Multiple sequence alignment - TraesCS7D01G348600

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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 TraesCS7D01G348600 chr7D 100.000 3371 0 0 1 3371 448332851 448336221 0.000000e+00 6226.0
1 TraesCS7D01G348600 chr7D 86.289 795 69 26 55 821 327343773 327342991 0.000000e+00 828.0
2 TraesCS7D01G348600 chr7D 86.272 794 70 25 55 821 332523778 332522997 0.000000e+00 826.0
3 TraesCS7D01G348600 chr7D 85.990 778 81 23 56 821 306059858 306060619 0.000000e+00 808.0
4 TraesCS7D01G348600 chr7D 85.283 795 77 25 55 821 327285513 327284731 0.000000e+00 784.0
5 TraesCS7D01G348600 chr7D 93.053 547 19 8 55 583 448268714 448269259 0.000000e+00 782.0
6 TraesCS7D01G348600 chr7B 94.974 1910 61 17 895 2783 465586182 465588077 0.000000e+00 2963.0
7 TraesCS7D01G348600 chr7B 96.115 592 14 5 2780 3371 465588196 465588778 0.000000e+00 957.0
8 TraesCS7D01G348600 chr7A 87.853 1663 139 37 987 2622 547641968 547640342 0.000000e+00 1893.0
9 TraesCS7D01G348600 chr7A 85.685 496 35 13 2899 3371 547574101 547573619 1.090000e-134 490.0
10 TraesCS7D01G348600 chr7A 94.595 74 4 0 2612 2685 547574256 547574183 7.640000e-22 115.0
11 TraesCS7D01G348600 chr2D 91.465 785 38 5 57 822 277721267 277722041 0.000000e+00 1051.0
12 TraesCS7D01G348600 chr2D 88.181 863 56 16 1 821 265296378 265295520 0.000000e+00 987.0
13 TraesCS7D01G348600 chr2D 88.945 787 47 17 55 821 265268683 265267917 0.000000e+00 935.0
14 TraesCS7D01G348600 chr2D 87.277 786 39 15 55 821 277713176 277713919 0.000000e+00 841.0
15 TraesCS7D01G348600 chr2D 84.977 852 73 31 1 821 265221398 265220571 0.000000e+00 813.0
16 TraesCS7D01G348600 chr2D 85.518 801 71 27 56 821 524000791 524000001 0.000000e+00 795.0
17 TraesCS7D01G348600 chr2D 90.435 115 10 1 2697 2811 512769344 512769231 2.100000e-32 150.0
18 TraesCS7D01G348600 chr2D 88.136 118 13 1 2697 2814 617101213 617101097 4.540000e-29 139.0
19 TraesCS7D01G348600 chr2D 86.992 123 12 4 2697 2819 463879034 463878916 5.870000e-28 135.0
20 TraesCS7D01G348600 chr2D 100.000 56 0 0 1 56 265268759 265268704 1.650000e-18 104.0
21 TraesCS7D01G348600 chr6D 89.594 788 61 10 55 822 215317058 215317844 0.000000e+00 981.0
22 TraesCS7D01G348600 chr6D 86.559 863 71 26 1 821 268747105 268746246 0.000000e+00 909.0
23 TraesCS7D01G348600 chr6D 87.913 786 42 22 55 821 209876245 209876996 0.000000e+00 876.0
24 TraesCS7D01G348600 chr6D 85.284 863 61 38 1 821 220832878 220832040 0.000000e+00 830.0
25 TraesCS7D01G348600 chr5D 87.748 857 67 16 1 821 117365566 117364712 0.000000e+00 966.0
26 TraesCS7D01G348600 chr5D 85.731 862 54 32 1 821 117357742 117356909 0.000000e+00 846.0
27 TraesCS7D01G348600 chr5D 82.624 869 83 38 1 821 154773415 154772567 0.000000e+00 706.0
28 TraesCS7D01G348600 chr5D 84.466 103 14 2 2002 2103 407106823 407106722 2.140000e-17 100.0
29 TraesCS7D01G348600 chr2A 87.694 772 76 17 56 821 323276327 323277085 0.000000e+00 881.0
30 TraesCS7D01G348600 chr2A 88.983 118 12 1 2697 2814 747272327 747272211 9.750000e-31 145.0
