Multiple sequence alignment - TraesCS5D01G364300

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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 TraesCS5D01G364300 chr5D 100.000 3318 0 0 1 3318 441888688 441885371 0.000000e+00 6128.0
1 TraesCS5D01G364300 chr5D 91.215 683 43 12 1 674 325838620 325839294 0.000000e+00 913.0
2 TraesCS5D01G364300 chr5D 90.741 162 9 3 823 979 403746754 403746594 9.330000e-51 211.0
3 TraesCS5D01G364300 chr5A 94.817 1505 68 5 977 2478 558252232 558250735 0.000000e+00 2338.0
4 TraesCS5D01G364300 chr5A 89.870 849 54 13 2476 3318 558250691 558249869 0.000000e+00 1062.0
5 TraesCS5D01G364300 chr5A 90.385 156 11 2 823 977 349387798 349387950 5.610000e-48 202.0
6 TraesCS5D01G364300 chr5B 94.820 1448 60 3 1038 2478 537906765 537905326 0.000000e+00 2244.0
7 TraesCS5D01G364300 chr5B 90.284 844 55 14 2477 3318 537905208 537904390 0.000000e+00 1079.0
8 TraesCS5D01G364300 chr3D 91.155 701 46 11 1 697 242190614 242191302 0.000000e+00 937.0
9 TraesCS5D01G364300 chr3D 91.556 675 47 6 1 674 582242221 582241556 0.000000e+00 922.0
10 TraesCS5D01G364300 chr3D 80.970 268 30 9 712 974 129191745 129191996 3.380000e-45 193.0
11 TraesCS5D01G364300 chr6D 92.553 658 38 9 1 654 42363830 42363180 0.000000e+00 933.0
12 TraesCS5D01G364300 chr6D 97.368 38 1 0 800 837 415625014 415625051 7.680000e-07 65.8
13 TraesCS5D01G364300 chr6D 97.368 38 1 0 800 837 441376277 441376314 7.680000e-07 65.8
14 TraesCS5D01G364300 chr1D 90.309 712 51 11 1 707 164981428 164982126 0.000000e+00 917.0
15 TraesCS5D01G364300 chr1D 90.000 700 57 11 1 697 244892517 244891828 0.000000e+00 893.0
16 TraesCS5D01G364300 chr1D 97.368 38 1 0 800 837 162358293 162358330 7.680000e-07 65.8
17 TraesCS5D01G364300 chr1B 91.933 657 45 6 1 655 591406289 591406939 0.000000e+00 913.0
18 TraesCS5D01G364300 chr7A 89.645 705 59 8 1 704 65643937 65643246 0.000000e+00 885.0
19 TraesCS5D01G364300 chr7D 89.563 709 52 15 1 707 375634826 375634138 0.000000e+00 880.0
20 TraesCS5D01G364300 chr2D 92.405 158 8 2 823 976 563098711 563098554 4.310000e-54 222.0
21 TraesCS5D01G364300 chr2D 88.387 155 15 1 823 974 109556673 109556519 2.030000e-42 183.0
22 TraesCS5D01G364300 chr4D 91.503 153 10 1 824 973 24692370 24692522 1.210000e-49 207.0
23 TraesCS5D01G364300 chr4D 88.961 154 13 4 823 973 410624358 410624510 1.570000e-43 187.0
24 TraesCS5D01G364300 chr4A 89.474 152 9 5 823 973 260708692 260708837 5.650000e-43 185.0
25 TraesCS5D01G364300 chr4A 89.404 151 10 2 823 973 512989042 512989186 5.650000e-43 185.0
26 TraesCS5D01G364300 chr6A 93.333 45 2 1 800 844 62931945 62931988 7.680000e-07 65.8


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 TraesCS5D01G364300 chr5D 441885371 441888688 3317 True 6128.0 6128 100.0000 1 3318 1 chr5D.!!$R2 3317
1 TraesCS5D01G364300 chr5D 325838620 325839294 674 False 913.0 913 91.2150 1 674 1 chr5D.!!$F1 673
2 TraesCS5D01G364300 chr5A 558249869 558252232 2363 True 1700.0 2338 92.3435 977 3318 2 chr5A.!!$R1 2341
3 TraesCS5D01G364300 chr5B 537904390 537906765 2375 True 1661.5 2244 92.5520 1038 3318 2 chr5B.!!$R1 2280
4 TraesCS5D01G364300 chr3D 242190614 242191302 688 False 937.0 937 91.1550 1 697 1 chr3D.!!$F2 696
5 TraesCS5D01G364300 chr3D 582241556 582242221 665 True 922.0 922 91.5560 1 674 1 chr3D.!!$R1 673
6 TraesCS5D01G364300 chr6D 42363180 42363830 650 True 933.0 933 92.5530 1 654 1 chr6D.!!$R1 653
7 TraesCS5D01G364300 chr1D 164981428 164982126 698 False 917.0 917 90.3090 1 707 1 chr1D.!!$F2 706
8 TraesCS5D01G364300 chr1D 244891828 244892517 689 True 893.0 893 90.0000 1 697 1 chr1D.!!$R1 696
9 TraesCS5D01G364300 chr1B 591406289 591406939 650 False 913.0 913 91.9330 1 655 1 chr1B.!!$F1 654
10 TraesCS5D01G364300 chr7A 65643246 65643937 691 True 885.0 885 89.6450 1 704 1 chr7A.!!$R1 703
11 TraesCS5D01G364300 chr7D 375634138 375634826 688 True 880.0 880 89.5630 1 707 1 chr7D.!!$R1 706

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
171 175 0.037590 CCGAATTCAACAGGGGGACA 59.962 55.0 6.22 0.0 0.0 4.02 F
907 925 0.179073 AGTGGCGTGATGATAGTGGC 60.179 55.0 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1449 0.033504 GGTGCCAGTCGAAACAGAGA 59.966 55.0 0.0 0.0 0.0 3.10 R
2732 2888 0.698238 AGCCTCCCACAAATACTGCA 59.302 50.0 0.0 0.0 0.0 4.41 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
163 167 6.203145 TCGAAAAGTTACATCCGAATTCAACA 59.797 34.615 6.22 0.00 0.00 3.33
170 174 0.326927 TCCGAATTCAACAGGGGGAC 59.673 55.000 6.22 0.00 0.00 4.46
171 175 0.037590 CCGAATTCAACAGGGGGACA 59.962 55.000 6.22 0.00 0.00 4.02
