Multiple sequence alignment - TraesCS5B01G572000

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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 TraesCS5B01G572000 chr5B 100.000 3938 0 0 1 3938 712865177 712861240 0.000000e+00 7273.0
1 TraesCS5B01G572000 chr5B 92.985 841 31 9 2845 3661 118165652 118164816 0.000000e+00 1201.0
2 TraesCS5B01G572000 chr5B 78.801 901 133 31 3019 3889 712857103 712856231 1.600000e-153 553.0
3 TraesCS5B01G572000 chr5D 88.758 3131 173 65 870 3938 562351563 562348550 0.000000e+00 3666.0
4 TraesCS5B01G572000 chr5D 77.466 892 142 36 3059 3928 562344284 562343430 2.750000e-131 479.0
5 TraesCS5B01G572000 chr5D 86.667 240 10 6 493 732 562351841 562351624 3.040000e-61 246.0
6 TraesCS5B01G572000 chr5D 87.013 77 4 1 3851 3927 559666855 559666785 9.070000e-12 82.4
7 TraesCS5B01G572000 chr7B 88.614 1695 96 32 850 2520 257125 258746 0.000000e+00 1971.0
8 TraesCS5B01G572000 chr7B 93.365 1040 28 19 2322 3324 258698 259733 0.000000e+00 1500.0
9 TraesCS5B01G572000 chr7B 86.696 684 30 23 56 729 256411 257043 0.000000e+00 702.0
10 TraesCS5B01G572000 chr6B 92.697 849 25 9 2846 3661 592468441 592467597 0.000000e+00 1190.0
11 TraesCS5B01G572000 chr3B 92.033 841 29 11 2846 3661 194479981 194480808 0.000000e+00 1147.0


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 TraesCS5B01G572000 chr5B 712861240 712865177 3937 True 7273 7273 100.000000 1 3938 1 chr5B.!!$R3 3937
1 TraesCS5B01G572000 chr5B 118164816 118165652 836 True 1201 1201 92.985000 2845 3661 1 chr5B.!!$R1 816
2 TraesCS5B01G572000 chr5B 712856231 712857103 872 True 553 553 78.801000 3019 3889 1 chr5B.!!$R2 870
3 TraesCS5B01G572000 chr5D 562348550 562351841 3291 True 1956 3666 87.712500 493 3938 2 chr5D.!!$R3 3445
4 TraesCS5B01G572000 chr5D 562343430 562344284 854 True 479 479 77.466000 3059 3928 1 chr5D.!!$R2 869
5 TraesCS5B01G572000 chr7B 256411 259733 3322 False 1391 1971 89.558333 56 3324 3 chr7B.!!$F1 3268
6 TraesCS5B01G572000 chr6B 592467597 592468441 844 True 1190 1190 92.697000 2846 3661 1 chr6B.!!$R1 815
7 TraesCS5B01G572000 chr3B 194479981 194480808 827 False 1147 1147 92.033000 2846 3661 1 chr3B.!!$F1 815

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
834 858 0.459899 CATGGATGCATGCTGCTGTT 59.540 50.0 20.33 0.0 45.31 3.16 F
1265 1296 0.039618 CAACCAAGTACAGCCCCCAT 59.960 55.0 0.00 0.0 0.00 4.00 F
1656 1690 0.032615 AACACCACCACCAACACCAT 60.033 50.0 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1684 0.036388 GGTCCATGACGTGATGGTGT 60.036 55.0 29.57 0.0 43.20 4.16 R
2812 3017 0.179702 CCAGCAGCAGGAGCAGATAA 59.820 55.0 0.00 0.0 45.49 1.75 R
3384 3691 0.609131 ACATTGTTGGCTCTTCCCCG 60.609 55.0 0.00 0.0 0.00 5.73 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
23 24 6.628919 GAACAACTTAAAGGGCTAACAGAA 57.371 37.500 0.00 0.00 0.00 3.02
24 25 7.034685 GAACAACTTAAAGGGCTAACAGAAA 57.965 36.000 0.00 0.00 0.00 2.52
25 26 6.387041 ACAACTTAAAGGGCTAACAGAAAC 57.613 37.500 0.00 0.00 0.00 2.78
26 27 5.301045 ACAACTTAAAGGGCTAACAGAAACC 59.699 40.000 0.00 0.00 0.00 3.27
27 28 5.056553 ACTTAAAGGGCTAACAGAAACCA 57.943 39.130 0.00 0.00 0.00 3.67
28 29 5.641155 ACTTAAAGGGCTAACAGAAACCAT 58.359 37.500 0.00 0.00 0.00 3.55
29 30 5.476945 ACTTAAAGGGCTAACAGAAACCATG 59.523 40.000 0.00 0.00 0.00 3.66
30 31 3.806949 AAGGGCTAACAGAAACCATGA 57.193 42.857 0.00 0.00 0.00 3.07
31 32 3.806949 AGGGCTAACAGAAACCATGAA 57.193 42.857 0.00 0.00 0.00 2.57
32 33 3.421844 AGGGCTAACAGAAACCATGAAC 58.578 45.455 0.00 0.00 0.00 3.18
33 34 2.161609 GGGCTAACAGAAACCATGAACG 59.838 50.000 0.00 0.00 0.00 3.95
34 35 3.071479 GGCTAACAGAAACCATGAACGA 58.929 45.455 0.00 0.00 0.00 3.85
35 36 3.125316 GGCTAACAGAAACCATGAACGAG 59.875 47.826 0.00 0.00 0.00 4.18
36 37 3.746492 GCTAACAGAAACCATGAACGAGT 59.254 43.478 0.00 0.00 0.00 4.18
37 38 4.927425 GCTAACAGAAACCATGAACGAGTA 59.073 41.667 0.00 0.00 0.00 2.59
38 39 5.062308 GCTAACAGAAACCATGAACGAGTAG 59.938 44.000 0.00 0.00 0.00 2.57
39 40 3.326747 ACAGAAACCATGAACGAGTAGC 58.673 45.455 0.00 0.00 0.00 3.58
40 41 3.244078 ACAGAAACCATGAACGAGTAGCA 60.244 43.478 0.00 0.00 0.00 3.49
41 42 3.369147 CAGAAACCATGAACGAGTAGCAG 59.631 47.826 0.00 0.00 0.00 4.24
42 43 3.006967 AGAAACCATGAACGAGTAGCAGT 59.993 43.478 0.00 0.00 0.00 4.40
43 44 2.370281 ACCATGAACGAGTAGCAGTG 57.630 50.000 0.00 0.00 0.00 3.66
44 45 1.618837 ACCATGAACGAGTAGCAGTGT 59.381 47.619 0.00 0.00 0.00 3.55
45 46 2.037251 ACCATGAACGAGTAGCAGTGTT 59.963 45.455 0.00 0.00 0.00 3.32
46 47 2.413112 CCATGAACGAGTAGCAGTGTTG 59.587 50.000 0.00 0.00 0.00 3.33
47 48 2.882927 TGAACGAGTAGCAGTGTTGT 57.117 45.000 0.00 0.00 0.00 3.32
48 49 3.173668 TGAACGAGTAGCAGTGTTGTT 57.826 42.857 0.00 0.00 0.00 2.83
49 50 4.310357 TGAACGAGTAGCAGTGTTGTTA 57.690 40.909 0.00 0.00 0.00 2.41
50 51 4.878439 TGAACGAGTAGCAGTGTTGTTAT 58.122 39.130 0.00 0.00 0.00 1.89
51 52 5.294356 TGAACGAGTAGCAGTGTTGTTATT 58.706 37.500 0.00 0.00 0.00 1.40
52 53 5.756347 TGAACGAGTAGCAGTGTTGTTATTT 59.244 36.000 0.00 0.00 0.00 1.40
