Multiple sequence alignment - TraesCS3D01G442400

Loading Multiple Alignment...

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 TraesCS3D01G442400 chr3D 100.000 2660 0 0 1 2660 552531595 552528936 0.000000e+00 4913.0
1 TraesCS3D01G442400 chr3D 86.644 599 64 12 1049 1645 552627430 552626846 0.000000e+00 649.0
2 TraesCS3D01G442400 chr3D 85.806 620 71 13 1049 1666 552571150 552570546 2.230000e-180 641.0
3 TraesCS3D01G442400 chr3D 97.619 42 1 0 326 367 552616988 552617029 3.670000e-09 73.1
4 TraesCS3D01G442400 chr7D 93.866 913 49 7 1754 2660 145920052 145919141 0.000000e+00 1369.0
5 TraesCS3D01G442400 chr7D 92.873 912 53 8 1754 2660 576645035 576644131 0.000000e+00 1314.0
6 TraesCS3D01G442400 chr7D 92.747 910 60 5 1754 2660 616465909 616465003 0.000000e+00 1310.0
7 TraesCS3D01G442400 chr7D 92.484 918 58 10 1748 2660 164762185 164761274 0.000000e+00 1303.0
8 TraesCS3D01G442400 chr2D 93.880 915 45 10 1754 2660 276936753 276935842 0.000000e+00 1369.0
9 TraesCS3D01G442400 chr2D 93.943 908 46 8 1758 2660 285349014 285349917 0.000000e+00 1363.0
10 TraesCS3D01G442400 chr1D 92.763 912 58 8 1754 2660 467389062 467389970 0.000000e+00 1312.0
11 TraesCS3D01G442400 chr1D 92.857 910 48 15 1758 2660 318104510 318105409 0.000000e+00 1304.0
12 TraesCS3D01G442400 chr5D 92.723 907 58 7 1758 2660 508156424 508157326 0.000000e+00 1303.0
13 TraesCS3D01G442400 chr5D 100.000 116 0 0 799 914 72366829 72366714 5.770000e-52 215.0
14 TraesCS3D01G442400 chr3A 90.606 809 44 9 1 799 688966034 688965248 0.000000e+00 1044.0
15 TraesCS3D01G442400 chr3A 88.290 854 81 12 912 1757 688965244 688964402 0.000000e+00 1005.0
16 TraesCS3D01G442400 chr3A 89.130 644 56 13 1038 1676 688899012 688898378 0.000000e+00 789.0
17 TraesCS3D01G442400 chr3A 84.890 728 83 18 946 1670 688978129 688977426 0.000000e+00 710.0
18 TraesCS3D01G442400 chr3A 82.416 745 94 20 935 1672 688992937 688993651 1.350000e-172 616.0
19 TraesCS3D01G442400 chr3B 89.314 627 56 9 1049 1670 732841640 732841020 0.000000e+00 776.0
20 TraesCS3D01G442400 chr3B 84.160 726 87 19 946 1670 733257762 733257064 0.000000e+00 678.0
21 TraesCS3D01G442400 chr3B 85.323 620 76 11 1049 1667 732998749 732998144 6.250000e-176 627.0
22 TraesCS3D01G442400 chr3B 93.103 116 8 0 799 914 637664783 637664898 1.270000e-38 171.0
23 TraesCS3D01G442400 chr2B 93.103 116 8 0 799 914 712622253 712622138 1.270000e-38 171.0
24 TraesCS3D01G442400 chr4A 96.471 85 3 0 799 883 96540152 96540236 9.930000e-30 141.0


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 TraesCS3D01G442400 chr3D 552528936 552531595 2659 True 4913.0 4913 100.000 1 2660 1 chr3D.!!$R1 2659
1 TraesCS3D01G442400 chr3D 552626846 552627430 584 True 649.0 649 86.644 1049 1645 1 chr3D.!!$R3 596
2 TraesCS3D01G442400 chr3D 552570546 552571150 604 True 641.0 641 85.806 1049 1666 1 chr3D.!!$R2 617
3 TraesCS3D01G442400 chr7D 145919141 145920052 911 True 1369.0 1369 93.866 1754 2660 1 chr7D.!!$R1 906
4 TraesCS3D01G442400 chr7D 576644131 576645035 904 True 1314.0 1314 92.873 1754 2660 1 chr7D.!!$R3 906
5 TraesCS3D01G442400 chr7D 616465003 616465909 906 True 1310.0 1310 92.747 1754 2660 1 chr7D.!!$R4 906
6 TraesCS3D01G442400 chr7D 164761274 164762185 911 True 1303.0 1303 92.484 1748 2660 1 chr7D.!!$R2 912
7 TraesCS3D01G442400 chr2D 276935842 276936753 911 True 1369.0 1369 93.880 1754 2660 1 chr2D.!!$R1 906
8 TraesCS3D01G442400 chr2D 285349014 285349917 903 False 1363.0 1363 93.943 1758 2660 1 chr2D.!!$F1 902
9 TraesCS3D01G442400 chr1D 467389062 467389970 908 False 1312.0 1312 92.763 1754 2660 1 chr1D.!!$F2 906
10 TraesCS3D01G442400 chr1D 318104510 318105409 899 False 1304.0 1304 92.857 1758 2660 1 chr1D.!!$F1 902
11 TraesCS3D01G442400 chr5D 508156424 508157326 902 False 1303.0 1303 92.723 1758 2660 1 chr5D.!!$F1 902
12 TraesCS3D01G442400 chr3A 688964402 688966034 1632 True 1024.5 1044 89.448 1 1757 2 chr3A.!!$R3 1756
13 TraesCS3D01G442400 chr3A 688898378 688899012 634 True 789.0 789 89.130 1038 1676 1 chr3A.!!$R1 638
14 TraesCS3D01G442400 chr3A 688977426 688978129 703 True 710.0 710 84.890 946 1670 1 chr3A.!!$R2 724
15 TraesCS3D01G442400 chr3A 688992937 688993651 714 False 616.0 616 82.416 935 1672 1 chr3A.!!$F1 737
16 TraesCS3D01G442400 chr3B 732841020 732841640 620 True 776.0 776 89.314 1049 1670 1 chr3B.!!$R1 621
17 TraesCS3D01G442400 chr3B 733257064 733257762 698 True 678.0 678 84.160 946 1670 1 chr3B.!!$R3 724
18 TraesCS3D01G442400 chr3B 732998144 732998749 605 True 627.0 627 85.323 1049 1667 1 chr3B.!!$R2 618

