Multiple sequence alignment - TraesCS7D01G271300

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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 TraesCS7D01G271300 chr7D 100.000 2222 0 0 1 2222 259802950 259805171 0.000000e+00 4104.0
1 TraesCS7D01G271300 chr7D 94.771 918 48 0 1305 2222 124188666 124189583 0.000000e+00 1430.0
2 TraesCS7D01G271300 chr7D 93.682 918 58 0 1305 2222 260649855 260648938 0.000000e+00 1375.0
3 TraesCS7D01G271300 chr7D 88.750 880 77 10 1 870 259617863 259618730 0.000000e+00 1057.0
4 TraesCS7D01G271300 chr7D 84.312 886 117 13 1 870 58506323 58505444 0.000000e+00 846.0
5 TraesCS7D01G271300 chr7D 83.102 722 103 10 147 849 493544429 493545150 6.690000e-180 640.0
6 TraesCS7D01G271300 chr7D 91.791 134 10 1 855 987 386666780 386666647 3.770000e-43 185.0
7 TraesCS7D01G271300 chr7D 98.462 65 1 0 1245 1309 635511936 635511872 5.010000e-22 115.0
8 TraesCS7D01G271300 chr3D 94.227 918 52 1 1305 2222 226532799 226531883 0.000000e+00 1400.0
9 TraesCS7D01G271300 chr3D 87.677 779 83 6 1 767 274724660 274723883 0.000000e+00 894.0
10 TraesCS7D01G271300 chr3D 87.436 780 83 8 1 767 274488962 274488185 0.000000e+00 883.0
11 TraesCS7D01G271300 chr3D 84.086 886 121 13 1 870 93174004 93173123 0.000000e+00 837.0
12 TraesCS7D01G271300 chr3D 96.498 257 9 0 988 1244 10748188 10747932 2.040000e-115 425.0
13 TraesCS7D01G271300 chr3D 91.538 130 9 2 859 987 54323225 54323097 6.300000e-41 178.0
14 TraesCS7D01G271300 chr3D 98.462 65 1 0 1245 1309 604112526 604112590 5.010000e-22 115.0
15 TraesCS7D01G271300 chr1D 94.130 920 50 1 1307 2222 159760355 159761274 0.000000e+00 1397.0
16 TraesCS7D01G271300 chr1D 93.900 918 56 0 1305 2222 185207539 185208456 0.000000e+00 1386.0
17 TraesCS7D01G271300 chr1D 94.002 917 50 4 1305 2220 117956218 117955306 0.000000e+00 1384.0
18 TraesCS7D01G271300 chr1D 84.904 881 121 9 1 870 124695377 124696256 0.000000e+00 880.0
19 TraesCS7D01G271300 chr1D 84.509 865 108 13 1 849 463954714 463953860 0.000000e+00 832.0
20 TraesCS7D01G271300 chr1D 83.146 890 127 13 1 870 142029729 142028843 0.000000e+00 791.0
21 TraesCS7D01G271300 chr1D 83.834 866 102 18 1 855 124898214 124899052 0.000000e+00 789.0
22 TraesCS7D01G271300 chr1D 96.887 257 8 0 988 1244 254499280 254499536 4.380000e-117 431.0
23 TraesCS7D01G271300 chr1D 98.462 65 1 0 1245 1309 446739731 446739667 5.010000e-22 115.0
24 TraesCS7D01G271300 chr6D 93.900 918 53 1 1305 2222 283969898 283968984 0.000000e+00 1382.0
25 TraesCS7D01G271300 chr6D 93.682 918 58 0 1305 2222 357683005 357683922 0.000000e+00 1375.0
26 TraesCS7D01G271300 chr6D 86.322 870 101 12 1 855 103606532 103607398 0.000000e+00 931.0
27 TraesCS7D01G271300 chr2D 93.886 916 54 2 1307 2222 29323955 29324868 0.000000e+00 1380.0
28 TraesCS7D01G271300 chr2D 98.462 65 1 0 1245 1309 9788123 9788187 5.010000e-22 115.0
29 TraesCS7D01G271300 chr5B 85.518 801 105 7 1 791 108409616 108410415 0.000000e+00 826.0
30 TraesCS7D01G271300 chr5B 95.000 120 5 1 868 986 92098496 92098615 1.050000e-43 187.0
31 TraesCS7D01G271300 chr7B 84.143 782 100 12 1 763 546858648 546857872 0.000000e+00 736.0
32 TraesCS7D01G271300 chr7B 79.791 861 128 36 1 844 383698396 383699227 3.180000e-163 584.0
33 TraesCS7D01G271300 chr7B 94.215 121 7 0 867 987 408679069 408679189 3.770000e-43 185.0
34 TraesCS7D01G271300 chr1B 81.512 860 124 16 15 854 191290276 191291120 0.000000e+00 675.0
35 TraesCS7D01G271300 chr7A 89.245 530 52 5 1 527 487643221 487642694 0.000000e+00 658.0
36 TraesCS7D01G271300 chr7A 92.063 126 10 0 862 987 304734312 304734187 6.300000e-41 178.0
37 TraesCS7D01G271300 chrUn 97.665 257 6 0 988 1244 445811781 445811525 2.020000e-120 442.0