53 54 6.259167 TGAACGAGTAGCAGTGTTGTTATTTT 59.741 34.615 0.00 0.00 0.00 1.82
54 55 5.985781 ACGAGTAGCAGTGTTGTTATTTTG 58.014 37.500 0.00 0.00 0.00 2.44
64 65 8.272866 GCAGTGTTGTTATTTTGGTCAAATTAC 58.727 33.333 0.00 0.00 36.43 1.89
75 76 7.775053 TTTGGTCAAATTACAGCCTCTTTAT 57.225 32.000 0.00 0.00 0.00 1.40
144 145 6.567687 TCTCCGAGAGACTTCATCATAATC 57.432 41.667 0.00 0.00 33.35 1.75
146 147 4.216472 TCCGAGAGACTTCATCATAATCCG 59.784 45.833 0.00 0.00 0.00 4.18
229 230 8.085296 AGACGTCACCAAAATATGCAAAATTTA 58.915 29.630 19.50 0.00 0.00 1.40
255 257 4.876107 GCAGATTTCAGATTACTTTCGGGA 59.124 41.667 0.00 0.00 0.00 5.14
277 281 5.123979 GGATTGTGAGTTTCCAGTATTCACC 59.876 44.000 0.00 0.00 37.85 4.02
281 285 5.888724 TGTGAGTTTCCAGTATTCACCAAAA 59.111 36.000 0.00 0.00 37.85 2.44
344 350 6.381801 ACTTGTAATCTGGCTCAAAATTTCG 58.618 36.000 0.00 0.00 0.00 3.46
382 388 6.528537 TGAGACCCACCAAAATATGAAATG 57.471 37.500 0.00 0.00 0.00 2.32
383 389 6.015918 TGAGACCCACCAAAATATGAAATGT 58.984 36.000 0.00 0.00 0.00 2.71
399 405 4.339814 TGAAATGTCAACCCTGGTTTGTAC 59.660 41.667 3.79 2.48 36.00 2.90
400 406 1.956297 TGTCAACCCTGGTTTGTACG 58.044 50.000 3.79 0.00 36.00 3.67
401 407 1.209990 TGTCAACCCTGGTTTGTACGT 59.790 47.619 3.79 0.00 36.00 3.57
402 408 2.433604 TGTCAACCCTGGTTTGTACGTA 59.566 45.455 3.79 0.00 36.00 3.57
403 409 3.118482 TGTCAACCCTGGTTTGTACGTAA 60.118 43.478 3.79 0.00 36.00 3.18
423 429 1.408969 TTTGTTGGAGCTTGAACCCC 58.591 50.000 6.39 0.00 0.00 4.95
555 574 4.141914 ACAAGAATAGTAGTAGCAGGTGGC 60.142 45.833 0.00 0.00 45.30 5.01
577 596 4.402528 CGGCGTGGATGGACCCAA 62.403 66.667 0.00 0.00 38.06 4.12
599 618 0.978151 AAAATGCCATTCCTGCAGCA 59.022 45.000 8.66 2.81 42.92 4.41
648 672 1.264288 GACTGCCTTCCTCAACAAACG 59.736 52.381 0.00 0.00 0.00 3.60
680 704 8.945195 TCTACCGATTAATTAAGATCCTGGTA 57.055 34.615 3.94 7.97 0.00 3.25
681 705 9.370930 TCTACCGATTAATTAAGATCCTGGTAA 57.629 33.333 3.94 0.00 0.00 2.85
684 708 9.284968 ACCGATTAATTAAGATCCTGGTAATTG 57.715 33.333 3.94 1.83 31.58 2.32
685 709 9.502091 CCGATTAATTAAGATCCTGGTAATTGA 57.498 33.333 3.94 3.54 31.58 2.57
729 753 3.793842 AATTCCCTCTCCTCTCCTCTT 57.206 47.619 0.00 0.00 0.00 2.85
732 756 1.850345 TCCCTCTCCTCTCCTCTTCTC 59.150 57.143 0.00 0.00 0.00 2.87
734 758 2.158608 CCCTCTCCTCTCCTCTTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
735 759 2.158608 CCTCTCCTCTCCTCTTCTCTCC 60.159 59.091 0.00 0.00 0.00 3.71
736 760 2.780010 CTCTCCTCTCCTCTTCTCTCCT 59.220 54.545 0.00 0.00 0.00 3.69
737 761 2.509548 TCTCCTCTCCTCTTCTCTCCTG 59.490 54.545 0.00 0.00 0.00 3.86
738 762 2.242196 CTCCTCTCCTCTTCTCTCCTGT 59.758 54.545 0.00 0.00 0.00 4.00
739 763 3.458118 CTCCTCTCCTCTTCTCTCCTGTA 59.542 52.174 0.00 0.00 0.00 2.74
740 764 3.853181 TCCTCTCCTCTTCTCTCCTGTAA 59.147 47.826 0.00 0.00 0.00 2.41
741 765 4.480537 TCCTCTCCTCTTCTCTCCTGTAAT 59.519 45.833 0.00 0.00 0.00 1.89
742 766 4.827284 CCTCTCCTCTTCTCTCCTGTAATC 59.173 50.000 0.00 0.00 0.00 1.75
743 767 5.445069 CTCTCCTCTTCTCTCCTGTAATCA 58.555 45.833 0.00 0.00 0.00 2.57
744 768 5.832221 TCTCCTCTTCTCTCCTGTAATCAA 58.168 41.667 0.00 0.00 0.00 2.57
745 769 6.439487 TCTCCTCTTCTCTCCTGTAATCAAT 58.561 40.000 0.00 0.00 0.00 2.57
746 770 6.549364 TCTCCTCTTCTCTCCTGTAATCAATC 59.451 42.308 0.00 0.00 0.00 2.67
747 771 6.197903 TCCTCTTCTCTCCTGTAATCAATCA 58.802 40.000 0.00 0.00 0.00 2.57
748 772 6.669591 TCCTCTTCTCTCCTGTAATCAATCAA 59.330 38.462 0.00 0.00 0.00 2.57
749 773 7.180946 TCCTCTTCTCTCCTGTAATCAATCAAA 59.819 37.037 0.00 0.00 0.00 2.69
750 774 7.279758 CCTCTTCTCTCCTGTAATCAATCAAAC 59.720 40.741 0.00 0.00 0.00 2.93
751 775 6.813649 TCTTCTCTCCTGTAATCAATCAAACG 59.186 38.462 0.00 0.00 0.00 3.60
752 776 6.280855 TCTCTCCTGTAATCAATCAAACGA 57.719 37.500 0.00 0.00 0.00 3.85
753 777 6.878317 TCTCTCCTGTAATCAATCAAACGAT 58.122 36.000 0.00 0.00 0.00 3.73
754 778 6.758416 TCTCTCCTGTAATCAATCAAACGATG 59.242 38.462 0.00 0.00 0.00 3.84
755 779 5.817296 TCTCCTGTAATCAATCAAACGATGG 59.183 40.000 0.00 0.00 0.00 3.51
775 799 4.498241 TGGATCGATCGATTCATTCATCC 58.502 43.478 30.85 24.30 35.37 3.51
776 800 4.221482 TGGATCGATCGATTCATTCATCCT 59.779 41.667 30.85 7.06 35.37 3.24
777 801 5.174395 GGATCGATCGATTCATTCATCCTT 58.826 41.667 29.89 5.36 34.60 3.36
778 802 5.063186 GGATCGATCGATTCATTCATCCTTG 59.937 44.000 29.89 0.00 34.60 3.61
779 803 4.309933 TCGATCGATTCATTCATCCTTGG 58.690 43.478 15.15 0.00 0.00 3.61
780 804 4.060900 CGATCGATTCATTCATCCTTGGT 58.939 43.478 10.26 0.00 0.00 3.67
781 805 4.512944 CGATCGATTCATTCATCCTTGGTT 59.487 41.667 10.26 0.00 0.00 3.67
782 806 5.559608 CGATCGATTCATTCATCCTTGGTTG 60.560 44.000 10.26 0.00 0.00 3.77
783 807 3.378112 TCGATTCATTCATCCTTGGTTGC 59.622 43.478 0.00 0.00 0.00 4.17
784 808 3.379372 CGATTCATTCATCCTTGGTTGCT 59.621 43.478 0.00 0.00 0.00 3.91
785 809 4.142315 CGATTCATTCATCCTTGGTTGCTT 60.142 41.667 0.00 0.00 0.00 3.91
786 810 4.524316 TTCATTCATCCTTGGTTGCTTG 57.476 40.909 0.00 0.00 0.00 4.01