31 TraesCS7D01G348600 chr3D 87.595 790 57 22 55 821 284586031 284586802 0.000000e+00 878.0
32 TraesCS7D01G348600 chr1D 82.111 777 116 20 55 821 160744258 160745021 0.000000e+00 643.0
33 TraesCS7D01G348600 chr6A 81.782 752 110 25 79 821 309109054 309109787 3.720000e-169 604.0
34 TraesCS7D01G348600 chr6A 85.938 128 14 3 2697 2821 99403182 99403056 2.110000e-27 134.0
35 TraesCS7D01G348600 chr6B 89.076 119 12 1 2697 2815 233039225 233039342 2.710000e-31 147.0
36 TraesCS7D01G348600 chr5A 88.696 115 12 1 2697 2811 321920631 321920744 4.540000e-29 139.0
37 TraesCS7D01G348600 chr5A 82.692 104 16 2 2001 2103 512601301 512601403 1.290000e-14 91.6
38 TraesCS7D01G348600 chr4A 87.603 121 11 3 2696 2815 649809657 649809774 1.630000e-28 137.0
39 TraesCS7D01G348600 chr1B 86.508 126 14 3 2697 2822 250423692 250423814 5.870000e-28 135.0
40 TraesCS7D01G348600 chr5B 82.075 106 19 0 1998 2103 488112880 488112985 1.290000e-14 91.6


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 TraesCS7D01G348600 chr7D 448332851 448336221 3370 False 6226.0 6226 100.0000 1 3371 1 chr7D.!!$F3 3370
1 TraesCS7D01G348600 chr7D 327342991 327343773 782 True 828.0 828 86.2890 55 821 1 chr7D.!!$R2 766
2 TraesCS7D01G348600 chr7D 332522997 332523778 781 True 826.0 826 86.2720 55 821 1 chr7D.!!$R3 766
3 TraesCS7D01G348600 chr7D 306059858 306060619 761 False 808.0 808 85.9900 56 821 1 chr7D.!!$F1 765
4 TraesCS7D01G348600 chr7D 327284731 327285513 782 True 784.0 784 85.2830 55 821 1 chr7D.!!$R1 766
5 TraesCS7D01G348600 chr7D 448268714 448269259 545 False 782.0 782 93.0530 55 583 1 chr7D.!!$F2 528
6 TraesCS7D01G348600 chr7B 465586182 465588778 2596 False 1960.0 2963 95.5445 895 3371 2 chr7B.!!$F1 2476
7 TraesCS7D01G348600 chr7A 547640342 547641968 1626 True 1893.0 1893 87.8530 987 2622 1 chr7A.!!$R1 1635
8 TraesCS7D01G348600 chr7A 547573619 547574256 637 True 302.5 490 90.1400 2612 3371 2 chr7A.!!$R2 759
9 TraesCS7D01G348600 chr2D 277721267 277722041 774 False 1051.0 1051 91.4650 57 822 1 chr2D.!!$F2 765
10 TraesCS7D01G348600 chr2D 265295520 265296378 858 True 987.0 987 88.1810 1 821 1 chr2D.!!$R2 820
11 TraesCS7D01G348600 chr2D 277713176 277713919 743 False 841.0 841 87.2770 55 821 1 chr2D.!!$F1 766
12 TraesCS7D01G348600 chr2D 265220571 265221398 827 True 813.0 813 84.9770 1 821 1 chr2D.!!$R1 820
13 TraesCS7D01G348600 chr2D 524000001 524000791 790 True 795.0 795 85.5180 56 821 1 chr2D.!!$R5 765
14 TraesCS7D01G348600 chr2D 265267917 265268759 842 True 519.5 935 94.4725 1 821 2 chr2D.!!$R7 820
15 TraesCS7D01G348600 chr6D 215317058 215317844 786 False 981.0 981 89.5940 55 822 1 chr6D.!!$F2 767
16 TraesCS7D01G348600 chr6D 268746246 268747105 859 True 909.0 909 86.5590 1 821 1 chr6D.!!$R2 820
17 TraesCS7D01G348600 chr6D 209876245 209876996 751 False 876.0 876 87.9130 55 821 1 chr6D.!!$F1 766
18 TraesCS7D01G348600 chr6D 220832040 220832878 838 True 830.0 830 85.2840 1 821 1 chr6D.!!$R1 820
19 TraesCS7D01G348600 chr5D 117364712 117365566 854 True 966.0 966 87.7480 1 821 1 chr5D.!!$R2 820