38 TraesCS7D01G271300 chrUn 96.887 257 8 0 988 1244 30306069 30305813 4.380000e-117 431.0
39 TraesCS7D01G271300 chr3B 97.665 257 6 0 988 1244 201514920 201515176 2.020000e-120 442.0
40 TraesCS7D01G271300 chr3B 96.887 257 8 0 988 1244 201515962 201516218 4.380000e-117 431.0
41 TraesCS7D01G271300 chr5D 96.887 257 8 0 988 1244 560873750 560874006 4.380000e-117 431.0
42 TraesCS7D01G271300 chr5D 96.498 257 9 0 988 1244 6200000 6199744 2.040000e-115 425.0
43 TraesCS7D01G271300 chr5D 98.462 65 1 0 1245 1309 6177985 6177921 5.010000e-22 115.0
44 TraesCS7D01G271300 chr5D 98.462 65 1 0 1245 1309 28033817 28033881 5.010000e-22 115.0
45 TraesCS7D01G271300 chr5D 98.462 65 1 0 1245 1309 513585423 513585359 5.010000e-22 115.0
46 TraesCS7D01G271300 chr6B 96.109 257 10 0 988 1244 121820995 121820739 9.490000e-114 420.0
47 TraesCS7D01G271300 chr3A 95.041 121 5 1 866 986 338790876 338790995 2.910000e-44 189.0
48 TraesCS7D01G271300 chr4D 95.000 120 5 1 868 986 277797064 277796945 1.050000e-43 187.0
49 TraesCS7D01G271300 chr4B 95.690 116 5 0 872 987 476981030 476980915 1.050000e-43 187.0
50 TraesCS7D01G271300 chr4B 92.248 129 9 1 859 987 111802279 111802406 4.870000e-42 182.0
51 TraesCS7D01G271300 chr1A 98.462 65 1 0 1245 1309 554461445 554461509 5.010000e-22 115.0
52 TraesCS7D01G271300 chr1A 98.462 65 1 0 1245 1309 554461992 554462056 5.010000e-22 115.0
53 TraesCS7D01G271300 chr4A 76.705 176 35 6 347 519 460991809 460991637 2.350000e-15 93.5


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 TraesCS7D01G271300 chr7D 259802950 259805171 2221 False 4104.0 4104 100.000 1 2222 1 chr7D.!!$F3 2221
1 TraesCS7D01G271300 chr7D 124188666 124189583 917 False 1430.0 1430 94.771 1305 2222 1 chr7D.!!$F1 917
2 TraesCS7D01G271300 chr7D 260648938 260649855 917 True 1375.0 1375 93.682 1305 2222 1 chr7D.!!$R2 917
3 TraesCS7D01G271300 chr7D 259617863 259618730 867 False 1057.0 1057 88.750 1 870 1 chr7D.!!$F2 869
4 TraesCS7D01G271300 chr7D 58505444 58506323 879 True 846.0 846 84.312 1 870 1 chr7D.!!$R1 869
5 TraesCS7D01G271300 chr7D 493544429 493545150 721 False 640.0 640 83.102 147 849 1 chr7D.!!$F4 702
6 TraesCS7D01G271300 chr3D 226531883 226532799 916 True 1400.0 1400 94.227 1305 2222 1 chr3D.!!$R4 917
7 TraesCS7D01G271300 chr3D 274723883 274724660 777 True 894.0 894 87.677 1 767 1 chr3D.!!$R6 766
8 TraesCS7D01G271300 chr3D 274488185 274488962 777 True 883.0 883 87.436 1 767 1 chr3D.!!$R5 766
9 TraesCS7D01G271300 chr3D 93173123 93174004 881 True 837.0 837 84.086 1 870 1 chr3D.!!$R3 869
10 TraesCS7D01G271300 chr1D 159760355 159761274 919 False 1397.0 1397 94.130 1307 2222 1 chr1D.!!$F3 915
11 TraesCS7D01G271300 chr1D 185207539 185208456 917 False 1386.0 1386 93.900 1305 2222 1 chr1D.!!$F4 917
12 TraesCS7D01G271300 chr1D 117955306 117956218 912 True 1384.0 1384 94.002 1305 2220 1 chr1D.!!$R1 915
13 TraesCS7D01G271300 chr1D 124695377 124696256 879 False 880.0 880 84.904 1 870 1 chr1D.!!$F1 869
14 TraesCS7D01G271300 chr1D 463953860 463954714 854 True 832.0 832 84.509 1 849 1 chr1D.!!$R4 848
15 TraesCS7D01G271300 chr1D 142028843 142029729 886 True 791.0 791 83.146 1 870 1 chr1D.!!$R2 869
16 TraesCS7D01G271300 chr1D 124898214 124899052 838 False 789.0 789 83.834 1 855 1 chr1D.!!$F2 854
17 TraesCS7D01G271300 chr6D 283968984 283969898 914 True 1382.0 1382 93.900 1305 2222 1 chr6D.!!$R1 917
18 TraesCS7D01G271300 chr6D 357683005 357683922 917 False 1375.0 1375 93.682 1305 2222 1 chr6D.!!$F2 917
19 TraesCS7D01G271300 chr6D 103606532 103607398 866 False 931.0 931 86.322 1 855 1 chr6D.!!$F1 854
20 TraesCS7D01G271300 chr2D 29323955 29324868 913 False 1380.0 1380 93.886 1307 2222 1 chr2D.!!$F2 915
