Multiple sequence alignment - TraesCS1B01G165000

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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 TraesCS1B01G165000 chr1B 100.000 3469 0 0 1 3469 288172958 288169490 0.000000e+00 6407
1 TraesCS1B01G165000 chr1B 80.854 726 114 15 1 715 211628921 211629632 6.550000e-152 547
2 TraesCS1B01G165000 chr1A 94.332 1870 84 8 934 2802 252772058 252773906 0.000000e+00 2846
3 TraesCS1B01G165000 chr1A 86.957 667 65 11 2816 3467 351585677 351586336 0.000000e+00 730
4 TraesCS1B01G165000 chr1A 92.647 272 13 3 1030 1300 252734170 252734435 5.430000e-103 385
5 TraesCS1B01G165000 chr7D 88.626 677 44 16 2809 3469 178140787 178140128 0.000000e+00 793
6 TraesCS1B01G165000 chr7D 84.672 685 78 17 2805 3469 562386930 562386253 0.000000e+00 658
7 TraesCS1B01G165000 chr7D 87.421 159 19 1 711 869 554908840 554908683 7.650000e-42 182
8 TraesCS1B01G165000 chr4A 87.556 667 75 6 2805 3469 434041164 434040504 0.000000e+00 765
9 TraesCS1B01G165000 chr6D 87.209 688 63 9 2803 3469 285245327 285244644 0.000000e+00 760
10 TraesCS1B01G165000 chr6D 87.353 680 64 7 2805 3469 314624673 314624001 0.000000e+00 760
11 TraesCS1B01G165000 chr6D 86.291 693 63 17 2805 3469 411186857 411187545 0.000000e+00 725
12 TraesCS1B01G165000 chr6D 77.844 334 70 3 1276 1607 432672534 432672203 1.630000e-48 204
13 TraesCS1B01G165000 chr5D 85.379 725 89 14 1 713 256627416 256626697 0.000000e+00 736
14 TraesCS1B01G165000 chr6A 85.322 729 84 18 1 710 108938432 108939156 0.000000e+00 732
15 TraesCS1B01G165000 chr6A 78.638 426 72 14 1194 1605 578926117 578926537 7.380000e-67 265
16 TraesCS1B01G165000 chr1D 86.337 688 63 12 2805 3469 453303077 453302398 0.000000e+00 721
17 TraesCS1B01G165000 chr1D 85.116 692 54 25 2805 3469 63883159 63882490 0.000000e+00 662
18 TraesCS1B01G165000 chr1D 83.176 743 93 19 1 724 351510403 351509674 0.000000e+00 651
19 TraesCS1B01G165000 chr1D 85.816 282 27 10 2805 3080 455548342 455548616 1.580000e-73 287
20 TraesCS1B01G165000 chr4D 84.840 719 99 7 1 710 15312993 15313710 0.000000e+00 715
21 TraesCS1B01G165000 chr4D 89.777 538 52 3 2805 3341 222963718 222964253 0.000000e+00 686
22 TraesCS1B01G165000 chr3A 85.882 680 68 12 2805 3469 251041053 251040387 0.000000e+00 699
23 TraesCS1B01G165000 chr7B 85.298 687 70 15 2805 3469 263666162 263665485 0.000000e+00 680
24 TraesCS1B01G165000 chr7B 84.393 692 76 18 2803 3469 720343618 720342934 0.000000e+00 651
25 TraesCS1B01G165000 chr2B 83.425 724 100 16 4 713 291620704 291619987 0.000000e+00 654
26 TraesCS1B01G165000 chr2B 82.669 727 105 17 1 717 790773799 790774514 2.940000e-175 625
27 TraesCS1B01G165000 chr5A 83.032 719 94 21 7 714 650516575 650517276 8.170000e-176 627
28 TraesCS1B01G165000 chr5A 81.276 721 115 11 1 710 106753647 106752936 1.810000e-157 566
29 TraesCS1B01G165000 chr3D 85.970 335 30 6 2805 3125 528805767 528805436 3.320000e-90 342
30 TraesCS1B01G165000 chr5B 76.292 561 89 20 1277 1823 118591490 118592020 3.430000e-65 259
31 TraesCS1B01G165000 chr4B 80.588 340 58 8 1273 1608 477371468 477371133 4.440000e-64 255
32 TraesCS1B01G165000 chr4B 80.588 340 58 8 1273 1608 477389407 477389072 4.440000e-64 255


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 TraesCS1B01G165000 chr1B 288169490 288172958 3468 True 6407 6407 100.000 1 3469 1 chr1B.!!$R1 3468
1 TraesCS1B01G165000 chr1B 211628921 211629632 711 False 547 547 80.854 1 715 1 chr1B.!!$F1 714
2 TraesCS1B01G165000 chr1A 252772058 252773906 1848 False 2846 2846 94.332 934 2802 1 chr1A.!!$F2 1868
3 TraesCS1B01G165000 chr1A 351585677 351586336 659 False 730 730 86.957 2816 3467 1 chr1A.!!$F3 651
4 TraesCS1B01G165000 chr7D 178140128 178140787 659 True 793 793 88.626 2809 3469 1 chr7D.!!$R1 660
5 TraesCS1B01G165000 chr7D 562386253 562386930 677 True 658 658 84.672 2805 3469 1 chr7D.!!$R3 664
6 TraesCS1B01G165000 chr4A 434040504 434041164 660 True 765 765 87.556 2805 3469 1 chr4A.!!$R1 664
7 TraesCS1B01G165000 chr6D 285244644 285245327 683 True 760 760 87.209 2803 3469 1 chr6D.!!$R1 666
8 TraesCS1B01G165000 chr6D 314624001 314624673 672 True 760 760 87.353 2805 3469 1 chr6D.!!$R2 664
9 TraesCS1B01G165000 chr6D 411186857 411187545 688 False 725 725 86.291 2805 3469 1 chr6D.!!$F1 664
10 TraesCS1B01G165000 chr5D 256626697 256627416 719 True 736 736 85.379 1 713 1 chr5D.!!$R1 712
11 TraesCS1B01G165000 chr6A 108938432 108939156 724 False 732 732 85.322 1 710 1 chr6A.!!$F1 709
12 TraesCS1B01G165000 chr1D 453302398 453303077 679 True 721 721 86.337 2805 3469 1 chr1D.!!$R3 664
13 TraesCS1B01G165000 chr1D 63882490 63883159 669 True 662 662 85.116 2805 3469 1 chr1D.!!$R1 664
14 TraesCS1B01G165000 chr1D 351509674 351510403 729 True 651 651 83.176 1 724 1 chr1D.!!$R2 723
15 TraesCS1B01G165000 chr4D 15312993 15313710 717 False 715 715 84.840 1 710 1 chr4D.!!$F1 709
16 TraesCS1B01G165000 chr4D 222963718 222964253 535 False 686 686 89.777 2805 3341 1 chr4D.!!$F2 536
17 TraesCS1B01G165000 chr3A 251040387 251041053 666 True 699 699 85.882 2805 3469 1 chr3A.!!$R1 664
18 TraesCS1B01G165000 chr7B 263665485 263666162 677 True 680 680 85.298 2805 3469 1 chr7B.!!$R1 664
19 TraesCS1B01G165000 chr7B 720342934 720343618 684 True 651 651 84.393 2803 3469 1 chr7B.!!$R2 666
20 TraesCS1B01G165000 chr2B 291619987 291620704 717 True 654 654 83.425 4 713 1 chr2B.!!$R1 709