192 197 6.391227 ACACCGTTGAAGATTTTCAGAATT 57.609 33.333 0.00 0.00 43.76 2.17
193 198 6.805713 ACACCGTTGAAGATTTTCAGAATTT 58.194 32.000 0.00 0.00 43.76 1.82
194 199 6.697019 ACACCGTTGAAGATTTTCAGAATTTG 59.303 34.615 0.00 0.00 43.76 2.32
199 204 7.580165 CGTTGAAGATTTTCAGAATTTGCAAAC 59.420 33.333 15.41 2.49 43.76 2.93
299 305 4.319133 ACCATTTGCTAGGTGCGG 57.681 55.556 0.00 0.00 46.63 5.69
431 441 8.394971 TCACACTCATGAATATGAACAAAGTT 57.605 30.769 0.00 0.00 42.48 2.66
435 445 9.979270 CACTCATGAATATGAACAAAGTTCTAC 57.021 33.333 10.79 0.50 42.48 2.59
446 456 7.247728 TGAACAAAGTTCTACACATCAACAAC 58.752 34.615 10.79 0.00 0.00 3.32
460 470 8.234546 ACACATCAACAACGTTTAATAGGATTC 58.765 33.333 0.00 0.00 0.00 2.52
531 541 5.355910 GGGTTGGATAGAATTGCGAAGTTAA 59.644 40.000 0.00 0.00 0.00 2.01
532 542 6.039382 GGGTTGGATAGAATTGCGAAGTTAAT 59.961 38.462 0.00 0.00 0.00 1.40
533 543 7.227910 GGGTTGGATAGAATTGCGAAGTTAATA 59.772 37.037 0.00 0.00 0.00 0.98
618 629 4.201714 TGCGATTTGACTTGAGATTAAGCG 60.202 41.667 0.00 0.00 0.00 4.68
719 737 3.676291 AAAAATTGGTGCGCCATTACT 57.324 38.095 21.95 4.89 45.56 2.24
720 738 2.652941 AAATTGGTGCGCCATTACTG 57.347 45.000 21.95 0.00 45.56 2.74
721 739 1.832883 AATTGGTGCGCCATTACTGA 58.167 45.000 21.95 3.79 45.56 3.41
722 740 1.094785 ATTGGTGCGCCATTACTGAC 58.905 50.000 21.95 0.00 45.56 3.51
723 741 0.958382 TTGGTGCGCCATTACTGACC 60.958 55.000 21.95 3.18 45.56 4.02
724 742 2.112815 GGTGCGCCATTACTGACCC 61.113 63.158 12.58 0.00 34.09 4.46
725 743 2.125310 TGCGCCATTACTGACCCG 60.125 61.111 4.18 0.00 0.00 5.28
726 744 2.185867 GCGCCATTACTGACCCGA 59.814 61.111 0.00 0.00 0.00 5.14
727 745 1.883084 GCGCCATTACTGACCCGAG 60.883 63.158 0.00 0.00 0.00 4.63
728 746 1.813859 CGCCATTACTGACCCGAGA 59.186 57.895 0.00 0.00 0.00 4.04
729 747 0.389391 CGCCATTACTGACCCGAGAT 59.611 55.000 0.00 0.00 0.00 2.75
730 748 1.202533 CGCCATTACTGACCCGAGATT 60.203 52.381 0.00 0.00 0.00 2.40
731 749 2.035449 CGCCATTACTGACCCGAGATTA 59.965 50.000 0.00 0.00 0.00 1.75
732 750 3.491964 CGCCATTACTGACCCGAGATTAA 60.492 47.826 0.00 0.00 0.00 1.40
733 751 4.058817 GCCATTACTGACCCGAGATTAAG 58.941 47.826 0.00 0.00 0.00 1.85
734 752 4.202223 GCCATTACTGACCCGAGATTAAGA 60.202 45.833 0.00 0.00 0.00 2.10
735 753 5.684030 GCCATTACTGACCCGAGATTAAGAA 60.684 44.000 0.00 0.00 0.00 2.52
736 754 6.346096 CCATTACTGACCCGAGATTAAGAAA 58.654 40.000 0.00 0.00 0.00 2.52
737 755 6.821665 CCATTACTGACCCGAGATTAAGAAAA 59.178 38.462 0.00 0.00 0.00 2.29
738 756 7.335924 CCATTACTGACCCGAGATTAAGAAAAA 59.664 37.037 0.00 0.00 0.00 1.94
817 835 5.607119 AAAAGTGGTGCGTCATTACTAAG 57.393 39.130 0.00 0.00 0.00 2.18
818 836 3.955650 AGTGGTGCGTCATTACTAAGT 57.044 42.857 0.00 0.00 0.00 2.24
819 837 3.846360 AGTGGTGCGTCATTACTAAGTC 58.154 45.455 0.00 0.00 0.00 3.01
820 838 2.928116 GTGGTGCGTCATTACTAAGTCC 59.072 50.000 0.00 0.00 0.00 3.85
821 839 2.190981 GGTGCGTCATTACTAAGTCCG 58.809 52.381 0.00 0.00 0.00 4.79
822 840 2.159338 GGTGCGTCATTACTAAGTCCGA 60.159 50.000 0.00 0.00 0.00 4.55
823 841 3.490419 GGTGCGTCATTACTAAGTCCGAT 60.490 47.826 0.00 0.00 0.00 4.18
824 842 4.261322 GGTGCGTCATTACTAAGTCCGATA 60.261 45.833 0.00 0.00 0.00 2.92
825 843 4.910456 GTGCGTCATTACTAAGTCCGATAG 59.090 45.833 0.00 0.00 0.00 2.08
826 844 4.577693 TGCGTCATTACTAAGTCCGATAGT 59.422 41.667 0.00 0.00 37.39 2.12
827 845 5.759763 TGCGTCATTACTAAGTCCGATAGTA 59.240 40.000 0.00 0.00 35.34 1.82
828 846 6.260714 TGCGTCATTACTAAGTCCGATAGTAA 59.739 38.462 8.19 8.19 45.13 2.24
833 851 4.500603 ACTAAGTCCGATAGTAATGGCG 57.499 45.455 0.00 0.00 31.96 5.69
834 852 2.150397 AAGTCCGATAGTAATGGCGC 57.850 50.000 0.00 0.00 0.00 6.53
835 853 1.037493 AGTCCGATAGTAATGGCGCA 58.963 50.000 10.83 0.00 0.00 6.09
836 854 1.137513 GTCCGATAGTAATGGCGCAC 58.862 55.000 10.83 0.00 0.00 5.34
837 855 1.037493 TCCGATAGTAATGGCGCACT 58.963 50.000 10.83 6.53 0.00 4.40
838 856 2.030540 GTCCGATAGTAATGGCGCACTA 60.031 50.000 10.83 8.93 0.00 2.74
839 857 2.823747 TCCGATAGTAATGGCGCACTAT 59.176 45.455 15.65 15.65 39.97 2.12
840 858 2.923655 CCGATAGTAATGGCGCACTATG 59.076 50.000 19.38 12.57 37.94 2.23
841 859 3.575630 CGATAGTAATGGCGCACTATGT 58.424 45.455 19.38 1.43 37.94 2.29
842 860 3.364920 CGATAGTAATGGCGCACTATGTG 59.635 47.826 19.38 10.13 37.94 3.21
843 861 1.953559 AGTAATGGCGCACTATGTGG 58.046 50.000 10.83 0.00 33.64 4.17
844 862 1.209504 AGTAATGGCGCACTATGTGGT 59.790 47.619 10.83 0.00 33.64 4.16
845 863 1.330521 GTAATGGCGCACTATGTGGTG 59.669 52.381 10.83 0.00 39.91 4.17
860 878 2.238942 TGGTGCGCCACTATTATCTG 57.761 50.000 16.89 0.00 40.46 2.90