21 TraesCS7D01G271300 chr5B 108409616 108410415 799 False 826.0 826 85.518 1 791 1 chr5B.!!$F2 790
22 TraesCS7D01G271300 chr7B 546857872 546858648 776 True 736.0 736 84.143 1 763 1 chr7B.!!$R1 762
23 TraesCS7D01G271300 chr7B 383698396 383699227 831 False 584.0 584 79.791 1 844 1 chr7B.!!$F1 843
24 TraesCS7D01G271300 chr1B 191290276 191291120 844 False 675.0 675 81.512 15 854 1 chr1B.!!$F1 839
25 TraesCS7D01G271300 chr7A 487642694 487643221 527 True 658.0 658 89.245 1 527 1 chr7A.!!$R2 526
26 TraesCS7D01G271300 chr3B 201514920 201516218 1298 False 436.5 442 97.276 988 1244 2 chr3B.!!$F1 256

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
922 966 0.028242 CGATCAGAGACCCTTCGACG 59.972 60.0 0.0 0.0 29.06 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1946 0.385029 TGTGTGTGCAAAGGTCATGC 59.615 50.0 0.0 0.0 44.08 4.06 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
60 61 0.819582 CACAATGGAATGTGGCTCCC 59.180 55.000 0.00 0.00 45.47 4.30
75 76 0.838122 CTCCCAGGTGACCTCAACCT 60.838 60.000 0.00 0.00 32.98 3.50
269 289 1.064017 GGAGGAGAGAGAGGCAAGAGA 60.064 57.143 0.00 0.00 0.00 3.10
389 412 1.067425 CGGTACAACCAGGATTCACGA 60.067 52.381 0.00 0.00 38.47 4.35
532 569 0.468648 ACCCCTATAGCAAAGCGGTC 59.531 55.000 0.00 0.00 0.00 4.79
626 666 4.581824 TCACCGGTAGTATGGTTATCAGAC 59.418 45.833 6.87 0.00 35.96 3.51
653 693 2.519780 GAAAACCGGGCCACCACA 60.520 61.111 6.32 0.00 36.13 4.17
679 719 0.257039 GGACTGCCCCATCACAGAAT 59.743 55.000 0.00 0.00 37.35 2.40
690 731 3.133003 CCATCACAGAATAGAGTCCGGTT 59.867 47.826 0.00 0.00 0.00 4.44
696 737 2.007608 GAATAGAGTCCGGTTGTTGGC 58.992 52.381 0.00 0.00 0.00 4.52
805 848 2.117156 GCTGCGCATGAACCTGGAT 61.117 57.895 12.24 0.00 0.00 3.41
824 868 1.380785 CAGCAACCCAGGGCATCAT 60.381 57.895 4.91 0.00 0.00 2.45
855 899 0.180642 TGGTTGTGCCGGTTGAACTA 59.819 50.000 1.90 0.00 41.21 2.24
885 929 6.465439 TGGTACAATCACTACTACAGGATG 57.535 41.667 0.00 0.00 37.61 3.51
886 930 5.163447 TGGTACAATCACTACTACAGGATGC 60.163 44.000 0.00 0.00 34.51 3.91
887 931 5.069251 GGTACAATCACTACTACAGGATGCT 59.931 44.000 0.00 0.00 42.53 3.79
888 932 5.016051 ACAATCACTACTACAGGATGCTG 57.984 43.478 13.34 13.34 42.53 4.41
889 933 3.742433 ATCACTACTACAGGATGCTGC 57.258 47.619 14.95 0.00 42.53 5.25
890 934 2.739943 TCACTACTACAGGATGCTGCT 58.260 47.619 14.95 4.43 42.53 4.24
891 935 3.898482 TCACTACTACAGGATGCTGCTA 58.102 45.455 14.95 5.37 42.53 3.49
892 936 4.278310 TCACTACTACAGGATGCTGCTAA 58.722 43.478 14.95 0.00 42.53 3.09
893 937 4.098044 TCACTACTACAGGATGCTGCTAAC 59.902 45.833 14.95 0.00 42.53 2.34
894 938 2.586258 ACTACAGGATGCTGCTAACG 57.414 50.000 14.95 1.02 42.53 3.18
895 939 1.825474 ACTACAGGATGCTGCTAACGT 59.175 47.619 14.95 1.65 42.53 3.99
896 940 2.196749 CTACAGGATGCTGCTAACGTG 58.803 52.381 14.95 6.79 42.53 4.49
897 941 0.608130 ACAGGATGCTGCTAACGTGA 59.392 50.000 14.95 0.00 42.53 4.35
898 942 1.002366 CAGGATGCTGCTAACGTGAC 58.998 55.000 0.00 0.00 0.00 3.67
899 943 0.608130 AGGATGCTGCTAACGTGACA 59.392 50.000 0.00 0.00 0.00 3.58
900 944 0.721718 GGATGCTGCTAACGTGACAC 59.278 55.000 0.00 0.00 0.00 3.67
901 945 1.673033 GGATGCTGCTAACGTGACACT 60.673 52.381 3.68 0.00 0.00 3.55
902 946 2.416836 GGATGCTGCTAACGTGACACTA 60.417 50.000 3.68 0.00 0.00 2.74
903 947 2.060326 TGCTGCTAACGTGACACTAC 57.940 50.000 3.68 0.00 0.00 2.73
905 949 1.400629 GCTGCTAACGTGACACTACGA 60.401 52.381 3.68 0.00 46.46 3.43
906 950 2.731341 GCTGCTAACGTGACACTACGAT 60.731 50.000 3.68 0.00 46.46 3.73
907 951 3.099362 CTGCTAACGTGACACTACGATC 58.901 50.000 3.68 0.00 46.46 3.69
908 952 2.485038 TGCTAACGTGACACTACGATCA 59.515 45.455 3.68 0.00 46.46 2.92
909 953 3.099362 GCTAACGTGACACTACGATCAG 58.901 50.000 3.68 0.86 46.46 2.90