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
135 136 0.040336 TTCTACGCTCCATCGATCGC 60.040 55.0 11.09 0.0 30.77 4.58 F
1035 1048 0.037139 AACAGCAGCAGAGCAGAGAG 60.037 55.0 0.00 0.0 36.85 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1065 0.254178 TCTTGGCCATTGGAGAGAGC 59.746 55.0 6.09 0.0 0.0 4.09 R
1889 1923 0.387202 CATAGGCGTGTGAGAGGGAG 59.613 60.0 0.00 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
23 24 5.501715 ACTGATATGTACGTACCGTAAACG 58.498 41.667 22.43 8.45 43.95 3.60
36 37 2.088360 CCGTAAACGCGCAAAGAAATTG 59.912 45.455 5.73 0.00 38.92 2.32
43 44 2.138596 CGCAAAGAAATTGTGTGCCT 57.861 45.000 0.00 0.00 43.14 4.75
107 108 2.433970 AGCTTTCTCTCTGATGGCTACC 59.566 50.000 0.00 0.00 33.46 3.18
110 111 0.105453 TCTCTCTGATGGCTACCCCC 60.105 60.000 0.00 0.00 0.00 5.40
114 115 0.846015 TCTGATGGCTACCCCCATTG 59.154 55.000 0.00 0.00 45.41 2.82
121 122 2.441750 TGGCTACCCCCATTGATTCTAC 59.558 50.000 0.00 0.00 0.00 2.59
123 124 2.767505 CTACCCCCATTGATTCTACGC 58.232 52.381 0.00 0.00 0.00 4.42
125 126 1.141053 ACCCCCATTGATTCTACGCTC 59.859 52.381 0.00 0.00 0.00 5.03
135 136 0.040336 TTCTACGCTCCATCGATCGC 60.040 55.000 11.09 0.00 30.77 4.58
136 137 1.442857 CTACGCTCCATCGATCGCC 60.443 63.158 11.09 0.00 30.77 5.54
152 153 1.729131 GCCGCCGTGTGTTGATTTG 60.729 57.895 0.00 0.00 0.00 2.32
154 155 1.729131 CGCCGTGTGTTGATTTGGC 60.729 57.895 0.00 0.00 39.10 4.52
172 173 3.135994 TGGCCTCGTTTCAGTAGAAAAC 58.864 45.455 3.32 0.00 44.75 2.43
188 189 8.822855 CAGTAGAAAACAGTGTTGTGTGTATTA 58.177 33.333 9.79 0.00 37.67 0.98
229 230 3.126858 CCACGGAACAATGGTGATTACTG 59.873 47.826 0.00 0.00 33.58 2.74
233 234 5.815740 ACGGAACAATGGTGATTACTGATAC 59.184 40.000 0.00 0.00 0.00 2.24
275 278 4.461431 TGCAGAGCATGAAACTGATTGAAT 59.539 37.500 15.00 0.00 31.71 2.57
283 286 7.544566 AGCATGAAACTGATTGAATAAAGCTTG 59.455 33.333 0.00 0.00 0.00 4.01
287 290 9.241919 TGAAACTGATTGAATAAAGCTTGGATA 57.758 29.630 0.00 0.00 0.00 2.59
297 300 9.631257 TGAATAAAGCTTGGATAATGATGAAGA 57.369 29.630 0.00 0.00 0.00 2.87
323 326 4.615588 ATGTAGCTTGCTCTTAGGGATC 57.384 45.455 0.00 0.00 0.00 3.36
447 455 4.952957 TGCCTGCTTAATTTATTAGGTGCA 59.047 37.500 0.00 0.00 0.00 4.57
461 469 9.609346 TTTATTAGGTGCAAGTACTTATCCTTC 57.391 33.333 21.91 7.40 0.00 3.46
508 516 1.538950 CTGCTTTCTTTCTGCTCACCC 59.461 52.381 0.00 0.00 0.00 4.61
521 529 1.541588 GCTCACCCAACAGAACAATCC 59.458 52.381 0.00 0.00 0.00 3.01
527 535 5.835819 TCACCCAACAGAACAATCCATTTTA 59.164 36.000 0.00 0.00 0.00 1.52
544 552 5.069516 CCATTTTATGACTAGCAGCCCAAAT 59.930 40.000 0.00 0.00 0.00 2.32
570 578 3.495753 ACCATCCGTAGTTCGTTTTGTTC 59.504 43.478 0.00 0.00 37.94 3.18
627 635 4.683832 CCTGTACTCATGTAAGCACCTAC 58.316 47.826 0.00 0.00 0.00 3.18
628 636 4.159693 CCTGTACTCATGTAAGCACCTACA 59.840 45.833 0.00 0.00 36.27 2.74
629 637 5.337250 CCTGTACTCATGTAAGCACCTACAA 60.337 44.000 0.00 0.00 35.48 2.41
630 638 5.720202 TGTACTCATGTAAGCACCTACAAG 58.280 41.667 0.00 0.00 35.48 3.16
631 639 4.891992 ACTCATGTAAGCACCTACAAGT 57.108 40.909 0.00 0.00 35.48 3.16
632 640 5.228945 ACTCATGTAAGCACCTACAAGTT 57.771 39.130 0.00 0.00 35.48 2.66
633 641 5.621193 ACTCATGTAAGCACCTACAAGTTT 58.379 37.500 0.00 0.00 35.48 2.66
634 642 5.470098 ACTCATGTAAGCACCTACAAGTTTG 59.530 40.000 0.00 0.00 35.48 2.93
635 643 5.373222 TCATGTAAGCACCTACAAGTTTGT 58.627 37.500 2.75 2.75 44.86 2.83
636 644 6.526526 TCATGTAAGCACCTACAAGTTTGTA 58.473 36.000 4.78 4.78 42.35 2.41
637 645 6.993308 TCATGTAAGCACCTACAAGTTTGTAA 59.007 34.615 6.23 0.00 42.55 2.41
638 646 7.663905 TCATGTAAGCACCTACAAGTTTGTAAT 59.336 33.333 6.23 0.00 42.55 1.89
639 647 7.811117 TGTAAGCACCTACAAGTTTGTAATT 57.189 32.000 6.23 0.00 42.55 1.40
640 648 8.905660 TGTAAGCACCTACAAGTTTGTAATTA 57.094 30.769 6.23 0.00 42.55 1.40
641 649 9.339850 TGTAAGCACCTACAAGTTTGTAATTAA 57.660 29.630 6.23 0.00 42.55 1.40
642 650 9.603298 GTAAGCACCTACAAGTTTGTAATTAAC 57.397 33.333 6.23 0.00 42.55 2.01
643 651 8.459911 AAGCACCTACAAGTTTGTAATTAACT 57.540 30.769 6.23 0.00 42.55 2.24
644 652 7.871853 AGCACCTACAAGTTTGTAATTAACTG 58.128 34.615 6.23 0.00 42.55 3.16
645 653 7.501225 AGCACCTACAAGTTTGTAATTAACTGT 59.499 33.333 6.23 0.00 42.55 3.55
646 654 7.589954 GCACCTACAAGTTTGTAATTAACTGTG 59.410 37.037 6.23 0.00 42.55 3.66
647 655 7.589954 CACCTACAAGTTTGTAATTAACTGTGC 59.410 37.037 6.23 0.00 42.55 4.57
659 667 5.671742 ATTAACTGTGCAAATTTGTTGCC 57.328 34.783 19.03 3.53 44.32 4.52
677 685 1.809547 GCCAAGAGAAGAGCTCCAAAC 59.190 52.381 10.93 0.06 45.10 2.93
