Multiple sequence alignment - TraesCS7D01G161700

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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 TraesCS7D01G161700 chr7D 100.000 2879 0 0 1 2879 111747233 111744355 0.000000e+00 5317.0
1 TraesCS7D01G161700 chr7D 88.485 964 83 16 1921 2879 34478897 34479837 0.000000e+00 1140.0
2 TraesCS7D01G161700 chr7D 84.048 583 69 11 1922 2486 125783505 125782929 9.080000e-150 540.0
3 TraesCS7D01G161700 chr7D 78.821 831 137 25 1091 1910 111728688 111727886 9.140000e-145 523.0
4 TraesCS7D01G161700 chr1B 89.804 971 83 9 1919 2879 162355681 162356645 0.000000e+00 1230.0
5 TraesCS7D01G161700 chr1B 90.674 772 62 7 2112 2879 677023418 677022653 0.000000e+00 1018.0
6 TraesCS7D01G161700 chr1B 88.068 528 44 8 195 712 468219356 468218838 2.450000e-170 608.0
7 TraesCS7D01G161700 chr7A 94.486 798 26 7 1 784 116774900 116774107 0.000000e+00 1214.0
8 TraesCS7D01G161700 chr7A 85.464 399 30 13 1021 1408 116759046 116758665 9.670000e-105 390.0
9 TraesCS7D01G161700 chr7A 80.040 506 71 18 1423 1910 116746904 116746411 5.900000e-92 348.0
10 TraesCS7D01G161700 chr1D 89.106 973 89 11 1921 2879 439140939 439139970 0.000000e+00 1194.0
11 TraesCS7D01G161700 chr4D 88.513 975 92 10 1922 2879 50772601 50773572 0.000000e+00 1162.0
12 TraesCS7D01G161700 chr3D 88.434 977 91 15 1919 2879 7961772 7960802 0.000000e+00 1158.0
13 TraesCS7D01G161700 chr3D 88.095 966 82 18 1923 2879 21607132 21606191 0.000000e+00 1116.0
14 TraesCS7D01G161700 chr3D 92.135 712 51 3 2173 2879 173482227 173481516 0.000000e+00 1000.0
15 TraesCS7D01G161700 chr3D 92.176 703 48 4 2178 2879 32416576 32415880 0.000000e+00 987.0
16 TraesCS7D01G161700 chr3D 85.669 314 36 7 1923 2230 173482539 173482229 3.580000e-84 322.0
17 TraesCS7D01G161700 chrUn 87.851 996 82 19 1920 2879 153388029 153387037 0.000000e+00 1133.0
18 TraesCS7D01G161700 chr6A 87.307 969 102 15 1923 2879 600963662 600962703 0.000000e+00 1088.0
19 TraesCS7D01G161700 chr7B 90.261 842 51 11 2 832 71276403 71275582 0.000000e+00 1072.0
20 TraesCS7D01G161700 chr7B 90.141 639 58 4 1020 1657 71256261 71255627 0.000000e+00 826.0
21 TraesCS7D01G161700 chr7B 87.534 730 61 15 1 726 428782948 428783651 0.000000e+00 817.0
22 TraesCS7D01G161700 chr7B 78.614 837 135 26 1092 1910 71240476 71239666 5.500000e-142 514.0
23 TraesCS7D01G161700 chr7B 94.545 55 3 0 826 880 71275563 71275509 5.110000e-13 86.1
24 TraesCS7D01G161700 chr2B 85.685 971 121 9 1921 2879 523239862 523238898 0.000000e+00 1007.0
25 TraesCS7D01G161700 chr3A 85.880 949 99 18 1943 2879 621592970 621593895 0.000000e+00 977.0
26 TraesCS7D01G161700 chr3A 82.353 85 10 4 1552 1632 647802861 647802778 5.150000e-08 69.4
27 TraesCS7D01G161700 chr2D 90.634 726 46 12 1 726 245573791 245573088 0.000000e+00 944.0
28 TraesCS7D01G161700 chr4A 86.098 856 99 13 1920 2758 624843982 624844834 0.000000e+00 904.0
29 TraesCS7D01G161700 chr4A 86.088 726 76 11 1 726 7883595 7884295 0.000000e+00 758.0
30 TraesCS7D01G161700 chr4A 84.414 725 81 14 2 726 535940772 535941464 0.000000e+00 684.0
31 TraesCS7D01G161700 chr2A 86.992 738 62 20 1 726 424539217 424538502 0.000000e+00 800.0
32 TraesCS7D01G161700 chr2A 86.621 725 71 12 2 726 302435664 302436362 0.000000e+00 778.0
33 TraesCS7D01G161700 chr5A 84.986 726 84 11 2 726 222770820 222770119 0.000000e+00 713.0
34 TraesCS7D01G161700 chr6B 86.551 632 47 16 100 726 637178829 637179427 0.000000e+00 662.0
35 TraesCS7D01G161700 chr5B 88.783 419 33 6 110 527 291615307 291614902 4.280000e-138 501.0
36 TraesCS7D01G161700 chr5B 88.785 214 13 3 517 726 291606131 291605925 4.760000e-63 252.0


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 TraesCS7D01G161700 chr7D 111744355 111747233 2878 True 5317.00 5317 100.000 1 2879 1 chr7D.!!$R2 2878
1 TraesCS7D01G161700 chr7D 34478897 34479837 940 False 1140.00 1140 88.485 1921 2879 1 chr7D.!!$F1 958
2 TraesCS7D01G161700 chr7D 125782929 125783505 576 True 540.00 540 84.048 1922 2486 1 chr7D.!!$R3 564
3 TraesCS7D01G161700 chr7D 111727886 111728688 802 True 523.00 523 78.821 1091 1910 1 chr7D.!!$R1 819
4 TraesCS7D01G161700 chr1B 162355681 162356645 964 False 1230.00 1230 89.804 1919 2879 1 chr1B.!!$F1 960