21 TraesCS1B01G165000 chr2B 790773799 790774514 715 False 625 625 82.669 1 717 1 chr2B.!!$F1 716
22 TraesCS1B01G165000 chr5A 650516575 650517276 701 False 627 627 83.032 7 714 1 chr5A.!!$F1 707
23 TraesCS1B01G165000 chr5A 106752936 106753647 711 True 566 566 81.276 1 710 1 chr5A.!!$R1 709
24 TraesCS1B01G165000 chr5B 118591490 118592020 530 False 259 259 76.292 1277 1823 1 chr5B.!!$F1 546

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
763 817 0.030235 GGGACAACACGGTGCTTTTC 59.970 55.0 8.3 4.85 0.00 2.29 F
856 910 0.031721 GACGTTTGGTCCGACAGACT 59.968 55.0 0.0 0.00 45.54 3.24 F
887 941 0.100682 CGTGTTGATCGGGTCGAGAT 59.899 55.0 0.0 0.00 39.91 2.75 F
1985 2048 0.099436 GAAACGATGACAGGGCATGC 59.901 55.0 9.9 9.90 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1811 0.107459 GAATGACCTCCCACCTCAGC 60.107 60.0 0.00 0.0 0.00 4.26 R
1963 2026 0.109532 TGCCCTGTCATCGTTTCCAA 59.890 50.0 0.00 0.0 0.00 3.53 R
2057 2120 0.398696 TGAGAAACAAAGCCCGGCTA 59.601 50.0 13.73 0.0 38.25 3.93 R
2874 2940 0.826672 AACCGAGACGTTCTGAGGGT 60.827 55.0 0.00 0.0 0.00 4.34 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
27 28 1.149401 TGATGGACCAACACGGCAA 59.851 52.632 0.00 0.00 39.03 4.52
134 138 6.295011 CCATTTTGTACCTTGGCAAACTATCA 60.295 38.462 0.00 0.00 34.77 2.15
239 247 4.293648 CGTGCCGGTGTCAGGACA 62.294 66.667 1.90 0.00 39.32 4.02
418 454 0.393808 GGCAGAGGCACCGGAAAATA 60.394 55.000 9.46 0.00 43.71 1.40
479 516 6.514012 TTGCTATTGAAATGGGAGAGGATA 57.486 37.500 0.00 0.00 0.00 2.59
501 538 0.673333 CAATGTGCCACCGACTAGCA 60.673 55.000 0.00 0.00 0.00 3.49
566 608 2.690778 GCCGACGCAAATGAGGCTT 61.691 57.895 0.00 0.00 44.06 4.35
568 610 0.373716 CCGACGCAAATGAGGCTTAC 59.626 55.000 0.00 0.00 0.00 2.34
572 614 3.234386 GACGCAAATGAGGCTTACAAAC 58.766 45.455 0.00 0.00 0.00 2.93
659 704 2.668550 ACTTTTCTGTCCGCGCCC 60.669 61.111 0.00 0.00 0.00 6.13
717 771 3.063997 CGCTTTGGAGTTGCTATAAGGTG 59.936 47.826 0.00 0.00 0.00 4.00
718 772 3.181496 GCTTTGGAGTTGCTATAAGGTGC 60.181 47.826 0.00 0.00 0.00 5.01
719 773 2.309528 TGGAGTTGCTATAAGGTGCG 57.690 50.000 0.00 0.00 0.00 5.34
720 774 1.134521 TGGAGTTGCTATAAGGTGCGG 60.135 52.381 0.00 0.00 0.00 5.69
721 775 0.938008 GAGTTGCTATAAGGTGCGGC 59.062 55.000 0.00 0.00 0.00 6.53
722 776 0.541863 AGTTGCTATAAGGTGCGGCT 59.458 50.000 0.00 0.00 0.00 5.52
723 777 1.065418 AGTTGCTATAAGGTGCGGCTT 60.065 47.619 0.00 0.00 0.00 4.35
724 778 1.743394 GTTGCTATAAGGTGCGGCTTT 59.257 47.619 0.00 0.00 0.00 3.51
725 779 1.378531 TGCTATAAGGTGCGGCTTTG 58.621 50.000 0.00 0.00 0.00 2.77
726 780 0.663153 GCTATAAGGTGCGGCTTTGG 59.337 55.000 0.00 0.00 0.00 3.28
727 781 0.663153 CTATAAGGTGCGGCTTTGGC 59.337 55.000 0.00 0.00 37.82 4.52
736 790 2.351276 GGCTTTGGCGAGGAGGAA 59.649 61.111 0.00 0.00 39.81 3.36
737 791 1.746991 GGCTTTGGCGAGGAGGAAG 60.747 63.158 0.00 0.00 39.81 3.46
738 792 1.296715 GCTTTGGCGAGGAGGAAGA 59.703 57.895 0.00 0.00 0.00 2.87
739 793 1.021920 GCTTTGGCGAGGAGGAAGAC 61.022 60.000 0.00 0.00 0.00 3.01
740 794 0.737715 CTTTGGCGAGGAGGAAGACG 60.738 60.000 0.00 0.00 0.00 4.18
741 795 1.469335 TTTGGCGAGGAGGAAGACGT 61.469 55.000 0.00 0.00 0.00 4.34
742 796 1.469335 TTGGCGAGGAGGAAGACGTT 61.469 55.000 0.00 0.00 0.00 3.99
743 797 1.153804 GGCGAGGAGGAAGACGTTC 60.154 63.158 0.00 0.00 0.00 3.95
744 798 1.514443 GCGAGGAGGAAGACGTTCG 60.514 63.158 0.00 0.00 32.92 3.95
745 799 1.136984 CGAGGAGGAAGACGTTCGG 59.863 63.158 0.00 0.00 32.92 4.30
746 800 1.511768 GAGGAGGAAGACGTTCGGG 59.488 63.158 0.00 0.00 32.92 5.14
747 801 0.964358 GAGGAGGAAGACGTTCGGGA 60.964 60.000 0.00 0.00 32.92 5.14
748 802 1.214853 GGAGGAAGACGTTCGGGAC 59.785 63.158 0.00 0.00 32.92 4.46
749 803 1.530013 GGAGGAAGACGTTCGGGACA 61.530 60.000 0.00 0.00 32.92 4.02
750 804 0.316204 GAGGAAGACGTTCGGGACAA 59.684 55.000 0.00 0.00 32.92 3.18
751 805 0.033090 AGGAAGACGTTCGGGACAAC 59.967 55.000 0.00 0.00 32.92 3.32
752 806 0.249573 GGAAGACGTTCGGGACAACA 60.250 55.000 0.00 0.00 32.92 3.33
753 807 0.857287 GAAGACGTTCGGGACAACAC 59.143 55.000 0.00 0.00 0.00 3.32
754 808 0.872881 AAGACGTTCGGGACAACACG 60.873 55.000 0.00 0.00 45.08 4.49
755 809 2.279650 ACGTTCGGGACAACACGG 60.280 61.111 0.00 0.00 43.75 4.94
756 810 2.279650 CGTTCGGGACAACACGGT 60.280 61.111 0.00 0.00 43.75 4.83
757 811 2.591311 CGTTCGGGACAACACGGTG 61.591 63.158 6.58 6.58 43.75 4.94
758 812 2.589442 TTCGGGACAACACGGTGC 60.589 61.111 8.30 0.00 43.75 5.01
759 813 3.096633 TTCGGGACAACACGGTGCT 62.097 57.895 8.30 0.00 43.75 4.40
760 814 2.590575 CGGGACAACACGGTGCTT 60.591 61.111 8.30 0.00 39.47 3.91
761 815 2.184167 CGGGACAACACGGTGCTTT 61.184 57.895 8.30 0.00 39.47 3.51
762 816 1.720694 CGGGACAACACGGTGCTTTT 61.721 55.000 8.30 0.00 39.47 2.27
763 817 0.030235 GGGACAACACGGTGCTTTTC 59.970 55.000 8.30 4.85 0.00 2.29
764 818 0.030235 GGACAACACGGTGCTTTTCC 59.970 55.000 8.30 9.80 0.00 3.13
774 828 3.430333 GGTGCTTTTCCGAACAAAGAA 57.570 42.857 5.44 0.00 33.69 2.52
775 829 3.776340 GGTGCTTTTCCGAACAAAGAAA 58.224 40.909 5.44 0.00 33.69 2.52
776 830 4.177783 GGTGCTTTTCCGAACAAAGAAAA 58.822 39.130 5.44 0.00 39.12 2.29
777 831 4.032445 GGTGCTTTTCCGAACAAAGAAAAC 59.968 41.667 5.44 0.00 37.13 2.43
778 832 3.854809 TGCTTTTCCGAACAAAGAAAACG 59.145 39.130 5.44 0.00 37.13 3.60
779 833 3.301579 GCTTTTCCGAACAAAGAAAACGC 60.302 43.478 5.44 0.00 37.13 4.84
780 834 3.768468 TTTCCGAACAAAGAAAACGCT 57.232 38.095 0.00 0.00 0.00 5.07
781 835 2.748461 TCCGAACAAAGAAAACGCTG 57.252 45.000 0.00 0.00 0.00 5.18