861 879 1.202639 TGGTGCGCCACTATTATCTGG 60.203 52.381 16.89 0.00 40.46 3.86
862 880 1.202651 GGTGCGCCACTATTATCTGGT 60.203 52.381 12.58 0.00 34.40 4.00
863 881 2.036733 GGTGCGCCACTATTATCTGGTA 59.963 50.000 12.58 0.00 34.40 3.25
864 882 3.306780 GGTGCGCCACTATTATCTGGTAT 60.307 47.826 12.58 0.00 34.40 2.73
865 883 4.081862 GGTGCGCCACTATTATCTGGTATA 60.082 45.833 12.58 0.00 34.40 1.47
866 884 5.395324 GGTGCGCCACTATTATCTGGTATAT 60.395 44.000 12.58 0.00 34.40 0.86
867 885 5.520288 GTGCGCCACTATTATCTGGTATATG 59.480 44.000 4.18 0.00 0.00 1.78
868 886 4.508124 GCGCCACTATTATCTGGTATATGC 59.492 45.833 0.00 0.00 0.00 3.14
869 887 4.740205 CGCCACTATTATCTGGTATATGCG 59.260 45.833 0.00 0.00 0.00 4.73
870 888 5.661458 GCCACTATTATCTGGTATATGCGT 58.339 41.667 0.00 0.00 0.00 5.24
871 889 5.749109 GCCACTATTATCTGGTATATGCGTC 59.251 44.000 0.00 0.00 0.00 5.19
872 890 6.627287 GCCACTATTATCTGGTATATGCGTCA 60.627 42.308 0.00 0.00 0.00 4.35
873 891 7.492524 CCACTATTATCTGGTATATGCGTCAT 58.507 38.462 0.00 0.00 0.00 3.06
874 892 7.981789 CCACTATTATCTGGTATATGCGTCATT 59.018 37.037 0.00 0.00 0.00 2.57
880 898 7.704578 ATCTGGTATATGCGTCATTAGTACT 57.295 36.000 0.00 0.00 0.00 2.73
881 899 7.520451 TCTGGTATATGCGTCATTAGTACTT 57.480 36.000 0.00 0.00 0.00 2.24
882 900 7.368059 TCTGGTATATGCGTCATTAGTACTTG 58.632 38.462 0.00 0.00 0.00 3.16
883 901 7.013942 TCTGGTATATGCGTCATTAGTACTTGT 59.986 37.037 0.00 0.00 0.00 3.16
884 902 7.494211 TGGTATATGCGTCATTAGTACTTGTT 58.506 34.615 0.00 0.00 0.00 2.83
885 903 8.631797 TGGTATATGCGTCATTAGTACTTGTTA 58.368 33.333 0.00 0.00 0.00 2.41
886 904 8.909671 GGTATATGCGTCATTAGTACTTGTTAC 58.090 37.037 0.00 0.00 0.00 2.50
887 905 9.674824 GTATATGCGTCATTAGTACTTGTTACT 57.325 33.333 0.00 0.00 43.89 2.24
889 907 9.894783 ATATGCGTCATTAGTACTTGTTACTAG 57.105 33.333 0.00 0.00 42.99 2.57
890 908 7.149569 TGCGTCATTAGTACTTGTTACTAGT 57.850 36.000 0.00 0.00 42.99 2.57
891 909 7.025365 TGCGTCATTAGTACTTGTTACTAGTG 58.975 38.462 5.39 3.67 45.77 2.74
892 910 6.471519 GCGTCATTAGTACTTGTTACTAGTGG 59.528 42.308 5.39 0.00 45.05 4.00
893 911 6.471519 CGTCATTAGTACTTGTTACTAGTGGC 59.528 42.308 5.39 9.89 45.52 5.01
894 912 6.471519 GTCATTAGTACTTGTTACTAGTGGCG 59.528 42.308 5.39 0.00 45.05 5.69
895 913 5.964958 TTAGTACTTGTTACTAGTGGCGT 57.035 39.130 5.39 0.00 42.99 5.68
896 914 4.170292 AGTACTTGTTACTAGTGGCGTG 57.830 45.455 5.39 0.00 39.45 5.34
897 915 3.822735 AGTACTTGTTACTAGTGGCGTGA 59.177 43.478 5.39 0.00 39.45 4.35
898 916 3.955650 ACTTGTTACTAGTGGCGTGAT 57.044 42.857 5.39 0.00 0.00 3.06
899 917 3.585862 ACTTGTTACTAGTGGCGTGATG 58.414 45.455 5.39 0.00 0.00 3.07
900 918 3.257375 ACTTGTTACTAGTGGCGTGATGA 59.743 43.478 5.39 0.00 0.00 2.92
901 919 4.081642 ACTTGTTACTAGTGGCGTGATGAT 60.082 41.667 5.39 0.00 0.00 2.45
902 920 5.126545 ACTTGTTACTAGTGGCGTGATGATA 59.873 40.000 5.39 0.00 0.00 2.15
903 921 5.183014 TGTTACTAGTGGCGTGATGATAG 57.817 43.478 5.39 0.00 0.00 2.08
904 922 4.643334 TGTTACTAGTGGCGTGATGATAGT 59.357 41.667 5.39 0.00 0.00 2.12
905 923 3.717400 ACTAGTGGCGTGATGATAGTG 57.283 47.619 0.00 0.00 0.00 2.74
906 924 2.362397 ACTAGTGGCGTGATGATAGTGG 59.638 50.000 0.00 0.00 0.00 4.00
907 925 0.179073 AGTGGCGTGATGATAGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
908 926 1.227234 TGGCGTGATGATAGTGGCG 60.227 57.895 0.00 0.00 0.00 5.69
909 927 2.598632 GGCGTGATGATAGTGGCGC 61.599 63.158 0.00 0.00 43.46 6.53
910 928 1.882625 GCGTGATGATAGTGGCGCA 60.883 57.895 10.83 0.00 43.62 6.09
911 929 1.927210 CGTGATGATAGTGGCGCAC 59.073 57.895 10.83 5.73 34.10 5.34
912 930 1.490693 CGTGATGATAGTGGCGCACC 61.491 60.000 10.83 0.00 34.49 5.01
913 931 0.179073 GTGATGATAGTGGCGCACCT 60.179 55.000 10.83 6.50 34.49 4.00
914 932 1.068588 GTGATGATAGTGGCGCACCTA 59.931 52.381 10.83 8.88 34.49 3.08
915 933 1.970640 TGATGATAGTGGCGCACCTAT 59.029 47.619 10.83 13.75 34.49 2.57
916 934 3.056821 GTGATGATAGTGGCGCACCTATA 60.057 47.826 10.83 3.93 34.49 1.31
917 935 3.193479 TGATGATAGTGGCGCACCTATAG 59.807 47.826 10.83 0.00 34.49 1.31
918 936 2.594131 TGATAGTGGCGCACCTATAGT 58.406 47.619 10.83 0.00 34.49 2.12
930 948 4.668576 CACCTATAGTGCGCCATTAATG 57.331 45.455 4.18 8.58 40.28 1.90
931 949 3.436704 CACCTATAGTGCGCCATTAATGG 59.563 47.826 27.35 27.35 44.70 3.16
945 963 4.925054 CCATTAATGGCCAAAATAGATGCG 59.075 41.667 21.32 0.00 41.75 4.73
946 964 2.514205 AATGGCCAAAATAGATGCGC 57.486 45.000 10.96 0.00 0.00 6.09
947 965 0.675633 ATGGCCAAAATAGATGCGCC 59.324 50.000 10.96 0.00 35.77 6.53
948 966 0.682532 TGGCCAAAATAGATGCGCCA 60.683 50.000 0.61 0.00 39.90 5.69
949 967 0.249031 GGCCAAAATAGATGCGCCAC 60.249 55.000 4.18 0.00 35.49 5.01