700 708 3.861840 AGCACTATGTAAACGTGATGCT 58.138 40.909 8.53 8.53 34.56 3.79
715 723 2.366590 TGATGCTAATCGGATGCTGACT 59.633 45.455 0.00 0.00 35.37 3.41
716 724 2.515926 TGCTAATCGGATGCTGACTC 57.484 50.000 0.00 0.00 0.00 3.36
717 725 1.269257 TGCTAATCGGATGCTGACTCG 60.269 52.381 0.00 0.00 0.00 4.18
718 726 1.269309 GCTAATCGGATGCTGACTCGT 60.269 52.381 0.00 0.00 0.00 4.18
722 733 1.170442 TCGGATGCTGACTCGTACAA 58.830 50.000 0.00 0.00 0.00 2.41
756 767 3.228749 CATAAACAAGTTCAGTGCAGCG 58.771 45.455 0.00 0.00 0.00 5.18
799 810 2.094258 CGCACACACTGCCATTAACTAG 59.906 50.000 0.00 0.00 43.84 2.57
800 811 3.074412 GCACACACTGCCATTAACTAGT 58.926 45.455 0.00 0.00 40.42 2.57
801 812 3.120199 GCACACACTGCCATTAACTAGTG 60.120 47.826 0.00 0.00 44.52 2.74
808 819 7.121974 CACTGCCATTAACTAGTGTATATGC 57.878 40.000 0.00 0.88 36.63 3.14
809 820 6.147821 CACTGCCATTAACTAGTGTATATGCC 59.852 42.308 0.00 0.00 36.63 4.40
810 821 5.556915 TGCCATTAACTAGTGTATATGCCC 58.443 41.667 0.00 0.00 0.00 5.36
811 822 4.941873 GCCATTAACTAGTGTATATGCCCC 59.058 45.833 0.00 0.00 0.00 5.80
812 823 5.514136 GCCATTAACTAGTGTATATGCCCCA 60.514 44.000 0.00 0.00 0.00 4.96
813 824 5.938125 CCATTAACTAGTGTATATGCCCCAC 59.062 44.000 0.00 0.00 0.00 4.61
814 825 5.556006 TTAACTAGTGTATATGCCCCACC 57.444 43.478 0.00 0.00 0.00 4.61
815 826 3.054779 ACTAGTGTATATGCCCCACCA 57.945 47.619 0.00 0.00 0.00 4.17
816 827 2.972713 ACTAGTGTATATGCCCCACCAG 59.027 50.000 0.00 0.00 0.00 4.00
817 828 2.190398 AGTGTATATGCCCCACCAGA 57.810 50.000 0.00 0.00 0.00 3.86
818 829 1.768870 AGTGTATATGCCCCACCAGAC 59.231 52.381 0.00 0.00 0.00 3.51
819 830 1.488812 GTGTATATGCCCCACCAGACA 59.511 52.381 0.00 0.00 0.00 3.41
820 831 2.092646 GTGTATATGCCCCACCAGACAA 60.093 50.000 0.00 0.00 0.00 3.18
821 832 2.782925 TGTATATGCCCCACCAGACAAT 59.217 45.455 0.00 0.00 0.00 2.71
822 833 3.977326 TGTATATGCCCCACCAGACAATA 59.023 43.478 0.00 0.00 0.00 1.90
823 834 4.413851 TGTATATGCCCCACCAGACAATAA 59.586 41.667 0.00 0.00 0.00 1.40
824 835 2.442236 ATGCCCCACCAGACAATAAG 57.558 50.000 0.00 0.00 0.00 1.73
825 836 1.072266 TGCCCCACCAGACAATAAGT 58.928 50.000 0.00 0.00 0.00 2.24
826 837 1.271871 TGCCCCACCAGACAATAAGTG 60.272 52.381 0.00 0.00 0.00 3.16
827 838 1.463674 CCCCACCAGACAATAAGTGC 58.536 55.000 0.00 0.00 0.00 4.40
828 839 1.271871 CCCCACCAGACAATAAGTGCA 60.272 52.381 0.00 0.00 0.00 4.57
829 840 1.812571 CCCACCAGACAATAAGTGCAC 59.187 52.381 9.40 9.40 0.00 4.57
830 841 2.553028 CCCACCAGACAATAAGTGCACT 60.553 50.000 15.25 15.25 0.00 4.40
831 842 2.485426 CCACCAGACAATAAGTGCACTG 59.515 50.000 22.49 11.42 35.80 3.66
832 843 3.402110 CACCAGACAATAAGTGCACTGA 58.598 45.455 22.49 14.63 37.22 3.41
833 844 4.005650 CACCAGACAATAAGTGCACTGAT 58.994 43.478 22.49 16.67 37.22 2.90
834 845 4.093998 CACCAGACAATAAGTGCACTGATC 59.906 45.833 22.49 13.29 37.22 2.92
835 846 3.624861 CCAGACAATAAGTGCACTGATCC 59.375 47.826 22.49 11.14 37.22 3.36
836 847 4.256110 CAGACAATAAGTGCACTGATCCA 58.744 43.478 22.49 3.94 37.22 3.41
837 848 4.696877 CAGACAATAAGTGCACTGATCCAA 59.303 41.667 22.49 2.41 37.22 3.53
838 849 4.697352 AGACAATAAGTGCACTGATCCAAC 59.303 41.667 22.49 10.71 0.00 3.77
839 850 3.436704 ACAATAAGTGCACTGATCCAACG 59.563 43.478 22.49 7.90 0.00 4.10
840 851 2.831685 TAAGTGCACTGATCCAACGT 57.168 45.000 22.49 3.34 0.00 3.99
841 852 1.967319 AAGTGCACTGATCCAACGTT 58.033 45.000 22.49 0.00 0.00 3.99
842 853 2.831685 AGTGCACTGATCCAACGTTA 57.168 45.000 20.97 0.00 0.00 3.18
843 854 3.334583 AGTGCACTGATCCAACGTTAT 57.665 42.857 20.97 0.00 0.00 1.89
844 855 3.674997 AGTGCACTGATCCAACGTTATT 58.325 40.909 20.97 0.00 0.00 1.40
845 856 3.436704 AGTGCACTGATCCAACGTTATTG 59.563 43.478 20.97 0.00 0.00 1.90
846 857 3.188460 GTGCACTGATCCAACGTTATTGT 59.812 43.478 10.32 0.00 0.00 2.71
847 858 3.818210 TGCACTGATCCAACGTTATTGTT 59.182 39.130 0.00 0.00 0.00 2.83
848 859 4.277174 TGCACTGATCCAACGTTATTGTTT 59.723 37.500 0.00 0.00 0.00 2.83
849 860 5.470437 TGCACTGATCCAACGTTATTGTTTA 59.530 36.000 0.00 0.00 0.00 2.01
850 861 6.021596 GCACTGATCCAACGTTATTGTTTAG 58.978 40.000 0.00 0.00 0.00 1.85
851 862 6.128391 GCACTGATCCAACGTTATTGTTTAGA 60.128 38.462 0.00 0.00 0.00 2.10
852 863 7.572353 GCACTGATCCAACGTTATTGTTTAGAA 60.572 37.037 0.00 0.00 0.00 2.10
853 864 8.286800 CACTGATCCAACGTTATTGTTTAGAAA 58.713 33.333 0.00 0.00 0.00 2.52
854 865 8.842280 ACTGATCCAACGTTATTGTTTAGAAAA 58.158 29.630 0.00 0.00 0.00 2.29
855 866 9.329913 CTGATCCAACGTTATTGTTTAGAAAAG 57.670 33.333 0.00 0.00 0.00 2.27
856 867 8.842280 TGATCCAACGTTATTGTTTAGAAAAGT 58.158 29.630 0.00 0.00 0.00 2.66