5 TraesCS7D01G161700 chr1B 677022653 677023418 765 True 1018.00 1018 90.674 2112 2879 1 chr1B.!!$R2 767
6 TraesCS7D01G161700 chr1B 468218838 468219356 518 True 608.00 608 88.068 195 712 1 chr1B.!!$R1 517
7 TraesCS7D01G161700 chr7A 116774107 116774900 793 True 1214.00 1214 94.486 1 784 1 chr7A.!!$R3 783
8 TraesCS7D01G161700 chr1D 439139970 439140939 969 True 1194.00 1194 89.106 1921 2879 1 chr1D.!!$R1 958
9 TraesCS7D01G161700 chr4D 50772601 50773572 971 False 1162.00 1162 88.513 1922 2879 1 chr4D.!!$F1 957
10 TraesCS7D01G161700 chr3D 7960802 7961772 970 True 1158.00 1158 88.434 1919 2879 1 chr3D.!!$R1 960
11 TraesCS7D01G161700 chr3D 21606191 21607132 941 True 1116.00 1116 88.095 1923 2879 1 chr3D.!!$R2 956
12 TraesCS7D01G161700 chr3D 32415880 32416576 696 True 987.00 987 92.176 2178 2879 1 chr3D.!!$R3 701
13 TraesCS7D01G161700 chr3D 173481516 173482539 1023 True 661.00 1000 88.902 1923 2879 2 chr3D.!!$R4 956
14 TraesCS7D01G161700 chrUn 153387037 153388029 992 True 1133.00 1133 87.851 1920 2879 1 chrUn.!!$R1 959
15 TraesCS7D01G161700 chr6A 600962703 600963662 959 True 1088.00 1088 87.307 1923 2879 1 chr6A.!!$R1 956
16 TraesCS7D01G161700 chr7B 71255627 71256261 634 True 826.00 826 90.141 1020 1657 1 chr7B.!!$R2 637
17 TraesCS7D01G161700 chr7B 428782948 428783651 703 False 817.00 817 87.534 1 726 1 chr7B.!!$F1 725
18 TraesCS7D01G161700 chr7B 71275509 71276403 894 True 579.05 1072 92.403 2 880 2 chr7B.!!$R3 878
19 TraesCS7D01G161700 chr7B 71239666 71240476 810 True 514.00 514 78.614 1092 1910 1 chr7B.!!$R1 818
20 TraesCS7D01G161700 chr2B 523238898 523239862 964 True 1007.00 1007 85.685 1921 2879 1 chr2B.!!$R1 958
21 TraesCS7D01G161700 chr3A 621592970 621593895 925 False 977.00 977 85.880 1943 2879 1 chr3A.!!$F1 936
22 TraesCS7D01G161700 chr2D 245573088 245573791 703 True 944.00 944 90.634 1 726 1 chr2D.!!$R1 725
23 TraesCS7D01G161700 chr4A 624843982 624844834 852 False 904.00 904 86.098 1920 2758 1 chr4A.!!$F3 838
24 TraesCS7D01G161700 chr4A 7883595 7884295 700 False 758.00 758 86.088 1 726 1 chr4A.!!$F1 725
25 TraesCS7D01G161700 chr4A 535940772 535941464 692 False 684.00 684 84.414 2 726 1 chr4A.!!$F2 724
26 TraesCS7D01G161700 chr2A 424538502 424539217 715 True 800.00 800 86.992 1 726 1 chr2A.!!$R1 725
27 TraesCS7D01G161700 chr2A 302435664 302436362 698 False 778.00 778 86.621 2 726 1 chr2A.!!$F1 724
28 TraesCS7D01G161700 chr5A 222770119 222770820 701 True 713.00 713 84.986 2 726 1 chr5A.!!$R1 724
29 TraesCS7D01G161700 chr6B 637178829 637179427 598 False 662.00 662 86.551 100 726 1 chr6B.!!$F1 626

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
940 1033 0.107017 AATCAATCTCCCGCCACCAG 60.107 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2022 0.035343 GAGTTGGCCTAAGGGTGGTC 60.035 60.0 3.32 0.0 34.45 4.02 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
258 274 4.719369 GGAGAGCGGTGCGTCGTT 62.719 66.667 0.00 0.00 0.00 3.85
636 687 3.506067 ACCGTCCCTTGATTGATTTGTTC 59.494 43.478 0.00 0.00 0.00 3.18
684 745 5.466058 TCACCATGATTTGTTGATTTGTTGC 59.534 36.000 0.00 0.00 0.00 4.17
690 751 9.320406 CATGATTTGTTGATTTGTTGCATTTAC 57.680 29.630 0.00 0.00 0.00 2.01
752 819 1.341852 TCCACGTCAACCGATTCTGAA 59.658 47.619 0.00 0.00 40.70 3.02
758 825 3.301835 CGTCAACCGATTCTGAAATAGCG 60.302 47.826 0.00 0.00 39.56 4.26
789 856 7.447545 ACATTCACATTACTCGACCTAGCTATA 59.552 37.037 0.00 0.00 0.00 1.31
790 857 7.997773 TTCACATTACTCGACCTAGCTATAT 57.002 36.000 0.00 0.00 0.00 0.86
791 858 9.682465 ATTCACATTACTCGACCTAGCTATATA 57.318 33.333 0.00 0.00 0.00 0.86
792 859 9.682465 TTCACATTACTCGACCTAGCTATATAT 57.318 33.333 0.00 0.00 0.00 0.86
795 862 6.939132 TTACTCGACCTAGCTATATATGGC 57.061 41.667 12.86 12.86 34.12 4.40
799 866 3.243569 CGACCTAGCTATATATGGCAGCC 60.244 52.174 21.51 3.66 36.66 4.85
808 875 6.157645 AGCTATATATGGCAGCCTGAATTAGT 59.842 38.462 21.51 0.00 36.66 2.24
809 876 7.345653 AGCTATATATGGCAGCCTGAATTAGTA 59.654 37.037 21.51 0.00 36.66 1.82
810 877 7.655328 GCTATATATGGCAGCCTGAATTAGTAG 59.345 40.741 14.15 6.20 34.10 2.57
811 878 3.498774 ATGGCAGCCTGAATTAGTAGG 57.501 47.619 14.15 0.00 37.14 3.18
863 956 0.384309 TCGGATCGGAACTTCGGATG 59.616 55.000 14.72 4.17 36.70 3.51
867 960 2.297597 GGATCGGAACTTCGGATGAGAT 59.702 50.000 14.72 0.00 36.70 2.75