950 968 0.740737 GCCAAAATAGATGCGCCACT 59.259 50.000 4.18 6.83 0.00 4.00
951 969 1.946768 GCCAAAATAGATGCGCCACTA 59.053 47.619 4.18 9.11 0.00 2.74
952 970 2.357637 GCCAAAATAGATGCGCCACTAA 59.642 45.455 4.18 0.00 0.00 2.24
953 971 3.792124 GCCAAAATAGATGCGCCACTAAC 60.792 47.826 4.18 0.00 0.00 2.34
954 972 3.376859 CCAAAATAGATGCGCCACTAACA 59.623 43.478 4.18 0.00 0.00 2.41
955 973 4.496341 CCAAAATAGATGCGCCACTAACAG 60.496 45.833 4.18 1.38 0.00 3.16
956 974 2.533266 ATAGATGCGCCACTAACAGG 57.467 50.000 4.18 0.00 0.00 4.00
964 982 0.888619 GCCACTAACAGGCCTTTTCC 59.111 55.000 7.60 0.00 46.50 3.13
965 983 1.547901 GCCACTAACAGGCCTTTTCCT 60.548 52.381 7.60 0.00 46.50 3.36
966 984 2.290705 GCCACTAACAGGCCTTTTCCTA 60.291 50.000 7.60 0.00 46.50 2.94
967 985 3.610911 CCACTAACAGGCCTTTTCCTAG 58.389 50.000 7.60 2.80 33.95 3.02
968 986 3.009143 CCACTAACAGGCCTTTTCCTAGT 59.991 47.826 7.60 3.49 33.95 2.57
969 987 4.224370 CCACTAACAGGCCTTTTCCTAGTA 59.776 45.833 7.60 0.00 33.95 1.82
970 988 5.420409 CACTAACAGGCCTTTTCCTAGTAG 58.580 45.833 7.60 1.27 33.95 2.57
971 989 5.046520 CACTAACAGGCCTTTTCCTAGTAGT 60.047 44.000 7.60 1.94 36.34 2.73
972 990 3.983044 ACAGGCCTTTTCCTAGTAGTG 57.017 47.619 0.00 0.00 33.95 2.74
973 991 2.027100 ACAGGCCTTTTCCTAGTAGTGC 60.027 50.000 0.00 0.00 33.95 4.40
974 992 2.027192 CAGGCCTTTTCCTAGTAGTGCA 60.027 50.000 0.00 0.00 33.95 4.57
975 993 2.846827 AGGCCTTTTCCTAGTAGTGCAT 59.153 45.455 0.00 0.00 33.95 3.96
976 994 4.037927 AGGCCTTTTCCTAGTAGTGCATA 58.962 43.478 0.00 0.00 33.95 3.14
977 995 4.660771 AGGCCTTTTCCTAGTAGTGCATAT 59.339 41.667 0.00 0.00 33.95 1.78
978 996 4.757149 GGCCTTTTCCTAGTAGTGCATATG 59.243 45.833 0.00 0.00 0.00 1.78
979 997 4.214332 GCCTTTTCCTAGTAGTGCATATGC 59.786 45.833 21.09 21.09 42.50 3.14
980 998 4.449068 CCTTTTCCTAGTAGTGCATATGCG 59.551 45.833 22.21 6.38 45.83 4.73
1036 1055 5.944135 AGTATCTCTAGTTACCCCACTCTC 58.056 45.833 0.00 0.00 0.00 3.20
1064 1083 2.848679 TCCACCACTGCCTGCAGA 60.849 61.111 24.88 0.00 46.30 4.26
1144 1163 2.178273 CATCGGTCGTCGTCTGCA 59.822 61.111 0.00 0.00 40.32 4.41
1187 1206 4.012374 CTGTTCATTGTGGATGGCTACTT 58.988 43.478 0.00 0.00 36.37 2.24
1191 1210 3.196901 TCATTGTGGATGGCTACTTACGT 59.803 43.478 0.00 0.00 36.37 3.57
1399 1418 0.803768 CGACCAGATCGTCAAGCAGG 60.804 60.000 2.31 0.00 46.25 4.85
1401 1420 0.247736 ACCAGATCGTCAAGCAGGAC 59.752 55.000 0.00 0.00 34.42 3.85
1425 1444 1.201921 GCACGCATTCACTTAACCGAG 60.202 52.381 0.00 0.00 0.00 4.63
1428 1447 1.659098 CGCATTCACTTAACCGAGGTC 59.341 52.381 0.00 0.00 0.00 3.85
1429 1448 2.695359 GCATTCACTTAACCGAGGTCA 58.305 47.619 0.00 0.00 0.00 4.02
1430 1449 3.270877 GCATTCACTTAACCGAGGTCAT 58.729 45.455 0.00 0.00 0.00 3.06
1435 1454 3.444034 TCACTTAACCGAGGTCATCTCTG 59.556 47.826 0.00 0.00 40.30 3.35
1551 1570 1.634225 CGACGTGTTTGTTGCGACT 59.366 52.632 5.50 0.00 0.00 4.18
1583 1602 2.185310 ATTGCTCCCACCTCGACCAC 62.185 60.000 0.00 0.00 0.00 4.16
1676 1695 3.518998 CGAGGTCGGTGGCGAGAT 61.519 66.667 0.00 0.00 35.37 2.75
1929 1954 7.961351 AGTCGGAAGAAGAATATGATGAAGAT 58.039 34.615 0.00 0.00 45.01 2.40
2108 2133 2.811317 GAAGGAGGAGTGCGTGCG 60.811 66.667 0.00 0.00 0.00 5.34
2154 2179 7.081349 CCGCAAAGTTACAAATCTTATTGTCA 58.919 34.615 0.00 0.00 42.33 3.58
2325 2358 6.880822 GTGTTCATCACATTGAATGAATGG 57.119 37.500 12.80 0.00 45.20 3.16
2463 2496 1.129251 GAACCATGTGCTGATGTGACG 59.871 52.381 0.00 0.00 0.00 4.35
2471 2504 1.601903 TGCTGATGTGACGGTGAAAAC 59.398 47.619 0.00 0.00 0.00 2.43
2472 2505 1.601903 GCTGATGTGACGGTGAAAACA 59.398 47.619 0.00 0.00 0.00 2.83
2473 2506 2.349817 GCTGATGTGACGGTGAAAACAG 60.350 50.000 0.00 0.00 0.00 3.16
2474 2507 2.872245 CTGATGTGACGGTGAAAACAGT 59.128 45.455 0.00 0.00 0.00 3.55
2515 2668 6.867816 TCATGGTATTGTTTGAATCTTTGCAC 59.132 34.615 0.00 0.00 0.00 4.57
2524 2677 9.469807 TTGTTTGAATCTTTGCACGTATTTTAT 57.530 25.926 0.00 0.00 0.00 1.40
2576 2729 7.740519 AGTACAAAAATTGCAAGCGAATATC 57.259 32.000 4.94 0.00 0.00 1.63
2577 2730 5.685195 ACAAAAATTGCAAGCGAATATCG 57.315 34.783 4.94 0.00 43.89 2.92
2578 2731 4.562394 ACAAAAATTGCAAGCGAATATCGG 59.438 37.500 4.94 0.00 40.84 4.18
2579 2732 4.630894 AAAATTGCAAGCGAATATCGGA 57.369 36.364 4.94 0.00 40.84 4.55
2592 2745 9.817809 AAGCGAATATCGGAATATGTATTGTAT 57.182 29.630 1.64 0.00 40.84 2.29
2614 2767 3.689347 TGTATGGAGATTGCAGCAACTT 58.311 40.909 10.85 0.81 0.00 2.66
2620 2773 3.985925 GGAGATTGCAGCAACTTTTTCTG 59.014 43.478 10.85 0.00 0.00 3.02
2630 2785 5.292589 CAGCAACTTTTTCTGACAATGCTTT 59.707 36.000 1.51 0.00 40.62 3.51