20 TraesCS7D01G348600 chr5D 117356909 117357742 833 True 846.0 846 85.7310 1 821 1 chr5D.!!$R1 820
21 TraesCS7D01G348600 chr5D 154772567 154773415 848 True 706.0 706 82.6240 1 821 1 chr5D.!!$R3 820
22 TraesCS7D01G348600 chr2A 323276327 323277085 758 False 881.0 881 87.6940 56 821 1 chr2A.!!$F1 765
23 TraesCS7D01G348600 chr3D 284586031 284586802 771 False 878.0 878 87.5950 55 821 1 chr3D.!!$F1 766
24 TraesCS7D01G348600 chr1D 160744258 160745021 763 False 643.0 643 82.1110 55 821 1 chr1D.!!$F1 766
25 TraesCS7D01G348600 chr6A 309109054 309109787 733 False 604.0 604 81.7820 79 821 1 chr6A.!!$F1 742

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
901 985 0.251787 ACCCATGGTTCCAAAGCTCC 60.252 55.0 11.73 0.00 27.29 4.70 F
1482 1577 0.372334 CCGGCGAGGTAATTTTCGTG 59.628 55.0 9.30 3.05 38.96 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2031 0.323178 CCCAGCTTGTCCTTGAGCAT 60.323 55.000 0.00 0.0 41.31 3.79 R
2386 2496 1.956477 ACCTGCAGTGAATTTGTGGAC 59.044 47.619 13.81 0.0 0.00 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
92 115 0.535102 ACAACAGCCCAAGGAACTCG 60.535 55.000 0.00 0.00 38.49 4.18
140 163 3.677648 CGACCAGGACCGGACGTT 61.678 66.667 9.46 0.00 39.02 3.99
707 789 7.442364 GCATATGTGTGACTATATCTTGTTGGT 59.558 37.037 4.29 0.00 0.00 3.67
741 825 4.142249 CCTCTTGTGTTTTCCCTCGTTTTT 60.142 41.667 0.00 0.00 0.00 1.94
823 907 1.471119 GGTCTCACCCTACATCACGA 58.529 55.000 0.00 0.00 30.04 4.35
824 908 1.405821 GGTCTCACCCTACATCACGAG 59.594 57.143 0.00 0.00 30.04 4.18
825 909 2.366533 GTCTCACCCTACATCACGAGA 58.633 52.381 0.00 0.00 0.00 4.04
826 910 2.753452 GTCTCACCCTACATCACGAGAA 59.247 50.000 0.00 0.00 31.74 2.87
827 911 3.381908 GTCTCACCCTACATCACGAGAAT 59.618 47.826 0.00 0.00 31.74 2.40
828 912 4.579340 GTCTCACCCTACATCACGAGAATA 59.421 45.833 0.00 0.00 31.74 1.75
829 913 4.579340 TCTCACCCTACATCACGAGAATAC 59.421 45.833 0.00 0.00 0.00 1.89
830 914 3.314357 TCACCCTACATCACGAGAATACG 59.686 47.826 0.00 0.00 39.31 3.06
831 915 2.034305 ACCCTACATCACGAGAATACGC 59.966 50.000 0.00 0.00 36.70 4.42
832 916 2.293677 CCCTACATCACGAGAATACGCT 59.706 50.000 0.00 0.00 36.70 5.07
833 917 3.501062 CCCTACATCACGAGAATACGCTA 59.499 47.826 0.00 0.00 36.70 4.26
834 918 4.023450 CCCTACATCACGAGAATACGCTAA 60.023 45.833 0.00 0.00 36.70 3.09
835 919 5.506815 CCCTACATCACGAGAATACGCTAAA 60.507 44.000 0.00 0.00 36.70 1.85
836 920 5.975344 CCTACATCACGAGAATACGCTAAAA 59.025 40.000 0.00 0.00 36.70 1.52
837 921 6.474427 CCTACATCACGAGAATACGCTAAAAA 59.526 38.462 0.00 0.00 36.70 1.94
838 922 6.091123 ACATCACGAGAATACGCTAAAAAC 57.909 37.500 0.00 0.00 36.70 2.43
839 923 5.867716 ACATCACGAGAATACGCTAAAAACT 59.132 36.000 0.00 0.00 36.70 2.66
840 924 5.756950 TCACGAGAATACGCTAAAAACTG 57.243 39.130 0.00 0.00 36.70 3.16
841 925 5.463286 TCACGAGAATACGCTAAAAACTGA 58.537 37.500 0.00 0.00 36.70 3.41
842 926 6.097356 TCACGAGAATACGCTAAAAACTGAT 58.903 36.000 0.00 0.00 36.70 2.90
843 927 6.252869 TCACGAGAATACGCTAAAAACTGATC 59.747 38.462 0.00 0.00 36.70 2.92
844 928 6.253727 CACGAGAATACGCTAAAAACTGATCT 59.746 38.462 0.00 0.00 36.70 2.75