869 962 1.202417 TCGGAACTTCGGATGAGATGC 60.202 52.381 0.00 0.00 0.00 3.91
880 973 3.380142 GGATGAGATGCTCTTCTTCGTC 58.620 50.000 9.32 0.00 35.73 4.20
881 974 2.551355 TGAGATGCTCTTCTTCGTCG 57.449 50.000 0.00 0.00 0.00 5.12
882 975 1.813178 TGAGATGCTCTTCTTCGTCGT 59.187 47.619 0.00 0.00 0.00 4.34
883 976 2.159503 TGAGATGCTCTTCTTCGTCGTC 60.160 50.000 0.00 0.00 0.00 4.20
884 977 1.184349 GATGCTCTTCTTCGTCGTCG 58.816 55.000 0.00 0.00 38.55 5.12
885 978 0.803117 ATGCTCTTCTTCGTCGTCGA 59.197 50.000 0.00 0.00 44.66 4.20
886 979 0.803117 TGCTCTTCTTCGTCGTCGAT 59.197 50.000 5.44 0.00 45.65 3.59
887 980 1.199327 TGCTCTTCTTCGTCGTCGATT 59.801 47.619 5.44 0.00 45.65 3.34
888 981 2.417586 TGCTCTTCTTCGTCGTCGATTA 59.582 45.455 5.44 0.00 45.65 1.75
889 982 2.777305 GCTCTTCTTCGTCGTCGATTAC 59.223 50.000 5.44 0.00 45.65 1.89
901 994 2.933495 TCGATTACGACTTGGACTGG 57.067 50.000 0.00 0.00 43.81 4.00
902 995 2.439409 TCGATTACGACTTGGACTGGA 58.561 47.619 0.00 0.00 43.81 3.86
903 996 3.021695 TCGATTACGACTTGGACTGGAT 58.978 45.455 0.00 0.00 43.81 3.41
904 997 3.116300 CGATTACGACTTGGACTGGATG 58.884 50.000 0.00 0.00 42.66 3.51
905 998 3.428999 CGATTACGACTTGGACTGGATGT 60.429 47.826 0.00 0.00 42.66 3.06
906 999 4.504858 GATTACGACTTGGACTGGATGTT 58.495 43.478 0.00 0.00 0.00 2.71
907 1000 2.457366 ACGACTTGGACTGGATGTTC 57.543 50.000 0.00 0.00 0.00 3.18
908 1001 1.002087 ACGACTTGGACTGGATGTTCC 59.998 52.381 0.00 0.00 36.96 3.62
909 1002 1.676014 CGACTTGGACTGGATGTTCCC 60.676 57.143 0.00 0.00 35.03 3.97
910 1003 0.698818 ACTTGGACTGGATGTTCCCC 59.301 55.000 0.00 0.00 35.03 4.81
911 1004 0.995024 CTTGGACTGGATGTTCCCCT 59.005 55.000 0.00 0.00 35.03 4.79
912 1005 0.991920 TTGGACTGGATGTTCCCCTC 59.008 55.000 0.00 0.00 35.03 4.30
913 1006 0.119155 TGGACTGGATGTTCCCCTCT 59.881 55.000 0.00 0.00 35.03 3.69
914 1007 1.364678 TGGACTGGATGTTCCCCTCTA 59.635 52.381 0.00 0.00 35.03 2.43
915 1008 1.763545 GGACTGGATGTTCCCCTCTAC 59.236 57.143 0.00 0.00 35.03 2.59
916 1009 2.627217 GGACTGGATGTTCCCCTCTACT 60.627 54.545 0.00 0.00 35.03 2.57
917 1010 2.432510 GACTGGATGTTCCCCTCTACTG 59.567 54.545 0.00 0.00 35.03 2.74
918 1011 2.044492 ACTGGATGTTCCCCTCTACTGA 59.956 50.000 0.00 0.00 35.03 3.41
919 1012 3.310954 ACTGGATGTTCCCCTCTACTGAT 60.311 47.826 0.00 0.00 35.03 2.90
920 1013 4.078571 ACTGGATGTTCCCCTCTACTGATA 60.079 45.833 0.00 0.00 35.03 2.15
921 1014 4.890988 TGGATGTTCCCCTCTACTGATAA 58.109 43.478 0.00 0.00 35.03 1.75
922 1015 5.285401 TGGATGTTCCCCTCTACTGATAAA 58.715 41.667 0.00 0.00 35.03 1.40
923 1016 5.911178 TGGATGTTCCCCTCTACTGATAAAT 59.089 40.000 0.00 0.00 35.03 1.40
924 1017 6.043243 TGGATGTTCCCCTCTACTGATAAATC 59.957 42.308 0.00 0.00 35.03 2.17
925 1018 6.043243 GGATGTTCCCCTCTACTGATAAATCA 59.957 42.308 0.00 0.00 35.16 2.57
926 1019 6.884472 TGTTCCCCTCTACTGATAAATCAA 57.116 37.500 0.00 0.00 36.18 2.57
927 1020 7.451731 TGTTCCCCTCTACTGATAAATCAAT 57.548 36.000 0.00 0.00 36.18 2.57
928 1021 7.509546 TGTTCCCCTCTACTGATAAATCAATC 58.490 38.462 0.00 0.00 36.18 2.67
929 1022 7.348274 TGTTCCCCTCTACTGATAAATCAATCT 59.652 37.037 0.00 0.00 36.18 2.40
930 1023 7.546250 TCCCCTCTACTGATAAATCAATCTC 57.454 40.000 0.00 0.00 36.18 2.75
931 1024 6.498651 TCCCCTCTACTGATAAATCAATCTCC 59.501 42.308 0.00 0.00 36.18 3.71
932 1025 6.296145 CCCCTCTACTGATAAATCAATCTCCC 60.296 46.154 0.00 0.00 36.18 4.30
933 1026 6.393990 CCTCTACTGATAAATCAATCTCCCG 58.606 44.000 0.00 0.00 36.18 5.14
934 1027 5.784177 TCTACTGATAAATCAATCTCCCGC 58.216 41.667 0.00 0.00 36.18 6.13
935 1028 3.744660 ACTGATAAATCAATCTCCCGCC 58.255 45.455 0.00 0.00 36.18 6.13
936 1029 3.136443 ACTGATAAATCAATCTCCCGCCA 59.864 43.478 0.00 0.00 36.18 5.69
937 1030 3.476552 TGATAAATCAATCTCCCGCCAC 58.523 45.455 0.00 0.00 33.08 5.01
938 1031 2.341846 TAAATCAATCTCCCGCCACC 57.658 50.000 0.00 0.00 0.00 4.61
939 1032 0.331278 AAATCAATCTCCCGCCACCA 59.669 50.000 0.00 0.00 0.00 4.17
940 1033 0.107017 AATCAATCTCCCGCCACCAG 60.107 55.000 0.00 0.00 0.00 4.00
941 1034 0.982852 ATCAATCTCCCGCCACCAGA 60.983 55.000 0.00 0.00 0.00 3.86
942 1035 1.450312 CAATCTCCCGCCACCAGAC 60.450 63.158 0.00 0.00 0.00 3.51
943 1036 2.670148 AATCTCCCGCCACCAGACC 61.670 63.158 0.00 0.00 0.00 3.85
944 1037 3.924013 ATCTCCCGCCACCAGACCA 62.924 63.158 0.00 0.00 0.00 4.02