2637 2792 7.550196 ACTTTTTCTGACAATGCTTTGAAACAT 59.450 29.630 18.35 0.00 36.64 2.71
2640 2795 9.545105 TTTTCTGACAATGCTTTGAAACATTAT 57.455 25.926 18.35 0.00 34.80 1.28
2641 2796 8.523523 TTCTGACAATGCTTTGAAACATTATG 57.476 30.769 18.35 0.00 34.80 1.90
2665 2821 9.778741 ATGAACAAGATGTCAACTAAGAAACTA 57.221 29.630 0.00 0.00 0.00 2.24
2683 2839 4.720649 ACTATACGCAGTTGACAGACAT 57.279 40.909 0.00 0.00 37.78 3.06
2690 2846 2.413765 GCAGTTGACAGACATGACATGC 60.414 50.000 15.49 8.35 32.72 4.06
2691 2847 2.809696 CAGTTGACAGACATGACATGCA 59.190 45.455 15.49 2.09 31.23 3.96
2692 2848 3.439129 CAGTTGACAGACATGACATGCAT 59.561 43.478 15.49 0.00 37.85 3.96
2732 2888 4.907809 TCGGTCGAGATCCATCTAACTAT 58.092 43.478 0.00 0.00 37.25 2.12
2734 2890 4.673061 CGGTCGAGATCCATCTAACTATGC 60.673 50.000 0.00 0.00 37.25 3.14
2736 2892 5.398169 GTCGAGATCCATCTAACTATGCAG 58.602 45.833 0.00 0.00 37.25 4.41
2740 2896 7.394641 TCGAGATCCATCTAACTATGCAGTATT 59.605 37.037 0.00 0.00 37.25 1.89
2744 2900 8.613060 ATCCATCTAACTATGCAGTATTTGTG 57.387 34.615 0.00 0.00 33.48 3.33
2786 2942 1.856265 CGGCAGCAAACTTGTCCTCC 61.856 60.000 0.00 0.00 0.00 4.30
2797 2953 2.108168 CTTGTCCTCCGGATAGAACCA 58.892 52.381 3.57 0.00 32.73 3.67
2798 2954 1.776662 TGTCCTCCGGATAGAACCAG 58.223 55.000 3.57 0.00 32.73 4.00
2808 2964 3.443681 CGGATAGAACCAGGCAACAATTT 59.556 43.478 0.00 0.00 41.41 1.82
2831 2987 0.760567 TCTCATCCCACCATCTCCCG 60.761 60.000 0.00 0.00 0.00 5.14
2846 3002 1.048724 TCCCGCCCATCTCGATCTTT 61.049 55.000 0.00 0.00 0.00 2.52
2864 3020 4.631131 TCTTTCAAAGATTCGAGCTGTCA 58.369 39.130 0.00 0.00 31.20 3.58
2867 3023 4.257267 TCAAAGATTCGAGCTGTCAAGA 57.743 40.909 0.00 0.00 0.00 3.02
2882 3038 3.382227 TGTCAAGACACGAGTACTCCAAA 59.618 43.478 17.23 0.00 36.21 3.28
3023 3179 1.069022 CCGTAAAACTCGTCGTCCTCA 60.069 52.381 0.00 0.00 0.00 3.86
3093 3249 2.290464 CTCCGTCTTCGTGAGGTAGAT 58.710 52.381 0.00 0.00 33.81 1.98
3155 3314 4.164802 GTGTACATAAGCACGTTCATCG 57.835 45.455 0.00 0.00 46.00 3.84
3238 3397 2.573462 AGAAGCCAGGCAGAATCAAGTA 59.427 45.455 15.80 0.00 0.00 2.24
3302 3461 3.626028 AACAGAAATCGAGGCAAACAC 57.374 42.857 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 167 0.840722 ATCTTCAACGGTGTCCCCCT 60.841 55.000 0.00 0.00 0.00 4.79
170 174 6.346040 GCAAATTCTGAAAATCTTCAACGGTG 60.346 38.462 0.00 0.00 41.05 4.94
171 175 5.691754 GCAAATTCTGAAAATCTTCAACGGT 59.308 36.000 0.00 0.00 41.05 4.83
192 197 8.001881 TCTTTTATTCTGTTAGGTGTTTGCAA 57.998 30.769 0.00 0.00 0.00 4.08
193 198 7.575414 TCTTTTATTCTGTTAGGTGTTTGCA 57.425 32.000 0.00 0.00 0.00 4.08
199 204 7.040409 GCCCCATATCTTTTATTCTGTTAGGTG 60.040 40.741 0.00 0.00 0.00 4.00
220 225 4.325816 CCCCTCTAGATTTTAAAAGCCCCA 60.326 45.833 12.38 0.00 0.00 4.96
431 441 8.089597 TCCTATTAAACGTTGTTGATGTGTAGA 58.910 33.333 0.00 0.00 0.00 2.59
435 445 8.233868 TGAATCCTATTAAACGTTGTTGATGTG 58.766 33.333 0.00 0.00 0.00 3.21
531 541 1.750399 CCAGCCCAAGCACGCTTAT 60.750 57.895 3.53 0.00 43.56 1.73
532 542 2.359850 CCAGCCCAAGCACGCTTA 60.360 61.111 3.53 0.00 43.56 3.09
533 543 4.269523 TCCAGCCCAAGCACGCTT 62.270 61.111 0.00 0.00 43.56 4.68
576 586 3.326747 GCACTCCGTGATCAAACTTACT 58.673 45.455 0.00 0.00 35.23 2.24
578 588 2.029739 TCGCACTCCGTGATCAAACTTA 60.030 45.455 0.00 0.00 35.23 2.24
587 597 0.317160 AGTCAAATCGCACTCCGTGA 59.683 50.000 0.00 0.00 38.83 4.35
708 726 2.125310 CGGGTCAGTAATGGCGCA 60.125 61.111 10.83 0.00 0.00 6.09
709 727 1.883084 CTCGGGTCAGTAATGGCGC 60.883 63.158 0.00 0.00 0.00 6.53
710 728 0.389391 ATCTCGGGTCAGTAATGGCG 59.611 55.000 0.00 0.00 0.00 5.69
711 729 2.622064 AATCTCGGGTCAGTAATGGC 57.378 50.000 0.00 0.00 0.00 4.40
712 730 5.531122 TCTTAATCTCGGGTCAGTAATGG 57.469 43.478 0.00 0.00 0.00 3.16
713 731 7.843490 TTTTCTTAATCTCGGGTCAGTAATG 57.157 36.000 0.00 0.00 0.00 1.90
794 812 5.529800 ACTTAGTAATGACGCACCACTTTTT 59.470 36.000 0.00 0.00 0.00 1.94
795 813 5.061179 ACTTAGTAATGACGCACCACTTTT 58.939 37.500 0.00 0.00 0.00 2.27
796 814 4.638304 ACTTAGTAATGACGCACCACTTT 58.362 39.130 0.00 0.00 0.00 2.66
797 815 4.243270 GACTTAGTAATGACGCACCACTT 58.757 43.478 0.00 0.00 0.00 3.16
798 816 3.368116 GGACTTAGTAATGACGCACCACT 60.368 47.826 0.00 0.00 0.00 4.00
799 817 2.928116 GGACTTAGTAATGACGCACCAC 59.072 50.000 0.00 0.00 0.00 4.16
800 818 2.416296 CGGACTTAGTAATGACGCACCA 60.416 50.000 0.00 0.00 0.00 4.17
801 819 2.159338 TCGGACTTAGTAATGACGCACC 60.159 50.000 0.00 0.00 0.00 5.01
802 820 3.141002 TCGGACTTAGTAATGACGCAC 57.859 47.619 0.00 0.00 0.00 5.34
803 821 4.577693 ACTATCGGACTTAGTAATGACGCA 59.422 41.667 0.00 0.00 0.00 5.24
804 822 5.105834 ACTATCGGACTTAGTAATGACGC 57.894 43.478 0.00 0.00 0.00 5.19