787 811 2.231964 TCATTCATCCTTGGTTGCTTGC 59.768 45.455 0.00 0.00 0.00 4.01
788 812 1.999648 TTCATCCTTGGTTGCTTGCT 58.000 45.000 0.00 0.00 0.00 3.91
789 813 1.999648 TCATCCTTGGTTGCTTGCTT 58.000 45.000 0.00 0.00 0.00 3.91
790 814 1.614903 TCATCCTTGGTTGCTTGCTTG 59.385 47.619 0.00 0.00 0.00 4.01
792 816 0.756442 TCCTTGGTTGCTTGCTTGCT 60.756 50.000 3.47 0.00 0.00 3.91
794 818 1.214367 CTTGGTTGCTTGCTTGCTTG 58.786 50.000 3.47 0.00 0.00 4.01
805 829 4.685628 GCTTGCTTGCTTGCTTGTTAATTA 59.314 37.500 3.47 0.00 0.00 1.40
810 834 7.374272 TGCTTGCTTGCTTGTTAATTACATTA 58.626 30.769 3.47 0.00 36.44 1.90
811 835 7.328249 TGCTTGCTTGCTTGTTAATTACATTAC 59.672 33.333 3.47 0.00 36.44 1.89
812 836 7.328249 GCTTGCTTGCTTGTTAATTACATTACA 59.672 33.333 0.00 0.00 36.44 2.41
819 843 9.800433 TGCTTGTTAATTACATTACATTCATGG 57.200 29.630 0.00 0.00 36.44 3.66
823 847 9.964303 TGTTAATTACATTACATTCATGGATGC 57.036 29.630 14.28 0.00 32.30 3.91
824 848 9.964303 GTTAATTACATTACATTCATGGATGCA 57.036 29.630 14.28 0.00 32.30 3.96
827 851 4.878439 ACATTACATTCATGGATGCATGC 58.122 39.130 21.37 11.82 35.30 4.06
828 852 4.587262 ACATTACATTCATGGATGCATGCT 59.413 37.500 21.37 9.03 35.30 3.79
829 853 4.577834 TTACATTCATGGATGCATGCTG 57.422 40.909 21.37 20.76 35.30 4.41
830 854 1.068588 ACATTCATGGATGCATGCTGC 59.931 47.619 21.37 10.47 45.29 5.25
831 855 1.341209 CATTCATGGATGCATGCTGCT 59.659 47.619 21.37 3.26 45.31 4.24
832 856 0.744281 TTCATGGATGCATGCTGCTG 59.256 50.000 21.37 13.39 45.31 4.41
834 858 0.459899 CATGGATGCATGCTGCTGTT 59.540 50.000 20.33 0.00 45.31 3.16
835 859 0.459899 ATGGATGCATGCTGCTGTTG 59.540 50.000 20.33 0.00 45.31 3.33
836 860 0.896479 TGGATGCATGCTGCTGTTGT 60.896 50.000 20.33 0.00 45.31 3.32
839 863 0.677288 ATGCATGCTGCTGTTGTTGT 59.323 45.000 20.33 0.00 45.31 3.32
840 864 0.460722 TGCATGCTGCTGTTGTTGTT 59.539 45.000 20.33 0.00 45.31 2.83
841 865 0.856641 GCATGCTGCTGTTGTTGTTG 59.143 50.000 11.37 0.00 40.96 3.33
843 867 2.542597 CATGCTGCTGTTGTTGTTGTT 58.457 42.857 0.00 0.00 0.00 2.83
845 869 1.271934 TGCTGCTGTTGTTGTTGTTGT 59.728 42.857 0.00 0.00 0.00 3.32
848 872 3.486841 GCTGCTGTTGTTGTTGTTGTATG 59.513 43.478 0.00 0.00 0.00 2.39
868 892 3.995199 TGCGTAGGATTGGAGATCATTC 58.005 45.455 0.00 0.00 0.00 2.67
874 898 5.926580 AGGATTGGAGATCATTCCATTCT 57.073 39.130 18.24 9.17 46.22 2.40
893 917 9.182214 TCCATTCTTTCCTGATTATTCTTCTTG 57.818 33.333 0.00 0.00 0.00 3.02
913 937 5.997129 TCTTGTGCTGTTATTGTCTTGATGA 59.003 36.000 0.00 0.00 0.00 2.92
914 938 6.656270 TCTTGTGCTGTTATTGTCTTGATGAT 59.344 34.615 0.00 0.00 0.00 2.45
915 939 6.185852 TGTGCTGTTATTGTCTTGATGATG 57.814 37.500 0.00 0.00 0.00 3.07
916 940 5.032863 GTGCTGTTATTGTCTTGATGATGC 58.967 41.667 0.00 0.00 0.00 3.91
1010 1038 3.770040 CGGTGCCATGGACGAGGA 61.770 66.667 18.40 0.00 0.00 3.71
1011 1039 2.187946 GGTGCCATGGACGAGGAG 59.812 66.667 18.40 0.00 0.00 3.69
1012 1040 2.187946 GTGCCATGGACGAGGAGG 59.812 66.667 18.40 0.00 0.00 4.30
1023 1054 2.379972 GACGAGGAGGAGGAGATTGAA 58.620 52.381 0.00 0.00 0.00 2.69
1028 1059 0.472044 GAGGAGGAGATTGAAGGGGC 59.528 60.000 0.00 0.00 0.00 5.80
1060 1091 3.999285 ACCGCCACCCTCTCCTCT 61.999 66.667 0.00 0.00 0.00 3.69
1064 1095 0.395862 CGCCACCCTCTCCTCTTCTA 60.396 60.000 0.00 0.00 0.00 2.10
1133 1164 4.514577 CTTCATCCTCGCCGCCGT 62.515 66.667 0.00 0.00 35.54 5.68
1218 1249 2.315925 ATGACCCGCATGTCTACAAG 57.684 50.000 0.00 0.00 35.42 3.16
1226 1257 3.553511 CCGCATGTCTACAAGAAGATCAC 59.446 47.826 0.00 0.00 0.00 3.06
1254 1285 0.752054 CACCACAATGCCAACCAAGT 59.248 50.000 0.00 0.00 0.00 3.16
1257 1288 1.959985 CCACAATGCCAACCAAGTACA 59.040 47.619 0.00 0.00 0.00 2.90
1258 1289 2.030007 CCACAATGCCAACCAAGTACAG 60.030 50.000 0.00 0.00 0.00 2.74
1260 1291 1.067635 CAATGCCAACCAAGTACAGCC 60.068 52.381 0.00 0.00 0.00 4.85
1261 1292 0.611896 ATGCCAACCAAGTACAGCCC 60.612 55.000 0.00 0.00 0.00 5.19
1262 1293 1.977009 GCCAACCAAGTACAGCCCC 60.977 63.158 0.00 0.00 0.00 5.80
1264 1295 1.458486 CAACCAAGTACAGCCCCCA 59.542 57.895 0.00 0.00 0.00 4.96
1265 1296 0.039618 CAACCAAGTACAGCCCCCAT 59.960 55.000 0.00 0.00 0.00 4.00
1267 1298 1.153168 CCAAGTACAGCCCCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
1268 1299 1.153168 CAAGTACAGCCCCCATCGG 60.153 63.158 0.00 0.00 0.00 4.18
1269 1300 1.306654 AAGTACAGCCCCCATCGGA 60.307 57.895 0.00 0.00 0.00 4.55
1270 1301 1.338136 AAGTACAGCCCCCATCGGAG 61.338 60.000 0.00 0.00 0.00 4.63
1271 1302 2.445845 TACAGCCCCCATCGGAGG 60.446 66.667 0.00 0.00 0.00 4.30
1279 1310 3.083349 CCATCGGAGGGAGCACCA 61.083 66.667 1.63 0.00 43.89 4.17
1280 1311 2.503061 CATCGGAGGGAGCACCAG 59.497 66.667 1.58 0.00 43.89 4.00
1283 1314 4.463879 CGGAGGGAGCACCAGCAG 62.464 72.222 1.58 0.00 45.49 4.24
1298 1329 1.302752 GCAGCAGACATCACCACCA 60.303 57.895 0.00 0.00 0.00 4.17
1299 1330 1.303799 GCAGCAGACATCACCACCAG 61.304 60.000 0.00 0.00 0.00 4.00
1306 1337 2.125912 ATCACCACCAGCCCTCCT 59.874 61.111 0.00 0.00 0.00 3.69
1321 1352 0.317103 CTCCTACGAATCCAGCGACG 60.317 60.000 0.00 0.00 0.00 5.12