945 1038 4.087892 CTCCCGCCACCAGACCAG 62.088 72.222 0.00 0.00 0.00 4.00
950 1043 4.314440 GCCACCAGACCAGCGTCA 62.314 66.667 0.00 0.00 41.87 4.35
951 1044 2.357517 CCACCAGACCAGCGTCAC 60.358 66.667 0.00 0.00 41.87 3.67
952 1045 2.737180 CACCAGACCAGCGTCACT 59.263 61.111 0.00 0.00 41.87 3.41
953 1046 1.069765 CACCAGACCAGCGTCACTT 59.930 57.895 0.00 0.00 41.87 3.16
954 1047 0.946221 CACCAGACCAGCGTCACTTC 60.946 60.000 0.00 0.00 41.87 3.01
955 1048 1.367471 CCAGACCAGCGTCACTTCA 59.633 57.895 0.00 0.00 41.87 3.02
956 1049 0.668706 CCAGACCAGCGTCACTTCAG 60.669 60.000 0.00 0.00 41.87 3.02
957 1050 0.315251 CAGACCAGCGTCACTTCAGA 59.685 55.000 0.00 0.00 41.87 3.27
958 1051 1.040646 AGACCAGCGTCACTTCAGAA 58.959 50.000 0.00 0.00 41.87 3.02
959 1052 1.620819 AGACCAGCGTCACTTCAGAAT 59.379 47.619 0.00 0.00 41.87 2.40
960 1053 1.996191 GACCAGCGTCACTTCAGAATC 59.004 52.381 0.00 0.00 38.99 2.52
961 1054 1.338200 ACCAGCGTCACTTCAGAATCC 60.338 52.381 0.00 0.00 0.00 3.01
962 1055 1.338105 CCAGCGTCACTTCAGAATCCA 60.338 52.381 0.00 0.00 0.00 3.41
963 1056 2.416747 CAGCGTCACTTCAGAATCCAA 58.583 47.619 0.00 0.00 0.00 3.53
964 1057 3.005554 CAGCGTCACTTCAGAATCCAAT 58.994 45.455 0.00 0.00 0.00 3.16
965 1058 3.063180 CAGCGTCACTTCAGAATCCAATC 59.937 47.826 0.00 0.00 0.00 2.67
966 1059 3.055530 AGCGTCACTTCAGAATCCAATCT 60.056 43.478 0.00 0.00 0.00 2.40
967 1060 3.686726 GCGTCACTTCAGAATCCAATCTT 59.313 43.478 0.00 0.00 0.00 2.40
968 1061 4.201763 GCGTCACTTCAGAATCCAATCTTC 60.202 45.833 0.00 0.00 0.00 2.87
969 1062 4.331168 CGTCACTTCAGAATCCAATCTTCC 59.669 45.833 0.00 0.00 0.00 3.46
970 1063 4.331168 GTCACTTCAGAATCCAATCTTCCG 59.669 45.833 0.00 0.00 0.00 4.30
971 1064 4.222810 TCACTTCAGAATCCAATCTTCCGA 59.777 41.667 0.00 0.00 0.00 4.55
972 1065 4.937620 CACTTCAGAATCCAATCTTCCGAA 59.062 41.667 0.00 0.00 0.00 4.30
973 1066 5.587844 CACTTCAGAATCCAATCTTCCGAAT 59.412 40.000 0.00 0.00 0.00 3.34
974 1067 6.094603 CACTTCAGAATCCAATCTTCCGAATT 59.905 38.462 0.00 0.00 0.00 2.17
975 1068 6.317391 ACTTCAGAATCCAATCTTCCGAATTC 59.683 38.462 0.00 0.00 0.00 2.17
976 1069 5.126067 TCAGAATCCAATCTTCCGAATTCC 58.874 41.667 0.00 0.00 0.00 3.01
977 1070 4.024556 CAGAATCCAATCTTCCGAATTCCG 60.025 45.833 0.00 0.00 38.18 4.30
978 1071 3.838244 ATCCAATCTTCCGAATTCCGA 57.162 42.857 0.00 0.00 41.76 4.55
979 1072 3.838244 TCCAATCTTCCGAATTCCGAT 57.162 42.857 0.00 0.00 41.76 4.18
980 1073 4.150897 TCCAATCTTCCGAATTCCGATT 57.849 40.909 0.00 1.17 41.76 3.34
981 1074 5.284861 TCCAATCTTCCGAATTCCGATTA 57.715 39.130 0.00 0.00 41.76 1.75
982 1075 5.297547 TCCAATCTTCCGAATTCCGATTAG 58.702 41.667 0.00 0.00 41.76 1.73
983 1076 4.452455 CCAATCTTCCGAATTCCGATTAGG 59.548 45.833 0.00 0.00 41.76 2.69
984 1077 3.107642 TCTTCCGAATTCCGATTAGGC 57.892 47.619 0.00 0.00 41.76 3.93
985 1078 2.698797 TCTTCCGAATTCCGATTAGGCT 59.301 45.455 0.00 0.00 41.76 4.58
986 1079 2.526304 TCCGAATTCCGATTAGGCTG 57.474 50.000 0.00 0.00 41.76 4.85
987 1080 2.036387 TCCGAATTCCGATTAGGCTGA 58.964 47.619 0.00 0.00 41.76 4.26
988 1081 2.632996 TCCGAATTCCGATTAGGCTGAT 59.367 45.455 0.00 0.00 41.76 2.90
989 1082 2.996621 CCGAATTCCGATTAGGCTGATC 59.003 50.000 9.11 9.11 41.76 2.92
990 1083 3.554960 CCGAATTCCGATTAGGCTGATCA 60.555 47.826 18.07 0.00 41.76 2.92
991 1084 3.677121 CGAATTCCGATTAGGCTGATCAG 59.323 47.826 18.84 18.84 41.76 2.90
992 1085 3.692257 ATTCCGATTAGGCTGATCAGG 57.308 47.619 23.89 17.88 40.77 3.86
993 1086 2.381752 TCCGATTAGGCTGATCAGGA 57.618 50.000 23.89 20.54 40.77 3.86
994 1087 2.894731 TCCGATTAGGCTGATCAGGAT 58.105 47.619 23.89 1.19 40.77 3.24
995 1088 2.828520 TCCGATTAGGCTGATCAGGATC 59.171 50.000 23.89 7.53 40.77 3.36
996 1089 2.564504 CCGATTAGGCTGATCAGGATCA 59.435 50.000 23.89 11.22 44.83 2.92
1004 1097 0.683412 TGATCAGGATCAGCGATGGG 59.317 55.000 7.86 0.00 42.42 4.00
1005 1098 0.673022 GATCAGGATCAGCGATGGGC 60.673 60.000 0.00 0.00 44.05 5.36
1037 1130 3.075641 GGGGTCCTCCTCCACGTC 61.076 72.222 0.00 0.00 35.33 4.34
1041 1134 1.674980 GTCCTCCTCCACGTCGTCT 60.675 63.158 0.00 0.00 0.00 4.18
1071 1164 4.436998 CGGGAGTGGGACTGCGAC 62.437 72.222 0.00 0.00 37.44 5.19
1151 1245 4.554363 CTCGACGGGCGGCTACAG 62.554 72.222 9.56 0.63 41.33 2.74
1155 1249 4.530857 ACGGGCGGCTACAGCATC 62.531 66.667 9.56 0.00 44.36 3.91