857 868 9.673454 GATCCAACGTTATTGTTTAGAAAAGTT 57.327 29.630 0.00 0.00 0.00 2.66
868 879 8.426881 TTGTTTAGAAAAGTTAATTGGCAACC 57.573 30.769 0.00 0.00 0.00 3.77
869 880 7.787028 TGTTTAGAAAAGTTAATTGGCAACCT 58.213 30.769 0.00 0.00 0.00 3.50
870 881 7.708752 TGTTTAGAAAAGTTAATTGGCAACCTG 59.291 33.333 0.00 0.00 0.00 4.00
871 882 5.869649 AGAAAAGTTAATTGGCAACCTGT 57.130 34.783 0.00 0.00 0.00 4.00
872 883 6.969993 AGAAAAGTTAATTGGCAACCTGTA 57.030 33.333 0.00 0.00 0.00 2.74
873 884 6.745116 AGAAAAGTTAATTGGCAACCTGTAC 58.255 36.000 0.00 0.00 0.00 2.90
874 885 5.462530 AAAGTTAATTGGCAACCTGTACC 57.537 39.130 0.00 0.00 0.00 3.34
875 886 4.107127 AGTTAATTGGCAACCTGTACCA 57.893 40.909 0.00 0.00 0.00 3.25
876 887 3.824443 AGTTAATTGGCAACCTGTACCAC 59.176 43.478 0.00 0.00 31.83 4.16
877 888 1.627864 AATTGGCAACCTGTACCACC 58.372 50.000 0.00 0.00 31.83 4.61
878 889 0.777446 ATTGGCAACCTGTACCACCT 59.223 50.000 0.00 0.00 31.83 4.00
879 890 0.179004 TTGGCAACCTGTACCACCTG 60.179 55.000 0.00 0.00 31.83 4.00
880 891 1.971695 GGCAACCTGTACCACCTGC 60.972 63.158 0.00 0.00 0.00 4.85
881 892 1.228124 GCAACCTGTACCACCTGCA 60.228 57.895 0.00 0.00 0.00 4.41
882 893 0.609131 GCAACCTGTACCACCTGCAT 60.609 55.000 0.00 0.00 0.00 3.96
883 894 1.453155 CAACCTGTACCACCTGCATC 58.547 55.000 0.00 0.00 0.00 3.91
884 895 1.003580 CAACCTGTACCACCTGCATCT 59.996 52.381 0.00 0.00 0.00 2.90
885 896 0.905357 ACCTGTACCACCTGCATCTC 59.095 55.000 0.00 0.00 0.00 2.75
886 897 1.198713 CCTGTACCACCTGCATCTCT 58.801 55.000 0.00 0.00 0.00 3.10
887 898 1.137872 CCTGTACCACCTGCATCTCTC 59.862 57.143 0.00 0.00 0.00 3.20
888 899 2.106566 CTGTACCACCTGCATCTCTCT 58.893 52.381 0.00 0.00 0.00 3.10
889 900 2.499289 CTGTACCACCTGCATCTCTCTT 59.501 50.000 0.00 0.00 0.00 2.85
890 901 2.497675 TGTACCACCTGCATCTCTCTTC 59.502 50.000 0.00 0.00 0.00 2.87
891 902 1.649321 ACCACCTGCATCTCTCTTCA 58.351 50.000 0.00 0.00 0.00 3.02
892 903 1.277557 ACCACCTGCATCTCTCTTCAC 59.722 52.381 0.00 0.00 0.00 3.18
893 904 1.638133 CACCTGCATCTCTCTTCACG 58.362 55.000 0.00 0.00 0.00 4.35
894 905 1.067283 CACCTGCATCTCTCTTCACGT 60.067 52.381 0.00 0.00 0.00 4.49
895 906 1.620819 ACCTGCATCTCTCTTCACGTT 59.379 47.619 0.00 0.00 0.00 3.99
896 907 2.826128 ACCTGCATCTCTCTTCACGTTA 59.174 45.455 0.00 0.00 0.00 3.18
897 908 3.182967 CCTGCATCTCTCTTCACGTTAC 58.817 50.000 0.00 0.00 0.00 2.50
898 909 3.367395 CCTGCATCTCTCTTCACGTTACA 60.367 47.826 0.00 0.00 0.00 2.41
899 910 3.838120 TGCATCTCTCTTCACGTTACAG 58.162 45.455 0.00 0.00 0.00 2.74
900 911 3.255888 TGCATCTCTCTTCACGTTACAGT 59.744 43.478 0.00 0.00 0.00 3.55
901 912 4.238514 GCATCTCTCTTCACGTTACAGTT 58.761 43.478 0.00 0.00 0.00 3.16
902 913 5.048294 TGCATCTCTCTTCACGTTACAGTTA 60.048 40.000 0.00 0.00 0.00 2.24
903 914 5.862323 GCATCTCTCTTCACGTTACAGTTAA 59.138 40.000 0.00 0.00 0.00 2.01
904 915 6.034044 GCATCTCTCTTCACGTTACAGTTAAG 59.966 42.308 0.00 0.00 0.00 1.85
905 916 6.872628 TCTCTCTTCACGTTACAGTTAAGA 57.127 37.500 0.00 4.79 34.41 2.10
906 917 6.900189 TCTCTCTTCACGTTACAGTTAAGAG 58.100 40.000 16.97 16.97 46.14 2.85
908 919 6.914760 CTCTTCACGTTACAGTTAAGAGAC 57.085 41.667 17.62 0.00 47.00 3.36
909 920 6.381481 TCTTCACGTTACAGTTAAGAGACA 57.619 37.500 0.00 0.00 31.66 3.41
910 921 6.798482 TCTTCACGTTACAGTTAAGAGACAA 58.202 36.000 0.00 0.00 31.66 3.18
918 929 7.514747 CGTTACAGTTAAGAGACAATAATCCGC 60.515 40.741 0.00 0.00 0.00 5.54
919 930 4.804139 ACAGTTAAGAGACAATAATCCGCG 59.196 41.667 0.00 0.00 0.00 6.46
952 963 4.201881 ACGAACAAACTAGTTCAAGCAACC 60.202 41.667 8.95 0.00 46.32 3.77
1005 1018 2.439135 ACCATCCCAATCATCGATGTCA 59.561 45.455 24.09 7.29 33.09 3.58
1034 1047 0.320508 CAACAGCAGCAGAGCAGAGA 60.321 55.000 0.00 0.00 36.85 3.10
1035 1048 0.037139 AACAGCAGCAGAGCAGAGAG 60.037 55.000 0.00 0.00 36.85 3.20
1047 1065 3.879295 AGAGCAGAGAGATCTTCTTCGAG 59.121 47.826 0.00 0.00 40.91 4.04
1106 1127 3.080121 AGCCTCGCCTTCTCCCTG 61.080 66.667 0.00 0.00 0.00 4.45
1107 1128 4.847444 GCCTCGCCTTCTCCCTGC 62.847 72.222 0.00 0.00 0.00 4.85
1111 1132 4.521062 CGCCTTCTCCCTGCTCCG 62.521 72.222 0.00 0.00 0.00 4.63
1117 1138 1.330655 TTCTCCCTGCTCCGGTGATC 61.331 60.000 7.92 0.00 0.00 2.92
1119 1140 2.187946 CCCTGCTCCGGTGATCAC 59.812 66.667 17.91 17.91 0.00 3.06
1130 1154 1.078143 GTGATCACCACCAGAGCCC 60.078 63.158 15.31 0.00 39.86 5.19
1323 1347 1.442769 GCTTCGGCATGTTCAAGAGA 58.557 50.000 0.00 0.00 41.33 3.10
1338 1362 2.039624 AGATGGGAGGTCTGCCGT 59.960 61.111 2.80 2.80 44.85 5.68
1633 1657 3.476031 CTGGGCTTGGTCGTGGTGT 62.476 63.158 0.00 0.00 0.00 4.16
1635 1659 3.660111 GGCTTGGTCGTGGTGTGC 61.660 66.667 0.00 0.00 0.00 4.57