809 827 6.618811 CGCCATTACTATCGGACTTAGTAAT 58.381 40.000 14.16 14.16 46.39 1.89
810 828 5.563475 GCGCCATTACTATCGGACTTAGTAA 60.563 44.000 11.59 11.59 42.95 2.24
811 829 4.083110 GCGCCATTACTATCGGACTTAGTA 60.083 45.833 0.00 0.00 32.35 1.82
812 830 3.305199 GCGCCATTACTATCGGACTTAGT 60.305 47.826 0.00 0.00 34.40 2.24
813 831 3.243336 GCGCCATTACTATCGGACTTAG 58.757 50.000 0.00 0.00 0.00 2.18
814 832 2.624364 TGCGCCATTACTATCGGACTTA 59.376 45.455 4.18 0.00 0.00 2.24
815 833 1.411246 TGCGCCATTACTATCGGACTT 59.589 47.619 4.18 0.00 0.00 3.01
816 834 1.037493 TGCGCCATTACTATCGGACT 58.963 50.000 4.18 0.00 0.00 3.85
817 835 1.137513 GTGCGCCATTACTATCGGAC 58.862 55.000 4.18 0.00 36.27 4.79
818 836 1.037493 AGTGCGCCATTACTATCGGA 58.963 50.000 4.18 0.00 0.00 4.55
819 837 2.717580 TAGTGCGCCATTACTATCGG 57.282 50.000 4.18 0.00 0.00 4.18
820 838 3.364920 CACATAGTGCGCCATTACTATCG 59.635 47.826 13.51 11.80 37.87 2.92
821 839 3.679980 CCACATAGTGCGCCATTACTATC 59.320 47.826 13.51 0.00 37.87 2.08
822 840 3.071023 ACCACATAGTGCGCCATTACTAT 59.929 43.478 4.18 8.71 39.91 2.12
823 841 2.432874 ACCACATAGTGCGCCATTACTA 59.567 45.455 4.18 6.34 34.23 1.82
824 842 1.209504 ACCACATAGTGCGCCATTACT 59.790 47.619 4.18 3.74 31.34 2.24
825 843 1.330521 CACCACATAGTGCGCCATTAC 59.669 52.381 4.18 0.00 31.34 1.89
826 844 1.662517 CACCACATAGTGCGCCATTA 58.337 50.000 4.18 0.00 31.34 1.90
827 845 2.481212 CACCACATAGTGCGCCATT 58.519 52.632 4.18 0.00 31.34 3.16
828 846 4.223800 CACCACATAGTGCGCCAT 57.776 55.556 4.18 0.00 31.34 4.40
841 859 1.202639 CCAGATAATAGTGGCGCACCA 60.203 52.381 10.83 0.00 46.51 4.17
842 860 1.202651 ACCAGATAATAGTGGCGCACC 60.203 52.381 10.83 0.00 37.34 5.01
843 861 2.240493 ACCAGATAATAGTGGCGCAC 57.760 50.000 10.83 5.73 37.34 5.34
844 862 5.660460 CATATACCAGATAATAGTGGCGCA 58.340 41.667 10.83 0.00 37.34 6.09
845 863 4.508124 GCATATACCAGATAATAGTGGCGC 59.492 45.833 0.00 0.00 37.34 6.53
846 864 4.740205 CGCATATACCAGATAATAGTGGCG 59.260 45.833 0.00 0.00 37.34 5.69
847 865 5.661458 ACGCATATACCAGATAATAGTGGC 58.339 41.667 0.00 0.00 37.34 5.01
848 866 6.863275 TGACGCATATACCAGATAATAGTGG 58.137 40.000 0.00 0.00 39.98 4.00
849 867 8.932945 AATGACGCATATACCAGATAATAGTG 57.067 34.615 0.00 0.00 0.00 2.74
854 872 9.239551 AGTACTAATGACGCATATACCAGATAA 57.760 33.333 0.00 0.00 0.00 1.75
855 873 8.803397 AGTACTAATGACGCATATACCAGATA 57.197 34.615 0.00 0.00 0.00 1.98
856 874 7.704578 AGTACTAATGACGCATATACCAGAT 57.295 36.000 0.00 0.00 0.00 2.90
857 875 7.013942 ACAAGTACTAATGACGCATATACCAGA 59.986 37.037 0.00 0.00 0.00 3.86
858 876 7.145985 ACAAGTACTAATGACGCATATACCAG 58.854 38.462 0.00 0.00 0.00 4.00
859 877 7.046292 ACAAGTACTAATGACGCATATACCA 57.954 36.000 0.00 0.00 0.00 3.25
860 878 7.941795 AACAAGTACTAATGACGCATATACC 57.058 36.000 0.00 0.00 0.00 2.73
861 879 9.674824 AGTAACAAGTACTAATGACGCATATAC 57.325 33.333 0.00 0.00 41.51 1.47
863 881 9.894783 CTAGTAACAAGTACTAATGACGCATAT 57.105 33.333 0.00 0.00 43.31 1.78
864 882 8.896744 ACTAGTAACAAGTACTAATGACGCATA 58.103 33.333 0.00 0.00 43.31 3.14
865 883 7.701078 CACTAGTAACAAGTACTAATGACGCAT 59.299 37.037 0.00 0.00 42.59 4.73
866 884 7.025365 CACTAGTAACAAGTACTAATGACGCA 58.975 38.462 0.00 0.00 42.59 5.24
867 885 6.471519 CCACTAGTAACAAGTACTAATGACGC 59.528 42.308 0.00 0.00 42.59 5.19
868 886 6.471519 GCCACTAGTAACAAGTACTAATGACG 59.528 42.308 0.00 0.00 42.59 4.35
869 887 6.471519 CGCCACTAGTAACAAGTACTAATGAC 59.528 42.308 0.00 0.00 42.59 3.06
870 888 6.151648 ACGCCACTAGTAACAAGTACTAATGA 59.848 38.462 0.00 0.00 42.59 2.57
871 889 6.252869 CACGCCACTAGTAACAAGTACTAATG 59.747 42.308 0.00 0.00 43.31 1.90
872 890 6.151648 TCACGCCACTAGTAACAAGTACTAAT 59.848 38.462 0.00 0.00 43.31 1.73
873 891 5.473162 TCACGCCACTAGTAACAAGTACTAA 59.527 40.000 0.00 0.00 43.31 2.24
874 892 5.003160 TCACGCCACTAGTAACAAGTACTA 58.997 41.667 0.00 0.00 41.51 1.82
875 893 3.822735 TCACGCCACTAGTAACAAGTACT 59.177 43.478 0.00 0.00 45.42 2.73
876 894 4.164822 TCACGCCACTAGTAACAAGTAC 57.835 45.455 0.00 0.00 0.00 2.73
877 895 4.460034 TCATCACGCCACTAGTAACAAGTA 59.540 41.667 0.00 0.00 0.00 2.24
878 896 3.257375 TCATCACGCCACTAGTAACAAGT 59.743 43.478 0.00 0.00 0.00 3.16
879 897 3.845178 TCATCACGCCACTAGTAACAAG 58.155 45.455 0.00 0.00 0.00 3.16
880 898 3.945981 TCATCACGCCACTAGTAACAA 57.054 42.857 0.00 0.00 0.00 2.83
881 899 4.643334 ACTATCATCACGCCACTAGTAACA 59.357 41.667 0.00 0.00 0.00 2.41
882 900 4.976731 CACTATCATCACGCCACTAGTAAC 59.023 45.833 0.00 0.00 0.00 2.50
883 901 4.037565 CCACTATCATCACGCCACTAGTAA 59.962 45.833 0.00 0.00 0.00 2.24