910 954 3.181513 GCTAACGTGACACTACGATCAGA 60.182 47.826 3.68 0.00 46.46 3.27
911 955 3.473093 AACGTGACACTACGATCAGAG 57.527 47.619 3.68 0.00 46.46 3.35
912 956 2.696506 ACGTGACACTACGATCAGAGA 58.303 47.619 3.68 0.00 46.46 3.10
913 957 2.415857 ACGTGACACTACGATCAGAGAC 59.584 50.000 3.68 0.00 46.46 3.36
914 958 2.223066 CGTGACACTACGATCAGAGACC 60.223 54.545 3.68 0.00 46.46 3.85
915 959 2.097791 GTGACACTACGATCAGAGACCC 59.902 54.545 0.00 0.00 0.00 4.46
916 960 2.026169 TGACACTACGATCAGAGACCCT 60.026 50.000 0.00 0.00 0.00 4.34
917 961 3.018149 GACACTACGATCAGAGACCCTT 58.982 50.000 0.00 0.00 0.00 3.95
918 962 3.018149 ACACTACGATCAGAGACCCTTC 58.982 50.000 0.00 0.00 0.00 3.46
919 963 2.032302 CACTACGATCAGAGACCCTTCG 59.968 54.545 0.00 0.00 32.82 3.79
920 964 2.093075 ACTACGATCAGAGACCCTTCGA 60.093 50.000 0.00 0.00 31.47 3.71
921 965 1.096416 ACGATCAGAGACCCTTCGAC 58.904 55.000 0.00 0.00 31.47 4.20
922 966 0.028242 CGATCAGAGACCCTTCGACG 59.972 60.000 0.00 0.00 29.06 5.12
923 967 1.380524 GATCAGAGACCCTTCGACGA 58.619 55.000 0.00 0.00 0.00 4.20
924 968 1.743958 GATCAGAGACCCTTCGACGAA 59.256 52.381 10.34 10.34 0.00 3.85
925 969 1.612676 TCAGAGACCCTTCGACGAAA 58.387 50.000 12.03 0.00 0.00 3.46
926 970 1.268899 TCAGAGACCCTTCGACGAAAC 59.731 52.381 12.03 4.05 0.00 2.78
927 971 1.269998 CAGAGACCCTTCGACGAAACT 59.730 52.381 12.03 8.53 0.00 2.66
928 972 1.269998 AGAGACCCTTCGACGAAACTG 59.730 52.381 12.03 5.54 0.00 3.16
929 973 1.000496 GAGACCCTTCGACGAAACTGT 60.000 52.381 12.03 8.66 0.00 3.55
930 974 1.137513 GACCCTTCGACGAAACTGTG 58.862 55.000 12.03 0.00 0.00 3.66
931 975 0.462789 ACCCTTCGACGAAACTGTGT 59.537 50.000 12.03 2.05 0.00 3.72
932 976 0.859232 CCCTTCGACGAAACTGTGTG 59.141 55.000 12.03 0.00 0.00 3.82
933 977 1.567504 CCTTCGACGAAACTGTGTGT 58.432 50.000 12.03 0.00 0.00 3.72
934 978 1.257936 CCTTCGACGAAACTGTGTGTG 59.742 52.381 12.03 0.00 0.00 3.82
935 979 0.648441 TTCGACGAAACTGTGTGTGC 59.352 50.000 8.05 0.00 0.00 4.57
936 980 0.179121 TCGACGAAACTGTGTGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
937 981 0.043053 CGACGAAACTGTGTGTGCTG 60.043 55.000 0.00 0.00 0.00 4.41
938 982 0.316196 GACGAAACTGTGTGTGCTGC 60.316 55.000 0.00 0.00 0.00 5.25
939 983 1.024046 ACGAAACTGTGTGTGCTGCA 61.024 50.000 0.00 0.00 0.00 4.41
940 984 0.098552 CGAAACTGTGTGTGCTGCAA 59.901 50.000 2.77 0.00 0.00 4.08
941 985 1.268692 CGAAACTGTGTGTGCTGCAAT 60.269 47.619 2.77 0.00 0.00 3.56
942 986 2.032117 CGAAACTGTGTGTGCTGCAATA 60.032 45.455 2.77 0.00 0.00 1.90
943 987 3.547813 CGAAACTGTGTGTGCTGCAATAA 60.548 43.478 2.77 0.00 0.00 1.40
944 988 4.549458 GAAACTGTGTGTGCTGCAATAAT 58.451 39.130 2.77 0.00 0.00 1.28
945 989 3.837213 ACTGTGTGTGCTGCAATAATC 57.163 42.857 2.77 0.00 0.00 1.75
946 990 2.160219 ACTGTGTGTGCTGCAATAATCG 59.840 45.455 2.77 0.00 0.00 3.34
947 991 1.135717 TGTGTGTGCTGCAATAATCGC 60.136 47.619 2.77 0.00 0.00 4.58
948 992 1.135717 GTGTGTGCTGCAATAATCGCA 60.136 47.619 2.77 1.11 37.88 5.10
949 993 1.538950 TGTGTGCTGCAATAATCGCAA 59.461 42.857 2.77 0.00 39.30 4.85
950 994 2.030451 TGTGTGCTGCAATAATCGCAAA 60.030 40.909 2.77 0.00 39.30 3.68
951 995 3.181397 GTGTGCTGCAATAATCGCAAAT 58.819 40.909 2.77 0.00 39.30 2.32
952 996 3.000476 GTGTGCTGCAATAATCGCAAATG 60.000 43.478 2.77 0.00 39.30 2.32
953 997 2.536803 GTGCTGCAATAATCGCAAATGG 59.463 45.455 2.77 0.00 39.30 3.16
954 998 2.166050 TGCTGCAATAATCGCAAATGGT 59.834 40.909 0.00 0.00 39.30 3.55
955 999 2.536803 GCTGCAATAATCGCAAATGGTG 59.463 45.455 0.00 0.00 39.30 4.17
1015 1059 4.980573 AGAACTTATGGCTACACAAACCA 58.019 39.130 0.00 0.00 37.99 3.67
1024 1068 4.458989 TGGCTACACAAACCATTGAAGATC 59.541 41.667 0.00 0.00 38.94 2.75