1676 1703 1.684450 GTGATGGATGCATGCATGGAA 59.316 47.619 36.73 21.30 39.04 3.53
1677 1704 1.684450 TGATGGATGCATGCATGGAAC 59.316 47.619 36.73 21.58 39.04 3.62
1678 1705 0.671796 ATGGATGCATGCATGGAACG 59.328 50.000 36.73 0.14 37.46 3.95
1680 1707 1.299620 GATGCATGCATGGAACGGC 60.300 57.895 36.73 16.99 36.70 5.68
1695 1724 2.813179 CGGCCGGCAATCTTCTTCG 61.813 63.158 30.85 15.38 0.00 3.79
1700 1729 1.130561 CCGGCAATCTTCTTCGGTTTC 59.869 52.381 0.00 0.00 36.38 2.78
1714 1743 1.067915 CGGTTTCCATGCGGTTTCATT 60.068 47.619 0.00 0.00 0.00 2.57
1724 1753 4.497473 TGCGGTTTCATTTCCAAACTAG 57.503 40.909 0.00 0.00 34.66 2.57
1735 1764 7.066781 TCATTTCCAAACTAGGAAGTTCCTTT 58.933 34.615 29.09 15.75 46.91 3.11
1736 1765 7.563556 TCATTTCCAAACTAGGAAGTTCCTTTT 59.436 33.333 29.09 20.45 46.91 2.27
1740 1769 7.808218 TCCAAACTAGGAAGTTCCTTTTTAGA 58.192 34.615 29.09 21.19 46.91 2.10
1746 1775 6.133253 AGGAAGTTCCTTTTTAGATGAGCT 57.867 37.500 19.27 0.00 46.91 4.09
1782 1811 1.144969 CGATAACTGCCACACGTGTT 58.855 50.000 20.79 5.94 0.00 3.32
1784 1813 1.871039 GATAACTGCCACACGTGTTGT 59.129 47.619 20.79 12.57 39.97 3.32
1796 1825 2.018515 ACGTGTTGTTGTTAAGGGGTG 58.981 47.619 0.00 0.00 0.00 4.61
1801 1830 0.553819 TGTTGTTAAGGGGTGTGCCT 59.446 50.000 0.00 0.00 34.45 4.75
1817 1849 4.477302 GTGCCTACACGTTTTGTATGTT 57.523 40.909 0.00 0.00 40.06 2.71
1837 1869 2.561209 TAAGAGGACCAGCCCATACA 57.439 50.000 0.00 0.00 37.37 2.29
1865 1897 1.874872 GTGGGTAAAACAACTAGCGCA 59.125 47.619 11.47 0.00 0.00 6.09
1868 1900 2.486592 GGGTAAAACAACTAGCGCACAT 59.513 45.455 11.47 0.00 0.00 3.21
1871 1903 4.152759 GGTAAAACAACTAGCGCACATACA 59.847 41.667 11.47 0.00 0.00 2.29
1875 1907 2.289444 ACAACTAGCGCACATACACCTT 60.289 45.455 11.47 0.00 0.00 3.50
1938 1974 2.325583 ATGAATAACGCCCACACGAT 57.674 45.000 0.00 0.00 36.70 3.73
1939 1975 1.364721 TGAATAACGCCCACACGATG 58.635 50.000 0.00 0.00 36.70 3.84
1965 2001 1.982938 GCCACCTACCTCACGGTCT 60.983 63.158 0.00 0.00 44.21 3.85
1971 2007 1.535833 CTACCTCACGGTCTCACACT 58.464 55.000 0.00 0.00 44.21 3.55
1997 2033 2.335369 GACAGTCACCACGCGTCT 59.665 61.111 9.86 0.00 30.88 4.18
2046 2082 2.225491 TCAATGTCCGTTTAACTGCAGC 59.775 45.455 15.27 0.00 0.00 5.25
2062 2098 1.077930 AGCTGCCATGTCGCTGAAT 60.078 52.632 0.00 0.00 31.82 2.57
2254 2291 6.835320 CACTAAGCAGTTGCCATGTATGGTT 61.835 44.000 12.21 0.33 40.79 3.67
2292 2329 6.271488 TGCCATGATTTGAAAACCTTAGAG 57.729 37.500 0.00 0.00 0.00 2.43
2352 2391 4.379813 CGCTACAAAGAGACATGGCAAAAT 60.380 41.667 0.00 0.00 0.00 1.82
2441 2481 0.582960 GCAAAACACATGGCAACTGC 59.417 50.000 0.00 0.00 41.14 4.40
2642 2684 0.179043 TGTGGGCGAACTGCTAAACA 60.179 50.000 0.00 0.00 45.43 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.508213 GGCACACAATTTCTTTGCGC 59.492 50.000 0.00 0.00 39.03 6.09
36 37 0.949105 CCAGTTGACGGTAGGCACAC 60.949 60.000 0.00 0.00 33.22 3.82
40 41 4.592426 GTCCAGTTGACGGTAGGC 57.408 61.111 0.00 0.00 33.49 3.93
107 108 1.140852 TGGAGCGTAGAATCAATGGGG 59.859 52.381 0.00 0.00 0.00 4.96
110 111 3.642705 TCGATGGAGCGTAGAATCAATG 58.357 45.455 0.00 0.00 0.00 2.82
114 115 2.510874 CGATCGATGGAGCGTAGAATC 58.489 52.381 10.26 0.00 46.35 2.52
135 136 1.081509 CCAAATCAACACACGGCGG 60.082 57.895 13.24 2.35 0.00 6.13
136 137 1.729131 GCCAAATCAACACACGGCG 60.729 57.895 4.80 4.80 0.00 6.46
152 153 3.135994 TGTTTTCTACTGAAACGAGGCC 58.864 45.455 0.00 0.00 41.34 5.19
154 155 4.809426 ACACTGTTTTCTACTGAAACGAGG 59.191 41.667 0.00 0.00 41.34 4.63
172 173 6.142139 CACCATGTTAATACACACAACACTG 58.858 40.000 0.00 0.00 37.03 3.66
188 189 1.227943 AGCACGCAGACACCATGTT 60.228 52.632 0.00 0.00 0.00 2.71
214 215 8.806429 TCATTTGTATCAGTAATCACCATTGT 57.194 30.769 0.00 0.00 0.00 2.71
253 254 4.430137 TTCAATCAGTTTCATGCTCTGC 57.570 40.909 0.00 0.00 0.00 4.26
323 326 3.143675 CCACACATGGGAGAACTCG 57.856 57.895 0.00 0.00 43.04 4.18
437 445 7.286087 TCGAAGGATAAGTACTTGCACCTAATA 59.714 37.037 18.56 9.04 0.00 0.98
447 455 4.338682 ACGCTGATCGAAGGATAAGTACTT 59.661 41.667 13.68 13.68 41.67 2.24
461 469 1.001268 AGCCATGTACTACGCTGATCG 60.001 52.381 0.00 0.00 45.38 3.69
508 516 9.778993 CTAGTCATAAAATGGATTGTTCTGTTG 57.221 33.333 0.00 0.00 0.00 3.33
521 529 5.581126 TTTGGGCTGCTAGTCATAAAATG 57.419 39.130 0.00 0.00 0.00 2.32
527 535 1.565759 TCCATTTGGGCTGCTAGTCAT 59.434 47.619 0.00 0.00 36.21 3.06
544 552 1.259609 ACGAACTACGGATGGTTCCA 58.740 50.000 0.00 0.00 41.92 3.53
570 578 5.104374 GGATGTGATTAAACCACAATGCAG 58.896 41.667 15.12 0.00 46.12 4.41
610 618 4.891992 ACTTGTAGGTGCTTACATGAGT 57.108 40.909 0.00 4.45 33.81 3.41