782 836 2.281517 TCCGAACAAAGAAAACGCTGA 58.718 42.857 0.00 0.00 0.00 4.26
783 837 2.031191 TCCGAACAAAGAAAACGCTGAC 59.969 45.455 0.00 0.00 0.00 3.51
795 849 3.657537 CGCTGACGTGGTTGATTTC 57.342 52.632 0.00 0.00 33.53 2.17
796 850 0.165944 CGCTGACGTGGTTGATTTCC 59.834 55.000 0.00 0.00 33.53 3.13
797 851 1.523758 GCTGACGTGGTTGATTTCCT 58.476 50.000 0.00 0.00 0.00 3.36
798 852 1.880027 GCTGACGTGGTTGATTTCCTT 59.120 47.619 0.00 0.00 0.00 3.36
799 853 2.293399 GCTGACGTGGTTGATTTCCTTT 59.707 45.455 0.00 0.00 0.00 3.11
800 854 3.853307 GCTGACGTGGTTGATTTCCTTTG 60.853 47.826 0.00 0.00 0.00 2.77
801 855 2.034053 TGACGTGGTTGATTTCCTTTGC 59.966 45.455 0.00 0.00 0.00 3.68
802 856 2.293399 GACGTGGTTGATTTCCTTTGCT 59.707 45.455 0.00 0.00 0.00 3.91
803 857 2.693074 ACGTGGTTGATTTCCTTTGCTT 59.307 40.909 0.00 0.00 0.00 3.91
804 858 3.132111 ACGTGGTTGATTTCCTTTGCTTT 59.868 39.130 0.00 0.00 0.00 3.51
805 859 4.119136 CGTGGTTGATTTCCTTTGCTTTT 58.881 39.130 0.00 0.00 0.00 2.27
806 860 5.163499 ACGTGGTTGATTTCCTTTGCTTTTA 60.163 36.000 0.00 0.00 0.00 1.52
807 861 5.925969 CGTGGTTGATTTCCTTTGCTTTTAT 59.074 36.000 0.00 0.00 0.00 1.40
808 862 6.128849 CGTGGTTGATTTCCTTTGCTTTTATG 60.129 38.462 0.00 0.00 0.00 1.90
809 863 6.928492 GTGGTTGATTTCCTTTGCTTTTATGA 59.072 34.615 0.00 0.00 0.00 2.15
810 864 7.603784 GTGGTTGATTTCCTTTGCTTTTATGAT 59.396 33.333 0.00 0.00 0.00 2.45
811 865 8.156165 TGGTTGATTTCCTTTGCTTTTATGATT 58.844 29.630 0.00 0.00 0.00 2.57
812 866 8.659491 GGTTGATTTCCTTTGCTTTTATGATTC 58.341 33.333 0.00 0.00 0.00 2.52
813 867 8.375465 GTTGATTTCCTTTGCTTTTATGATTCG 58.625 33.333 0.00 0.00 0.00 3.34
814 868 7.601856 TGATTTCCTTTGCTTTTATGATTCGT 58.398 30.769 0.00 0.00 0.00 3.85
815 869 7.541783 TGATTTCCTTTGCTTTTATGATTCGTG 59.458 33.333 0.00 0.00 0.00 4.35
816 870 4.732784 TCCTTTGCTTTTATGATTCGTGC 58.267 39.130 0.00 0.00 0.00 5.34
817 871 3.859386 CCTTTGCTTTTATGATTCGTGCC 59.141 43.478 0.00 0.00 0.00 5.01
818 872 4.380867 CCTTTGCTTTTATGATTCGTGCCT 60.381 41.667 0.00 0.00 0.00 4.75
819 873 3.763097 TGCTTTTATGATTCGTGCCTG 57.237 42.857 0.00 0.00 0.00 4.85
820 874 2.159393 TGCTTTTATGATTCGTGCCTGC 60.159 45.455 0.00 0.00 0.00 4.85
821 875 2.159393 GCTTTTATGATTCGTGCCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
822 876 3.673052 GCTTTTATGATTCGTGCCTGCAA 60.673 43.478 0.00 0.00 0.00 4.08
823 877 4.675510 CTTTTATGATTCGTGCCTGCAAT 58.324 39.130 0.00 0.00 0.00 3.56
824 878 3.969117 TTATGATTCGTGCCTGCAATC 57.031 42.857 0.00 0.00 0.00 2.67
825 879 1.753930 ATGATTCGTGCCTGCAATCA 58.246 45.000 7.27 7.27 40.07 2.57
826 880 1.532523 TGATTCGTGCCTGCAATCAA 58.467 45.000 3.20 0.00 34.35 2.57
827 881 1.199789 TGATTCGTGCCTGCAATCAAC 59.800 47.619 3.20 0.00 34.35 3.18
828 882 0.168788 ATTCGTGCCTGCAATCAACG 59.831 50.000 0.00 4.93 0.00 4.10
829 883 1.851021 TTCGTGCCTGCAATCAACGG 61.851 55.000 9.96 0.00 0.00 4.44
830 884 2.616330 CGTGCCTGCAATCAACGGT 61.616 57.895 0.00 0.00 0.00 4.83
831 885 1.295357 CGTGCCTGCAATCAACGGTA 61.295 55.000 0.00 0.00 0.00 4.02
832 886 0.168128 GTGCCTGCAATCAACGGTAC 59.832 55.000 0.00 0.00 0.00 3.34
833 887 0.250510 TGCCTGCAATCAACGGTACA 60.251 50.000 0.00 0.00 0.00 2.90
834 888 0.447801 GCCTGCAATCAACGGTACAG 59.552 55.000 0.00 0.00 0.00 2.74
835 889 1.943968 GCCTGCAATCAACGGTACAGA 60.944 52.381 0.00 0.00 0.00 3.41
836 890 1.732259 CCTGCAATCAACGGTACAGAC 59.268 52.381 0.00 0.00 0.00 3.51
837 891 1.390123 CTGCAATCAACGGTACAGACG 59.610 52.381 0.00 0.00 37.36 4.18
838 892 1.000052 TGCAATCAACGGTACAGACGA 60.000 47.619 0.00 0.00 34.93 4.20
839 893 1.389106 GCAATCAACGGTACAGACGAC 59.611 52.381 0.00 0.00 34.93 4.34
840 894 1.647213 CAATCAACGGTACAGACGACG 59.353 52.381 0.00 0.00 34.93 5.12
841 895 0.877071 ATCAACGGTACAGACGACGT 59.123 50.000 0.00 0.00 41.88 4.34
843 897 1.065401 TCAACGGTACAGACGACGTTT 59.935 47.619 0.13 0.00 45.97 3.60
844 898 1.188573 CAACGGTACAGACGACGTTTG 59.811 52.381 16.20 16.20 45.97 2.93
845 899 0.318107 ACGGTACAGACGACGTTTGG 60.318 55.000 20.95 7.12 35.90 3.28
846 900 0.318107 CGGTACAGACGACGTTTGGT 60.318 55.000 20.95 12.95 0.00 3.67
847 901 1.412387 GGTACAGACGACGTTTGGTC 58.588 55.000 20.95 13.16 42.48 4.02
848 902 1.412387 GTACAGACGACGTTTGGTCC 58.588 55.000 20.95 6.12 42.99 4.46
849 903 0.040157 TACAGACGACGTTTGGTCCG 60.040 55.000 20.95 1.69 42.99 4.79
850 904 1.008194 CAGACGACGTTTGGTCCGA 60.008 57.895 10.51 0.00 42.99 4.55
851 905 1.008079 AGACGACGTTTGGTCCGAC 60.008 57.895 0.13 0.00 42.99 4.79
852 906 1.299316 GACGACGTTTGGTCCGACA 60.299 57.895 0.13 0.00 42.99 4.35
853 907 1.273455 GACGACGTTTGGTCCGACAG 61.273 60.000 0.13 0.00 42.99 3.51
854 908 1.008194 CGACGTTTGGTCCGACAGA 60.008 57.895 0.00 0.00 42.99 3.41
855 909 1.273455 CGACGTTTGGTCCGACAGAC 61.273 60.000 0.00 0.00 42.99 3.51
856 910 0.031721 GACGTTTGGTCCGACAGACT 59.968 55.000 0.00 0.00 45.54 3.24
857 911 1.267806 GACGTTTGGTCCGACAGACTA 59.732 52.381 0.00 0.00 45.54 2.59
858 912 1.682854 ACGTTTGGTCCGACAGACTAA 59.317 47.619 0.00 0.00 45.54 2.24
879 933 4.988065 ACAGGACGTGTTGATCGG 57.012 55.556 0.00 0.00 34.94 4.18
880 934 1.292223 ACAGGACGTGTTGATCGGG 59.708 57.895 0.00 0.00 34.94 5.14
881 935 1.292223 CAGGACGTGTTGATCGGGT 59.708 57.895 0.00 0.00 0.00 5.28
882 936 0.736325 CAGGACGTGTTGATCGGGTC 60.736 60.000 0.00 0.00 0.00 4.46
883 937 1.804326 GGACGTGTTGATCGGGTCG 60.804 63.158 0.00 0.00 0.00 4.79
884 938 1.210931 GACGTGTTGATCGGGTCGA 59.789 57.895 0.00 0.00 41.13 4.20