845 929 7.431376 CACGAGAATACGCTAAAAACTGATCTA 59.569 37.037 0.00 0.00 36.70 1.98
846 930 7.431668 ACGAGAATACGCTAAAAACTGATCTAC 59.568 37.037 0.00 0.00 36.70 2.59
847 931 7.431376 CGAGAATACGCTAAAAACTGATCTACA 59.569 37.037 0.00 0.00 0.00 2.74
848 932 8.997621 AGAATACGCTAAAAACTGATCTACAA 57.002 30.769 0.00 0.00 0.00 2.41
849 933 9.088512 AGAATACGCTAAAAACTGATCTACAAG 57.911 33.333 0.00 0.00 0.00 3.16
850 934 5.532025 ACGCTAAAAACTGATCTACAAGC 57.468 39.130 0.00 0.00 0.00 4.01
851 935 4.994852 ACGCTAAAAACTGATCTACAAGCA 59.005 37.500 0.00 0.00 0.00 3.91
852 936 5.468746 ACGCTAAAAACTGATCTACAAGCAA 59.531 36.000 0.00 0.00 0.00 3.91
853 937 6.149474 ACGCTAAAAACTGATCTACAAGCAAT 59.851 34.615 0.00 0.00 0.00 3.56
854 938 7.023575 CGCTAAAAACTGATCTACAAGCAATT 58.976 34.615 0.00 0.00 0.00 2.32
855 939 7.538678 CGCTAAAAACTGATCTACAAGCAATTT 59.461 33.333 0.00 0.00 0.00 1.82
856 940 8.642020 GCTAAAAACTGATCTACAAGCAATTTG 58.358 33.333 0.00 0.00 42.68 2.32
857 941 7.951530 AAAAACTGATCTACAAGCAATTTGG 57.048 32.000 0.00 0.00 41.25 3.28
858 942 6.655078 AAACTGATCTACAAGCAATTTGGT 57.345 33.333 0.00 0.00 41.25 3.67
859 943 7.759489 AAACTGATCTACAAGCAATTTGGTA 57.241 32.000 0.82 0.00 41.25 3.25
860 944 6.992063 ACTGATCTACAAGCAATTTGGTAG 57.008 37.500 0.82 3.67 41.25 3.18
861 945 6.711277 ACTGATCTACAAGCAATTTGGTAGA 58.289 36.000 13.10 13.10 41.25 2.59
862 946 6.820656 ACTGATCTACAAGCAATTTGGTAGAG 59.179 38.462 14.92 8.24 41.25 2.43
863 947 6.711277 TGATCTACAAGCAATTTGGTAGAGT 58.289 36.000 14.92 10.96 41.25 3.24
864 948 6.595326 TGATCTACAAGCAATTTGGTAGAGTG 59.405 38.462 14.92 7.81 41.25 3.51
865 949 5.245531 TCTACAAGCAATTTGGTAGAGTGG 58.754 41.667 0.82 4.14 41.25 4.00
866 950 3.157087 ACAAGCAATTTGGTAGAGTGGG 58.843 45.455 0.82 0.00 41.25 4.61
867 951 3.181434 ACAAGCAATTTGGTAGAGTGGGA 60.181 43.478 0.82 0.00 41.25 4.37
868 952 3.806949 AGCAATTTGGTAGAGTGGGAA 57.193 42.857 0.00 0.00 0.00 3.97
869 953 3.690460 AGCAATTTGGTAGAGTGGGAAG 58.310 45.455 0.00 0.00 0.00 3.46
870 954 2.755103 GCAATTTGGTAGAGTGGGAAGG 59.245 50.000 0.00 0.00 0.00 3.46
871 955 3.561313 GCAATTTGGTAGAGTGGGAAGGA 60.561 47.826 0.00 0.00 0.00 3.36
872 956 4.265073 CAATTTGGTAGAGTGGGAAGGAG 58.735 47.826 0.00 0.00 0.00 3.69
873 957 3.269592 TTTGGTAGAGTGGGAAGGAGA 57.730 47.619 0.00 0.00 0.00 3.71
874 958 3.269592 TTGGTAGAGTGGGAAGGAGAA 57.730 47.619 0.00 0.00 0.00 2.87
875 959 3.269592 TGGTAGAGTGGGAAGGAGAAA 57.730 47.619 0.00 0.00 0.00 2.52
876 960 2.904434 TGGTAGAGTGGGAAGGAGAAAC 59.096 50.000 0.00 0.00 0.00 2.78
877 961 2.236644 GGTAGAGTGGGAAGGAGAAACC 59.763 54.545 0.00 0.00 39.35 3.27
888 972 1.839424 GGAGAAACCTTCCACCCATG 58.161 55.000 0.00 0.00 34.74 3.66
889 973 1.616994 GGAGAAACCTTCCACCCATGG 60.617 57.143 4.14 4.14 40.66 3.66
890 974 4.228649 GGAGAAACCTTCCACCCATGGT 62.229 54.545 11.73 0.00 40.39 3.55
891 975 5.671839 GGAGAAACCTTCCACCCATGGTT 62.672 52.174 11.73 0.00 43.73 3.67
898 982 1.974543 CCACCCATGGTTCCAAAGC 59.025 57.895 11.73 0.00 41.64 3.51
899 983 0.542702 CCACCCATGGTTCCAAAGCT 60.543 55.000 11.73 0.00 41.64 3.74