629 637 9.377312 ACAAATTTGCACAGTTAATTACAAACT 57.623 25.926 18.12 0.00 37.67 2.66
630 638 9.980780 AACAAATTTGCACAGTTAATTACAAAC 57.019 25.926 18.12 0.00 30.60 2.93
631 639 9.979270 CAACAAATTTGCACAGTTAATTACAAA 57.021 25.926 18.12 0.00 0.00 2.83
632 640 8.119226 GCAACAAATTTGCACAGTTAATTACAA 58.881 29.630 18.12 0.00 44.34 2.41
633 641 7.254590 GGCAACAAATTTGCACAGTTAATTACA 60.255 33.333 18.12 0.00 46.58 2.41
634 642 7.068955 GGCAACAAATTTGCACAGTTAATTAC 58.931 34.615 18.12 0.00 46.58 1.89
635 643 7.183580 GGCAACAAATTTGCACAGTTAATTA 57.816 32.000 18.12 0.00 46.58 1.40
636 644 6.058827 GGCAACAAATTTGCACAGTTAATT 57.941 33.333 18.12 0.00 46.58 1.40
637 645 5.671742 GGCAACAAATTTGCACAGTTAAT 57.328 34.783 18.12 0.00 46.58 1.40
659 667 2.992543 CTCGTTTGGAGCTCTTCTCTTG 59.007 50.000 14.64 0.00 41.60 3.02
677 685 3.301835 GCATCACGTTTACATAGTGCTCG 60.302 47.826 0.00 0.00 35.97 5.03
700 708 2.946990 TGTACGAGTCAGCATCCGATTA 59.053 45.455 0.00 0.00 0.00 1.75
715 723 1.402968 GCTCGACCCAGTATTGTACGA 59.597 52.381 0.00 0.00 0.00 3.43
716 724 1.133598 TGCTCGACCCAGTATTGTACG 59.866 52.381 0.00 0.00 0.00 3.67
717 725 2.953466 TGCTCGACCCAGTATTGTAC 57.047 50.000 0.00 0.00 0.00 2.90
718 726 5.105269 TGTTTATGCTCGACCCAGTATTGTA 60.105 40.000 0.00 0.00 0.00 2.41
722 733 4.081087 ACTTGTTTATGCTCGACCCAGTAT 60.081 41.667 0.00 0.00 0.00 2.12
756 767 1.398390 CACGCCTTTGGATAGAACAGC 59.602 52.381 0.00 0.00 0.00 4.40
788 799 4.941873 GGGGCATATACACTAGTTAATGGC 59.058 45.833 15.94 15.94 40.44 4.40
799 810 1.488812 TGTCTGGTGGGGCATATACAC 59.511 52.381 0.00 0.00 0.00 2.90
800 811 1.886422 TGTCTGGTGGGGCATATACA 58.114 50.000 0.00 0.00 0.00 2.29
801 812 3.508845 ATTGTCTGGTGGGGCATATAC 57.491 47.619 0.00 0.00 0.00 1.47
802 813 4.663120 ACTTATTGTCTGGTGGGGCATATA 59.337 41.667 0.00 0.00 0.00 0.86
803 814 3.463329 ACTTATTGTCTGGTGGGGCATAT 59.537 43.478 0.00 0.00 0.00 1.78
804 815 2.849943 ACTTATTGTCTGGTGGGGCATA 59.150 45.455 0.00 0.00 0.00 3.14
805 816 1.640670 ACTTATTGTCTGGTGGGGCAT 59.359 47.619 0.00 0.00 0.00 4.40
806 817 1.072266 ACTTATTGTCTGGTGGGGCA 58.928 50.000 0.00 0.00 0.00 5.36
807 818 1.463674 CACTTATTGTCTGGTGGGGC 58.536 55.000 0.00 0.00 0.00 5.80
808 819 1.271871 TGCACTTATTGTCTGGTGGGG 60.272 52.381 0.00 0.00 0.00 4.96
809 820 1.812571 GTGCACTTATTGTCTGGTGGG 59.187 52.381 10.32 0.00 0.00 4.61
810 821 2.485426 CAGTGCACTTATTGTCTGGTGG 59.515 50.000 18.94 0.00 0.00 4.61
811 822 3.402110 TCAGTGCACTTATTGTCTGGTG 58.598 45.455 18.94 1.94 33.27 4.17
812 823 3.769739 TCAGTGCACTTATTGTCTGGT 57.230 42.857 18.94 0.00 33.27 4.00
813 824 3.624861 GGATCAGTGCACTTATTGTCTGG 59.375 47.826 18.94 2.28 33.27 3.86
814 825 4.256110 TGGATCAGTGCACTTATTGTCTG 58.744 43.478 18.94 4.17 33.52 3.51
815 826 4.558226 TGGATCAGTGCACTTATTGTCT 57.442 40.909 18.94 0.00 0.00 3.41
816 827 4.436050 CGTTGGATCAGTGCACTTATTGTC 60.436 45.833 18.94 10.49 0.00 3.18
817 828 3.436704 CGTTGGATCAGTGCACTTATTGT 59.563 43.478 18.94 0.91 0.00 2.71
818 829 3.436704 ACGTTGGATCAGTGCACTTATTG 59.563 43.478 18.94 7.10 0.00 1.90
819 830 3.674997 ACGTTGGATCAGTGCACTTATT 58.325 40.909 18.94 4.44 0.00 1.40
820 831 3.334583 ACGTTGGATCAGTGCACTTAT 57.665 42.857 18.94 15.86 0.00 1.73
821 832 2.831685 ACGTTGGATCAGTGCACTTA 57.168 45.000 18.94 10.56 0.00 2.24
822 833 1.967319 AACGTTGGATCAGTGCACTT 58.033 45.000 18.94 2.95 0.00 3.16
823 834 2.831685 TAACGTTGGATCAGTGCACT 57.168 45.000 15.25 15.25 0.00 4.40
824 835 3.188460 ACAATAACGTTGGATCAGTGCAC 59.812 43.478 11.99 9.40 0.00 4.57
825 836 3.407698 ACAATAACGTTGGATCAGTGCA 58.592 40.909 11.99 0.00 0.00 4.57
826 837 4.419522 AACAATAACGTTGGATCAGTGC 57.580 40.909 11.99 0.00 0.00 4.40
827 838 7.359262 TCTAAACAATAACGTTGGATCAGTG 57.641 36.000 11.99 2.21 0.00 3.66
828 839 7.972832 TTCTAAACAATAACGTTGGATCAGT 57.027 32.000 11.99 0.00 0.00 3.41
829 840 9.329913 CTTTTCTAAACAATAACGTTGGATCAG 57.670 33.333 11.99 0.00 0.00 2.90
830 841 8.842280 ACTTTTCTAAACAATAACGTTGGATCA 58.158 29.630 11.99 0.00 0.00 2.92
831 842 9.673454 AACTTTTCTAAACAATAACGTTGGATC 57.327 29.630 11.99 0.00 0.00 3.36
842 853 9.051679 GGTTGCCAATTAACTTTTCTAAACAAT 57.948 29.630 0.00 0.00 0.00 2.71
843 854 8.261522 AGGTTGCCAATTAACTTTTCTAAACAA 58.738 29.630 0.00 0.00 0.00 2.83
844 855 7.708752 CAGGTTGCCAATTAACTTTTCTAAACA 59.291 33.333 0.00 0.00 0.00 2.83
845 856 7.709182 ACAGGTTGCCAATTAACTTTTCTAAAC 59.291 33.333 0.00 0.00 0.00 2.01
846 857 7.787028 ACAGGTTGCCAATTAACTTTTCTAAA 58.213 30.769 0.00 0.00 0.00 1.85
847 858 7.354751 ACAGGTTGCCAATTAACTTTTCTAA 57.645 32.000 0.00 0.00 0.00 2.10