885 939 0.797249 GACGTGTTGATCGGGTCGAG 60.797 60.000 0.00 0.00 39.91 4.04
886 940 1.239296 ACGTGTTGATCGGGTCGAGA 61.239 55.000 0.00 0.00 39.91 4.04
887 941 0.100682 CGTGTTGATCGGGTCGAGAT 59.899 55.000 0.00 0.00 39.91 2.75
888 942 1.332686 CGTGTTGATCGGGTCGAGATA 59.667 52.381 0.00 0.00 39.91 1.98
889 943 2.728922 GTGTTGATCGGGTCGAGATAC 58.271 52.381 0.00 0.00 39.91 2.24
890 944 2.098607 GTGTTGATCGGGTCGAGATACA 59.901 50.000 0.00 0.00 39.91 2.29
891 945 2.956333 TGTTGATCGGGTCGAGATACAT 59.044 45.455 0.00 0.00 39.91 2.29
892 946 3.383505 TGTTGATCGGGTCGAGATACATT 59.616 43.478 0.00 0.00 39.91 2.71
893 947 3.643159 TGATCGGGTCGAGATACATTG 57.357 47.619 0.00 0.00 39.91 2.82
894 948 2.296190 TGATCGGGTCGAGATACATTGG 59.704 50.000 0.00 0.00 39.91 3.16
895 949 2.061509 TCGGGTCGAGATACATTGGA 57.938 50.000 0.00 0.00 0.00 3.53
896 950 2.380941 TCGGGTCGAGATACATTGGAA 58.619 47.619 0.00 0.00 0.00 3.53
897 951 2.361119 TCGGGTCGAGATACATTGGAAG 59.639 50.000 0.00 0.00 0.00 3.46
898 952 2.545952 CGGGTCGAGATACATTGGAAGG 60.546 54.545 0.00 0.00 0.00 3.46
899 953 2.224305 GGGTCGAGATACATTGGAAGGG 60.224 54.545 0.00 0.00 0.00 3.95
900 954 2.698797 GGTCGAGATACATTGGAAGGGA 59.301 50.000 0.00 0.00 0.00 4.20
901 955 3.325135 GGTCGAGATACATTGGAAGGGAT 59.675 47.826 0.00 0.00 0.00 3.85
902 956 4.202367 GGTCGAGATACATTGGAAGGGATT 60.202 45.833 0.00 0.00 0.00 3.01
903 957 5.368989 GTCGAGATACATTGGAAGGGATTT 58.631 41.667 0.00 0.00 0.00 2.17
904 958 6.463897 GGTCGAGATACATTGGAAGGGATTTA 60.464 42.308 0.00 0.00 0.00 1.40
905 959 6.424207 GTCGAGATACATTGGAAGGGATTTAC 59.576 42.308 0.00 0.00 0.00 2.01
906 960 5.405571 CGAGATACATTGGAAGGGATTTACG 59.594 44.000 0.00 0.00 0.00 3.18
907 961 5.063880 AGATACATTGGAAGGGATTTACGC 58.936 41.667 0.00 0.00 0.00 4.42
908 962 2.014128 ACATTGGAAGGGATTTACGCG 58.986 47.619 3.53 3.53 36.53 6.01
909 963 1.333619 CATTGGAAGGGATTTACGCGG 59.666 52.381 12.47 0.00 36.53 6.46
910 964 0.614294 TTGGAAGGGATTTACGCGGA 59.386 50.000 12.47 0.00 36.53 5.54
911 965 0.614294 TGGAAGGGATTTACGCGGAA 59.386 50.000 12.47 4.81 36.53 4.30
912 966 1.003349 TGGAAGGGATTTACGCGGAAA 59.997 47.619 20.56 20.56 36.53 3.13
913 967 1.399440 GGAAGGGATTTACGCGGAAAC 59.601 52.381 20.71 12.84 36.53 2.78
914 968 2.078392 GAAGGGATTTACGCGGAAACA 58.922 47.619 20.71 0.00 36.53 2.83
915 969 2.188062 AGGGATTTACGCGGAAACAA 57.812 45.000 20.71 0.00 36.53 2.83
916 970 1.808343 AGGGATTTACGCGGAAACAAC 59.192 47.619 20.71 13.23 36.53 3.32
917 971 1.536331 GGGATTTACGCGGAAACAACA 59.464 47.619 20.71 0.00 0.00 3.33
918 972 2.413634 GGGATTTACGCGGAAACAACAG 60.414 50.000 20.71 0.00 0.00 3.16
919 973 2.413634 GGATTTACGCGGAAACAACAGG 60.414 50.000 20.71 0.00 0.00 4.00
920 974 0.945813 TTTACGCGGAAACAACAGGG 59.054 50.000 13.67 0.00 0.00 4.45
921 975 1.508808 TTACGCGGAAACAACAGGGC 61.509 55.000 12.47 0.00 0.00 5.19
922 976 4.383602 CGCGGAAACAACAGGGCG 62.384 66.667 0.00 0.00 37.56 6.13
923 977 2.975799 GCGGAAACAACAGGGCGA 60.976 61.111 0.00 0.00 0.00 5.54
924 978 2.966309 GCGGAAACAACAGGGCGAG 61.966 63.158 0.00 0.00 0.00 5.03
925 979 1.301401 CGGAAACAACAGGGCGAGA 60.301 57.895 0.00 0.00 0.00 4.04
926 980 1.566018 CGGAAACAACAGGGCGAGAC 61.566 60.000 0.00 0.00 0.00 3.36
927 981 1.566018 GGAAACAACAGGGCGAGACG 61.566 60.000 0.00 0.00 0.00 4.18
928 982 1.566018 GAAACAACAGGGCGAGACGG 61.566 60.000 0.00 0.00 0.00 4.79
929 983 2.319890 AAACAACAGGGCGAGACGGT 62.320 55.000 0.00 0.00 0.00 4.83
930 984 1.466025 AACAACAGGGCGAGACGGTA 61.466 55.000 0.00 0.00 0.00 4.02
931 985 1.445582 CAACAGGGCGAGACGGTAC 60.446 63.158 0.00 0.00 0.00 3.34
932 986 2.643232 AACAGGGCGAGACGGTACC 61.643 63.158 0.16 0.16 0.00 3.34
949 1003 4.386711 GGTACCATCTTTCCCTTATTCGG 58.613 47.826 7.15 0.00 0.00 4.30
953 1007 5.576128 ACCATCTTTCCCTTATTCGGAAAA 58.424 37.500 3.80 0.00 46.19 2.29
954 1008 5.417894 ACCATCTTTCCCTTATTCGGAAAAC 59.582 40.000 3.80 0.00 46.19 2.43
955 1009 5.417580 CCATCTTTCCCTTATTCGGAAAACA 59.582 40.000 3.80 0.00 46.19 2.83
960 1014 8.425703 TCTTTCCCTTATTCGGAAAACAAAAAT 58.574 29.630 3.80 0.00 46.19 1.82
974 1028 9.337396 GGAAAACAAAAATTCTCCCTAAAACAT 57.663 29.630 0.00 0.00 0.00 2.71
1034 1088 3.434637 CTCTTGTCCCGTTTTGTTGTTG 58.565 45.455 0.00 0.00 0.00 3.33
1035 1089 2.820787 TCTTGTCCCGTTTTGTTGTTGT 59.179 40.909 0.00 0.00 0.00 3.32
1036 1090 3.256136 TCTTGTCCCGTTTTGTTGTTGTT 59.744 39.130 0.00 0.00 0.00 2.83
1037 1091 3.219052 TGTCCCGTTTTGTTGTTGTTC 57.781 42.857 0.00 0.00 0.00 3.18
1038 1092 2.178783 GTCCCGTTTTGTTGTTGTTCG 58.821 47.619 0.00 0.00 0.00 3.95
1059 1113 1.287730 CCTGCGCCTGATCGATAAGC 61.288 60.000 4.18 4.10 0.00 3.09
1081 1135 1.966451 GTGCGGGTGTGGGAGAAAG 60.966 63.158 0.00 0.00 0.00 2.62
1110 1164 1.743995 GAAATGTGTCCGTCCGGGG 60.744 63.158 0.00 0.00 36.01 5.73
1194 1248 4.735358 GGGCCCCTGAACCGGAAC 62.735 72.222 12.23 1.34 0.00 3.62
1195 1249 4.735358 GGCCCCTGAACCGGAACC 62.735 72.222 9.46 0.00 0.00 3.62
1240 1294 3.471244 CTCTCCCGACCGACATCGC 62.471 68.421 0.00 0.00 40.87 4.58
1790 1853 0.395311 ATGGCATGGTGGAGCTTCAG 60.395 55.000 0.00 0.00 0.00 3.02
1796 1859 2.260844 TGGTGGAGCTTCAGAACTTG 57.739 50.000 0.00 0.00 0.00 3.16
1888 1951 2.620585 GCAAAATCTCCATGGCCTACTC 59.379 50.000 6.96 0.00 0.00 2.59
1963 2026 2.818714 GATGCTCGTGCTGCAGCT 60.819 61.111 36.61 17.15 44.04 4.24
1985 2048 0.099436 GAAACGATGACAGGGCATGC 59.901 55.000 9.90 9.90 0.00 4.06
2057 2120 0.040058 TGCCCATCTGCAATCTTGGT 59.960 50.000 0.00 0.00 38.56 3.67