1142 1186 0.626382 TTTATGGGGGTCGCAATGGA 59.374 50.000 0.00 0.00 0.00 3.41
1150 1194 3.222603 GGGGTCGCAATGGATTTATTCT 58.777 45.455 0.00 0.00 0.00 2.40
1245 1289 8.143673 AGGTTTCTACTAACTAAAACTAGGGG 57.856 38.462 0.00 0.00 33.27 4.79
1246 1290 7.958016 AGGTTTCTACTAACTAAAACTAGGGGA 59.042 37.037 0.00 0.00 33.27 4.81
1247 1291 8.597167 GGTTTCTACTAACTAAAACTAGGGGAA 58.403 37.037 0.00 0.00 33.27 3.97
1252 1296 6.647229 ACTAACTAAAACTAGGGGAAATCCG 58.353 40.000 0.00 0.00 36.71 4.18
1253 1297 5.509832 AACTAAAACTAGGGGAAATCCGT 57.490 39.130 0.00 0.00 36.71 4.69
1255 1299 2.124277 AAACTAGGGGAAATCCGTGC 57.876 50.000 0.00 0.00 36.71 5.34
1256 1300 0.988832 AACTAGGGGAAATCCGTGCA 59.011 50.000 0.00 0.00 36.71 4.57
1257 1301 0.541863 ACTAGGGGAAATCCGTGCAG 59.458 55.000 0.00 0.00 36.71 4.41
1258 1302 0.815615 CTAGGGGAAATCCGTGCAGC 60.816 60.000 0.00 0.00 36.71 5.25
1268 1312 3.578456 CGTGCAGCGGAAAATCCT 58.422 55.556 0.00 0.00 33.30 3.24
1269 1313 1.135315 CGTGCAGCGGAAAATCCTG 59.865 57.895 0.00 0.00 33.30 3.86
1270 1314 1.298157 CGTGCAGCGGAAAATCCTGA 61.298 55.000 0.00 0.00 33.30 3.86
1271 1315 0.881118 GTGCAGCGGAAAATCCTGAA 59.119 50.000 0.00 0.00 33.30 3.02
1272 1316 1.474077 GTGCAGCGGAAAATCCTGAAT 59.526 47.619 0.00 0.00 33.30 2.57
1273 1317 2.094545 GTGCAGCGGAAAATCCTGAATT 60.095 45.455 0.00 0.00 33.30 2.17
1274 1318 2.562298 TGCAGCGGAAAATCCTGAATTT 59.438 40.909 0.00 0.00 39.30 1.82
1275 1319 2.925563 GCAGCGGAAAATCCTGAATTTG 59.074 45.455 0.00 0.00 37.64 2.32
1276 1320 3.367292 GCAGCGGAAAATCCTGAATTTGA 60.367 43.478 0.00 0.00 37.64 2.69
1277 1321 4.418392 CAGCGGAAAATCCTGAATTTGAG 58.582 43.478 0.00 0.00 37.64 3.02
1278 1322 4.156556 CAGCGGAAAATCCTGAATTTGAGA 59.843 41.667 0.00 0.00 37.64 3.27
1279 1323 4.156739 AGCGGAAAATCCTGAATTTGAGAC 59.843 41.667 0.00 0.00 37.64 3.36
1280 1324 4.156739 GCGGAAAATCCTGAATTTGAGACT 59.843 41.667 0.00 0.00 37.64 3.24
1281 1325 5.335976 GCGGAAAATCCTGAATTTGAGACTT 60.336 40.000 0.00 0.00 37.64 3.01
1282 1326 6.681777 CGGAAAATCCTGAATTTGAGACTTT 58.318 36.000 0.00 0.00 37.64 2.66
1283 1327 6.803807 CGGAAAATCCTGAATTTGAGACTTTC 59.196 38.462 0.00 0.00 37.64 2.62
1284 1328 7.308830 CGGAAAATCCTGAATTTGAGACTTTCT 60.309 37.037 6.50 0.00 37.64 2.52
1285 1329 9.014297 GGAAAATCCTGAATTTGAGACTTTCTA 57.986 33.333 6.50 0.00 37.64 2.10
1286 1330 9.833182 GAAAATCCTGAATTTGAGACTTTCTAC 57.167 33.333 0.00 0.00 37.64 2.59
1287 1331 8.924511 AAATCCTGAATTTGAGACTTTCTACA 57.075 30.769 0.00 0.00 36.20 2.74
1288 1332 7.913674 ATCCTGAATTTGAGACTTTCTACAC 57.086 36.000 0.00 0.00 0.00 2.90
1289 1333 6.231211 TCCTGAATTTGAGACTTTCTACACC 58.769 40.000 0.00 0.00 0.00 4.16
1290 1334 5.997746 CCTGAATTTGAGACTTTCTACACCA 59.002 40.000 0.00 0.00 0.00 4.17
1291 1335 6.486657 CCTGAATTTGAGACTTTCTACACCAA 59.513 38.462 0.00 0.00 0.00 3.67
1292 1336 7.013274 CCTGAATTTGAGACTTTCTACACCAAA 59.987 37.037 0.00 0.00 0.00 3.28
1293 1337 8.287439 TGAATTTGAGACTTTCTACACCAAAA 57.713 30.769 0.00 0.00 0.00 2.44
1294 1338 8.744652 TGAATTTGAGACTTTCTACACCAAAAA 58.255 29.630 0.00 0.00 0.00 1.94
1295 1339 9.750125 GAATTTGAGACTTTCTACACCAAAAAT 57.250 29.630 0.00 0.00 0.00 1.82
1300 1344 9.793259 TGAGACTTTCTACACCAAAAATATTCT 57.207 29.630 0.00 0.00 0.00 2.40
1368 1412 2.669569 GCGTGTGTGATGCAGGGT 60.670 61.111 0.00 0.00 36.49 4.34
1373 1417 2.159099 CGTGTGTGATGCAGGGTATACT 60.159 50.000 2.25 0.00 0.00 2.12
1529 1573 0.792640 CAGATCAAGGTGTGTGCGAC 59.207 55.000 0.00 0.00 0.00 5.19
1549 1593 1.130373 CATACGGCATGCGTTTCACTT 59.870 47.619 17.80 0.00 0.00 3.16
1567 1611 5.129634 TCACTTGGATGAACTGTTTGCTTA 58.870 37.500 0.00 0.00 0.00 3.09
1580 1624 4.655963 TGTTTGCTTAGAGCCAAGAGAAT 58.344 39.130 0.00 0.00 41.51 2.40