848 859 6.969993 ACAGGTTGCCAATTAACTTTTCTA 57.030 33.333 0.00 0.00 0.00 2.10
849 860 5.869649 ACAGGTTGCCAATTAACTTTTCT 57.130 34.783 0.00 0.00 0.00 2.52
850 861 5.924254 GGTACAGGTTGCCAATTAACTTTTC 59.076 40.000 0.00 0.00 0.00 2.29
851 862 5.364157 TGGTACAGGTTGCCAATTAACTTTT 59.636 36.000 0.00 0.00 0.00 2.27
852 863 4.896482 TGGTACAGGTTGCCAATTAACTTT 59.104 37.500 0.00 0.00 0.00 2.66
853 864 4.279922 GTGGTACAGGTTGCCAATTAACTT 59.720 41.667 0.00 0.00 41.80 2.66
854 865 3.824443 GTGGTACAGGTTGCCAATTAACT 59.176 43.478 0.00 0.00 41.80 2.24
855 866 3.057104 GGTGGTACAGGTTGCCAATTAAC 60.057 47.826 0.00 0.00 41.80 2.01
856 867 3.158676 GGTGGTACAGGTTGCCAATTAA 58.841 45.455 0.00 0.00 41.80 1.40
857 868 2.377193 AGGTGGTACAGGTTGCCAATTA 59.623 45.455 0.00 0.00 41.80 1.40
858 869 1.146982 AGGTGGTACAGGTTGCCAATT 59.853 47.619 0.00 0.00 41.80 2.32
859 870 0.777446 AGGTGGTACAGGTTGCCAAT 59.223 50.000 0.00 0.00 41.80 3.16
860 871 0.179004 CAGGTGGTACAGGTTGCCAA 60.179 55.000 0.00 0.00 41.80 4.52
861 872 1.454104 CAGGTGGTACAGGTTGCCA 59.546 57.895 0.00 0.00 41.80 4.92
862 873 1.971695 GCAGGTGGTACAGGTTGCC 60.972 63.158 0.00 0.00 41.80 4.52
863 874 0.609131 ATGCAGGTGGTACAGGTTGC 60.609 55.000 0.00 0.00 41.80 4.17
864 875 1.003580 AGATGCAGGTGGTACAGGTTG 59.996 52.381 0.00 0.00 41.80 3.77
865 876 1.279271 GAGATGCAGGTGGTACAGGTT 59.721 52.381 0.00 0.00 41.80 3.50
866 877 0.905357 GAGATGCAGGTGGTACAGGT 59.095 55.000 0.00 0.00 41.80 4.00
867 878 1.137872 GAGAGATGCAGGTGGTACAGG 59.862 57.143 0.00 0.00 41.80 4.00
868 879 2.106566 AGAGAGATGCAGGTGGTACAG 58.893 52.381 0.00 0.00 41.80 2.74
869 880 2.238084 AGAGAGATGCAGGTGGTACA 57.762 50.000 0.00 0.00 0.00 2.90
870 881 2.497675 TGAAGAGAGATGCAGGTGGTAC 59.502 50.000 0.00 0.00 0.00 3.34
871 882 2.497675 GTGAAGAGAGATGCAGGTGGTA 59.502 50.000 0.00 0.00 0.00 3.25
872 883 1.277557 GTGAAGAGAGATGCAGGTGGT 59.722 52.381 0.00 0.00 0.00 4.16
873 884 1.738365 CGTGAAGAGAGATGCAGGTGG 60.738 57.143 0.00 0.00 0.00 4.61
874 885 1.067283 ACGTGAAGAGAGATGCAGGTG 60.067 52.381 0.00 0.00 0.00 4.00
875 886 1.261480 ACGTGAAGAGAGATGCAGGT 58.739 50.000 0.00 0.00 0.00 4.00
876 887 2.376808 AACGTGAAGAGAGATGCAGG 57.623 50.000 0.00 0.00 0.00 4.85
877 888 3.838120 TGTAACGTGAAGAGAGATGCAG 58.162 45.455 0.00 0.00 0.00 4.41
878 889 3.255888 ACTGTAACGTGAAGAGAGATGCA 59.744 43.478 0.00 0.00 0.00 3.96
879 890 3.839293 ACTGTAACGTGAAGAGAGATGC 58.161 45.455 0.00 0.00 0.00 3.91
880 891 7.306213 TCTTAACTGTAACGTGAAGAGAGATG 58.694 38.462 0.00 0.00 31.01 2.90
881 892 7.450124 TCTTAACTGTAACGTGAAGAGAGAT 57.550 36.000 0.00 0.00 31.01 2.75
882 893 6.872628 TCTTAACTGTAACGTGAAGAGAGA 57.127 37.500 0.00 0.00 31.01 3.10
885 896 6.436261 TGTCTCTTAACTGTAACGTGAAGAG 58.564 40.000 10.48 10.48 46.89 2.85
886 897 6.381481 TGTCTCTTAACTGTAACGTGAAGA 57.619 37.500 0.00 0.00 34.12 2.87
887 898 7.639162 ATTGTCTCTTAACTGTAACGTGAAG 57.361 36.000 0.00 0.00 0.00 3.02
888 899 9.701098 ATTATTGTCTCTTAACTGTAACGTGAA 57.299 29.630 0.00 0.00 0.00 3.18
889 900 9.350357 GATTATTGTCTCTTAACTGTAACGTGA 57.650 33.333 0.00 0.00 0.00 4.35
890 901 8.592998 GGATTATTGTCTCTTAACTGTAACGTG 58.407 37.037 0.00 0.00 0.00 4.49
891 902 7.487189 CGGATTATTGTCTCTTAACTGTAACGT 59.513 37.037 0.00 0.00 0.00 3.99
892 903 7.514747 GCGGATTATTGTCTCTTAACTGTAACG 60.515 40.741 0.00 0.00 0.00 3.18
893 904 7.514747 CGCGGATTATTGTCTCTTAACTGTAAC 60.515 40.741 0.00 0.00 0.00 2.50
894 905 6.474427 CGCGGATTATTGTCTCTTAACTGTAA 59.526 38.462 0.00 0.00 0.00 2.41
895 906 5.975344 CGCGGATTATTGTCTCTTAACTGTA 59.025 40.000 0.00 0.00 0.00 2.74
896 907 4.804139 CGCGGATTATTGTCTCTTAACTGT 59.196 41.667 0.00 0.00 0.00 3.55
897 908 4.318121 GCGCGGATTATTGTCTCTTAACTG 60.318 45.833 8.83 0.00 0.00 3.16
898 909 3.802685 GCGCGGATTATTGTCTCTTAACT 59.197 43.478 8.83 0.00 0.00 2.24
899 910 3.554324 TGCGCGGATTATTGTCTCTTAAC 59.446 43.478 8.83 0.00 0.00 2.01
900 911 3.554324 GTGCGCGGATTATTGTCTCTTAA 59.446 43.478 8.83 0.00 0.00 1.85
901 912 3.120792 GTGCGCGGATTATTGTCTCTTA 58.879 45.455 8.83 0.00 0.00 2.10
902 913 1.933853 GTGCGCGGATTATTGTCTCTT 59.066 47.619 8.83 0.00 0.00 2.85
903 914 1.571919 GTGCGCGGATTATTGTCTCT 58.428 50.000 8.83 0.00 0.00 3.10
904 915 0.229753 CGTGCGCGGATTATTGTCTC 59.770 55.000 12.87 0.00 0.00 3.36
905 916 2.297625 CGTGCGCGGATTATTGTCT 58.702 52.632 12.87 0.00 0.00 3.41
906 917 4.872476 CGTGCGCGGATTATTGTC 57.128 55.556 12.87 0.00 0.00 3.18
918 929 2.096614 AGTTTGTTCGTTATTCCGTGCG 60.097 45.455 0.00 0.00 0.00 5.34
919 930 3.531262 AGTTTGTTCGTTATTCCGTGC 57.469 42.857 0.00 0.00 0.00 5.34