1322 1353 0.745486 TCCTACGAATCCAGCGACGA 60.745 55.000 0.00 0.00 0.00 4.20
1323 1354 0.591741 CCTACGAATCCAGCGACGAC 60.592 60.000 0.00 0.00 0.00 4.34
1332 1366 2.041115 CAGCGACGACTCCTCCTCA 61.041 63.158 0.00 0.00 0.00 3.86
1337 1371 2.065906 GACGACTCCTCCTCATCCGC 62.066 65.000 0.00 0.00 0.00 5.54
1338 1372 2.121538 CGACTCCTCCTCATCCGCA 61.122 63.158 0.00 0.00 0.00 5.69
1339 1373 1.439644 GACTCCTCCTCATCCGCAC 59.560 63.158 0.00 0.00 0.00 5.34
1351 1385 1.196581 CATCCGCACACGAAAATGACA 59.803 47.619 0.00 0.00 43.93 3.58
1355 1389 1.394697 GCACACGAAAATGACAACCG 58.605 50.000 0.00 0.00 0.00 4.44
1364 1398 3.567579 ATGACAACCGCCCACCCAG 62.568 63.158 0.00 0.00 0.00 4.45
1386 1420 2.284625 ATGTCCACCGCCTCCTCA 60.285 61.111 0.00 0.00 0.00 3.86
1409 1443 4.772231 CTCCTTCCCCGACCCCGA 62.772 72.222 0.00 0.00 38.22 5.14
1434 1468 2.746277 GCCGCCAACACCGAATCT 60.746 61.111 0.00 0.00 0.00 2.40
1455 1489 2.567169 TGAATCAACCGACTCTGACCAT 59.433 45.455 0.00 0.00 0.00 3.55
1479 1513 0.175531 AAAAGCAGCACAACCACCAC 59.824 50.000 0.00 0.00 0.00 4.16
1486 1520 4.265056 ACAACCACCACCGCTCCC 62.265 66.667 0.00 0.00 0.00 4.30
1488 1522 4.265056 AACCACCACCGCTCCCAC 62.265 66.667 0.00 0.00 0.00 4.61
1638 1672 3.636231 CAGCGACCCCTCCACCAA 61.636 66.667 0.00 0.00 0.00 3.67
1647 1681 1.528309 CCTCCACCAACACCACCAC 60.528 63.158 0.00 0.00 0.00 4.16
1648 1682 1.528309 CTCCACCAACACCACCACC 60.528 63.158 0.00 0.00 0.00 4.61
1649 1683 2.277072 CCACCAACACCACCACCA 59.723 61.111 0.00 0.00 0.00 4.17
1650 1684 1.380515 CCACCAACACCACCACCAA 60.381 57.895 0.00 0.00 0.00 3.67
1653 1687 0.968393 ACCAACACCACCACCAACAC 60.968 55.000 0.00 0.00 0.00 3.32
1656 1690 0.032615 AACACCACCACCAACACCAT 60.033 50.000 0.00 0.00 0.00 3.55
1668 1702 1.464608 CAACACCATCACGTCATGGAC 59.535 52.381 26.51 0.00 45.79 4.02
1672 1706 0.528466 CCATCACGTCATGGACCTCG 60.528 60.000 14.10 0.00 45.79 4.63
1673 1707 1.141881 ATCACGTCATGGACCTCGC 59.858 57.895 0.00 0.00 0.00 5.03
1674 1708 2.298158 ATCACGTCATGGACCTCGCC 62.298 60.000 0.00 0.00 0.00 5.54
1704 1738 1.744368 CAAGCTCAGCATCGCCACT 60.744 57.895 0.00 0.00 0.00 4.00
1705 1739 1.449246 AAGCTCAGCATCGCCACTC 60.449 57.895 0.00 0.00 0.00 3.51
1821 1855 4.137543 GCAACCCCTTCTTCGATGATATT 58.862 43.478 1.37 0.00 0.00 1.28
1980 2023 1.153823 CAGGCCCTACTTCGTCACG 60.154 63.158 0.00 0.00 0.00 4.35
2079 2128 2.273449 GGTGCCACTGCCTATGCT 59.727 61.111 0.00 0.00 38.71 3.79
2082 2131 1.017387 GTGCCACTGCCTATGCTTAC 58.983 55.000 0.00 0.00 38.71 2.34
2135 2184 0.888285 GAGGCAGCAGCAGAACAAGT 60.888 55.000 2.65 0.00 44.61 3.16
2179 2240 1.550524 CAATGTCGGAGGAGGTGAAGA 59.449 52.381 0.00 0.00 0.00 2.87
2180 2241 1.479709 ATGTCGGAGGAGGTGAAGAG 58.520 55.000 0.00 0.00 0.00 2.85
2187 2248 2.356535 GGAGGAGGTGAAGAGTACCGTA 60.357 54.545 0.00 0.00 43.06 4.02
2277 2338 1.676635 CATGACACTGCCTGGTGGG 60.677 63.158 0.00 0.00 41.09 4.61
2301 2362 2.960384 CCATGCCCATAAAGAGCATCAA 59.040 45.455 0.00 0.00 45.16 2.57
2306 2367 3.565902 GCCCATAAAGAGCATCAAGTACC 59.434 47.826 0.00 0.00 37.82 3.34
2309 2370 4.442706 CATAAAGAGCATCAAGTACCGGT 58.557 43.478 13.98 13.98 37.82 5.28
2812 3017 4.730487 GCAGGGAGCAAGACATGT 57.270 55.556 0.00 0.00 44.79 3.21
2813 3018 2.952714 GCAGGGAGCAAGACATGTT 58.047 52.632 0.00 0.00 44.79 2.71
2814 3019 2.113860 GCAGGGAGCAAGACATGTTA 57.886 50.000 0.00 0.00 44.79 2.41
2986 3230 5.122519 TCTGTAGAAGACAACACATGCAAA 58.877 37.500 0.00 0.00 37.70 3.68
3144 3430 1.205417 GCTTTAGCAATGCACCACCAT 59.795 47.619 8.35 0.00 41.59 3.55
3254 3553 1.212688 CACACCTCATTCCCCTATGCA 59.787 52.381 0.00 0.00 0.00 3.96
3384 3691 2.076863 ACACAAGATAAGCGCCAAGTC 58.923 47.619 2.29 0.00 0.00 3.01
3529 3840 6.127619 TGACAGATGTGATTCACGAGTTCTAT 60.128 38.462 11.97 1.67 37.14 1.98
3619 3930 4.454504 CACGCTTCCTATTACAAACCACTT 59.545 41.667 0.00 0.00 0.00 3.16
3662 3991 5.482878 TCATCTGCTCCAATATCTCTGCATA 59.517 40.000 0.00 0.00 0.00 3.14
3663 3992 6.156429 TCATCTGCTCCAATATCTCTGCATAT 59.844 38.462 0.00 0.00 0.00 1.78
3664 3993 5.975282 TCTGCTCCAATATCTCTGCATATC 58.025 41.667 0.00 0.00 0.00 1.63
3665 3994 5.720520 TCTGCTCCAATATCTCTGCATATCT 59.279 40.000 0.00 0.00 0.00 1.98
3667 3996 5.482878 TGCTCCAATATCTCTGCATATCTGA 59.517 40.000 0.00 0.00 0.00 3.27
3672 4001 6.762187 CCAATATCTCTGCATATCTGACCATC 59.238 42.308 0.00 0.00 0.00 3.51
3675 4004 5.211174 TCTCTGCATATCTGACCATCAAG 57.789 43.478 0.00 0.00 0.00 3.02
3676 4005 4.040095 TCTCTGCATATCTGACCATCAAGG 59.960 45.833 0.00 0.00 45.67 3.61
3677 4006 2.812591 CTGCATATCTGACCATCAAGGC 59.187 50.000 0.00 0.00 43.14 4.35
3678 4007 2.173143 TGCATATCTGACCATCAAGGCA 59.827 45.455 0.00 0.00 43.14 4.75
3679 4008 3.216800 GCATATCTGACCATCAAGGCAA 58.783 45.455 0.00 0.00 43.14 4.52
3721 4056 4.766891 CCAAGTTCCCATACTCACAACAAT 59.233 41.667 0.00 0.00 0.00 2.71
3724 4059 7.305474 CAAGTTCCCATACTCACAACAATAAC 58.695 38.462 0.00 0.00 0.00 1.89
3727 4062 6.811253 TCCCATACTCACAACAATAACAAC 57.189 37.500 0.00 0.00 0.00 3.32
3817 4152 2.099592 GCCAAATTTGCCATCGATGAGA 59.900 45.455 26.86 9.52 0.00 3.27