900 984 0.890683 CACCCATGGTTCCAAAGCTC 59.109 55.000 11.73 0.00 31.02 4.09
901 985 0.251787 ACCCATGGTTCCAAAGCTCC 60.252 55.000 11.73 0.00 27.29 4.70
902 986 0.972471 CCCATGGTTCCAAAGCTCCC 60.972 60.000 11.73 0.00 0.00 4.30
925 1009 4.821260 CCATGTCACATCGGATTAATTCCA 59.179 41.667 0.00 0.00 45.78 3.53
938 1022 7.666388 TCGGATTAATTCCAAGTTGTTCCTTTA 59.334 33.333 1.45 0.00 45.78 1.85
939 1023 8.466798 CGGATTAATTCCAAGTTGTTCCTTTAT 58.533 33.333 1.45 0.00 45.78 1.40
959 1043 7.763985 CCTTTATATGTTTTTGTTCCCATGTCC 59.236 37.037 0.00 0.00 0.00 4.02
967 1051 1.270947 TGTTCCCATGTCCGGTTGTAC 60.271 52.381 0.00 0.00 0.00 2.90
969 1053 1.354101 TCCCATGTCCGGTTGTACTT 58.646 50.000 0.00 0.00 0.00 2.24
970 1054 1.700739 TCCCATGTCCGGTTGTACTTT 59.299 47.619 0.00 0.00 0.00 2.66
971 1055 1.810151 CCCATGTCCGGTTGTACTTTG 59.190 52.381 0.00 0.00 0.00 2.77
972 1056 2.500229 CCATGTCCGGTTGTACTTTGT 58.500 47.619 0.00 0.00 0.00 2.83
973 1057 2.882137 CCATGTCCGGTTGTACTTTGTT 59.118 45.455 0.00 0.00 0.00 2.83
974 1058 3.316868 CCATGTCCGGTTGTACTTTGTTT 59.683 43.478 0.00 0.00 0.00 2.83
975 1059 4.286910 CATGTCCGGTTGTACTTTGTTTG 58.713 43.478 0.00 0.00 0.00 2.93
1015 1099 2.063266 GTCTGATGGACGCGTACAAAA 58.937 47.619 30.63 18.43 35.07 2.44
1067 1151 1.346395 ACCACAGCATCTAACCGAACA 59.654 47.619 0.00 0.00 0.00 3.18
1070 1154 1.623811 ACAGCATCTAACCGAACACCT 59.376 47.619 0.00 0.00 0.00 4.00
1071 1155 2.002586 CAGCATCTAACCGAACACCTG 58.997 52.381 0.00 0.00 0.00 4.00
1153 1237 1.363744 CCGCCAACTAAGCTTCTCAG 58.636 55.000 0.00 0.00 0.00 3.35
1478 1573 1.001887 TGCCCGGCGAGGTAATTTT 60.002 52.632 9.30 0.00 38.74 1.82
1482 1577 0.372334 CCGGCGAGGTAATTTTCGTG 59.628 55.000 9.30 3.05 38.96 4.35
1705 1815 0.608130 CCTCATGTCCAAGGTCGACA 59.392 55.000 18.91 0.00 44.00 4.35
2172 2282 1.671328 CTCGAGGTGATCTACAAGCGA 59.329 52.381 3.91 0.00 0.00 4.93
2182 2292 2.176045 TCTACAAGCGAATCACCCTCA 58.824 47.619 0.00 0.00 0.00 3.86
2272 2382 3.316573 GAGGGCAAGGTCCAGGTCG 62.317 68.421 0.00 0.00 0.00 4.79
2301 2411 4.405671 TCCGACGGGCTCGAGAGT 62.406 66.667 15.95 12.50 46.14 3.24
2386 2496 3.434641 GGCATAGGATGAATCATGTCACG 59.565 47.826 0.00 0.00 0.00 4.35
2427 2540 0.034896 GTGTGTACTGTGGGGAGTGG 59.965 60.000 0.00 0.00 0.00 4.00
2463 2577 2.939103 GTTGTTCTGTTGAGCTGAGTGT 59.061 45.455 0.00 0.00 0.00 3.55
2467 2581 4.570772 TGTTCTGTTGAGCTGAGTGTTTAC 59.429 41.667 0.00 0.00 0.00 2.01
2720 2881 9.640963 CCTACTCCCTTCGTTCATAATTATAAG 57.359 37.037 0.00 0.00 0.00 1.73
2721 2882 9.640963 CTACTCCCTTCGTTCATAATTATAAGG 57.359 37.037 13.70 13.70 33.37 2.69
2724 2885 7.798071 TCCCTTCGTTCATAATTATAAGGTGT 58.202 34.615 17.16 0.00 31.98 4.16
2760 2929 7.290110 TCAATATGGACTACATACAGACTGG 57.710 40.000 7.51 0.00 44.41 4.00
2777 2946 5.916883 CAGACTGGAATGATTGAACAAACAC 59.083 40.000 0.00 0.00 0.00 3.32
2866 3157 9.725019 AGAACATCTTATAATTGTGAACAGACA 57.275 29.630 2.86 0.00 0.00 3.41
2868 3159 9.725019 AACATCTTATAATTGTGAACAGACAGA 57.275 29.630 2.86 0.00 0.00 3.41
2897 3188 8.428852 ACCATTTAAGCTCCAACAAAAACTTAT 58.571 29.630 0.00 0.00 0.00 1.73