2060 2123 1.952296 CCCATCTGCAATCTTGGTAGC 59.048 52.381 0.00 0.00 0.00 3.58
2080 2143 1.001378 CCGGGCTTTGTTTCTCAACAG 60.001 52.381 0.00 0.00 43.92 3.16
2084 2147 3.489229 GGGCTTTGTTTCTCAACAGTGAC 60.489 47.826 0.00 0.00 43.92 3.67
2125 2188 2.214347 CATGAGCTTGCCATCTCTCTG 58.786 52.381 0.00 0.00 0.00 3.35
2126 2189 0.107800 TGAGCTTGCCATCTCTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
2139 2202 1.808945 CTCTCTGCAGCAATTCGGTTT 59.191 47.619 9.47 0.00 0.00 3.27
2148 2211 5.030936 GCAGCAATTCGGTTTATTTCTCTC 58.969 41.667 0.00 0.00 0.00 3.20
2188 2251 1.201181 GATGCAGTCTCTGTCGAGTGT 59.799 52.381 0.00 0.00 38.45 3.55
2189 2252 1.892209 TGCAGTCTCTGTCGAGTGTA 58.108 50.000 0.00 0.00 38.45 2.90
2204 2267 3.285484 GAGTGTATTGTCCGAGGACCTA 58.715 50.000 18.57 8.03 43.97 3.08
2238 2301 3.381590 CCAGATACACGACATGAAGGAGA 59.618 47.826 0.00 0.00 0.00 3.71
2274 2337 0.169009 GCGACCTTTCACCATTGCTC 59.831 55.000 0.00 0.00 0.00 4.26
2340 2403 4.256920 GCTCATGTTTCATGAGTACCACT 58.743 43.478 28.47 0.00 45.38 4.00
2358 2421 6.919775 ACCACTATATACCAGACTCATTCC 57.080 41.667 0.00 0.00 0.00 3.01
2370 2433 5.046304 CCAGACTCATTCCAGGAACTAAAGA 60.046 44.000 3.18 0.00 36.02 2.52
2387 2450 9.181805 GAACTAAAGAAGAAAATAAAGGCACAC 57.818 33.333 0.00 0.00 0.00 3.82
2414 2477 0.320421 AAGTGCACATTCCGCGTACT 60.320 50.000 21.04 0.00 0.00 2.73
2415 2478 1.014044 AGTGCACATTCCGCGTACTG 61.014 55.000 21.04 0.00 0.00 2.74
2416 2479 1.739929 TGCACATTCCGCGTACTGG 60.740 57.895 4.92 0.00 0.00 4.00
2417 2480 1.447140 GCACATTCCGCGTACTGGA 60.447 57.895 4.92 0.00 0.00 3.86
2446 2509 1.681264 AGGAGGTTCAAAGGCAAAACG 59.319 47.619 0.00 0.00 0.00 3.60
2466 2529 9.776158 CAAAACGTTGCCATAATTAAGTATGTA 57.224 29.630 18.68 7.38 30.72 2.29
2573 2636 0.748005 CCCATGTTTCTACGGGCCTG 60.748 60.000 11.02 11.02 0.00 4.85
2580 2643 2.941064 GTTTCTACGGGCCTGTTTATCC 59.059 50.000 25.37 5.04 0.00 2.59
2584 2647 0.323087 ACGGGCCTGTTTATCCCAAC 60.323 55.000 12.85 0.00 40.05 3.77
2585 2648 0.034477 CGGGCCTGTTTATCCCAACT 60.034 55.000 2.29 0.00 40.05 3.16
2587 2650 2.356330 CGGGCCTGTTTATCCCAACTTA 60.356 50.000 2.29 0.00 40.05 2.24
2610 2673 6.765915 AGTCTTGCTCTTTCAAAAACTCTT 57.234 33.333 0.00 0.00 0.00 2.85
2612 2675 7.031975 AGTCTTGCTCTTTCAAAAACTCTTTG 58.968 34.615 0.00 0.00 0.00 2.77
2622 2685 8.742554 TTTCAAAAACTCTTTGTTCTCTTGAC 57.257 30.769 0.00 0.00 38.03 3.18
2646 2710 4.199432 AGTGGAGTCATTTAGCAGACAG 57.801 45.455 0.00 0.00 37.23 3.51
2748 2812 0.037605 ATGTCCACCGTTTCGTCCTC 60.038 55.000 0.00 0.00 0.00 3.71
2762 2826 2.238898 TCGTCCTCAGATCACCACTCTA 59.761 50.000 0.00 0.00 0.00 2.43
2763 2827 3.117851 TCGTCCTCAGATCACCACTCTAT 60.118 47.826 0.00 0.00 0.00 1.98
2783 2847 7.663493 ACTCTATTTTGCCTCAATAGCCTTATC 59.337 37.037 0.00 0.00 35.13 1.75
2886 2952 1.451067 CTCGTCTACCCTCAGAACGT 58.549 55.000 0.00 0.00 0.00 3.99
2920 2986 1.411501 GGGGAATCAATGGCAAGGCTA 60.412 52.381 0.00 0.00 0.00 3.93
2978 3086 2.125106 GGCGACGCATCCTTTCCT 60.125 61.111 23.09 0.00 0.00 3.36
2988 3096 3.726517 CCTTTCCTGCCACGCGTG 61.727 66.667 31.77 31.77 0.00 5.34
3132 3325 2.588877 CCGATGGCCGAGCGATTT 60.589 61.111 13.25 0.00 41.76 2.17
3324 3518 3.379445 ACGTCCCGCCATCTTCGT 61.379 61.111 0.00 0.00 0.00 3.85
3370 3564 3.753434 CTCACGGAGGAGCAGCGT 61.753 66.667 0.00 0.00 0.00 5.07
3386 3580 3.646715 GTGCCCTGCCCCAGTACA 61.647 66.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.648568 TGAGGAGGAGGAGATCTTGGT 59.351 52.381 0.00 0.00 0.00 3.67
134 138 3.660111 GACGCCCGCAAGCTGTTT 61.660 61.111 0.00 0.00 0.00 2.83
155 159 3.842925 TTCGCTGGCCGGCTCTTTT 62.843 57.895 33.12 0.00 37.59 2.27
239 247 4.729918 CGCCCTGCCAGCTCCTTT 62.730 66.667 0.00 0.00 0.00 3.11
479 516 1.836999 TAGTCGGTGGCACATTGGCT 61.837 55.000 20.82 16.81 44.52 4.75
566 608 1.377463 CATTCCCGGCCCGTTTGTA 60.377 57.895 0.85 0.00 0.00 2.41
568 610 2.675075 ACATTCCCGGCCCGTTTG 60.675 61.111 0.85 0.00 0.00 2.93
589 631 2.127383 GTTTTTCGTCCGCCTGCG 60.127 61.111 4.20 4.20 39.44 5.18
610 652 3.910914 CGACCCAAATGGACGCCCA 62.911 63.158 0.00 0.00 44.79 5.36
659 704 1.055235 CGCGCGTTCGTTTAGACTG 59.945 57.895 24.19 0.00 38.14 3.51
718 772 3.605749 TTCCTCCTCGCCAAAGCCG 62.606 63.158 0.00 0.00 34.57 5.52
719 773 1.746991 CTTCCTCCTCGCCAAAGCC 60.747 63.158 0.00 0.00 34.57 4.35
720 774 1.021920 GTCTTCCTCCTCGCCAAAGC 61.022 60.000 0.00 0.00 0.00 3.51
721 775 0.737715 CGTCTTCCTCCTCGCCAAAG 60.738 60.000 0.00 0.00 0.00 2.77
722 776 1.292223 CGTCTTCCTCCTCGCCAAA 59.708 57.895 0.00 0.00 0.00 3.28
723 777 1.469335 AACGTCTTCCTCCTCGCCAA 61.469 55.000 0.00 0.00 0.00 4.52
724 778 1.874345 GAACGTCTTCCTCCTCGCCA 61.874 60.000 0.00 0.00 0.00 5.69
725 779 1.153804 GAACGTCTTCCTCCTCGCC 60.154 63.158 0.00 0.00 0.00 5.54
726 780 1.514443 CGAACGTCTTCCTCCTCGC 60.514 63.158 0.00 0.00 0.00 5.03
727 781 1.136984 CCGAACGTCTTCCTCCTCG 59.863 63.158 0.00 0.00 0.00 4.63
728 782 0.964358 TCCCGAACGTCTTCCTCCTC 60.964 60.000 0.00 0.00 0.00 3.71
729 783 1.076192 TCCCGAACGTCTTCCTCCT 59.924 57.895 0.00 0.00 0.00 3.69
730 784 1.214853 GTCCCGAACGTCTTCCTCC 59.785 63.158 0.00 0.00 0.00 4.30
731 785 0.316204 TTGTCCCGAACGTCTTCCTC 59.684 55.000 0.00 0.00 0.00 3.71
732 786 0.033090 GTTGTCCCGAACGTCTTCCT 59.967 55.000 0.00 0.00 0.00 3.36
733 787 0.249573 TGTTGTCCCGAACGTCTTCC 60.250 55.000 0.00 0.00 0.00 3.46
734 788 0.857287 GTGTTGTCCCGAACGTCTTC 59.143 55.000 0.00 0.00 0.00 2.87