884 902 3.568430 CCACTATCATCACGCCACTAGTA 59.432 47.826 0.00 0.00 0.00 1.82
885 903 2.362397 CCACTATCATCACGCCACTAGT 59.638 50.000 0.00 0.00 0.00 2.57
886 904 2.864097 GCCACTATCATCACGCCACTAG 60.864 54.545 0.00 0.00 0.00 2.57
887 905 1.068588 GCCACTATCATCACGCCACTA 59.931 52.381 0.00 0.00 0.00 2.74
888 906 0.179073 GCCACTATCATCACGCCACT 60.179 55.000 0.00 0.00 0.00 4.00
889 907 1.490693 CGCCACTATCATCACGCCAC 61.491 60.000 0.00 0.00 0.00 5.01
890 908 1.227234 CGCCACTATCATCACGCCA 60.227 57.895 0.00 0.00 0.00 5.69
891 909 2.598632 GCGCCACTATCATCACGCC 61.599 63.158 0.00 0.00 40.43 5.68
892 910 1.882625 TGCGCCACTATCATCACGC 60.883 57.895 4.18 0.00 46.05 5.34
893 911 1.490693 GGTGCGCCACTATCATCACG 61.491 60.000 12.58 0.00 34.40 4.35
894 912 0.179073 AGGTGCGCCACTATCATCAC 60.179 55.000 20.59 0.00 37.19 3.06
895 913 1.408969 TAGGTGCGCCACTATCATCA 58.591 50.000 20.59 0.00 37.19 3.07
896 914 2.751166 ATAGGTGCGCCACTATCATC 57.249 50.000 20.59 0.00 37.19 2.92
897 915 3.056536 CACTATAGGTGCGCCACTATCAT 60.057 47.826 20.59 10.07 39.22 2.45
898 916 2.296190 CACTATAGGTGCGCCACTATCA 59.704 50.000 20.59 9.45 39.22 2.15
899 917 2.947852 CACTATAGGTGCGCCACTATC 58.052 52.381 20.59 0.00 39.22 2.08
909 927 3.436704 CCATTAATGGCGCACTATAGGTG 59.563 47.826 21.32 1.66 43.83 4.00
910 928 3.674997 CCATTAATGGCGCACTATAGGT 58.325 45.455 21.32 0.00 41.75 3.08
923 941 4.386652 GCGCATCTATTTTGGCCATTAATG 59.613 41.667 18.92 8.58 0.00 1.90
924 942 4.559153 GCGCATCTATTTTGGCCATTAAT 58.441 39.130 6.09 12.49 0.00 1.40
925 943 3.243704 GGCGCATCTATTTTGGCCATTAA 60.244 43.478 6.09 4.49 40.24 1.40
926 944 2.295909 GGCGCATCTATTTTGGCCATTA 59.704 45.455 6.09 0.00 40.24 1.90
927 945 1.069049 GGCGCATCTATTTTGGCCATT 59.931 47.619 6.09 0.00 40.24 3.16
928 946 0.675633 GGCGCATCTATTTTGGCCAT 59.324 50.000 6.09 0.00 40.24 4.40
929 947 2.114638 GGCGCATCTATTTTGGCCA 58.885 52.632 10.83 0.00 40.24 5.36
930 948 0.249031 GTGGCGCATCTATTTTGGCC 60.249 55.000 10.83 0.00 40.88 5.36
931 949 0.740737 AGTGGCGCATCTATTTTGGC 59.259 50.000 10.83 0.00 0.00 4.52
932 950 3.376859 TGTTAGTGGCGCATCTATTTTGG 59.623 43.478 10.83 0.00 0.00 3.28
933 951 4.496341 CCTGTTAGTGGCGCATCTATTTTG 60.496 45.833 10.83 2.67 0.00 2.44
934 952 3.627577 CCTGTTAGTGGCGCATCTATTTT 59.372 43.478 10.83 0.00 0.00 1.82
935 953 3.206150 CCTGTTAGTGGCGCATCTATTT 58.794 45.455 10.83 0.00 0.00 1.40
936 954 2.838736 CCTGTTAGTGGCGCATCTATT 58.161 47.619 10.83 0.00 0.00 1.73
937 955 1.541233 GCCTGTTAGTGGCGCATCTAT 60.541 52.381 10.83 0.00 41.03 1.98
938 956 0.179084 GCCTGTTAGTGGCGCATCTA 60.179 55.000 10.83 8.28 41.03 1.98
939 957 1.450312 GCCTGTTAGTGGCGCATCT 60.450 57.895 10.83 9.40 41.03 2.90
940 958 3.102097 GCCTGTTAGTGGCGCATC 58.898 61.111 10.83 0.41 41.03 3.91
946 964 2.586648 AGGAAAAGGCCTGTTAGTGG 57.413 50.000 8.60 0.00 36.76 4.00
947 965 4.287766 ACTAGGAAAAGGCCTGTTAGTG 57.712 45.455 8.60 2.12 39.08 2.74
948 966 5.046520 CACTACTAGGAAAAGGCCTGTTAGT 60.047 44.000 8.60 11.39 39.08 2.24
949 967 5.420409 CACTACTAGGAAAAGGCCTGTTAG 58.580 45.833 8.60 5.19 39.08 2.34
950 968 4.323257 GCACTACTAGGAAAAGGCCTGTTA 60.323 45.833 8.60 0.00 39.08 2.41
951 969 3.559384 GCACTACTAGGAAAAGGCCTGTT 60.559 47.826 8.30 8.30 39.08 3.16
952 970 2.027100 GCACTACTAGGAAAAGGCCTGT 60.027 50.000 5.69 0.00 39.08 4.00
953 971 2.027192 TGCACTACTAGGAAAAGGCCTG 60.027 50.000 5.69 0.00 39.08 4.85
954 972 2.266279 TGCACTACTAGGAAAAGGCCT 58.734 47.619 0.00 0.00 42.15 5.19
955 973 2.781681 TGCACTACTAGGAAAAGGCC 57.218 50.000 0.00 0.00 0.00 5.19
956 974 4.214332 GCATATGCACTACTAGGAAAAGGC 59.786 45.833 22.84 0.00 41.59 4.35
957 975 4.449068 CGCATATGCACTACTAGGAAAAGG 59.551 45.833 26.52 1.35 42.21 3.11
958 976 4.084328 GCGCATATGCACTACTAGGAAAAG 60.084 45.833 26.52 6.78 42.21 2.27
959 977 3.807622 GCGCATATGCACTACTAGGAAAA 59.192 43.478 26.52 0.00 42.21 2.29
960 978 3.181470 TGCGCATATGCACTACTAGGAAA 60.181 43.478 26.52 0.00 40.62 3.13
961 979 2.364002 TGCGCATATGCACTACTAGGAA 59.636 45.455 26.52 0.00 40.62 3.36
962 980 1.960689 TGCGCATATGCACTACTAGGA 59.039 47.619 26.52 7.50 40.62 2.94
963 981 2.438868 TGCGCATATGCACTACTAGG 57.561 50.000 26.52 9.29 40.62 3.02
980 998 1.202177 CCACTCATTAACACGCCATGC 60.202 52.381 0.00 0.00 0.00 4.06
981 999 2.083774 ACCACTCATTAACACGCCATG 58.916 47.619 0.00 0.00 0.00 3.66
982 1000 2.489938 ACCACTCATTAACACGCCAT 57.510 45.000 0.00 0.00 0.00 4.40
1014 1032 5.692928 TGAGAGTGGGGTAACTAGAGATAC 58.307 45.833 0.00 0.00 0.00 2.24
1036 1055 2.749621 GCAGTGGTGGAGTTAGGATTTG 59.250 50.000 0.00 0.00 0.00 2.32
1064 1083 2.507944 GCATGACGAGCCCAGGAT 59.492 61.111 0.00 0.00 0.00 3.24