3842 4177 1.623811 TCAAGGAGTAGAACCCACTGC 59.376 52.381 0.00 0.00 34.82 4.40
3846 4181 0.391793 GAGTAGAACCCACTGCTGCC 60.392 60.000 0.00 0.00 33.37 4.85
3849 4184 2.449031 TAGAACCCACTGCTGCCGTG 62.449 60.000 16.07 16.07 0.00 4.94
3853 4188 2.268920 CCACTGCTGCCGTGGTAT 59.731 61.111 28.49 0.00 45.36 2.73
3928 4263 0.250727 GTGGCAGGCAGTCTGGTAAA 60.251 55.000 3.66 0.00 43.54 2.01
3929 4264 0.036732 TGGCAGGCAGTCTGGTAAAG 59.963 55.000 3.66 0.00 43.54 1.85
3930 4265 0.036875 GGCAGGCAGTCTGGTAAAGT 59.963 55.000 3.66 0.00 43.54 2.66
3932 4267 2.347731 GCAGGCAGTCTGGTAAAGTAC 58.652 52.381 3.66 0.00 43.54 2.73
3933 4268 2.289444 GCAGGCAGTCTGGTAAAGTACA 60.289 50.000 3.66 0.00 43.54 2.90
3934 4269 3.619979 GCAGGCAGTCTGGTAAAGTACAT 60.620 47.826 3.66 0.00 43.54 2.29
3935 4270 3.935203 CAGGCAGTCTGGTAAAGTACATG 59.065 47.826 1.14 0.00 39.76 3.21
3936 4271 2.678336 GGCAGTCTGGTAAAGTACATGC 59.322 50.000 1.14 0.00 0.00 4.06
3937 4272 3.600388 GCAGTCTGGTAAAGTACATGCT 58.400 45.455 1.14 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.628919 TTCTGTTAGCCCTTTAAGTTGTTC 57.371 37.500 0.00 0.00 0.00 3.18
1 2 6.183360 GGTTTCTGTTAGCCCTTTAAGTTGTT 60.183 38.462 0.00 0.00 0.00 2.83
2 3 5.301045 GGTTTCTGTTAGCCCTTTAAGTTGT 59.699 40.000 0.00 0.00 0.00 3.32
3 4 5.300792 TGGTTTCTGTTAGCCCTTTAAGTTG 59.699 40.000 0.00 0.00 0.00 3.16
4 5 5.451354 TGGTTTCTGTTAGCCCTTTAAGTT 58.549 37.500 0.00 0.00 0.00 2.66
5 6 5.056553 TGGTTTCTGTTAGCCCTTTAAGT 57.943 39.130 0.00 0.00 0.00 2.24
6 7 5.710099 TCATGGTTTCTGTTAGCCCTTTAAG 59.290 40.000 0.00 0.00 0.00 1.85
7 8 5.636123 TCATGGTTTCTGTTAGCCCTTTAA 58.364 37.500 0.00 0.00 0.00 1.52
8 9 5.249780 TCATGGTTTCTGTTAGCCCTTTA 57.750 39.130 0.00 0.00 0.00 1.85
9 10 4.112634 TCATGGTTTCTGTTAGCCCTTT 57.887 40.909 0.00 0.00 0.00 3.11
10 11 3.806949 TCATGGTTTCTGTTAGCCCTT 57.193 42.857 0.00 0.00 0.00 3.95
11 12 3.421844 GTTCATGGTTTCTGTTAGCCCT 58.578 45.455 0.00 0.00 0.00 5.19
12 13 2.161609 CGTTCATGGTTTCTGTTAGCCC 59.838 50.000 0.00 0.00 0.00 5.19
13 14 3.071479 TCGTTCATGGTTTCTGTTAGCC 58.929 45.455 0.00 0.00 0.00 3.93
14 15 3.746492 ACTCGTTCATGGTTTCTGTTAGC 59.254 43.478 0.00 0.00 0.00 3.09
15 16 5.062308 GCTACTCGTTCATGGTTTCTGTTAG 59.938 44.000 0.00 0.00 0.00 2.34
16 17 4.927425 GCTACTCGTTCATGGTTTCTGTTA 59.073 41.667 0.00 0.00 0.00 2.41
17 18 3.746492 GCTACTCGTTCATGGTTTCTGTT 59.254 43.478 0.00 0.00 0.00 3.16
18 19 3.244078 TGCTACTCGTTCATGGTTTCTGT 60.244 43.478 0.00 0.00 0.00 3.41
19 20 3.325870 TGCTACTCGTTCATGGTTTCTG 58.674 45.455 0.00 0.00 0.00 3.02
20 21 3.006967 ACTGCTACTCGTTCATGGTTTCT 59.993 43.478 0.00 0.00 0.00 2.52
21 22 3.123621 CACTGCTACTCGTTCATGGTTTC 59.876 47.826 0.00 0.00 0.00 2.78
22 23 3.067106 CACTGCTACTCGTTCATGGTTT 58.933 45.455 0.00 0.00 0.00 3.27
23 24 2.037251 ACACTGCTACTCGTTCATGGTT 59.963 45.455 0.00 0.00 0.00 3.67
24 25 1.618837 ACACTGCTACTCGTTCATGGT 59.381 47.619 0.00 0.00 0.00 3.55
25 26 2.370281 ACACTGCTACTCGTTCATGG 57.630 50.000 0.00 0.00 0.00 3.66
26 27 3.059884 ACAACACTGCTACTCGTTCATG 58.940 45.455 0.00 0.00 0.00 3.07
27 28 3.386768 ACAACACTGCTACTCGTTCAT 57.613 42.857 0.00 0.00 0.00 2.57
28 29 2.882927 ACAACACTGCTACTCGTTCA 57.117 45.000 0.00 0.00 0.00 3.18
29 30 5.840940 AATAACAACACTGCTACTCGTTC 57.159 39.130 0.00 0.00 0.00 3.95
30 31 6.427150 CAAAATAACAACACTGCTACTCGTT 58.573 36.000 0.00 0.00 0.00 3.85
31 32 5.049680 CCAAAATAACAACACTGCTACTCGT 60.050 40.000 0.00 0.00 0.00 4.18
32 33 5.049680 ACCAAAATAACAACACTGCTACTCG 60.050 40.000 0.00 0.00 0.00 4.18
33 34 6.017440 TGACCAAAATAACAACACTGCTACTC 60.017 38.462 0.00 0.00 0.00 2.59
34 35 5.825679 TGACCAAAATAACAACACTGCTACT 59.174 36.000 0.00 0.00 0.00 2.57
35 36 6.067263 TGACCAAAATAACAACACTGCTAC 57.933 37.500 0.00 0.00 0.00 3.58
36 37 6.701145 TTGACCAAAATAACAACACTGCTA 57.299 33.333 0.00 0.00 0.00 3.49
37 38 5.590530 TTGACCAAAATAACAACACTGCT 57.409 34.783 0.00 0.00 0.00 4.24
38 39 6.843069 ATTTGACCAAAATAACAACACTGC 57.157 33.333 0.00 0.00 36.69 4.40
39 40 9.307121 TGTAATTTGACCAAAATAACAACACTG 57.693 29.630 0.00 0.00 37.51 3.66
40 41 9.528018 CTGTAATTTGACCAAAATAACAACACT 57.472 29.630 0.00 0.00 37.51 3.55
41 42 8.272866 GCTGTAATTTGACCAAAATAACAACAC 58.727 33.333 0.00 0.00 37.51 3.32
42 43 7.439655 GGCTGTAATTTGACCAAAATAACAACA 59.560 33.333 0.00 0.00 37.51 3.33
43 44 7.655732 AGGCTGTAATTTGACCAAAATAACAAC 59.344 33.333 0.00 1.28 37.51 3.32
44 45 7.731054 AGGCTGTAATTTGACCAAAATAACAA 58.269 30.769 0.00 0.00 37.51 2.83
45 46 7.232534 AGAGGCTGTAATTTGACCAAAATAACA 59.767 33.333 0.00 4.19 37.51 2.41
46 47 7.602753 AGAGGCTGTAATTTGACCAAAATAAC 58.397 34.615 0.00 0.17 37.51 1.89
47 48 7.775053 AGAGGCTGTAATTTGACCAAAATAA 57.225 32.000 0.00 0.00 37.51 1.40
48 49 7.775053 AAGAGGCTGTAATTTGACCAAAATA 57.225 32.000 0.00 0.00 37.51 1.40
49 50 6.670695 AAGAGGCTGTAATTTGACCAAAAT 57.329 33.333 0.00 0.00 40.32 1.82
50 51 6.478512 AAAGAGGCTGTAATTTGACCAAAA 57.521 33.333 0.00 0.00 33.56 2.44
51 52 7.775053 ATAAAGAGGCTGTAATTTGACCAAA 57.225 32.000 0.00 0.00 34.46 3.28