735 789 0.872881 CGTGTTGTCCCGAACGTCTT 60.873 55.000 0.00 0.00 0.00 3.01
736 790 1.299620 CGTGTTGTCCCGAACGTCT 60.300 57.895 0.00 0.00 0.00 4.18
737 791 2.305127 CCGTGTTGTCCCGAACGTC 61.305 63.158 0.00 0.00 34.30 4.34
738 792 2.279650 CCGTGTTGTCCCGAACGT 60.280 61.111 0.00 0.00 34.30 3.99
739 793 2.279650 ACCGTGTTGTCCCGAACG 60.280 61.111 0.00 0.00 35.85 3.95
740 794 2.888998 GCACCGTGTTGTCCCGAAC 61.889 63.158 0.00 0.00 0.00 3.95
741 795 2.589442 GCACCGTGTTGTCCCGAA 60.589 61.111 0.00 0.00 0.00 4.30
742 796 2.596553 AAAGCACCGTGTTGTCCCGA 62.597 55.000 0.00 0.00 0.00 5.14
743 797 1.720694 AAAAGCACCGTGTTGTCCCG 61.721 55.000 0.00 0.00 0.00 5.14
744 798 0.030235 GAAAAGCACCGTGTTGTCCC 59.970 55.000 0.00 0.00 0.00 4.46
745 799 0.030235 GGAAAAGCACCGTGTTGTCC 59.970 55.000 0.00 4.23 0.00 4.02
746 800 0.316689 CGGAAAAGCACCGTGTTGTC 60.317 55.000 0.00 0.00 44.57 3.18
747 801 1.725066 CGGAAAAGCACCGTGTTGT 59.275 52.632 0.00 0.00 44.57 3.32
748 802 4.607024 CGGAAAAGCACCGTGTTG 57.393 55.556 0.00 0.00 44.57 3.33
754 808 3.430333 TTCTTTGTTCGGAAAAGCACC 57.570 42.857 0.00 0.00 35.12 5.01
755 809 4.259253 CGTTTTCTTTGTTCGGAAAAGCAC 60.259 41.667 0.00 0.00 40.55 4.40
756 810 3.854809 CGTTTTCTTTGTTCGGAAAAGCA 59.145 39.130 0.00 0.00 40.55 3.91
757 811 3.301579 GCGTTTTCTTTGTTCGGAAAAGC 60.302 43.478 0.00 0.00 40.55 3.51
758 812 4.027702 CAGCGTTTTCTTTGTTCGGAAAAG 60.028 41.667 0.00 0.00 40.55 2.27
759 813 3.854809 CAGCGTTTTCTTTGTTCGGAAAA 59.145 39.130 0.00 0.00 38.55 2.29
760 814 3.127203 TCAGCGTTTTCTTTGTTCGGAAA 59.873 39.130 0.00 0.00 0.00 3.13
761 815 2.678836 TCAGCGTTTTCTTTGTTCGGAA 59.321 40.909 0.00 0.00 0.00 4.30
762 816 2.031191 GTCAGCGTTTTCTTTGTTCGGA 59.969 45.455 0.00 0.00 0.00 4.55
763 817 2.372350 GTCAGCGTTTTCTTTGTTCGG 58.628 47.619 0.00 0.00 0.00 4.30
764 818 2.026990 CGTCAGCGTTTTCTTTGTTCG 58.973 47.619 0.00 0.00 0.00 3.95
777 831 0.165944 GGAAATCAACCACGTCAGCG 59.834 55.000 0.00 0.00 44.93 5.18
778 832 1.523758 AGGAAATCAACCACGTCAGC 58.476 50.000 0.00 0.00 0.00 4.26
779 833 3.853307 GCAAAGGAAATCAACCACGTCAG 60.853 47.826 0.00 0.00 0.00 3.51
780 834 2.034053 GCAAAGGAAATCAACCACGTCA 59.966 45.455 0.00 0.00 0.00 4.35
781 835 2.293399 AGCAAAGGAAATCAACCACGTC 59.707 45.455 0.00 0.00 0.00 4.34
782 836 2.306847 AGCAAAGGAAATCAACCACGT 58.693 42.857 0.00 0.00 0.00 4.49
783 837 3.369546 AAGCAAAGGAAATCAACCACG 57.630 42.857 0.00 0.00 0.00 4.94
784 838 6.928492 TCATAAAAGCAAAGGAAATCAACCAC 59.072 34.615 0.00 0.00 0.00 4.16
785 839 7.060383 TCATAAAAGCAAAGGAAATCAACCA 57.940 32.000 0.00 0.00 0.00 3.67
786 840 8.552083 AATCATAAAAGCAAAGGAAATCAACC 57.448 30.769 0.00 0.00 0.00 3.77
787 841 8.375465 CGAATCATAAAAGCAAAGGAAATCAAC 58.625 33.333 0.00 0.00 0.00 3.18
788 842 8.087750 ACGAATCATAAAAGCAAAGGAAATCAA 58.912 29.630 0.00 0.00 0.00 2.57
789 843 7.541783 CACGAATCATAAAAGCAAAGGAAATCA 59.458 33.333 0.00 0.00 0.00 2.57
790 844 7.463251 GCACGAATCATAAAAGCAAAGGAAATC 60.463 37.037 0.00 0.00 0.00 2.17
791 845 6.311200 GCACGAATCATAAAAGCAAAGGAAAT 59.689 34.615 0.00 0.00 0.00 2.17
792 846 5.633182 GCACGAATCATAAAAGCAAAGGAAA 59.367 36.000 0.00 0.00 0.00 3.13
793 847 5.160641 GCACGAATCATAAAAGCAAAGGAA 58.839 37.500 0.00 0.00 0.00 3.36
794 848 4.380444 GGCACGAATCATAAAAGCAAAGGA 60.380 41.667 0.00 0.00 0.00 3.36
795 849 3.859386 GGCACGAATCATAAAAGCAAAGG 59.141 43.478 0.00 0.00 0.00 3.11
796 850 4.560035 CAGGCACGAATCATAAAAGCAAAG 59.440 41.667 0.00 0.00 0.00 2.77
797 851 4.484236 CAGGCACGAATCATAAAAGCAAA 58.516 39.130 0.00 0.00 0.00 3.68
798 852 3.673052 GCAGGCACGAATCATAAAAGCAA 60.673 43.478 0.00 0.00 0.00 3.91
799 853 2.159393 GCAGGCACGAATCATAAAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
800 854 2.159393 TGCAGGCACGAATCATAAAAGC 60.159 45.455 0.00 0.00 0.00 3.51
801 855 3.763097 TGCAGGCACGAATCATAAAAG 57.237 42.857 0.00 0.00 0.00 2.27
802 856 4.157472 TGATTGCAGGCACGAATCATAAAA 59.843 37.500 3.64 0.00 32.44 1.52
803 857 3.693578 TGATTGCAGGCACGAATCATAAA 59.306 39.130 3.64 0.00 32.44 1.40
804 858 3.277715 TGATTGCAGGCACGAATCATAA 58.722 40.909 3.64 0.00 32.44 1.90
805 859 2.916640 TGATTGCAGGCACGAATCATA 58.083 42.857 3.64 0.00 32.44 2.15
806 860 1.753930 TGATTGCAGGCACGAATCAT 58.246 45.000 3.64 0.00 32.44 2.45
807 861 1.199789 GTTGATTGCAGGCACGAATCA 59.800 47.619 3.64 3.64 34.94 2.57
808 862 1.791555 CGTTGATTGCAGGCACGAATC 60.792 52.381 0.00 0.00 0.00 2.52
809 863 0.168788 CGTTGATTGCAGGCACGAAT 59.831 50.000 0.00 0.00 0.00 3.34
810 864 1.573932 CGTTGATTGCAGGCACGAA 59.426 52.632 0.00 0.00 0.00 3.85
811 865 2.324330 CCGTTGATTGCAGGCACGA 61.324 57.895 10.34 0.00 0.00 4.35
812 866 1.295357 TACCGTTGATTGCAGGCACG 61.295 55.000 0.00 0.00 0.00 5.34
813 867 0.168128 GTACCGTTGATTGCAGGCAC 59.832 55.000 0.00 0.00 0.00 5.01
814 868 0.250510 TGTACCGTTGATTGCAGGCA 60.251 50.000 0.00 0.00 0.00 4.75
815 869 0.447801 CTGTACCGTTGATTGCAGGC 59.552 55.000 0.00 0.00 0.00 4.85
816 870 1.732259 GTCTGTACCGTTGATTGCAGG 59.268 52.381 0.00 0.00 0.00 4.85
817 871 1.390123 CGTCTGTACCGTTGATTGCAG 59.610 52.381 0.00 0.00 0.00 4.41
818 872 1.000052 TCGTCTGTACCGTTGATTGCA 60.000 47.619 0.00 0.00 0.00 4.08
819 873 1.389106 GTCGTCTGTACCGTTGATTGC 59.611 52.381 0.00 0.00 0.00 3.56
820 874 1.647213 CGTCGTCTGTACCGTTGATTG 59.353 52.381 0.00 0.00 0.00 2.67
821 875 1.267806 ACGTCGTCTGTACCGTTGATT 59.732 47.619 0.00 0.00 0.00 2.57
822 876 0.877071 ACGTCGTCTGTACCGTTGAT 59.123 50.000 0.00 0.00 0.00 2.57