1086 1105 1.067416 GATGACAGATACGCCGGCA 59.933 57.895 28.98 8.41 0.00 5.69
1187 1206 3.555586 GGGTGTTTTCTCCTTGCTACGTA 60.556 47.826 0.00 0.00 34.27 3.57
1191 1210 3.219281 GTTGGGTGTTTTCTCCTTGCTA 58.781 45.455 0.00 0.00 34.27 3.49
1203 1222 1.228154 GCTCTTCCCGTTGGGTGTT 60.228 57.895 1.04 0.00 44.74 3.32
1391 1410 2.343758 GTGCCGAGTCCTGCTTGA 59.656 61.111 1.49 0.00 0.00 3.02
1399 1418 1.291877 AAGTGAATGCGTGCCGAGTC 61.292 55.000 0.00 0.00 0.00 3.36
1401 1420 1.075542 TTAAGTGAATGCGTGCCGAG 58.924 50.000 0.00 0.00 0.00 4.63
1415 1434 3.432378 ACAGAGATGACCTCGGTTAAGT 58.568 45.455 0.00 0.00 45.87 2.24
1425 1444 2.611518 CCAGTCGAAACAGAGATGACC 58.388 52.381 0.00 0.00 0.00 4.02
1428 1447 1.728971 GTGCCAGTCGAAACAGAGATG 59.271 52.381 0.00 0.00 0.00 2.90
1429 1448 1.338200 GGTGCCAGTCGAAACAGAGAT 60.338 52.381 0.00 0.00 0.00 2.75
1430 1449 0.033504 GGTGCCAGTCGAAACAGAGA 59.966 55.000 0.00 0.00 0.00 3.10
1435 1454 1.300697 ACGAGGTGCCAGTCGAAAC 60.301 57.895 3.54 0.00 39.53 2.78
1480 1499 1.878656 CTCGACGCCTCAAAGTCCCT 61.879 60.000 0.00 0.00 34.10 4.20
1551 1570 2.817834 GCAATGCTACCGACGGCA 60.818 61.111 15.39 6.78 42.80 5.69
1617 1636 5.310409 ACTTGGTTTGAAGAAGATCTCCA 57.690 39.130 0.00 0.00 0.00 3.86
1929 1954 1.202440 AGCCACGTTACTTGTTCGTCA 60.202 47.619 0.00 0.00 35.62 4.35
2108 2133 2.665185 ACAGGAGTCGCGCAAACC 60.665 61.111 8.75 4.92 0.00 3.27
2154 2179 5.470462 GCTATATGCTTCCAGCCTTTGGTT 61.470 45.833 0.00 0.00 41.51 3.67
2322 2355 8.515414 GCACTTAAAATTGAGTCTAAAGACCAT 58.485 33.333 6.50 0.00 45.85 3.55
2323 2356 7.500892 TGCACTTAAAATTGAGTCTAAAGACCA 59.499 33.333 6.50 2.44 45.85 4.02
2324 2357 7.871853 TGCACTTAAAATTGAGTCTAAAGACC 58.128 34.615 6.50 0.00 45.85 3.85
2325 2358 9.334693 CATGCACTTAAAATTGAGTCTAAAGAC 57.665 33.333 1.72 1.72 45.08 3.01
2346 2379 1.687563 CAGATCAATGGAGCCATGCA 58.312 50.000 2.18 0.00 36.68 3.96
2575 2728 9.869757 CTCCATACAATACAATACATATTCCGA 57.130 33.333 0.00 0.00 0.00 4.55
2576 2729 9.869757 TCTCCATACAATACAATACATATTCCG 57.130 33.333 0.00 0.00 0.00 4.30
2592 2745 3.689347 AGTTGCTGCAATCTCCATACAA 58.311 40.909 19.11 0.00 0.00 2.41
2614 2767 7.846644 AATGTTTCAAAGCATTGTCAGAAAA 57.153 28.000 1.04 0.00 38.23 2.29
2620 2773 8.296799 TGTTCATAATGTTTCAAAGCATTGTC 57.703 30.769 13.14 0.00 39.63 3.18
2630 2785 8.849168 AGTTGACATCTTGTTCATAATGTTTCA 58.151 29.630 0.00 0.00 32.70 2.69
2640 2795 9.778741 ATAGTTTCTTAGTTGACATCTTGTTCA 57.221 29.630 0.00 0.00 0.00 3.18
2665 2821 3.254060 GTCATGTCTGTCAACTGCGTAT 58.746 45.455 0.00 0.00 0.00 3.06
2683 2839 5.072055 CCTATTAATCCACCATGCATGTCA 58.928 41.667 24.58 6.28 0.00 3.58
2690 2846 6.003950 ACCGAAATCCTATTAATCCACCATG 58.996 40.000 0.00 0.00 0.00 3.66
2691 2847 6.200878 ACCGAAATCCTATTAATCCACCAT 57.799 37.500 0.00 0.00 0.00 3.55
2692 2848 5.617252 GACCGAAATCCTATTAATCCACCA 58.383 41.667 0.00 0.00 0.00 4.17
2693 2849 4.689345 CGACCGAAATCCTATTAATCCACC 59.311 45.833 0.00 0.00 0.00 4.61
2694 2850 5.535333 TCGACCGAAATCCTATTAATCCAC 58.465 41.667 0.00 0.00 0.00 4.02
2695 2851 5.537295 TCTCGACCGAAATCCTATTAATCCA 59.463 40.000 0.00 0.00 0.00 3.41
2704 2860 1.776662 TGGATCTCGACCGAAATCCT 58.223 50.000 21.08 0.00 38.78 3.24
2722 2878 6.992123 TCCCACAAATACTGCATAGTTAGATG 59.008 38.462 0.00 0.00 38.36 2.90
2732 2888 0.698238 AGCCTCCCACAAATACTGCA 59.302 50.000 0.00 0.00 0.00 4.41
2734 2890 1.066143 ACGAGCCTCCCACAAATACTG 60.066 52.381 0.00 0.00 0.00 2.74
2736 2892 2.822764 CTACGAGCCTCCCACAAATAC 58.177 52.381 0.00 0.00 0.00 1.89
2740 2896 2.978824 GCTACGAGCCTCCCACAA 59.021 61.111 0.00 0.00 34.48 3.33
2786 2942 2.107950 TTGTTGCCTGGTTCTATCCG 57.892 50.000 0.00 0.00 0.00 4.18
2808 2964 1.487976 GAGATGGTGGGATGAGAAGCA 59.512 52.381 0.00 0.00 0.00 3.91
2831 2987 3.535561 TCTTTGAAAGATCGAGATGGGC 58.464 45.455 3.02 0.00 31.20 5.36
2846 3002 3.990469 GTCTTGACAGCTCGAATCTTTGA 59.010 43.478 0.00 0.00 0.00 2.69
2864 3020 5.048507 GTCTTTTTGGAGTACTCGTGTCTT 58.951 41.667 16.56 0.00 0.00 3.01
2867 3023 3.493873 GGGTCTTTTTGGAGTACTCGTGT 60.494 47.826 16.56 0.00 0.00 4.49
2882 3038 0.905337 CTGGAGTCGGGAGGGTCTTT 60.905 60.000 0.00 0.00 0.00 2.52
2942 3098 1.039856 GCAACCTGGTGAATGTGGTT 58.960 50.000 0.00 0.00 42.78 3.67
3023 3179 2.915659 TCGTCGCACCACCTCCTT 60.916 61.111 0.00 0.00 0.00 3.36
3155 3314 1.676967 CAAGCAACTCCCTCCAGGC 60.677 63.158 0.00 0.00 34.51 4.85
3238 3397 4.400884 TGTGTGTTTGTTTCAGCCATACTT 59.599 37.500 0.00 0.00 0.00 2.24
3292 3451 2.027192 TCCATACTCTGGTGTTTGCCTC 60.027 50.000 0.00 0.00 46.08 4.70


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

AutoCloner maintained by Alex Coulton.