52 53 7.775053 AATAAAGAGGCTGTAATTTGACCAA 57.225 32.000 0.00 0.00 0.00 3.67
53 54 7.309744 CCAAATAAAGAGGCTGTAATTTGACCA 60.310 37.037 23.03 0.00 31.59 4.02
54 55 7.035612 CCAAATAAAGAGGCTGTAATTTGACC 58.964 38.462 23.03 0.00 31.59 4.02
75 76 2.822561 TGCAAGATGAAATACGGCCAAA 59.177 40.909 2.24 0.00 0.00 3.28
102 103 4.216687 GGAGACATCTTCCTAGTGGTATCG 59.783 50.000 0.00 0.00 34.23 2.92
146 147 9.727627 ATGCTACAAACTAACTCGTATAACTAC 57.272 33.333 0.00 0.00 0.00 2.73
154 155 4.267349 ACCATGCTACAAACTAACTCGT 57.733 40.909 0.00 0.00 0.00 4.18
161 162 7.768120 TCAAAATTGAAAACCATGCTACAAACT 59.232 29.630 0.00 0.00 33.55 2.66
191 192 5.666969 TGGTGACGTCTGAAATTGTTTAG 57.333 39.130 17.92 0.00 0.00 1.85
192 193 6.438259 TTTGGTGACGTCTGAAATTGTTTA 57.562 33.333 17.92 0.00 0.00 2.01
229 230 6.127897 CCCGAAAGTAATCTGAAATCTGCTTT 60.128 38.462 0.00 0.00 0.00 3.51
238 240 5.800296 TCACAATCCCGAAAGTAATCTGAA 58.200 37.500 0.00 0.00 0.00 3.02
251 253 2.185004 ACTGGAAACTCACAATCCCG 57.815 50.000 0.00 0.00 32.01 5.14
255 257 5.630121 TGGTGAATACTGGAAACTCACAAT 58.370 37.500 3.23 0.00 38.50 2.71
344 350 3.704566 GGGTCTCAAATATTTGGAACCCC 59.295 47.826 34.49 27.86 46.36 4.95
382 388 1.957668 ACGTACAAACCAGGGTTGAC 58.042 50.000 25.01 15.49 38.47 3.18
383 389 3.834489 TTACGTACAAACCAGGGTTGA 57.166 42.857 25.01 4.74 38.47 3.18
399 405 4.226761 GGTTCAAGCTCCAACAAATTACG 58.773 43.478 9.35 0.00 0.00 3.18
400 406 4.556233 GGGTTCAAGCTCCAACAAATTAC 58.444 43.478 9.35 0.00 0.00 1.89
401 407 3.576550 GGGGTTCAAGCTCCAACAAATTA 59.423 43.478 9.35 0.00 0.00 1.40
402 408 2.368548 GGGGTTCAAGCTCCAACAAATT 59.631 45.455 9.35 0.00 0.00 1.82
403 409 1.970640 GGGGTTCAAGCTCCAACAAAT 59.029 47.619 9.35 0.00 0.00 2.32
423 429 6.212235 TGTTACATGTACAACAATGCCTTTG 58.788 36.000 10.99 0.00 41.36 2.77
487 493 7.285401 ACTGAGGACACACAAAATACATTTTCT 59.715 33.333 0.00 0.00 37.86 2.52
488 494 7.425606 ACTGAGGACACACAAAATACATTTTC 58.574 34.615 0.00 0.00 37.86 2.29
525 531 6.664714 TGCTACTACTATTCTTGTCTCCTCT 58.335 40.000 0.00 0.00 0.00 3.69
561 580 1.182385 TTTTTGGGTCCATCCACGCC 61.182 55.000 0.00 0.00 36.38 5.68
562 581 2.346597 TTTTTGGGTCCATCCACGC 58.653 52.632 0.00 0.00 36.38 5.34
586 605 1.442526 GACGGATGCTGCAGGAATGG 61.443 60.000 13.45 6.62 0.00 3.16
597 616 0.449388 CAGCCAAGAAAGACGGATGC 59.551 55.000 0.00 0.00 28.03 3.91
599 618 0.678048 GGCAGCCAAGAAAGACGGAT 60.678 55.000 6.55 0.00 0.00 4.18
729 753 6.280855 TCGTTTGATTGATTACAGGAGAGA 57.719 37.500 0.00 0.00 0.00 3.10
732 756 5.817296 TCCATCGTTTGATTGATTACAGGAG 59.183 40.000 0.00 0.00 30.49 3.69
734 758 6.564686 CGATCCATCGTTTGATTGATTACAGG 60.565 42.308 0.55 0.00 44.74 4.00
735 759 6.357980 CGATCCATCGTTTGATTGATTACAG 58.642 40.000 0.55 0.00 44.74 2.74
736 760 6.285790 CGATCCATCGTTTGATTGATTACA 57.714 37.500 0.55 0.00 44.74 2.41
739 763 8.479465 ATCGATCGATCCATCGTTTGATTGATT 61.479 37.037 24.60 0.00 44.51 2.57
740 764 7.067533 ATCGATCGATCCATCGTTTGATTGAT 61.068 38.462 24.60 10.16 44.51 2.57
741 765 5.793563 ATCGATCGATCCATCGTTTGATTGA 60.794 40.000 24.60 8.52 44.51 2.57
742 766 4.386954 ATCGATCGATCCATCGTTTGATTG 59.613 41.667 24.60 3.79 44.51 2.67
743 767 4.560128 ATCGATCGATCCATCGTTTGATT 58.440 39.130 24.60 0.00 44.51 2.57
744 768 4.560128 AATCGATCGATCCATCGTTTGAT 58.440 39.130 29.48 13.59 46.80 2.57
751 775 5.233902 GGATGAATGAATCGATCGATCCATC 59.766 44.000 27.02 27.04 28.13 3.51
752 776 5.105023 AGGATGAATGAATCGATCGATCCAT 60.105 40.000 29.48 25.89 30.79 3.41
753 777 4.221482 AGGATGAATGAATCGATCGATCCA 59.779 41.667 29.48 24.77 33.08 3.41
754 778 4.753233 AGGATGAATGAATCGATCGATCC 58.247 43.478 29.48 23.17 33.08 3.36
755 779 5.063186 CCAAGGATGAATGAATCGATCGATC 59.937 44.000 29.48 21.64 33.08 3.69
773 797 0.756442 AGCAAGCAAGCAACCAAGGA 60.756 50.000 3.19 0.00 36.85 3.36
774 798 0.105408 AAGCAAGCAAGCAACCAAGG 59.895 50.000 3.19 0.00 36.85 3.61
775 799 1.214367 CAAGCAAGCAAGCAACCAAG 58.786 50.000 3.19 0.00 36.85 3.61
776 800 0.810823 GCAAGCAAGCAAGCAACCAA 60.811 50.000 3.19 0.00 36.85 3.67
777 801 1.227321 GCAAGCAAGCAAGCAACCA 60.227 52.632 3.19 0.00 36.85 3.67
778 802 0.531311 AAGCAAGCAAGCAAGCAACC 60.531 50.000 10.52 0.00 36.85 3.77
779 803 0.580104 CAAGCAAGCAAGCAAGCAAC 59.420 50.000 10.52 0.00 36.85 4.17
780 804 0.176219 ACAAGCAAGCAAGCAAGCAA 59.824 45.000 10.52 0.00 36.85 3.91
781 805 0.176219 AACAAGCAAGCAAGCAAGCA 59.824 45.000 10.52 0.00 36.85 3.91
782 806 2.138596 TAACAAGCAAGCAAGCAAGC 57.861 45.000 3.19 0.00 36.85 4.01
783 807 5.691305 TGTAATTAACAAGCAAGCAAGCAAG 59.309 36.000 3.19 0.00 34.29 4.01
784 808 5.595885 TGTAATTAACAAGCAAGCAAGCAA 58.404 33.333 3.19 0.00 34.29 3.91
785 809 5.193663 TGTAATTAACAAGCAAGCAAGCA 57.806 34.783 3.19 0.00 34.29 3.91
786 810 6.710692 AATGTAATTAACAAGCAAGCAAGC 57.289 33.333 0.00 0.00 42.70 4.01
787 811 8.741101 TGTAATGTAATTAACAAGCAAGCAAG 57.259 30.769 0.00 0.00 41.12 4.01
788 812 9.703892 AATGTAATGTAATTAACAAGCAAGCAA 57.296 25.926 0.00 0.00 41.12 3.91
789 813 9.352784 GAATGTAATGTAATTAACAAGCAAGCA 57.647 29.630 0.00 0.00 41.12 3.91