823 877 0.662619 AACGTCGTCTGTACCGTTGA 59.337 50.000 0.00 0.00 41.47 3.18
824 878 1.188573 CAAACGTCGTCTGTACCGTTG 59.811 52.381 0.00 0.00 42.12 4.10
825 879 1.480205 CAAACGTCGTCTGTACCGTT 58.520 50.000 0.00 0.35 44.54 4.44
826 880 0.318107 CCAAACGTCGTCTGTACCGT 60.318 55.000 0.00 0.00 34.56 4.83
827 881 0.318107 ACCAAACGTCGTCTGTACCG 60.318 55.000 0.00 0.00 0.00 4.02
828 882 1.412387 GACCAAACGTCGTCTGTACC 58.588 55.000 0.00 0.00 0.00 3.34
829 883 1.412387 GGACCAAACGTCGTCTGTAC 58.588 55.000 0.00 0.00 42.99 2.90
830 884 0.040157 CGGACCAAACGTCGTCTGTA 60.040 55.000 0.00 0.00 42.99 2.74
831 885 1.299620 CGGACCAAACGTCGTCTGT 60.300 57.895 0.00 0.00 42.99 3.41
832 886 1.008194 TCGGACCAAACGTCGTCTG 60.008 57.895 0.00 11.19 42.99 3.51
833 887 1.008079 GTCGGACCAAACGTCGTCT 60.008 57.895 0.00 0.00 42.99 4.18
834 888 1.273455 CTGTCGGACCAAACGTCGTC 61.273 60.000 5.55 0.00 42.99 4.20
835 889 1.299620 CTGTCGGACCAAACGTCGT 60.300 57.895 5.55 0.00 42.99 4.34
836 890 1.008194 TCTGTCGGACCAAACGTCG 60.008 57.895 5.55 0.00 42.99 5.12
837 891 0.031721 AGTCTGTCGGACCAAACGTC 59.968 55.000 8.25 0.00 45.54 4.34
838 892 1.321474 TAGTCTGTCGGACCAAACGT 58.679 50.000 8.25 0.00 45.54 3.99
839 893 2.427232 TTAGTCTGTCGGACCAAACG 57.573 50.000 8.25 0.00 45.54 3.60
858 912 2.289547 CCGATCAACACGTCCTGTTTTT 59.710 45.455 0.00 0.00 41.50 1.94
859 913 1.871039 CCGATCAACACGTCCTGTTTT 59.129 47.619 0.00 0.00 41.50 2.43
860 914 1.508632 CCGATCAACACGTCCTGTTT 58.491 50.000 0.00 0.00 41.50 2.83
861 915 0.320421 CCCGATCAACACGTCCTGTT 60.320 55.000 0.00 0.00 44.51 3.16
862 916 1.292223 CCCGATCAACACGTCCTGT 59.708 57.895 0.00 0.00 32.89 4.00
863 917 0.736325 GACCCGATCAACACGTCCTG 60.736 60.000 0.00 0.00 0.00 3.86
864 918 1.590147 GACCCGATCAACACGTCCT 59.410 57.895 0.00 0.00 0.00 3.85
865 919 1.804326 CGACCCGATCAACACGTCC 60.804 63.158 0.00 0.00 0.00 4.79
866 920 0.797249 CTCGACCCGATCAACACGTC 60.797 60.000 0.00 0.00 34.61 4.34
867 921 1.211969 CTCGACCCGATCAACACGT 59.788 57.895 0.00 0.00 34.61 4.49
868 922 0.100682 ATCTCGACCCGATCAACACG 59.899 55.000 0.00 0.00 34.61 4.49
869 923 2.098607 TGTATCTCGACCCGATCAACAC 59.901 50.000 0.00 0.00 34.61 3.32
870 924 2.371306 TGTATCTCGACCCGATCAACA 58.629 47.619 0.00 0.00 34.61 3.33
871 925 3.644884 ATGTATCTCGACCCGATCAAC 57.355 47.619 0.00 0.00 34.61 3.18
872 926 3.243737 CCAATGTATCTCGACCCGATCAA 60.244 47.826 0.00 0.00 34.61 2.57
873 927 2.296190 CCAATGTATCTCGACCCGATCA 59.704 50.000 0.00 0.00 34.61 2.92
874 928 2.557056 TCCAATGTATCTCGACCCGATC 59.443 50.000 0.00 0.00 34.61 3.69
875 929 2.594131 TCCAATGTATCTCGACCCGAT 58.406 47.619 0.00 0.00 34.61 4.18
876 930 2.061509 TCCAATGTATCTCGACCCGA 57.938 50.000 0.00 0.00 0.00 5.14
877 931 2.545952 CCTTCCAATGTATCTCGACCCG 60.546 54.545 0.00 0.00 0.00 5.28
878 932 2.224305 CCCTTCCAATGTATCTCGACCC 60.224 54.545 0.00 0.00 0.00 4.46
879 933 2.698797 TCCCTTCCAATGTATCTCGACC 59.301 50.000 0.00 0.00 0.00 4.79
880 934 4.608948 ATCCCTTCCAATGTATCTCGAC 57.391 45.455 0.00 0.00 0.00 4.20
881 935 5.630415 AAATCCCTTCCAATGTATCTCGA 57.370 39.130 0.00 0.00 0.00 4.04
882 936 5.405571 CGTAAATCCCTTCCAATGTATCTCG 59.594 44.000 0.00 0.00 0.00 4.04
883 937 5.179555 GCGTAAATCCCTTCCAATGTATCTC 59.820 44.000 0.00 0.00 0.00 2.75
884 938 5.063880 GCGTAAATCCCTTCCAATGTATCT 58.936 41.667 0.00 0.00 0.00 1.98
885 939 4.084013 CGCGTAAATCCCTTCCAATGTATC 60.084 45.833 0.00 0.00 0.00 2.24
886 940 3.813166 CGCGTAAATCCCTTCCAATGTAT 59.187 43.478 0.00 0.00 0.00 2.29
887 941 3.199677 CGCGTAAATCCCTTCCAATGTA 58.800 45.455 0.00 0.00 0.00 2.29
888 942 2.014128 CGCGTAAATCCCTTCCAATGT 58.986 47.619 0.00 0.00 0.00 2.71
889 943 1.333619 CCGCGTAAATCCCTTCCAATG 59.666 52.381 4.92 0.00 0.00 2.82
890 944 1.210967 TCCGCGTAAATCCCTTCCAAT 59.789 47.619 4.92 0.00 0.00 3.16
891 945 0.614294 TCCGCGTAAATCCCTTCCAA 59.386 50.000 4.92 0.00 0.00 3.53
892 946 0.614294 TTCCGCGTAAATCCCTTCCA 59.386 50.000 4.92 0.00 0.00 3.53
893 947 1.399440 GTTTCCGCGTAAATCCCTTCC 59.601 52.381 4.92 0.00 0.00 3.46
894 948 2.078392 TGTTTCCGCGTAAATCCCTTC 58.922 47.619 4.92 0.00 0.00 3.46
895 949 2.188062 TGTTTCCGCGTAAATCCCTT 57.812 45.000 4.92 0.00 0.00 3.95
896 950 1.808343 GTTGTTTCCGCGTAAATCCCT 59.192 47.619 4.92 0.00 0.00 4.20
897 951 1.536331 TGTTGTTTCCGCGTAAATCCC 59.464 47.619 4.92 0.00 0.00 3.85
898 952 2.413634 CCTGTTGTTTCCGCGTAAATCC 60.414 50.000 4.92 0.00 0.00 3.01
899 953 2.413634 CCCTGTTGTTTCCGCGTAAATC 60.414 50.000 4.92 0.00 0.00 2.17
900 954 1.538075 CCCTGTTGTTTCCGCGTAAAT 59.462 47.619 4.92 0.00 0.00 1.40
901 955 0.945813 CCCTGTTGTTTCCGCGTAAA 59.054 50.000 4.92 0.00 0.00 2.01
902 956 1.508808 GCCCTGTTGTTTCCGCGTAA 61.509 55.000 4.92 0.00 0.00 3.18
903 957 1.962306 GCCCTGTTGTTTCCGCGTA 60.962 57.895 4.92 0.00 0.00 4.42
904 958 3.284449 GCCCTGTTGTTTCCGCGT 61.284 61.111 4.92 0.00 0.00 6.01
905 959 4.383602 CGCCCTGTTGTTTCCGCG 62.384 66.667 0.00 0.00 0.00 6.46
906 960 2.966309 CTCGCCCTGTTGTTTCCGC 61.966 63.158 0.00 0.00 0.00 5.54
907 961 1.301401 TCTCGCCCTGTTGTTTCCG 60.301 57.895 0.00 0.00 0.00 4.30
908 962 1.566018 CGTCTCGCCCTGTTGTTTCC 61.566 60.000 0.00 0.00 0.00 3.13
909 963 1.566018 CCGTCTCGCCCTGTTGTTTC 61.566 60.000 0.00 0.00 0.00 2.78
910 964 1.597027 CCGTCTCGCCCTGTTGTTT 60.597 57.895 0.00 0.00 0.00 2.83
911 965 1.466025 TACCGTCTCGCCCTGTTGTT 61.466 55.000 0.00 0.00 0.00 2.83
912 966 1.904865 TACCGTCTCGCCCTGTTGT 60.905 57.895 0.00 0.00 0.00 3.32
913 967 1.445582 GTACCGTCTCGCCCTGTTG 60.446 63.158 0.00 0.00 0.00 3.33