1657 1723 3.684305 TCATAAATGTGTGCGAAGACTGG 59.316 43.478 0.00 0.00 0.00 4.00
1798 1864 3.822167 TGTGATGTCATTGCACACAGAAT 59.178 39.130 3.78 0.00 37.60 2.40
1880 1946 6.145534 CCAATTACATATGTGGCTAGTACACG 59.854 42.308 18.81 4.04 41.64 4.49
1899 1965 0.385029 GCATGACCTTTGCACACACA 59.615 50.000 0.00 0.00 39.90 3.72
1971 2290 5.622041 ACAAAACGAACCGTGAATAATTTCG 59.378 36.000 0.00 0.00 39.99 3.46
2010 2470 4.024556 GCTACTATAGTTGCATGTTGCCTG 60.025 45.833 27.44 0.00 44.23 4.85
2178 2802 1.752683 TTTACCACAGCGTGTTGGTT 58.247 45.000 8.91 0.00 34.92 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.234908 CCTAGAAGGTTGAGGTCACCTG 59.765 54.545 0.00 0.00 31.76 4.00
84 85 2.510382 TGTTACTCTTGGGTGTTTGGGA 59.490 45.455 0.00 0.00 0.00 4.37
142 143 5.726793 ACCTAGATCTACACTTCCACCAAAT 59.273 40.000 0.00 0.00 0.00 2.32
242 246 3.900601 TGCCTCTCTCTCCTCCATTAATC 59.099 47.826 0.00 0.00 0.00 1.75
269 289 5.045066 GGGTTTCTTCCACCTACCTCTTTAT 60.045 44.000 0.00 0.00 34.36 1.40
309 332 3.150767 CTGTAACGGTTGGAAAATGGGA 58.849 45.455 3.07 0.00 0.00 4.37
389 412 2.420687 GCTAGGGTTTCTGCAGCATACT 60.421 50.000 9.47 5.95 32.46 2.12
452 476 0.393820 TGGTTGGTCCGGTTACTCAC 59.606 55.000 0.00 0.00 39.52 3.51
532 569 0.233848 GTGGTAGTTTCGGTGCAACG 59.766 55.000 20.47 20.47 38.12 4.10
626 666 2.294979 GCCCGGTTTTCCTGGTTATAG 58.705 52.381 0.00 0.00 44.74 1.31
679 719 1.122632 TGGCCAACAACCGGACTCTA 61.123 55.000 9.46 0.00 30.26 2.43
791 833 0.745486 TGCTGATCCAGGTTCATGCG 60.745 55.000 0.33 0.00 31.21 4.73
805 848 1.866483 ATGATGCCCTGGGTTGCTGA 61.866 55.000 15.56 0.00 0.00 4.26
855 899 6.553476 TGTAGTAGTGATTGTACCATATGCCT 59.447 38.462 0.00 0.00 0.00 4.75
860 904 7.255836 GCATCCTGTAGTAGTGATTGTACCATA 60.256 40.741 0.00 0.00 0.00 2.74
870 914 2.739943 AGCAGCATCCTGTAGTAGTGA 58.260 47.619 0.00 0.00 41.26 3.41
871 915 4.363999 GTTAGCAGCATCCTGTAGTAGTG 58.636 47.826 0.00 0.00 41.26 2.74
872 916 3.066900 CGTTAGCAGCATCCTGTAGTAGT 59.933 47.826 0.00 0.00 41.26 2.73
873 917 3.066900 ACGTTAGCAGCATCCTGTAGTAG 59.933 47.826 0.00 0.00 41.26 2.57
874 918 3.021695 ACGTTAGCAGCATCCTGTAGTA 58.978 45.455 0.00 0.00 41.26 1.82
875 919 1.825474 ACGTTAGCAGCATCCTGTAGT 59.175 47.619 0.00 0.00 41.26 2.73
876 920 2.159240 TCACGTTAGCAGCATCCTGTAG 60.159 50.000 0.00 0.00 41.26 2.74
877 921 1.822371 TCACGTTAGCAGCATCCTGTA 59.178 47.619 0.00 0.00 41.26 2.74
878 922 0.608130 TCACGTTAGCAGCATCCTGT 59.392 50.000 0.00 0.00 41.26 4.00
879 923 1.002366 GTCACGTTAGCAGCATCCTG 58.998 55.000 0.00 0.00 42.13 3.86
880 924 0.608130 TGTCACGTTAGCAGCATCCT 59.392 50.000 0.00 0.00 0.00 3.24
881 925 0.721718 GTGTCACGTTAGCAGCATCC 59.278 55.000 0.00 0.00 0.00 3.51
882 926 1.714794 AGTGTCACGTTAGCAGCATC 58.285 50.000 0.00 0.00 0.00 3.91
883 927 2.607187 GTAGTGTCACGTTAGCAGCAT 58.393 47.619 0.00 0.00 0.00 3.79
884 928 1.664874 CGTAGTGTCACGTTAGCAGCA 60.665 52.381 0.00 0.00 37.16 4.41
885 929 0.982673 CGTAGTGTCACGTTAGCAGC 59.017 55.000 0.00 0.00 37.16 5.25
886 930 2.606717 TCGTAGTGTCACGTTAGCAG 57.393 50.000 0.00 0.00 42.51 4.24
887 931 2.485038 TGATCGTAGTGTCACGTTAGCA 59.515 45.455 0.00 0.00 42.51 3.49
888 932 3.099362 CTGATCGTAGTGTCACGTTAGC 58.901 50.000 0.00 0.00 42.51 3.09
889 933 4.329256 TCTCTGATCGTAGTGTCACGTTAG 59.671 45.833 0.00 0.00 42.51 2.34
890 934 4.092529 GTCTCTGATCGTAGTGTCACGTTA 59.907 45.833 0.00 0.00 42.51 3.18
891 935 3.072211 TCTCTGATCGTAGTGTCACGTT 58.928 45.455 0.00 0.00 42.51 3.99
892 936 2.415857 GTCTCTGATCGTAGTGTCACGT 59.584 50.000 0.00 0.00 42.51 4.49
893 937 2.223066 GGTCTCTGATCGTAGTGTCACG 60.223 54.545 0.00 0.00 43.28 4.35
894 938 2.097791 GGGTCTCTGATCGTAGTGTCAC 59.902 54.545 0.00 0.00 0.00 3.67
895 939 2.026169 AGGGTCTCTGATCGTAGTGTCA 60.026 50.000 0.00 0.00 0.00 3.58