790 814 9.352784 TGAATGTAATGTAATTAACAAGCAAGC 57.647 29.630 0.00 0.00 41.12 4.01
823 847 2.212869 ACAACAACAACAGCAGCATG 57.787 45.000 0.00 0.00 40.87 4.06
824 848 2.094078 ACAACAACAACAACAGCAGCAT 60.094 40.909 0.00 0.00 0.00 3.79
825 849 1.271934 ACAACAACAACAACAGCAGCA 59.728 42.857 0.00 0.00 0.00 4.41
826 850 1.994916 ACAACAACAACAACAGCAGC 58.005 45.000 0.00 0.00 0.00 5.25
827 851 3.486841 GCATACAACAACAACAACAGCAG 59.513 43.478 0.00 0.00 0.00 4.24
828 852 3.443037 GCATACAACAACAACAACAGCA 58.557 40.909 0.00 0.00 0.00 4.41
829 853 2.467305 CGCATACAACAACAACAACAGC 59.533 45.455 0.00 0.00 0.00 4.40
830 854 3.690422 ACGCATACAACAACAACAACAG 58.310 40.909 0.00 0.00 0.00 3.16
831 855 3.766676 ACGCATACAACAACAACAACA 57.233 38.095 0.00 0.00 0.00 3.33
832 856 4.024725 TCCTACGCATACAACAACAACAAC 60.025 41.667 0.00 0.00 0.00 3.32
834 858 3.729966 TCCTACGCATACAACAACAACA 58.270 40.909 0.00 0.00 0.00 3.33
835 859 4.939509 ATCCTACGCATACAACAACAAC 57.060 40.909 0.00 0.00 0.00 3.32
836 860 4.155099 CCAATCCTACGCATACAACAACAA 59.845 41.667 0.00 0.00 0.00 2.83
839 863 4.081365 TCTCCAATCCTACGCATACAACAA 60.081 41.667 0.00 0.00 0.00 2.83
840 864 3.449377 TCTCCAATCCTACGCATACAACA 59.551 43.478 0.00 0.00 0.00 3.33
841 865 4.054780 TCTCCAATCCTACGCATACAAC 57.945 45.455 0.00 0.00 0.00 3.32
843 867 3.895041 TGATCTCCAATCCTACGCATACA 59.105 43.478 0.00 0.00 0.00 2.29
845 869 5.337571 GGAATGATCTCCAATCCTACGCATA 60.338 44.000 0.00 0.00 40.85 3.14
848 872 3.244215 TGGAATGATCTCCAATCCTACGC 60.244 47.826 1.25 0.00 43.73 4.42
868 892 8.964772 ACAAGAAGAATAATCAGGAAAGAATGG 58.035 33.333 0.00 0.00 0.00 3.16
874 898 6.716628 ACAGCACAAGAAGAATAATCAGGAAA 59.283 34.615 0.00 0.00 0.00 3.13
893 917 5.032863 GCATCATCAAGACAATAACAGCAC 58.967 41.667 0.00 0.00 0.00 4.40
916 940 1.000274 CATGGTGGATCTGCATGCATG 60.000 52.381 22.97 22.70 32.20 4.06
994 1022 2.187946 CTCCTCGTCCATGGCACC 59.812 66.667 6.96 0.00 0.00 5.01
995 1023 2.187946 CCTCCTCGTCCATGGCAC 59.812 66.667 6.96 5.56 0.00 5.01
996 1024 2.038813 TCCTCCTCGTCCATGGCA 59.961 61.111 6.96 0.00 0.00 4.92
997 1025 2.801631 CCTCCTCCTCGTCCATGGC 61.802 68.421 6.96 0.96 0.00 4.40
998 1026 1.075970 TCCTCCTCCTCGTCCATGG 60.076 63.158 4.97 4.97 0.00 3.66
999 1027 0.106469 TCTCCTCCTCCTCGTCCATG 60.106 60.000 0.00 0.00 0.00 3.66
1010 1038 1.341156 CGCCCCTTCAATCTCCTCCT 61.341 60.000 0.00 0.00 0.00 3.69
1011 1039 1.147153 CGCCCCTTCAATCTCCTCC 59.853 63.158 0.00 0.00 0.00 4.30
1012 1040 1.524849 GCGCCCCTTCAATCTCCTC 60.525 63.158 0.00 0.00 0.00 3.71
1060 1091 3.622630 CGAGGAAGAGGAGGAAGTAGAA 58.377 50.000 0.00 0.00 0.00 2.10
1064 1095 0.973496 GGCGAGGAAGAGGAGGAAGT 60.973 60.000 0.00 0.00 0.00 3.01
1141 1172 3.379445 GAGGGCGGTGAGGACGAA 61.379 66.667 0.00 0.00 0.00 3.85
1218 1249 2.124695 GGGCGGTGGGTGATCTTC 60.125 66.667 0.00 0.00 0.00 2.87
1226 1257 4.676951 ATTGTGGTGGGCGGTGGG 62.677 66.667 0.00 0.00 0.00 4.61
1254 1285 2.445845 CCTCCGATGGGGGCTGTA 60.446 66.667 0.00 0.00 36.01 2.74
1262 1293 3.083349 TGGTGCTCCCTCCGATGG 61.083 66.667 1.59 0.00 0.00 3.51
1264 1295 3.474570 GCTGGTGCTCCCTCCGAT 61.475 66.667 1.59 0.00 36.03 4.18
1267 1298 4.792804 GCTGCTGGTGCTCCCTCC 62.793 72.222 1.59 0.00 40.48 4.30
1268 1299 3.972971 CTGCTGCTGGTGCTCCCTC 62.973 68.421 1.59 0.00 40.48 4.30
1269 1300 4.031129 CTGCTGCTGGTGCTCCCT 62.031 66.667 1.59 0.00 40.48 4.20
1270 1301 4.025858 TCTGCTGCTGGTGCTCCC 62.026 66.667 6.69 0.00 40.48 4.30
1271 1302 2.745492 GTCTGCTGCTGGTGCTCC 60.745 66.667 6.69 0.00 40.48 4.70
1272 1303 1.367599 GATGTCTGCTGCTGGTGCTC 61.368 60.000 6.69 0.00 40.48 4.26
1273 1304 1.376942 GATGTCTGCTGCTGGTGCT 60.377 57.895 6.69 0.00 40.48 4.40
1274 1305 1.673337 TGATGTCTGCTGCTGGTGC 60.673 57.895 6.69 0.00 40.20 5.01
1275 1306 1.303799 GGTGATGTCTGCTGCTGGTG 61.304 60.000 6.69 0.00 0.00 4.17
1276 1307 1.002868 GGTGATGTCTGCTGCTGGT 60.003 57.895 6.69 0.00 0.00 4.00
1277 1308 1.002990 TGGTGATGTCTGCTGCTGG 60.003 57.895 6.69 0.00 0.00 4.85
1278 1309 1.303799 GGTGGTGATGTCTGCTGCTG 61.304 60.000 0.00 0.00 0.00 4.41
1279 1310 1.002868 GGTGGTGATGTCTGCTGCT 60.003 57.895 0.00 0.00 0.00 4.24
1280 1311 1.302752 TGGTGGTGATGTCTGCTGC 60.303 57.895 0.00 0.00 0.00 5.25
1283 1314 2.042831 GGCTGGTGGTGATGTCTGC 61.043 63.158 0.00 0.00 0.00 4.26
1298 1329 1.403687 GCTGGATTCGTAGGAGGGCT 61.404 60.000 0.00 0.00 0.00 5.19
1299 1330 1.069935 GCTGGATTCGTAGGAGGGC 59.930 63.158 0.00 0.00 0.00 5.19
1306 1337 0.376152 GAGTCGTCGCTGGATTCGTA 59.624 55.000 0.00 0.00 0.00 3.43
1321 1352 1.323271 TGTGCGGATGAGGAGGAGTC 61.323 60.000 0.00 0.00 0.00 3.36
1322 1353 1.305297 TGTGCGGATGAGGAGGAGT 60.305 57.895 0.00 0.00 0.00 3.85
1323 1354 1.142748 GTGTGCGGATGAGGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69
1332 1366 1.518325 TGTCATTTTCGTGTGCGGAT 58.482 45.000 0.00 0.00 38.89 4.18
1337 1371 1.394697 GCGGTTGTCATTTTCGTGTG 58.605 50.000 0.00 0.00 0.00 3.82
1338 1372 0.309612 GGCGGTTGTCATTTTCGTGT 59.690 50.000 0.00 0.00 0.00 4.49
1339 1373 0.386731 GGGCGGTTGTCATTTTCGTG 60.387 55.000 0.00 0.00 0.00 4.35