914 968 2.643232 GGTACCGTCTCGCCCTGTT 61.643 63.158 0.00 0.00 0.00 3.16
915 969 3.066814 GGTACCGTCTCGCCCTGT 61.067 66.667 0.00 0.00 0.00 4.00
916 970 2.351336 GATGGTACCGTCTCGCCCTG 62.351 65.000 24.44 0.00 0.00 4.45
917 971 2.043248 ATGGTACCGTCTCGCCCT 60.043 61.111 7.57 0.00 0.00 5.19
918 972 1.673808 AAGATGGTACCGTCTCGCCC 61.674 60.000 32.16 8.49 41.02 6.13
919 973 0.175073 AAAGATGGTACCGTCTCGCC 59.825 55.000 32.16 9.20 41.02 5.54
920 974 1.557651 GAAAGATGGTACCGTCTCGC 58.442 55.000 32.16 23.37 41.02 5.03
921 975 1.202382 GGGAAAGATGGTACCGTCTCG 60.202 57.143 32.16 0.00 41.02 4.04
922 976 2.108970 AGGGAAAGATGGTACCGTCTC 58.891 52.381 32.16 22.00 41.02 3.36
923 977 2.249309 AGGGAAAGATGGTACCGTCT 57.751 50.000 27.95 27.95 43.46 4.18
924 978 4.684484 ATAAGGGAAAGATGGTACCGTC 57.316 45.455 24.35 24.35 0.00 4.79
925 979 4.442472 CGAATAAGGGAAAGATGGTACCGT 60.442 45.833 6.24 6.24 0.00 4.83
926 980 4.056050 CGAATAAGGGAAAGATGGTACCG 58.944 47.826 7.57 0.00 0.00 4.02
927 981 4.102054 TCCGAATAAGGGAAAGATGGTACC 59.898 45.833 4.43 4.43 0.00 3.34
928 982 5.286267 TCCGAATAAGGGAAAGATGGTAC 57.714 43.478 0.00 0.00 0.00 3.34
929 983 5.961398 TTCCGAATAAGGGAAAGATGGTA 57.039 39.130 0.00 0.00 40.48 3.25
930 984 4.855298 TTCCGAATAAGGGAAAGATGGT 57.145 40.909 0.00 0.00 40.48 3.55
953 1007 7.855784 AGGATGTTTTAGGGAGAATTTTTGT 57.144 32.000 0.00 0.00 0.00 2.83
960 1014 9.555727 CGAAATTATAGGATGTTTTAGGGAGAA 57.444 33.333 0.00 0.00 0.00 2.87
974 1028 8.638629 TCCTTTGGAAAAACGAAATTATAGGA 57.361 30.769 0.00 0.00 0.00 2.94
985 1039 7.878036 TCCTTTTATACTCCTTTGGAAAAACG 58.122 34.615 0.00 0.00 0.00 3.60
1038 1092 0.032130 TTATCGATCAGGCGCAGGAC 59.968 55.000 10.83 0.00 0.00 3.85
1093 1147 2.349755 CCCCGGACGGACACATTT 59.650 61.111 13.13 0.00 37.50 2.32
1220 1274 1.777030 CGATGTCGGTCGGGAGAGAG 61.777 65.000 0.00 0.00 41.26 3.20
1229 1283 4.148825 AGGCCTGCGATGTCGGTC 62.149 66.667 3.11 0.00 40.23 4.79
1259 1313 3.706373 ACGTCCTCGCCCAGCAAT 61.706 61.111 0.00 0.00 41.18 3.56
1267 1321 2.338015 TAGTCCACCACGTCCTCGC 61.338 63.158 0.00 0.00 41.18 5.03
1748 1811 0.107459 GAATGACCTCCCACCTCAGC 60.107 60.000 0.00 0.00 0.00 4.26
1754 1817 1.683011 CCATGGTGAATGACCTCCCAC 60.683 57.143 2.57 0.00 46.32 4.61
1790 1853 1.341209 CCTTGGAAGGGCAACAAGTTC 59.659 52.381 0.00 0.00 42.66 3.01
1888 1951 3.753070 GACGGGTCGGCTAGCGAAG 62.753 68.421 9.00 2.77 0.00 3.79
1963 2026 0.109532 TGCCCTGTCATCGTTTCCAA 59.890 50.000 0.00 0.00 0.00 3.53
1985 2048 2.806945 TCCTGAAGGCATACTTTGGG 57.193 50.000 0.00 0.00 40.21 4.12
2057 2120 0.398696 TGAGAAACAAAGCCCGGCTA 59.601 50.000 13.73 0.00 38.25 3.93
2060 2123 1.001378 CTGTTGAGAAACAAAGCCCGG 60.001 52.381 0.00 0.00 40.36 5.73
2084 2147 1.742880 CGGGACACACAGGCATCTG 60.743 63.158 0.00 0.00 46.10 2.90
2125 2188 4.986622 AGAGAAATAAACCGAATTGCTGC 58.013 39.130 0.00 0.00 0.00 5.25
2126 2189 6.253746 CAGAGAGAAATAAACCGAATTGCTG 58.746 40.000 0.00 0.00 0.00 4.41
2188 2251 1.315690 CGCTAGGTCCTCGGACAATA 58.684 55.000 17.21 8.76 46.20 1.90
2189 2252 1.392710 CCGCTAGGTCCTCGGACAAT 61.393 60.000 17.21 8.10 46.20 2.71
2218 2281 4.950475 TCTTCTCCTTCATGTCGTGTATCT 59.050 41.667 0.00 0.00 0.00 1.98
2274 2337 5.723492 TTGCAATACGTGAGAAGATGATG 57.277 39.130 0.00 0.00 0.00 3.07
2340 2403 7.306013 AGTTCCTGGAATGAGTCTGGTATATA 58.694 38.462 13.07 0.00 0.00 0.86
2358 2421 8.576442 TGCCTTTATTTTCTTCTTTAGTTCCTG 58.424 33.333 0.00 0.00 0.00 3.86
2370 2433 6.321181 TGAGAACAGTGTGCCTTTATTTTCTT 59.679 34.615 0.00 0.00 0.00 2.52
2387 2450 2.096069 CGGAATGTGCACTTGAGAACAG 60.096 50.000 19.41 0.22 0.00 3.16
2414 2477 1.420138 GAACCTCCTGTTCCACTTCCA 59.580 52.381 0.00 0.00 46.35 3.53
2415 2478 2.186532 GAACCTCCTGTTCCACTTCC 57.813 55.000 0.00 0.00 46.35 3.46
2472 2535 7.391833 AGAAGTCTGTCTGTGAAGAAAGTTTTT 59.608 33.333 0.00 0.00 0.00 1.94
2573 2636 6.174049 AGAGCAAGACTAAGTTGGGATAAAC 58.826 40.000 0.00 0.00 0.00 2.01
2580 2643 6.377327 TTTGAAAGAGCAAGACTAAGTTGG 57.623 37.500 0.00 0.00 0.00 3.77
2584 2647 7.924940 AGAGTTTTTGAAAGAGCAAGACTAAG 58.075 34.615 0.00 0.00 30.93 2.18
2585 2648 7.865706 AGAGTTTTTGAAAGAGCAAGACTAA 57.134 32.000 0.00 0.00 30.93 2.24
2587 2650 6.765915 AAGAGTTTTTGAAAGAGCAAGACT 57.234 33.333 0.00 0.00 32.38 3.24
2610 2673 3.132289 ACTCCACTTCGTCAAGAGAACAA 59.868 43.478 0.00 0.00 33.34 2.83
2612 2675 3.243434 TGACTCCACTTCGTCAAGAGAAC 60.243 47.826 0.00 0.00 37.23 3.01
2622 2685 3.614616 GTCTGCTAAATGACTCCACTTCG 59.385 47.826 0.00 0.00 0.00 3.79
2666 2730 1.227031 CCAATGCGGCAATGCGAAT 60.227 52.632 12.50 0.00 37.81 3.34
2669 2733 2.580326 GACCAATGCGGCAATGCG 60.580 61.111 12.50 8.44 39.03 4.73
2748 2812 4.521146 AGGCAAAATAGAGTGGTGATCTG 58.479 43.478 0.00 0.00 0.00 2.90
2783 2847 4.624882 GCCTCAGCATCTATATCAAACTCG 59.375 45.833 0.00 0.00 39.53 4.18
2874 2940 0.826672 AACCGAGACGTTCTGAGGGT 60.827 55.000 0.00 0.00 0.00 4.34
2969 3077 2.436646 CGCGTGGCAGGAAAGGAT 60.437 61.111 12.03 0.00 0.00 3.24
3048 3169 1.820481 GAGAGGTAGAGCTCGCGGT 60.820 63.158 6.13 0.00 0.00 5.68
3049 3170 1.503818 GAGAGAGGTAGAGCTCGCGG 61.504 65.000 6.13 0.00 36.29 6.46
3256 3449 4.351054 CCCCCGTTGCTGAGCCTT 62.351 66.667 0.23 0.00 0.00 4.35
3310 3504 4.508128 GCGACGAAGATGGCGGGA 62.508 66.667 0.00 0.00 0.00 5.14
3370 3564 3.646715 GTGTACTGGGGCAGGGCA 61.647 66.667 0.00 0.00 35.51 5.36


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

AutoCloner maintained by Alex Coulton.