGGGCTCATCGTCGAG 61.210 66.667 0.00 0.27 36.02 4.04
3056 3325 0.174845 TTACAAGTCCGGGCTCATCG 59.825 55.000 10.20 0.31 0.00 3.84
3068 3337 1.745087 CAGCGGCATCCATTTACAAGT 59.255 47.619 1.45 0.00 0.00 3.16
3069 3338 1.534595 GCAGCGGCATCCATTTACAAG 60.535 52.381 3.18 0.00 40.72 3.16
3070 3339 0.455410 GCAGCGGCATCCATTTACAA 59.545 50.000 3.18 0.00 40.72 2.41
3071 3340 1.713937 CGCAGCGGCATCCATTTACA 61.714 55.000 7.00 0.00 41.24 2.41
3074 3343 2.751436 ACGCAGCGGCATCCATTT 60.751 55.556 21.15 0.00 41.24 2.32
3075 3344 3.511595 CACGCAGCGGCATCCATT 61.512 61.111 21.15 0.00 41.24 3.16
3080 3349 2.359354 TAAACCACGCAGCGGCAT 60.359 55.556 21.15 0.00 41.24 4.40
3081 3350 3.350612 GTAAACCACGCAGCGGCA 61.351 61.111 21.15 0.00 41.24 5.69
3082 3351 4.439472 CGTAAACCACGCAGCGGC 62.439 66.667 21.15 0.00 45.03 6.53
3164 3571 0.320683 TGTTGTCGGCTGATCTGTGG 60.321 55.000 0.00 0.00 0.00 4.17
3169 3576 0.390340 TGCTCTGTTGTCGGCTGATC 60.390 55.000 0.00 0.00 0.00 2.92
3196 3603 2.054453 GGCAAATGTCCTGGGCTCC 61.054 63.158 0.00 0.00 0.00 4.70
3203 3610 1.077265 CCCCACTGGCAAATGTCCT 59.923 57.895 0.00 0.00 0.00 3.85
3214 3621 4.498009 GCATTATCGAATTTCACCCCACTG 60.498 45.833 0.00 0.00 0.00 3.66
3237 3644 9.152595 GGAGTACTAAAAGACATAAAGTGGAAG 57.847 37.037 0.00 0.00 0.00 3.46
3267 3674 4.868314 AAAGGCACCGGTACTATCTATC 57.132 45.455 6.87 0.00 0.00 2.08
3272 3679 1.211212 GGGAAAAGGCACCGGTACTAT 59.789 52.381 6.87 1.40 0.00 2.12
3273 3680 0.614812 GGGAAAAGGCACCGGTACTA 59.385 55.000 6.87 0.00 0.00 1.82
3274 3681 1.377612 GGGAAAAGGCACCGGTACT 59.622 57.895 6.87 5.85 0.00 2.73
3275 3682 1.676635 GGGGAAAAGGCACCGGTAC 60.677 63.158 6.87 0.00 0.00 3.34
3347 3766 4.005650 TCTAGCAGCAATGGTTTTCTGAG 58.994 43.478 0.00 0.00 0.00 3.35
3388 3807 1.030457 ACGAACGAACAGACCAGTCT 58.970 50.000 0.14 0.00 41.37 3.24
3390 3809 3.441496 TTTACGAACGAACAGACCAGT 57.559 42.857 0.14 0.00 0.00 4.00
3393 3812 2.865551 TGGTTTTACGAACGAACAGACC 59.134 45.455 0.14 3.52 0.00 3.85
3394 3813 4.519191 TTGGTTTTACGAACGAACAGAC 57.481 40.909 0.14 0.00 0.00 3.51
3395 3814 4.896080 GTTTGGTTTTACGAACGAACAGA 58.104 39.130 0.14 0.00 0.00 3.41
3403 3822 1.267932 CGTGCCGTTTGGTTTTACGAA 60.268 47.619 0.00 0.00 40.03 3.85
3411 3830 3.409605 AAGGTCCGTGCCGTTTGGT 62.410 57.895 0.00 0.00 37.67 3.67
3418 3837 1.134220 TCATTATGGAAGGTCCGTGCC 60.134 52.381 0.00 0.00 40.17 5.01
3420 3839 3.565482 CCAATCATTATGGAAGGTCCGTG 59.435 47.826 0.00 0.00 40.17 4.94
3424 3843 2.893489 GGGCCAATCATTATGGAAGGTC 59.107 50.000 4.39 0.00 40.56 3.85
3429 3848 0.850100 ACGGGGCCAATCATTATGGA 59.150 50.000 4.39 0.00 40.56 3.41
3430 3849 2.159382 GTACGGGGCCAATCATTATGG 58.841 52.381 4.39 0.00 41.08 2.74
3431 3850 2.159382 GGTACGGGGCCAATCATTATG 58.841 52.381 4.39 0.00 0.00 1.90
3432 3851 1.074889 GGGTACGGGGCCAATCATTAT 59.925 52.381 4.39 0.00 0.00 1.28
3452 3871 1.798223 TCTCCGTTTTGTCGATTGCAG 59.202 47.619 0.00 0.00 0.00 4.41
3464 3883 1.089920 GCATGCATCACTCTCCGTTT 58.910 50.000 14.21 0.00 0.00 3.60
3465 3884 0.251354 AGCATGCATCACTCTCCGTT 59.749 50.000 21.98 0.00 0.00 4.44
3468 3887 1.445716 GCCAGCATGCATCACTCTCC 61.446 60.000 21.98 0.00 31.97 3.71
3487 3906 2.331805 CCGCCCGATCGTACTCTG 59.668 66.667 15.09 0.00 0.00 3.35
3547 3967 3.303132 GGAGTTGAGTTTGTTGCAGTACG 60.303 47.826 0.00 0.00 0.00 3.67
3563 3989 0.828022 TACATACCGCCAGGGAGTTG 59.172 55.000 0.00 0.00 43.47 3.16
3575 4001 4.444449 GGGAAAGTCCTGGACATACATACC 60.444 50.000 27.48 18.11 36.57 2.73
3576 4002 4.444449 GGGGAAAGTCCTGGACATACATAC 60.444 50.000 27.48 11.48 36.57 2.39
3577 4003 3.714798 GGGGAAAGTCCTGGACATACATA 59.285 47.826 27.48 0.00 36.57 2.29
3578 4004 2.509964 GGGGAAAGTCCTGGACATACAT 59.490 50.000 27.48 9.26 36.57 2.29
3579 4005 1.913419 GGGGAAAGTCCTGGACATACA 59.087 52.381 27.48 0.00 36.57 2.29


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

AutoCloner maintained by Alex Coulton.