896 940 2.645802 AGGGTCTCTGATCGTAGTGTC 58.354 52.381 0.00 0.00 0.00 3.67
897 941 2.810870 AGGGTCTCTGATCGTAGTGT 57.189 50.000 0.00 0.00 0.00 3.55
898 942 2.032302 CGAAGGGTCTCTGATCGTAGTG 59.968 54.545 0.00 0.00 0.00 2.74
899 943 2.093075 TCGAAGGGTCTCTGATCGTAGT 60.093 50.000 0.00 0.00 35.20 2.73
900 944 2.288458 GTCGAAGGGTCTCTGATCGTAG 59.712 54.545 0.00 0.00 35.20 3.51
901 945 2.286872 GTCGAAGGGTCTCTGATCGTA 58.713 52.381 0.00 0.00 35.20 3.43
902 946 1.096416 GTCGAAGGGTCTCTGATCGT 58.904 55.000 0.00 0.00 35.20 3.73
903 947 0.028242 CGTCGAAGGGTCTCTGATCG 59.972 60.000 0.00 0.00 34.98 3.69
904 948 1.380524 TCGTCGAAGGGTCTCTGATC 58.619 55.000 0.00 0.00 0.00 2.92
905 949 1.835494 TTCGTCGAAGGGTCTCTGAT 58.165 50.000 2.90 0.00 0.00 2.90
906 950 1.268899 GTTTCGTCGAAGGGTCTCTGA 59.731 52.381 7.86 0.00 0.00 3.27
907 951 1.269998 AGTTTCGTCGAAGGGTCTCTG 59.730 52.381 7.86 0.00 0.00 3.35
908 952 1.269998 CAGTTTCGTCGAAGGGTCTCT 59.730 52.381 7.86 0.00 0.00 3.10
909 953 1.000496 ACAGTTTCGTCGAAGGGTCTC 60.000 52.381 7.86 0.00 0.00 3.36
910 954 1.038280 ACAGTTTCGTCGAAGGGTCT 58.962 50.000 7.86 3.51 0.00 3.85
911 955 1.137513 CACAGTTTCGTCGAAGGGTC 58.862 55.000 7.86 1.35 0.00 4.46
912 956 0.462789 ACACAGTTTCGTCGAAGGGT 59.537 50.000 7.86 1.21 0.00 4.34
913 957 0.859232 CACACAGTTTCGTCGAAGGG 59.141 55.000 7.86 0.54 0.00 3.95
914 958 1.257936 CACACACAGTTTCGTCGAAGG 59.742 52.381 7.86 4.99 0.00 3.46
915 959 1.332028 GCACACACAGTTTCGTCGAAG 60.332 52.381 7.86 0.00 0.00 3.79
916 960 0.648441 GCACACACAGTTTCGTCGAA 59.352 50.000 2.90 2.90 0.00 3.71
917 961 0.179121 AGCACACACAGTTTCGTCGA 60.179 50.000 0.00 0.00 0.00 4.20
918 962 0.043053 CAGCACACACAGTTTCGTCG 60.043 55.000 0.00 0.00 0.00 5.12
919 963 0.316196 GCAGCACACACAGTTTCGTC 60.316 55.000 0.00 0.00 0.00 4.20
920 964 1.024046 TGCAGCACACACAGTTTCGT 61.024 50.000 0.00 0.00 0.00 3.85
921 965 0.098552 TTGCAGCACACACAGTTTCG 59.901 50.000 0.00 0.00 0.00 3.46
922 966 2.497107 ATTGCAGCACACACAGTTTC 57.503 45.000 0.00 0.00 0.00 2.78
923 967 4.549458 GATTATTGCAGCACACACAGTTT 58.451 39.130 0.00 0.00 0.00 2.66
924 968 3.365264 CGATTATTGCAGCACACACAGTT 60.365 43.478 0.00 0.00 0.00 3.16
925 969 2.160219 CGATTATTGCAGCACACACAGT 59.840 45.455 0.00 0.00 0.00 3.55
926 970 2.777494 CGATTATTGCAGCACACACAG 58.223 47.619 0.00 0.00 0.00 3.66
927 971 1.135717 GCGATTATTGCAGCACACACA 60.136 47.619 0.00 0.00 0.00 3.72
928 972 1.135717 TGCGATTATTGCAGCACACAC 60.136 47.619 2.51 0.00 37.44 3.82
929 973 1.163554 TGCGATTATTGCAGCACACA 58.836 45.000 2.51 0.00 37.44 3.72
930 974 2.261037 TTGCGATTATTGCAGCACAC 57.739 45.000 7.23 0.00 44.28 3.82
931 975 3.180613 CATTTGCGATTATTGCAGCACA 58.819 40.909 7.23 0.00 44.28 4.57
932 976 2.536803 CCATTTGCGATTATTGCAGCAC 59.463 45.455 7.23 0.00 44.28 4.40
933 977 2.166050 ACCATTTGCGATTATTGCAGCA 59.834 40.909 7.23 0.00 44.28 4.41
934 978 2.536803 CACCATTTGCGATTATTGCAGC 59.463 45.455 7.23 0.00 44.28 5.25
935 979 2.536803 GCACCATTTGCGATTATTGCAG 59.463 45.455 7.23 0.00 44.28 4.41
936 980 2.538437 GCACCATTTGCGATTATTGCA 58.462 42.857 2.51 2.51 42.79 4.08
972 1016 9.884636 AGTTCTATTTAAGTTTTGCACCTTTTT 57.115 25.926 0.00 0.00 0.00 1.94
973 1017 9.884636 AAGTTCTATTTAAGTTTTGCACCTTTT 57.115 25.926 0.00 0.00 0.00 2.27
977 1021 9.353999 CCATAAGTTCTATTTAAGTTTTGCACC 57.646 33.333 0.00 0.00 0.00 5.01
978 1022 8.860128 GCCATAAGTTCTATTTAAGTTTTGCAC 58.140 33.333 0.00 0.00 0.00 4.57
979 1023 8.802267 AGCCATAAGTTCTATTTAAGTTTTGCA 58.198 29.630 0.00 0.00 0.00 4.08
984 1028 9.953565 TGTGTAGCCATAAGTTCTATTTAAGTT 57.046 29.630 0.00 0.00 0.00 2.66
985 1029 9.953565 TTGTGTAGCCATAAGTTCTATTTAAGT 57.046 29.630 0.00 0.00 0.00 2.24
997 1041 5.895636 TCAATGGTTTGTGTAGCCATAAG 57.104 39.130 0.00 0.00 41.68 1.73