1242 1337 1.598962 CGCTGCCATCCGGATGAAT 60.599 57.895 40.01 7.89 41.20 2.57
1366 1465 2.400399 CAACCATCGTCTACAACACGT 58.600 47.619 0.00 0.00 38.45 4.49
1420 1519 4.052518 CTGGGGTCCCTGCCTTGG 62.053 72.222 8.15 0.00 36.94 3.61
1493 1592 2.743928 CTTGCAGGCCCTGTCGTC 60.744 66.667 13.35 0.00 33.43 4.20
1494 1593 4.680237 TTGCAGGCCCTGTCGTCG 62.680 66.667 13.35 0.00 33.43 5.12
1517 1621 1.546476 GGCTCCCATCGACGATAGATT 59.454 52.381 10.57 0.00 41.38 2.40
1520 1624 3.671971 GCTCCCATCGACGATAGATTGAG 60.672 52.174 10.57 12.08 41.38 3.02
1560 1670 4.953868 TGGAACACCGTGCCGTCG 62.954 66.667 0.00 0.00 32.81 5.12
1667 1777 0.242825 CATTGCTTGGACACCAGCAG 59.757 55.000 11.99 1.65 38.28 4.24
1668 1778 1.530013 ATTGCTTGGACACCAGCAGC 61.530 55.000 7.32 7.32 38.28 5.25
1709 1819 0.895100 GACTGGGTGCTGCCATTCAA 60.895 55.000 0.00 0.00 39.65 2.69
1719 1829 2.285024 GCCATTCAAAGGCCAGGCA 61.285 57.895 15.19 0.00 46.50 4.75
1730 1840 2.526120 GCCAGGCATACTTCGACGC 61.526 63.158 6.55 0.00 0.00 5.19
1735 1845 0.596859 GGCATACTTCGACGCCTACC 60.597 60.000 0.00 0.00 41.50 3.18
1736 1846 0.101759 GCATACTTCGACGCCTACCA 59.898 55.000 0.00 0.00 0.00 3.25
1737 1847 1.864435 GCATACTTCGACGCCTACCAG 60.864 57.143 0.00 0.00 0.00 4.00
1743 1853 2.184579 GACGCCTACCAGCTGGAC 59.815 66.667 39.19 22.07 38.94 4.02
1769 1879 0.830648 GTCGGGATCCATCACAAGGA 59.169 55.000 15.23 0.00 39.97 3.36
1770 1880 1.123077 TCGGGATCCATCACAAGGAG 58.877 55.000 15.23 0.00 38.83 3.69
1776 1886 2.342406 TCCATCACAAGGAGGAAGGA 57.658 50.000 0.00 0.00 0.00 3.36
1777 1887 2.631384 TCCATCACAAGGAGGAAGGAA 58.369 47.619 0.00 0.00 0.00 3.36
1778 1888 2.573462 TCCATCACAAGGAGGAAGGAAG 59.427 50.000 0.00 0.00 0.00 3.46
1779 1889 2.356535 CCATCACAAGGAGGAAGGAAGG 60.357 54.545 0.00 0.00 0.00 3.46
1780 1890 2.415983 TCACAAGGAGGAAGGAAGGA 57.584 50.000 0.00 0.00 0.00 3.36
1781 1891 2.921221 TCACAAGGAGGAAGGAAGGAT 58.079 47.619 0.00 0.00 0.00 3.24
1786 1896 2.668625 AGGAGGAAGGAAGGATACGTC 58.331 52.381 0.00 0.00 45.15 4.34
1798 1908 2.303549 GATACGTCTGCTGCTGCCCT 62.304 60.000 13.47 0.00 38.71 5.19
1869 1979 1.768684 AAGGAGAAGCTGTTCCGCCA 61.769 55.000 10.26 0.00 38.54 5.69
1883 1993 0.321564 CCGCCACAACAATGAGGAGA 60.322 55.000 0.00 0.00 38.95 3.71
1885 1995 1.877680 CGCCACAACAATGAGGAGACA 60.878 52.381 0.00 0.00 38.95 3.41
1889 1999 2.751259 CACAACAATGAGGAGACATGGG 59.249 50.000 0.00 0.00 0.00 4.00
1892 2002 2.269023 ACAATGAGGAGACATGGGTGA 58.731 47.619 0.00 0.00 0.00 4.02
1893 2003 2.026822 ACAATGAGGAGACATGGGTGAC 60.027 50.000 0.00 0.00 0.00 3.67
1912 2022 4.832608 GGCGGCCGGTACCTGAAG 62.833 72.222 29.38 2.33 0.00 3.02
1913 2023 3.766691 GCGGCCGGTACCTGAAGA 61.767 66.667 29.38 0.00 0.00 2.87
1914 2024 2.183555 CGGCCGGTACCTGAAGAC 59.816 66.667 20.10 0.00 0.00 3.01
1915 2025 2.582978 GGCCGGTACCTGAAGACC 59.417 66.667 10.90 0.00 0.00 3.85
1916 2026 2.288025 GGCCGGTACCTGAAGACCA 61.288 63.158 10.90 0.00 35.26 4.02
1917 2027 1.079336 GCCGGTACCTGAAGACCAC 60.079 63.158 10.90 0.00 35.26 4.16
2014 2124 1.078988 GGTCGTGTTCGGGCCATTA 60.079 57.895 4.39 0.00 37.69 1.90
2017 2127 0.108520 TCGTGTTCGGGCCATTACTC 60.109 55.000 4.39 0.00 37.69 2.59
2198 2346 1.318576 ACACAGCCAGCCTACAAAAC 58.681 50.000 0.00 0.00 0.00 2.43
2217 2427 1.073177 CGAATAGTTTTGTCGCCGGT 58.927 50.000 1.90 0.00 0.00 5.28
2227 2437 4.728102 TCGCCGGTAACACAGCCG 62.728 66.667 1.90 0.00 46.80 5.52
2255 2484 5.007034 TCAAAATGAATAGGTTTCTCGCCA 58.993 37.500 0.00 0.00 0.00 5.69
2316 2566 4.373116 GCCACGGCCGAAGAGACA 62.373 66.667 35.90 0.00 34.56 3.41
2393 2643 3.013921 ACCTCGTCTTCTCACTCATCTC 58.986 50.000 0.00 0.00 0.00 2.75
2553 2809 3.492309 CCTCCATGTCGATCTTCCTCTTG 60.492 52.174 0.00 0.00 0.00 3.02
2557 2813 2.688507 TGTCGATCTTCCTCTTGTTGC 58.311 47.619 0.00 0.00 0.00 4.17
2703 2960 2.514592 AAGGCCATGGATGACGCG 60.515 61.111 18.40 3.53 0.00 6.01
2726 2983 0.245539 CGTATGTCGTCCACCTTGGT 59.754 55.000 0.00 0.00 39.03 3.67
2832 3089 6.721571 TGAAGTTCACGGTATTGATCTTTC 57.278 37.500 0.08 0.00 36.23 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 2.281345 GCCCCTCCATCATCTGCG 60.281 66.667 0.00 0.00 0.00 5.18
393 412 2.264794 CCGTCCCAGTAGTGGCAC 59.735 66.667 10.29 10.29 43.44 5.01
594 645 1.210538 TGAGCATTGGCCATCTCTCT 58.789 50.000 22.64 10.98 42.56 3.10