925 936 7.254227 TGCTTGAACTAGTTTGTTCGTTATT 57.746 32.000 10.02 0.00 46.59 1.40
952 963 6.205464 CCAGTGGCTGGTTCTACATATTTATG 59.795 42.308 6.99 0.00 45.82 1.90
1005 1018 0.731417 GCTGCTGTTGCGATGAGAAT 59.269 50.000 0.00 0.00 43.34 2.40
1034 1047 3.214328 GGAGAGAGCTCGAAGAAGATCT 58.786 50.000 8.37 2.58 42.25 2.75
1035 1048 2.948979 TGGAGAGAGCTCGAAGAAGATC 59.051 50.000 8.37 0.00 42.25 2.75
1047 1065 0.254178 TCTTGGCCATTGGAGAGAGC 59.746 55.000 6.09 0.00 0.00 4.09
1089 1110 3.080121 CAGGGAGAAGGCGAGGCT 61.080 66.667 0.00 0.00 0.00 4.58
1090 1111 4.847444 GCAGGGAGAAGGCGAGGC 62.847 72.222 0.00 0.00 0.00 4.70
1091 1112 3.080121 AGCAGGGAGAAGGCGAGG 61.080 66.667 0.00 0.00 0.00 4.63
1092 1113 2.498726 GAGCAGGGAGAAGGCGAG 59.501 66.667 0.00 0.00 0.00 5.03
1093 1114 3.077556 GGAGCAGGGAGAAGGCGA 61.078 66.667 0.00 0.00 0.00 5.54
1094 1115 4.521062 CGGAGCAGGGAGAAGGCG 62.521 72.222 0.00 0.00 0.00 5.52
1095 1116 4.168291 CCGGAGCAGGGAGAAGGC 62.168 72.222 0.00 0.00 0.00 4.35
1096 1117 2.685380 ACCGGAGCAGGGAGAAGG 60.685 66.667 9.46 0.00 35.02 3.46
1097 1118 1.333636 ATCACCGGAGCAGGGAGAAG 61.334 60.000 9.46 0.00 35.02 2.85
1098 1119 1.306141 ATCACCGGAGCAGGGAGAA 60.306 57.895 9.46 0.00 35.02 2.87
1117 1138 2.033141 CTGTGGGCTCTGGTGGTG 59.967 66.667 0.00 0.00 0.00 4.17
1130 1154 1.754803 TCCAGACCTTATACGCCTGTG 59.245 52.381 0.00 0.00 0.00 3.66
1140 1164 2.166459 CAGCGACTTCATCCAGACCTTA 59.834 50.000 0.00 0.00 0.00 2.69
1142 1166 0.534412 CAGCGACTTCATCCAGACCT 59.466 55.000 0.00 0.00 0.00 3.85
1254 1278 1.003118 CCCTGACGGTCCATGAAGAAA 59.997 52.381 5.55 0.00 0.00 2.52
1285 1309 1.817099 CCTTGCGCCTGATCCTGAC 60.817 63.158 4.18 0.00 0.00 3.51
1323 1347 2.671070 CAACGGCAGACCTCCCAT 59.329 61.111 0.00 0.00 0.00 4.00
1436 1460 4.735132 TCCTGTAGCACGTGCCGC 62.735 66.667 35.51 27.26 43.38 6.53
1440 1464 0.861866 CGTCGATCCTGTAGCACGTG 60.862 60.000 12.28 12.28 0.00 4.49
1472 1496 1.185618 TCTGTACTCGGGCTTGTGCT 61.186 55.000 0.00 0.00 39.59 4.40
1475 1499 0.889306 GACTCTGTACTCGGGCTTGT 59.111 55.000 0.00 0.00 0.00 3.16
1608 1632 2.526873 ACCAAGCCCAGGACGAGT 60.527 61.111 0.00 0.00 0.00 4.18
1633 1657 2.923426 GATCGGTTCATGAGGCCGCA 62.923 60.000 26.22 12.99 44.58 5.69
1635 1659 1.595382 GGATCGGTTCATGAGGCCG 60.595 63.158 25.52 25.52 46.12 6.13
1676 1703 1.745489 GAAGAAGATTGCCGGCCGT 60.745 57.895 26.77 12.97 0.00 5.68
1677 1704 2.813179 CGAAGAAGATTGCCGGCCG 61.813 63.158 26.77 21.04 0.00 6.13
1678 1705 2.472909 CCGAAGAAGATTGCCGGCC 61.473 63.158 26.77 8.84 33.47 6.13
1680 1707 1.130561 GAAACCGAAGAAGATTGCCGG 59.869 52.381 0.00 0.00 45.09 6.13
1695 1724 2.741759 AATGAAACCGCATGGAAACC 57.258 45.000 0.00 0.00 39.21 3.27
1700 1729 2.736192 GTTTGGAAATGAAACCGCATGG 59.264 45.455 0.00 0.00 42.84 3.66
1724 1753 7.923414 TTAGCTCATCTAAAAAGGAACTTCC 57.077 36.000 0.00 0.00 38.11 3.46
1735 1764 8.073768 CGTCCAAAACTTTTTAGCTCATCTAAA 58.926 33.333 0.00 0.00 43.47 1.85
1736 1765 7.442969 TCGTCCAAAACTTTTTAGCTCATCTAA 59.557 33.333 0.00 0.00 35.57 2.10
1740 1769 5.560183 CGTCGTCCAAAACTTTTTAGCTCAT 60.560 40.000 0.00 0.00 0.00 2.90
1746 1775 7.346695 CAGTTATCGTCGTCCAAAACTTTTTA 58.653 34.615 0.00 0.00 0.00 1.52
1782 1811 0.553819 AGGCACACCCCTTAACAACA 59.446 50.000 0.00 0.00 36.11 3.33
1784 1813 1.775459 TGTAGGCACACCCCTTAACAA 59.225 47.619 0.00 0.00 36.41 2.83
1796 1825 4.477302 AACATACAAAACGTGTAGGCAC 57.523 40.909 0.00 0.00 46.26 5.01
1801 1830 7.171337 GGTCCTCTTAAACATACAAAACGTGTA 59.829 37.037 0.00 0.00 46.72 2.90
1817 1849 2.504175 GTGTATGGGCTGGTCCTCTTAA 59.496 50.000 0.00 0.00 34.39 1.85
1837 1869 3.118298 AGTTGTTTTACCCACACGTAGGT 60.118 43.478 8.89 8.89 40.31 3.08
1889 1923 0.387202 CATAGGCGTGTGAGAGGGAG 59.613 60.000 0.00 0.00 0.00 4.30
1922 1958 1.066430 AGACATCGTGTGGGCGTTATT 60.066 47.619 0.00 0.00 0.00 1.40
1938 1974 0.409876 AGGTAGGTGGCTGAGAGACA 59.590 55.000 0.00 0.00 0.00 3.41
1939 1975 1.107945 GAGGTAGGTGGCTGAGAGAC 58.892 60.000 0.00 0.00 0.00 3.36
1971 2007 3.986006 GTGACTGTCACGCGGGGA 61.986 66.667 23.54 2.91 37.67 4.81
1997 2033 2.359850 GACCATGGCAACTGCGGA 60.360 61.111 13.04 0.00 43.26 5.54
2046 2082 2.009051 TGTAATTCAGCGACATGGCAG 58.991 47.619 0.00 0.00 34.64 4.85
2062 2098 1.070914 TGTCCGACATGGCAACTGTAA 59.929 47.619 0.00 0.00 37.80 2.41
2178 2215 9.461312 TTCAAATCATGGCAACTATAGTAAACT 57.539 29.630 5.65 0.00 37.61 2.66
2254 2291 4.720046 TCATGGCAACTGTAGTAAACCAA 58.280 39.130 0.00 0.00 31.23 3.67
2352 2391 6.014840 ACTCTCTCTTTTACCCGAACATGTTA 60.015 38.462 11.95 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.