2898 3189 9.921637 CCATTTAAGCTCCAACAAAAACTTATA 57.078 29.630 0.00 0.00 0.00 0.98
2941 3236 4.213564 AGAGAGGAAACAGTGCATAAGG 57.786 45.455 0.00 0.00 0.00 2.69
3221 3534 6.984474 GCTATTAGTGGTGTATAAACTCTGCA 59.016 38.462 0.00 0.00 0.00 4.41
3282 3596 8.157476 ACTCAACTCAAAGTGGTTGTCTATAAT 58.843 33.333 0.00 0.00 42.15 1.28
3283 3597 9.653287 CTCAACTCAAAGTGGTTGTCTATAATA 57.347 33.333 0.00 0.00 42.15 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 115 2.671619 TGTAGCGTTTGCAGGCCC 60.672 61.111 0.00 0.00 46.23 5.80
140 163 2.750637 GAGCCTGGGAGTCGTCGA 60.751 66.667 0.00 0.00 0.00 4.20
583 652 1.280457 GTGAGGAGGTCTTGATGGGT 58.720 55.000 0.00 0.00 0.00 4.51
620 700 3.737266 GTCAACAACGGACGATACAAAGA 59.263 43.478 0.00 0.00 0.00 2.52
741 825 8.506168 ACTAAGAACATGAAGAACACAAAGAA 57.494 30.769 0.00 0.00 0.00 2.52
742 826 8.397906 CAACTAAGAACATGAAGAACACAAAGA 58.602 33.333 0.00 0.00 0.00 2.52
822 906 8.630278 TGTAGATCAGTTTTTAGCGTATTCTC 57.370 34.615 0.00 0.00 0.00 2.87
823 907 8.997621 TTGTAGATCAGTTTTTAGCGTATTCT 57.002 30.769 0.00 0.00 0.00 2.40
824 908 7.846592 GCTTGTAGATCAGTTTTTAGCGTATTC 59.153 37.037 0.00 0.00 0.00 1.75
825 909 7.333423 TGCTTGTAGATCAGTTTTTAGCGTATT 59.667 33.333 0.00 0.00 0.00 1.89
826 910 6.816640 TGCTTGTAGATCAGTTTTTAGCGTAT 59.183 34.615 0.00 0.00 0.00 3.06
827 911 6.160684 TGCTTGTAGATCAGTTTTTAGCGTA 58.839 36.000 0.00 0.00 0.00 4.42
828 912 4.994852 TGCTTGTAGATCAGTTTTTAGCGT 59.005 37.500 0.00 0.00 0.00 5.07
829 913 5.530519 TGCTTGTAGATCAGTTTTTAGCG 57.469 39.130 0.00 0.00 0.00 4.26
830 914 8.642020 CAAATTGCTTGTAGATCAGTTTTTAGC 58.358 33.333 0.00 0.00 0.00 3.09
831 915 9.132521 CCAAATTGCTTGTAGATCAGTTTTTAG 57.867 33.333 0.00 0.00 32.65 1.85
832 916 8.637986 ACCAAATTGCTTGTAGATCAGTTTTTA 58.362 29.630 0.00 0.00 32.65 1.52
833 917 7.500141 ACCAAATTGCTTGTAGATCAGTTTTT 58.500 30.769 0.00 0.00 32.65 1.94
834 918 7.054491 ACCAAATTGCTTGTAGATCAGTTTT 57.946 32.000 0.00 0.00 32.65 2.43
835 919 6.655078 ACCAAATTGCTTGTAGATCAGTTT 57.345 33.333 0.00 0.00 32.65 2.66
836 920 7.168219 TCTACCAAATTGCTTGTAGATCAGTT 58.832 34.615 6.52 0.00 32.65 3.16
837 921 6.711277 TCTACCAAATTGCTTGTAGATCAGT 58.289 36.000 6.52 0.00 32.65 3.41
838 922 6.820656 ACTCTACCAAATTGCTTGTAGATCAG 59.179 38.462 9.78 3.90 32.28 2.90
839 923 6.595326 CACTCTACCAAATTGCTTGTAGATCA 59.405 38.462 9.78 0.00 32.28 2.92
840 924 6.037610 CCACTCTACCAAATTGCTTGTAGATC 59.962 42.308 9.78 0.00 32.28 2.75
841 925 5.882557 CCACTCTACCAAATTGCTTGTAGAT 59.117 40.000 9.78 1.62 32.28 1.98
842 926 5.245531 CCACTCTACCAAATTGCTTGTAGA 58.754 41.667 9.22 9.22 32.65 2.59
843 927 4.396166 CCCACTCTACCAAATTGCTTGTAG 59.604 45.833 2.74 2.74 32.65 2.74
844 928 4.042311 TCCCACTCTACCAAATTGCTTGTA 59.958 41.667 0.00 0.00 32.65 2.41
845 929 3.157087 CCCACTCTACCAAATTGCTTGT 58.843 45.455 0.00 0.00 32.65 3.16
846 930 3.420893 TCCCACTCTACCAAATTGCTTG 58.579 45.455 0.00 0.00 34.52 4.01
847 931 3.806949 TCCCACTCTACCAAATTGCTT 57.193 42.857 0.00 0.00 0.00 3.91
848 932 3.562176 CCTTCCCACTCTACCAAATTGCT 60.562 47.826 0.00 0.00 0.00 3.91
849 933 2.755103 CCTTCCCACTCTACCAAATTGC 59.245 50.000 0.00 0.00 0.00 3.56