636 687 8.620416 TGATACCTAATCGAATTCAACAAATGG 58.380 33.333 6.22 1.40 37.42 3.16
684 745 8.870160 TTCATTTCTTTGTGTCCTTGTAAATG 57.130 30.769 0.00 0.00 35.45 2.32
690 751 8.971321 CATACTTTTCATTTCTTTGTGTCCTTG 58.029 33.333 0.00 0.00 0.00 3.61
752 819 6.341316 AGTAATGTGAATGTCTGACGCTATT 58.659 36.000 2.98 0.00 0.00 1.73
758 825 4.563184 GGTCGAGTAATGTGAATGTCTGAC 59.437 45.833 0.00 0.00 0.00 3.51
789 856 5.171339 CCTACTAATTCAGGCTGCCATAT 57.829 43.478 22.65 7.89 0.00 1.78
790 857 4.623932 CCTACTAATTCAGGCTGCCATA 57.376 45.455 22.65 5.02 0.00 2.74
791 858 3.498774 CCTACTAATTCAGGCTGCCAT 57.501 47.619 22.65 2.34 0.00 4.40
799 866 6.090088 CGCTAGCTAATTGCCTACTAATTCAG 59.910 42.308 13.93 0.00 44.23 3.02
808 875 1.412710 ACTGCGCTAGCTAATTGCCTA 59.587 47.619 13.93 0.00 45.42 3.93
809 876 0.179000 ACTGCGCTAGCTAATTGCCT 59.821 50.000 13.93 0.00 45.42 4.75
810 877 0.583917 GACTGCGCTAGCTAATTGCC 59.416 55.000 13.93 0.00 45.42 4.52
811 878 1.260033 CAGACTGCGCTAGCTAATTGC 59.740 52.381 13.93 8.89 45.42 3.56
812 879 2.544685 ACAGACTGCGCTAGCTAATTG 58.455 47.619 13.93 6.25 45.42 2.32
863 956 3.097330 CGACGACGAAGAAGAGCATCTC 61.097 54.545 0.00 0.00 44.06 2.75
867 960 2.241171 TCGACGACGAAGAAGAGCA 58.759 52.632 7.68 0.00 45.74 4.26
882 975 2.439409 TCCAGTCCAAGTCGTAATCGA 58.561 47.619 0.00 0.00 44.12 3.59
883 976 2.933495 TCCAGTCCAAGTCGTAATCG 57.067 50.000 0.00 0.00 38.55 3.34
884 977 4.124851 ACATCCAGTCCAAGTCGTAATC 57.875 45.455 0.00 0.00 0.00 1.75
885 978 4.504858 GAACATCCAGTCCAAGTCGTAAT 58.495 43.478 0.00 0.00 0.00 1.89
886 979 3.306502 GGAACATCCAGTCCAAGTCGTAA 60.307 47.826 0.00 0.00 36.28 3.18
887 980 2.232941 GGAACATCCAGTCCAAGTCGTA 59.767 50.000 0.00 0.00 36.28 3.43
888 981 1.002087 GGAACATCCAGTCCAAGTCGT 59.998 52.381 0.00 0.00 36.28 4.34
889 982 1.676014 GGGAACATCCAGTCCAAGTCG 60.676 57.143 0.00 0.00 38.64 4.18
890 983 1.340114 GGGGAACATCCAGTCCAAGTC 60.340 57.143 0.00 0.00 38.64 3.01
891 984 0.698818 GGGGAACATCCAGTCCAAGT 59.301 55.000 0.00 0.00 38.64 3.16
892 985 0.995024 AGGGGAACATCCAGTCCAAG 59.005 55.000 0.00 0.00 38.64 3.61
893 986 0.991920 GAGGGGAACATCCAGTCCAA 59.008 55.000 0.00 0.00 38.64 3.53
894 987 0.119155 AGAGGGGAACATCCAGTCCA 59.881 55.000 0.00 0.00 43.69 4.02
895 988 1.763545 GTAGAGGGGAACATCCAGTCC 59.236 57.143 0.00 0.00 43.69 3.85
896 989 2.432510 CAGTAGAGGGGAACATCCAGTC 59.567 54.545 0.00 0.00 43.69 3.51
897 990 2.044492 TCAGTAGAGGGGAACATCCAGT 59.956 50.000 0.00 0.00 43.69 4.00
898 991 2.752030 TCAGTAGAGGGGAACATCCAG 58.248 52.381 0.00 0.00 43.69 3.86
899 992 2.940514 TCAGTAGAGGGGAACATCCA 57.059 50.000 0.00 0.00 43.69 3.41
900 993 5.888982 TTTATCAGTAGAGGGGAACATCC 57.111 43.478 0.00 0.00 43.69 3.51
901 994 7.067496 TGATTTATCAGTAGAGGGGAACATC 57.933 40.000 0.00 0.00 35.27 3.06
902 995 7.451731 TTGATTTATCAGTAGAGGGGAACAT 57.548 36.000 0.00 0.00 38.19 2.71
903 996 6.884472 TTGATTTATCAGTAGAGGGGAACA 57.116 37.500 0.00 0.00 38.19 3.18
904 997 7.740805 AGATTGATTTATCAGTAGAGGGGAAC 58.259 38.462 0.00 0.00 38.19 3.62
905 998 7.016661 GGAGATTGATTTATCAGTAGAGGGGAA 59.983 40.741 0.00 0.00 38.19 3.97
906 999 6.498651 GGAGATTGATTTATCAGTAGAGGGGA 59.501 42.308 0.00 0.00 38.19 4.81
907 1000 6.296145 GGGAGATTGATTTATCAGTAGAGGGG 60.296 46.154 0.00 0.00 38.19 4.79
908 1001 6.573289 CGGGAGATTGATTTATCAGTAGAGGG 60.573 46.154 0.00 0.00 38.19 4.30
909 1002 6.393990 CGGGAGATTGATTTATCAGTAGAGG 58.606 44.000 0.00 0.00 38.19 3.69
910 1003 5.866633 GCGGGAGATTGATTTATCAGTAGAG 59.133 44.000 0.00 0.00 38.19 2.43
911 1004 5.279506 GGCGGGAGATTGATTTATCAGTAGA 60.280 44.000 0.00 0.00 38.19 2.59
912 1005 4.932200 GGCGGGAGATTGATTTATCAGTAG 59.068 45.833 0.00 0.00 38.19 2.57
913 1006 4.346709 TGGCGGGAGATTGATTTATCAGTA 59.653 41.667 0.00 0.00 38.19 2.74
914 1007 3.136443 TGGCGGGAGATTGATTTATCAGT 59.864 43.478 0.00 0.00 38.19 3.41
915 1008 3.499918 GTGGCGGGAGATTGATTTATCAG 59.500 47.826 0.00 0.00 38.19 2.90
916 1009 3.476552 GTGGCGGGAGATTGATTTATCA 58.523 45.455 0.00 0.00 34.44 2.15
917 1010 2.814336 GGTGGCGGGAGATTGATTTATC 59.186 50.000 0.00 0.00 0.00 1.75
918 1011 2.174639 TGGTGGCGGGAGATTGATTTAT 59.825 45.455 0.00 0.00 0.00 1.40
919 1012 1.562008 TGGTGGCGGGAGATTGATTTA 59.438 47.619 0.00 0.00 0.00 1.40
920 1013 0.331278 TGGTGGCGGGAGATTGATTT 59.669 50.000 0.00 0.00 0.00 2.17