1381 1415 2.283529 GGAAGGAGGCGTGTGAGGA 61.284 63.158 0.00 0.00 0.00 3.71
1434 1468 1.967779 TGGTCAGAGTCGGTTGATTCA 59.032 47.619 0.00 0.00 33.54 2.57
1455 1489 2.098614 TGGTTGTGCTGCTTTTCTTCA 58.901 42.857 0.00 0.00 0.00 3.02
1479 1513 1.852067 CGTCCTTTTTGTGGGAGCGG 61.852 60.000 0.00 0.00 31.66 5.52
1486 1520 1.657181 GCACCGCGTCCTTTTTGTG 60.657 57.895 4.92 4.29 0.00 3.33
1629 1663 1.528309 GTGGTGGTGTTGGTGGAGG 60.528 63.158 0.00 0.00 0.00 4.30
1638 1672 0.467290 GATGGTGTTGGTGGTGGTGT 60.467 55.000 0.00 0.00 0.00 4.16
1647 1681 0.804364 CCATGACGTGATGGTGTTGG 59.196 55.000 24.17 0.44 38.53 3.77
1648 1682 1.464608 GTCCATGACGTGATGGTGTTG 59.535 52.381 29.57 7.78 43.20 3.33
1649 1683 1.610624 GGTCCATGACGTGATGGTGTT 60.611 52.381 29.57 0.00 43.20 3.32
1650 1684 0.036388 GGTCCATGACGTGATGGTGT 60.036 55.000 29.57 0.00 43.20 4.16
1653 1687 0.528466 CGAGGTCCATGACGTGATGG 60.528 60.000 26.16 26.16 43.96 3.51
1656 1690 2.571757 GCGAGGTCCATGACGTGA 59.428 61.111 0.00 0.00 32.65 4.35
1704 1738 1.255667 CGAAGGGGTTCCTCTTCCGA 61.256 60.000 21.40 0.00 44.07 4.55
1705 1739 1.218316 CGAAGGGGTTCCTCTTCCG 59.782 63.158 21.40 14.35 44.07 4.30
1821 1855 1.309950 GGAGATGGAGATCGTCGTCA 58.690 55.000 11.33 0.00 36.53 4.35
1878 1921 0.957395 ACAGCATGGCGTTCTTCTGG 60.957 55.000 0.00 0.00 43.62 3.86
1908 1951 2.125912 CCCACGGTGAAGCTCTCG 60.126 66.667 10.28 0.00 0.00 4.04
1933 1976 2.805353 CCGGAAGTCGCTGACGTG 60.805 66.667 0.00 0.00 41.18 4.49
1938 1981 2.892425 GATGGCCGGAAGTCGCTG 60.892 66.667 5.05 0.00 37.59 5.18
1980 2023 1.153005 CTGGCCCTGCATCTTCTCC 60.153 63.158 0.00 0.00 0.00 3.71
2135 2184 2.934364 GCTGCTTCTGCTTCTGCTTCTA 60.934 50.000 0.00 0.00 40.48 2.10
2179 2240 2.015587 GCTGCTGTACTCTACGGTACT 58.984 52.381 0.00 0.00 41.64 2.73
2180 2241 1.741706 TGCTGCTGTACTCTACGGTAC 59.258 52.381 0.00 0.00 41.51 3.34
2187 2248 1.181786 GAGACCTGCTGCTGTACTCT 58.818 55.000 16.43 9.31 0.00 3.24
2294 2355 1.134788 GCTGTACCGGTACTTGATGCT 60.135 52.381 37.37 2.58 37.00 3.79
2298 2359 0.245539 GCTGCTGTACCGGTACTTGA 59.754 55.000 37.37 21.56 37.00 3.02
2301 2362 1.890894 CTGCTGCTGTACCGGTACT 59.109 57.895 37.37 7.33 37.00 2.73
2306 2367 3.494336 GCTGCTGCTGCTGTACCG 61.494 66.667 22.10 3.61 39.81 4.02
2309 2370 2.046604 CCTGCTGCTGCTGCTGTA 60.047 61.111 27.67 16.32 39.81 2.74
2809 3014 1.489649 AGCAGCAGGAGCAGATAACAT 59.510 47.619 0.00 0.00 45.49 2.71
2810 3015 0.907486 AGCAGCAGGAGCAGATAACA 59.093 50.000 0.00 0.00 45.49 2.41
2811 3016 1.297664 CAGCAGCAGGAGCAGATAAC 58.702 55.000 0.00 0.00 45.49 1.89
2812 3017 0.179702 CCAGCAGCAGGAGCAGATAA 59.820 55.000 0.00 0.00 45.49 1.75
2813 3018 0.979709 ACCAGCAGCAGGAGCAGATA 60.980 55.000 11.55 0.00 45.49 1.98
2814 3019 2.299429 ACCAGCAGCAGGAGCAGAT 61.299 57.895 11.55 0.00 45.49 2.90
2986 3230 3.073946 GTCCTGAGAGAGTATAGGAGGCT 59.926 52.174 0.00 0.00 39.84 4.58
3254 3553 3.101437 TGAATGCAGAAAGATGGCCAAT 58.899 40.909 10.96 0.00 0.00 3.16
3384 3691 0.609131 ACATTGTTGGCTCTTCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
3529 3840 2.305927 GTCCTTGTCATTGAGGGAGGAA 59.694 50.000 11.94 0.00 35.27 3.36
3619 3930 7.766278 GCAGATGAGAGAATAACCTTGAAGTTA 59.234 37.037 0.00 0.00 36.68 2.24
3662 3991 2.885135 TGTTGCCTTGATGGTCAGAT 57.115 45.000 0.00 0.00 38.35 2.90
3663 3992 2.622942 GTTTGTTGCCTTGATGGTCAGA 59.377 45.455 0.00 0.00 38.35 3.27
3664 3993 2.361757 TGTTTGTTGCCTTGATGGTCAG 59.638 45.455 0.00 0.00 38.35 3.51
3665 3994 2.382882 TGTTTGTTGCCTTGATGGTCA 58.617 42.857 0.00 0.00 38.35 4.02
3667 3996 3.902881 TTTGTTTGTTGCCTTGATGGT 57.097 38.095 0.00 0.00 38.35 3.55
3672 4001 9.862585 GTTCTAATTTATTTGTTTGTTGCCTTG 57.137 29.630 0.00 0.00 0.00 3.61
3675 4004 8.371770 TGGTTCTAATTTATTTGTTTGTTGCC 57.628 30.769 0.00 0.00 0.00 4.52
3676 4005 9.862585 CTTGGTTCTAATTTATTTGTTTGTTGC 57.137 29.630 0.00 0.00 0.00 4.17
3721 4056 2.808244 GCAGCAGCAAAGTTGTTGTTA 58.192 42.857 9.25 0.00 40.86 2.41
3807 4142 5.114780 ACTCCTTGACAAATCTCATCGATG 58.885 41.667 19.61 19.61 31.20 3.84
3817 4152 4.351111 AGTGGGTTCTACTCCTTGACAAAT 59.649 41.667 0.00 0.00 0.00 2.32
3842 4177 3.187058 GCCACAATACCACGGCAG 58.813 61.111 0.00 0.00 44.25 4.85
3846 4181 0.521291 CAAGGTGCCACAATACCACG 59.479 55.000 0.00 0.00 39.46 4.94
3849 4184 2.500392 TACCAAGGTGCCACAATACC 57.500 50.000 1.07 0.00 37.23 2.73
3853 4188 2.554344 GGATCTTACCAAGGTGCCACAA 60.554 50.000 1.07 0.00 0.00 3.33
3898 4233 7.069950 CCAGACTGCCTGCCACTTATATATATA 59.930 40.741 0.00 0.00 41.57 0.86
3899 4234 6.126940 CCAGACTGCCTGCCACTTATATATAT 60.127 42.308 0.00 0.00 41.57 0.86
3900 4235 5.187772 CCAGACTGCCTGCCACTTATATATA 59.812 44.000 0.00 0.00 41.57 0.86
3901 4236 4.019860 CCAGACTGCCTGCCACTTATATAT 60.020 45.833 0.00 0.00 41.57 0.86
3902 4237 3.324846 CCAGACTGCCTGCCACTTATATA 59.675 47.826 0.00 0.00 41.57 0.86
3903 4238 2.105477 CCAGACTGCCTGCCACTTATAT 59.895 50.000 0.00 0.00 41.57 0.86


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

AutoCloner maintained by Alex Coulton.