1015 1059 6.049790 GCCTAGGTTTAGAACGATCTTCAAT 58.950 40.000 11.31 0.00 37.10 2.57
1024 1068 3.120442 CGTTTTGGCCTAGGTTTAGAACG 60.120 47.826 11.31 15.73 30.79 3.95
1192 1236 7.527568 TGGTTAAAATTCCGTCCAGTAAAAT 57.472 32.000 0.00 0.00 0.00 1.82
1252 1296 0.881118 TTCAGGATTTTCCGCTGCAC 59.119 50.000 0.00 0.00 42.75 4.57
1253 1297 1.838112 ATTCAGGATTTTCCGCTGCA 58.162 45.000 0.00 0.00 42.75 4.41
1255 1299 4.156556 TCTCAAATTCAGGATTTTCCGCTG 59.843 41.667 0.00 0.00 42.75 5.18
1256 1300 4.156739 GTCTCAAATTCAGGATTTTCCGCT 59.843 41.667 0.00 0.00 42.75 5.52
1257 1301 4.156739 AGTCTCAAATTCAGGATTTTCCGC 59.843 41.667 0.00 0.00 42.75 5.54
1258 1302 5.886960 AGTCTCAAATTCAGGATTTTCCG 57.113 39.130 0.00 0.00 42.75 4.30
1261 1305 9.354673 TGTAGAAAGTCTCAAATTCAGGATTTT 57.645 29.630 0.00 0.00 35.79 1.82
1262 1306 8.787852 GTGTAGAAAGTCTCAAATTCAGGATTT 58.212 33.333 0.00 0.00 38.49 2.17
1263 1307 7.391833 GGTGTAGAAAGTCTCAAATTCAGGATT 59.608 37.037 0.00 0.00 0.00 3.01
1264 1308 6.881602 GGTGTAGAAAGTCTCAAATTCAGGAT 59.118 38.462 0.00 0.00 0.00 3.24
1265 1309 6.183361 TGGTGTAGAAAGTCTCAAATTCAGGA 60.183 38.462 0.00 0.00 0.00 3.86
1266 1310 5.997746 TGGTGTAGAAAGTCTCAAATTCAGG 59.002 40.000 0.00 0.00 0.00 3.86
1267 1311 7.496529 TTGGTGTAGAAAGTCTCAAATTCAG 57.503 36.000 0.00 0.00 0.00 3.02
1268 1312 7.873719 TTTGGTGTAGAAAGTCTCAAATTCA 57.126 32.000 0.00 0.00 0.00 2.57
1269 1313 9.750125 ATTTTTGGTGTAGAAAGTCTCAAATTC 57.250 29.630 0.00 0.00 0.00 2.17
1274 1318 9.793259 AGAATATTTTTGGTGTAGAAAGTCTCA 57.207 29.630 0.00 0.00 0.00 3.27
1287 1331 9.923786 GCAAACGTTTAAAAGAATATTTTTGGT 57.076 25.926 14.20 0.00 32.79 3.67
1288 1332 9.086996 CGCAAACGTTTAAAAGAATATTTTTGG 57.913 29.630 14.20 0.00 31.81 3.28
1289 1333 9.836739 TCGCAAACGTTTAAAAGAATATTTTTG 57.163 25.926 14.20 7.88 41.18 2.44
1292 1336 8.643752 CCATCGCAAACGTTTAAAAGAATATTT 58.356 29.630 14.20 0.00 41.18 1.40
1293 1337 7.201401 GCCATCGCAAACGTTTAAAAGAATATT 60.201 33.333 14.20 0.00 41.18 1.28
1294 1338 6.252655 GCCATCGCAAACGTTTAAAAGAATAT 59.747 34.615 14.20 0.00 41.18 1.28
1295 1339 5.569823 GCCATCGCAAACGTTTAAAAGAATA 59.430 36.000 14.20 0.00 41.18 1.75
1296 1340 4.384547 GCCATCGCAAACGTTTAAAAGAAT 59.615 37.500 14.20 0.00 41.18 2.40
1297 1341 3.731717 GCCATCGCAAACGTTTAAAAGAA 59.268 39.130 14.20 0.00 41.18 2.52
1298 1342 3.243101 TGCCATCGCAAACGTTTAAAAGA 60.243 39.130 14.20 10.73 43.74 2.52
1299 1343 3.046390 TGCCATCGCAAACGTTTAAAAG 58.954 40.909 14.20 2.25 43.74 2.27
1300 1344 3.046390 CTGCCATCGCAAACGTTTAAAA 58.954 40.909 14.20 2.02 46.66 1.52
1301 1345 2.290916 TCTGCCATCGCAAACGTTTAAA 59.709 40.909 14.20 2.39 46.66 1.52
1302 1346 1.874231 TCTGCCATCGCAAACGTTTAA 59.126 42.857 14.20 2.77 46.66 1.52
1303 1347 1.514003 TCTGCCATCGCAAACGTTTA 58.486 45.000 14.20 0.00 46.66 2.01
1320 1364 4.338012 TCTGAACCATGTTTGATGCATCT 58.662 39.130 26.32 3.81 0.00 2.90
1549 1593 3.753272 GCTCTAAGCAAACAGTTCATCCA 59.247 43.478 0.00 0.00 41.89 3.41
1567 1611 5.707066 ACCATTTCTATTCTCTTGGCTCT 57.293 39.130 0.00 0.00 0.00 4.09
1657 1723 4.330074 AGCAGCAATCGTCTGTGTTATTAC 59.670 41.667 0.00 0.00 34.21 1.89
1880 1946 0.385029 TGTGTGTGCAAAGGTCATGC 59.615 50.000 0.00 0.00 44.08 4.06
1899 1965 4.929819 AGGCATTTTGGAACGTACTTTT 57.070 36.364 0.00 0.00 0.00 2.27
1946 2012 6.791299 CGAAATTATTCACGGTTCGTTTTGTA 59.209 34.615 0.00 0.00 38.32 2.41
1947 2013 5.622041 CGAAATTATTCACGGTTCGTTTTGT 59.378 36.000 0.00 0.00 38.32 2.83
2010 2470 5.570234 TCCCGCCTTGATTTATTTTACAC 57.430 39.130 0.00 0.00 0.00 2.90
2178 2802 3.694926 TGGCATGGTGTTATGTCATTGA 58.305 40.909 0.00 0.00 37.72 2.57


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

AutoCloner maintained by Alex Coulton.