850 934 4.019321 TCTCCTTCCCACTCTACCAAATTG 60.019 45.833 0.00 0.00 0.00 2.32
851 935 4.175962 TCTCCTTCCCACTCTACCAAATT 58.824 43.478 0.00 0.00 0.00 1.82
852 936 3.803340 TCTCCTTCCCACTCTACCAAAT 58.197 45.455 0.00 0.00 0.00 2.32
853 937 3.269592 TCTCCTTCCCACTCTACCAAA 57.730 47.619 0.00 0.00 0.00 3.28
854 938 3.269592 TTCTCCTTCCCACTCTACCAA 57.730 47.619 0.00 0.00 0.00 3.67
855 939 2.904434 GTTTCTCCTTCCCACTCTACCA 59.096 50.000 0.00 0.00 0.00 3.25
856 940 2.236644 GGTTTCTCCTTCCCACTCTACC 59.763 54.545 0.00 0.00 0.00 3.18
857 941 3.174779 AGGTTTCTCCTTCCCACTCTAC 58.825 50.000 0.00 0.00 45.67 2.59
858 942 3.562108 AGGTTTCTCCTTCCCACTCTA 57.438 47.619 0.00 0.00 45.67 2.43
859 943 2.424684 AGGTTTCTCCTTCCCACTCT 57.575 50.000 0.00 0.00 45.67 3.24
869 953 1.839424 CATGGGTGGAAGGTTTCTCC 58.161 55.000 0.00 0.00 0.00 3.71
881 965 0.890683 GAGCTTTGGAACCATGGGTG 59.109 55.000 18.09 0.00 35.34 4.61
882 966 0.251787 GGAGCTTTGGAACCATGGGT 60.252 55.000 18.09 10.33 37.65 4.51
883 967 0.972471 GGGAGCTTTGGAACCATGGG 60.972 60.000 18.09 0.00 0.00 4.00
884 968 0.972471 GGGGAGCTTTGGAACCATGG 60.972 60.000 11.19 11.19 0.00 3.66
885 969 0.251742 TGGGGAGCTTTGGAACCATG 60.252 55.000 0.00 0.00 0.00 3.66
886 970 0.712380 ATGGGGAGCTTTGGAACCAT 59.288 50.000 0.00 0.00 34.08 3.55
887 971 0.251742 CATGGGGAGCTTTGGAACCA 60.252 55.000 0.00 0.00 0.00 3.67
888 972 0.251787 ACATGGGGAGCTTTGGAACC 60.252 55.000 0.00 0.00 0.00 3.62
889 973 1.177401 GACATGGGGAGCTTTGGAAC 58.823 55.000 0.00 0.00 0.00 3.62
890 974 0.776810 TGACATGGGGAGCTTTGGAA 59.223 50.000 0.00 0.00 0.00 3.53
891 975 0.038166 GTGACATGGGGAGCTTTGGA 59.962 55.000 0.00 0.00 0.00 3.53
892 976 0.251297 TGTGACATGGGGAGCTTTGG 60.251 55.000 0.00 0.00 0.00 3.28
893 977 1.747355 GATGTGACATGGGGAGCTTTG 59.253 52.381 1.23 0.00 0.00 2.77
894 978 1.679944 CGATGTGACATGGGGAGCTTT 60.680 52.381 1.23 0.00 0.00 3.51
895 979 0.107508 CGATGTGACATGGGGAGCTT 60.108 55.000 1.23 0.00 0.00 3.74
896 980 1.524002 CGATGTGACATGGGGAGCT 59.476 57.895 1.23 0.00 0.00 4.09
897 981 1.524621 CCGATGTGACATGGGGAGC 60.525 63.158 17.66 0.00 0.00 4.70
898 982 0.761187 ATCCGATGTGACATGGGGAG 59.239 55.000 23.59 1.85 0.00 4.30
899 983 1.212375 AATCCGATGTGACATGGGGA 58.788 50.000 23.59 19.06 0.00 4.81
900 984 2.928801 TAATCCGATGTGACATGGGG 57.071 50.000 23.59 14.79 0.00 4.96
901 985 4.216257 GGAATTAATCCGATGTGACATGGG 59.784 45.833 19.12 19.12 38.79 4.00
902 986 5.362556 GGAATTAATCCGATGTGACATGG 57.637 43.478 1.23 0.63 38.79 3.66
959 1043 4.268405 ACGTAGTCAAACAAAGTACAACCG 59.732 41.667 0.00 0.00 29.74 4.44
967 1051 9.784680 ATCACTATACTACGTAGTCAAACAAAG 57.215 33.333 30.53 18.62 43.93 2.77
969 1053 8.186163 CCATCACTATACTACGTAGTCAAACAA 58.814 37.037 30.53 13.49 43.93 2.83
970 1054 7.337689 ACCATCACTATACTACGTAGTCAAACA 59.662 37.037 30.53 14.24 43.93 2.83
971 1055 7.701445 ACCATCACTATACTACGTAGTCAAAC 58.299 38.462 30.53 0.00 43.93 2.93
972 1056 7.772292 AGACCATCACTATACTACGTAGTCAAA 59.228 37.037 30.53 15.00 43.93 2.69
973 1057 7.226128 CAGACCATCACTATACTACGTAGTCAA 59.774 40.741 30.53 18.50 43.93 3.18