921 1014 0.107017 CTGGTGGCGGGAGATTGATT 60.107 55.000 0.00 0.00 0.00 2.57
922 1015 0.982852 TCTGGTGGCGGGAGATTGAT 60.983 55.000 0.00 0.00 0.00 2.57
923 1016 1.612146 TCTGGTGGCGGGAGATTGA 60.612 57.895 0.00 0.00 0.00 2.57
924 1017 1.450312 GTCTGGTGGCGGGAGATTG 60.450 63.158 0.00 0.00 0.00 2.67
925 1018 2.670148 GGTCTGGTGGCGGGAGATT 61.670 63.158 0.00 0.00 0.00 2.40
926 1019 3.083997 GGTCTGGTGGCGGGAGAT 61.084 66.667 0.00 0.00 0.00 2.75
927 1020 4.631740 TGGTCTGGTGGCGGGAGA 62.632 66.667 0.00 0.00 0.00 3.71
928 1021 4.087892 CTGGTCTGGTGGCGGGAG 62.088 72.222 0.00 0.00 0.00 4.30
933 1026 4.314440 TGACGCTGGTCTGGTGGC 62.314 66.667 0.00 0.00 43.79 5.01
934 1027 2.357517 GTGACGCTGGTCTGGTGG 60.358 66.667 0.00 0.00 43.79 4.61
935 1028 0.946221 GAAGTGACGCTGGTCTGGTG 60.946 60.000 0.00 0.00 43.79 4.17
936 1029 1.367840 GAAGTGACGCTGGTCTGGT 59.632 57.895 0.00 0.00 43.79 4.00
937 1030 0.668706 CTGAAGTGACGCTGGTCTGG 60.669 60.000 0.00 0.00 43.79 3.86
938 1031 0.315251 TCTGAAGTGACGCTGGTCTG 59.685 55.000 0.00 0.00 43.79 3.51
939 1032 1.040646 TTCTGAAGTGACGCTGGTCT 58.959 50.000 0.00 0.00 43.79 3.85
940 1033 1.996191 GATTCTGAAGTGACGCTGGTC 59.004 52.381 0.00 0.00 43.71 4.02
941 1034 1.338200 GGATTCTGAAGTGACGCTGGT 60.338 52.381 0.00 0.00 0.00 4.00
942 1035 1.338105 TGGATTCTGAAGTGACGCTGG 60.338 52.381 0.00 0.00 0.00 4.85
943 1036 2.084610 TGGATTCTGAAGTGACGCTG 57.915 50.000 0.00 0.00 0.00 5.18
944 1037 2.839486 TTGGATTCTGAAGTGACGCT 57.161 45.000 0.00 0.00 0.00 5.07
945 1038 3.265791 AGATTGGATTCTGAAGTGACGC 58.734 45.455 0.00 0.00 0.00 5.19
946 1039 4.331168 GGAAGATTGGATTCTGAAGTGACG 59.669 45.833 0.00 0.00 0.00 4.35
947 1040 4.331168 CGGAAGATTGGATTCTGAAGTGAC 59.669 45.833 0.00 0.00 35.45 3.67
948 1041 4.222810 TCGGAAGATTGGATTCTGAAGTGA 59.777 41.667 0.00 0.00 38.73 3.41
949 1042 4.507710 TCGGAAGATTGGATTCTGAAGTG 58.492 43.478 0.00 0.00 38.73 3.16
950 1043 4.826274 TCGGAAGATTGGATTCTGAAGT 57.174 40.909 0.00 0.00 38.73 3.01
953 1046 5.126067 GGAATTCGGAAGATTGGATTCTGA 58.874 41.667 0.00 0.00 39.67 3.27
954 1047 4.024556 CGGAATTCGGAAGATTGGATTCTG 60.025 45.833 7.20 0.00 41.60 3.02
955 1048 4.130118 CGGAATTCGGAAGATTGGATTCT 58.870 43.478 7.20 0.00 41.60 2.40
956 1049 4.127171 TCGGAATTCGGAAGATTGGATTC 58.873 43.478 12.85 0.00 41.60 2.52
957 1050 4.150897 TCGGAATTCGGAAGATTGGATT 57.849 40.909 12.85 0.00 41.60 3.01
958 1051 3.838244 TCGGAATTCGGAAGATTGGAT 57.162 42.857 12.85 0.00 41.60 3.41
959 1052 3.838244 ATCGGAATTCGGAAGATTGGA 57.162 42.857 18.30 0.00 41.60 3.53
960 1053 4.452455 CCTAATCGGAATTCGGAAGATTGG 59.548 45.833 18.30 16.13 39.77 3.16
961 1054 4.083802 GCCTAATCGGAATTCGGAAGATTG 60.084 45.833 18.30 9.47 39.77 2.67
962 1055 4.065789 GCCTAATCGGAATTCGGAAGATT 58.934 43.478 18.30 16.89 39.77 2.40
963 1056 3.325135 AGCCTAATCGGAATTCGGAAGAT 59.675 43.478 18.30 10.89 39.77 2.40
964 1057 2.698797 AGCCTAATCGGAATTCGGAAGA 59.301 45.455 18.30 9.26 39.77 2.87
965 1058 2.802816 CAGCCTAATCGGAATTCGGAAG 59.197 50.000 18.30 12.34 39.77 3.46
966 1059 2.432874 TCAGCCTAATCGGAATTCGGAA 59.567 45.455 18.30 3.87 39.77 4.30
967 1060 2.036387 TCAGCCTAATCGGAATTCGGA 58.964 47.619 16.94 16.94 39.77 4.55
968 1061 2.526304 TCAGCCTAATCGGAATTCGG 57.474 50.000 6.67 6.67 39.77 4.30
969 1062 3.653344 TGATCAGCCTAATCGGAATTCG 58.347 45.455 0.00 0.00 40.90 3.34
970 1063 3.999663 CCTGATCAGCCTAATCGGAATTC 59.000 47.826 17.76 0.00 32.25 2.17
971 1064 3.648067 TCCTGATCAGCCTAATCGGAATT 59.352 43.478 17.76 0.00 32.25 2.17
972 1065 3.242867 TCCTGATCAGCCTAATCGGAAT 58.757 45.455 17.76 0.00 32.25 3.01
973 1066 2.677914 TCCTGATCAGCCTAATCGGAA 58.322 47.619 17.76 0.00 32.25 4.30
974 1067 2.381752 TCCTGATCAGCCTAATCGGA 57.618 50.000 17.76 4.55 32.25 4.55
975 1068 2.564504 TGATCCTGATCAGCCTAATCGG 59.435 50.000 17.76 1.95 42.42 4.18
976 1069 3.949842 TGATCCTGATCAGCCTAATCG 57.050 47.619 17.76 1.85 42.42 3.34
985 1078 0.683412 CCCATCGCTGATCCTGATCA 59.317 55.000 9.35 9.35 44.83 2.92
986 1079 0.673022 GCCCATCGCTGATCCTGATC 60.673 60.000 0.06 0.06 38.29 2.92
987 1080 1.374190 GCCCATCGCTGATCCTGAT 59.626 57.895 0.00 0.00 0.00 2.90
988 1081 2.824546 GCCCATCGCTGATCCTGA 59.175 61.111 0.00 0.00 0.00 3.86
989 1082 2.664185 CGCCCATCGCTGATCCTG 60.664 66.667 0.00 0.00 34.21 3.86
990 1083 3.933722 CCGCCCATCGCTGATCCT 61.934 66.667 0.00 0.00 36.73 3.24
992 1085 4.916293 TGCCGCCCATCGCTGATC 62.916 66.667 0.00 0.00 36.73 2.92
993 1086 4.923942 CTGCCGCCCATCGCTGAT 62.924 66.667 0.00 0.00 36.73 2.90
1059 1152 3.649277 ATCGCAGTCGCAGTCCCAC 62.649 63.158 0.00 0.00 38.40 4.61
1151 1245 3.885777 GCGTCAAGCTTGTAGATGC 57.114 52.632 25.19 18.66 44.04 3.91
1231 1326 4.361253 CGGCGAATTCATCCGGAT 57.639 55.556 21.79 12.38 39.52 4.18
1335 1434 1.146263 GATGGTTGGGGGAGCGTAG 59.854 63.158 0.00 0.00 0.00 3.51
1511 1610 4.220382 CCCTCTCTTGATCGCTCAATCTAT 59.780 45.833 1.59 0.00 40.52 1.98
1517 1621 2.079170 ATCCCTCTCTTGATCGCTCA 57.921 50.000 0.00 0.00 0.00 4.26
1520 1624 1.414181 TCCAATCCCTCTCTTGATCGC 59.586 52.381 0.00 0.00 0.00 4.58
1579 1689 4.711980 GTAGGCGACGACATCCAG 57.288 61.111 2.19 0.00 35.82 3.86
1672 1782 3.068691 CCCGAGCTCCTTCCACGA 61.069 66.667 8.47 0.00 0.00 4.35
1673 1783 4.148825 CCCCGAGCTCCTTCCACG 62.149 72.222 8.47 0.00 0.00 4.94
1674 1784 2.683933 TCCCCGAGCTCCTTCCAC 60.684 66.667 8.47 0.00 0.00 4.02
1704 1814 2.834638 AGTATGCCTGGCCTTTGAAT 57.165 45.000 17.53 4.08 0.00 2.57
1709 1819 0.107654 GTCGAAGTATGCCTGGCCTT 60.108 55.000 17.53 12.29 0.00 4.35
1713 1823 1.883084 GGCGTCGAAGTATGCCTGG 60.883 63.158 0.00 0.00 44.16 4.45
1719 1829 0.384669 GCTGGTAGGCGTCGAAGTAT 59.615 55.000 0.00 0.00 0.00 2.12
1730 1840 3.760035 ACGCGTCCAGCTGGTAGG 61.760 66.667 31.58 22.47 45.59 3.18
1732 1842 4.063967 CCACGCGTCCAGCTGGTA 62.064 66.667 31.58 16.12 45.59 3.25
1746 1856 1.146263 GTGATGGATCCCGACCCAC 59.854 63.158 9.90 6.33 34.92 4.61
1758 1868 2.356535 CCTTCCTTCCTCCTTGTGATGG 60.357 54.545 0.00 0.00 0.00 3.51
1769 1879 1.757699 GCAGACGTATCCTTCCTTCCT 59.242 52.381 0.00 0.00 0.00 3.36
1770 1880 1.757699 AGCAGACGTATCCTTCCTTCC 59.242 52.381 0.00 0.00 0.00 3.46
1776 1886 0.460987 GCAGCAGCAGACGTATCCTT 60.461 55.000 0.00 0.00 41.58 3.36
1777 1887 1.142748 GCAGCAGCAGACGTATCCT 59.857 57.895 0.00 0.00 41.58 3.24
1778 1888 1.884926 GGCAGCAGCAGACGTATCC 60.885 63.158 2.65 0.00 44.61 2.59
1779 1889 1.884926 GGGCAGCAGCAGACGTATC 60.885 63.158 2.65 0.00 44.61 2.24
1780 1890 2.187946 GGGCAGCAGCAGACGTAT 59.812 61.111 2.65 0.00 44.61 3.06
1781 1891 2.997315 AGGGCAGCAGCAGACGTA 60.997 61.111 2.65 0.00 44.61 3.57
1869 1979 2.376518 ACCCATGTCTCCTCATTGTTGT 59.623 45.455 0.00 0.00 0.00 3.32
1904 2014 2.829023 CCTAAGGGTGGTCTTCAGGTA 58.171 52.381 0.00 0.00 0.00 3.08
1907 2017 0.253327 GGCCTAAGGGTGGTCTTCAG 59.747 60.000 0.00 0.00 34.45 3.02
1910 2020 0.404426 GTTGGCCTAAGGGTGGTCTT 59.596 55.000 3.32 0.00 34.45 3.01
1911 2021 0.475828 AGTTGGCCTAAGGGTGGTCT 60.476 55.000 3.32 0.00 34.45 3.85
1912 2022 0.035343 GAGTTGGCCTAAGGGTGGTC 60.035 60.000 3.32 0.00 34.45 4.02
1913 2023 1.498176 GGAGTTGGCCTAAGGGTGGT 61.498 60.000 3.32 0.00 34.45 4.16
1914 2024 1.303282 GGAGTTGGCCTAAGGGTGG 59.697 63.158 3.32 0.00 34.45 4.61
1915 2025 0.404040 TTGGAGTTGGCCTAAGGGTG 59.596 55.000 3.32 0.00 34.45 4.61
1916 2026 0.404426 GTTGGAGTTGGCCTAAGGGT 59.596 55.000 3.32 0.00 34.45 4.34
1917 2027 0.676782 CGTTGGAGTTGGCCTAAGGG 60.677 60.000 3.32 0.00 0.00 3.95
2074 2187 6.256757 TCGAAAATTTGCGTTTGAAAAAGGAT 59.743 30.769 17.95 0.00 0.00 3.24
2157 2283 3.834799 GGCGAGGACGTGTAGGGG 61.835 72.222 0.00 0.00 41.98 4.79
2158 2284 4.189188 CGGCGAGGACGTGTAGGG 62.189 72.222 0.00 0.00 41.98 3.53
2198 2346 1.073177 ACCGGCGACAAAACTATTCG 58.927 50.000 9.30 0.00 35.82 3.34
2217 2427 2.058125 TTTGAGGGCCGGCTGTGTTA 62.058 55.000 28.56 5.50 0.00 2.41
2227 2437 4.711846 AGAAACCTATTCATTTTGAGGGCC 59.288 41.667 0.00 0.00 33.02 5.80
2372 2622 3.013921 GAGATGAGTGAGAAGACGAGGT 58.986 50.000 0.00 0.00 0.00 3.85
2393 2643 2.981898 TCATGAGCATGGACTTGACAG 58.018 47.619 10.31 0.00 39.24 3.51
2460 2710 1.449246 GCAGAGGCAGCTCGACATT 60.449 57.895 0.00 0.00 40.72 2.71
2553 2809 4.115199 ATGGAGGAGGCGGGCAAC 62.115 66.667 3.78 0.00 0.00 4.17
2557 2813 2.037620 CTTGAGATGGAGGAGGCGGG 62.038 65.000 0.00 0.00 0.00 6.13
2648 2904 3.003068 CGGCATGATGTCTCAAAAGGATC 59.997 47.826 0.00 0.00 34.37 3.36
2726 2983 2.429930 CGAGGGGCAAGACCAACA 59.570 61.111 0.00 0.00 42.05 3.33
2832 3089 5.389859 TCATCAACAATTGCCCTAAGTTG 57.610 39.130 5.05 0.84 40.53 3.16


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

AutoCloner maintained by Alex Coulton.