974 1058 6.704937 CAGACCATCACTATACTACGTAGTCA 59.295 42.308 30.53 18.54 43.93 3.41
975 1059 6.927936 TCAGACCATCACTATACTACGTAGTC 59.072 42.308 30.53 12.52 43.93 2.59
1015 1099 2.615912 GCGCAGATGCTTTCCTAGAAAT 59.384 45.455 0.30 0.00 39.32 2.17
1067 1151 1.070289 GGACGAGGACAAGAAACAGGT 59.930 52.381 0.00 0.00 0.00 4.00
1070 1154 1.000607 CGAGGACGAGGACAAGAAACA 60.001 52.381 0.00 0.00 42.66 2.83
1071 1155 1.669211 CCGAGGACGAGGACAAGAAAC 60.669 57.143 0.00 0.00 42.66 2.78
1153 1237 7.253684 GCAAGAACAAGCGGTCGATATATATAC 60.254 40.741 0.00 0.00 0.00 1.47
1223 1310 4.702081 GGATCGATCGGCGGACGG 62.702 72.222 18.81 4.69 44.45 4.79
1478 1573 4.124351 GCCGTCGATGGACCACGA 62.124 66.667 28.06 13.06 40.17 4.35
1519 1617 2.878406 AGAACGCAGCCGCATTAATAAT 59.122 40.909 0.00 0.00 38.40 1.28
1520 1618 2.031560 CAGAACGCAGCCGCATTAATAA 59.968 45.455 0.00 0.00 38.40 1.40
1521 1619 1.597195 CAGAACGCAGCCGCATTAATA 59.403 47.619 0.00 0.00 38.40 0.98
1678 1788 0.252057 TTGGACATGAGGAGGACGGA 60.252 55.000 0.00 0.00 0.00 4.69
1682 1792 1.573108 GACCTTGGACATGAGGAGGA 58.427 55.000 0.00 0.00 36.84 3.71
1684 1794 1.134965 GTCGACCTTGGACATGAGGAG 60.135 57.143 3.51 0.00 36.84 3.69
1921 2031 0.323178 CCCAGCTTGTCCTTGAGCAT 60.323 55.000 0.00 0.00 41.31 3.79
2154 2264 2.561733 TTCGCTTGTAGATCACCTCG 57.438 50.000 0.00 0.00 0.00 4.63
2386 2496 1.956477 ACCTGCAGTGAATTTGTGGAC 59.044 47.619 13.81 0.00 0.00 4.02
2427 2540 4.741676 CAGAACAACCTGCATTTCAGTTTC 59.258 41.667 0.00 0.00 41.25 2.78
2463 2577 9.585369 TCATGCCCATTATCAATTATGAGTAAA 57.415 29.630 0.00 0.00 39.39 2.01
2467 2581 6.860080 GGTCATGCCCATTATCAATTATGAG 58.140 40.000 0.00 0.00 39.39 2.90
2484 2598 4.081531 TCAAATTTCAATCAGGGGTCATGC 60.082 41.667 0.00 0.00 0.00 4.06
2569 2689 3.990469 GCGCTGCTAGATTAGATTTGCTA 59.010 43.478 0.00 0.00 0.00 3.49
2646 2767 3.291809 TCTGATGTTTGCATTGCTGTG 57.708 42.857 10.49 0.00 35.07 3.66
2733 2894 9.770097 CAGTCTGTATGTAGTCCATATTGAAAT 57.230 33.333 0.00 0.00 38.29 2.17
2735 2896 7.563556 TCCAGTCTGTATGTAGTCCATATTGAA 59.436 37.037 0.00 0.00 38.29 2.69
2750 2919 7.448161 TGTTTGTTCAATCATTCCAGTCTGTAT 59.552 33.333 0.00 0.00 0.00 2.29
2754 2923 5.593909 TGTGTTTGTTCAATCATTCCAGTCT 59.406 36.000 0.69 0.00 0.00 3.24
2760 2929 9.081997 TGTTTTAGTGTGTTTGTTCAATCATTC 57.918 29.630 0.69 0.00 0.00 2.67
2822 3113 3.186345 TACTCCCACGGCTGAGTAG 57.814 57.895 0.00 0.00 41.80 2.57
2866 3157 5.499004 TGTTGGAGCTTAAATGGTACTCT 57.501 39.130 0.00 0.00 0.00 3.24
2868 3159 6.969993 TTTTGTTGGAGCTTAAATGGTACT 57.030 33.333 0.00 0.00 0.00 2.73
2897 3188 9.778741 CTCTTCCTTTGGTAAATATGCATACTA 57.221 33.333 8.99 0.80 0.00 1.82
2898 3189 8.494433 TCTCTTCCTTTGGTAAATATGCATACT 58.506 33.333 8.99 0.00 0.00 2.12
2941 3236 4.342772 CACGGCTGAGTATACAAAATTGC 58.657 43.478 5.50 0.84 0.00 3.56
3282 3596 5.598830 GGAGTGATCTGATAGGTGTTCCTTA 59.401 44.000 0.00 0.00 42.12 2.69
3283 3597 4.407296 GGAGTGATCTGATAGGTGTTCCTT 59.593 45.833 0.00 0.00 42.12 3.36


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

AutoCloner maintained by Alex Coulton.