Multiple sequence alignment - TraesCS3B01G399400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G399400 chr3B 100.000 3950 0 0 1 3950 630585886 630589835 0 7295
1 TraesCS3B01G399400 chr3B 95.844 770 31 1 1 769 697089957 697089188 0 1243
2 TraesCS3B01G399400 chr3B 89.373 781 68 15 1 769 603460207 603460984 0 968
3 TraesCS3B01G399400 chr3D 95.649 2988 93 17 969 3950 474427764 474430720 0 4763
4 TraesCS3B01G399400 chr3D 96.055 2180 54 6 866 3040 474427686 474429838 0 3520
5 TraesCS3B01G399400 chr3A 94.167 3086 114 25 866 3950 616704426 616707446 0 4641
6 TraesCS3B01G399400 chr5D 93.782 772 42 6 1 769 378646106 378645338 0 1155
7 TraesCS3B01G399400 chr1A 92.774 775 47 7 1 769 130135591 130134820 0 1112
8 TraesCS3B01G399400 chr6A 92.506 774 48 9 1 769 593308190 593308958 0 1099
9 TraesCS3B01G399400 chr7A 92.358 772 54 5 1 769 41821031 41820262 0 1094
10 TraesCS3B01G399400 chr5B 91.417 769 56 9 5 769 631840990 631840228 0 1046
11 TraesCS3B01G399400 chr6B 91.395 767 56 7 6 769 631229624 631230383 0 1042
12 TraesCS3B01G399400 chr2A 89.313 786 59 22 1 769 698099109 698099886 0 963


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 TraesCS3B01G399400 chr3B 630585886 630589835 3949 False 7295.0 7295 100.000 1 3950 1 chr3B.!!$F2 3949
1 TraesCS3B01G399400 chr3B 697089188 697089957 769 True 1243.0 1243 95.844 1 769 1 chr3B.!!$R1 768
2 TraesCS3B01G399400 chr3B 603460207 603460984 777 False 968.0 968 89.373 1 769 1 chr3B.!!$F1 768
3 TraesCS3B01G399400 chr3D 474427686 474430720 3034 False 4141.5 4763 95.852 866 3950 2 chr3D.!!$F1 3084
4 TraesCS3B01G399400 chr3A 616704426 616707446 3020 False 4641.0 4641 94.167 866 3950 1 chr3A.!!$F1 3084
5 TraesCS3B01G399400 chr5D 378645338 378646106 768 True 1155.0 1155 93.782 1 769 1 chr5D.!!$R1 768
6 TraesCS3B01G399400 chr1A 130134820 130135591 771 True 1112.0 1112 92.774 1 769 1 chr1A.!!$R1 768
7 TraesCS3B01G399400 chr6A 593308190 593308958 768 False 1099.0 1099 92.506 1 769 1 chr6A.!!$F1 768
8 TraesCS3B01G399400 chr7A 41820262 41821031 769 True 1094.0 1094 92.358 1 769 1 chr7A.!!$R1 768
9 TraesCS3B01G399400 chr5B 631840228 631840990 762 True 1046.0 1046 91.417 5 769 1 chr5B.!!$R1 764
10 TraesCS3B01G399400 chr6B 631229624 631230383 759 False 1042.0 1042 91.395 6 769 1 chr6B.!!$F1 763
11 TraesCS3B01G399400 chr2A 698099109 698099886 777 False 963.0 963 89.313 1 769 1 chr2A.!!$F1 768

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
858 937 0.179067 TTTGGTCGGCTTGTTCGAGT 60.179 50.000 0.00 0.0 37.31 4.18 F
1322 1403 0.100682 TTCGAGAGAATTCCGAGCCG 59.899 55.000 0.65 0.0 46.92 5.52 F
1762 1843 1.409064 CAATAGCTGGTAGGACGCAGA 59.591 52.381 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1751 0.034767 TCCTTCTGCAAGCCATCCAG 60.035 55.000 0.00 0.0 0.0 3.86 R
2226 2307 1.135141 TGTTTCACACTTGGTTGCAGC 60.135 47.619 0.00 0.0 0.0 5.25 R
3452 3538 0.107643 TCCAGCAACACGTGATCCAA 59.892 50.000 25.01 0.0 0.0 3.53 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
184 185 6.044404 AGAGGAGATTGAAGTAGGTTTTCCAA 59.956 38.462 0.00 0.00 43.73 3.53
224 225 0.761802 GTGGGAGAGGATGATGGGAC 59.238 60.000 0.00 0.00 0.00 4.46
479 488 4.270153 ACTGGGAGGGTGGAGGCA 62.270 66.667 0.00 0.00 0.00 4.75
510 519 4.035102 GTGGTGGTGGAGGGAGGC 62.035 72.222 0.00 0.00 0.00 4.70
513 522 4.416738 GTGGTGGAGGGAGGCAGC 62.417 72.222 0.00 0.00 0.00 5.25
771 850 8.298030 TGTGCTAAATACATATCTCAACATCG 57.702 34.615 0.00 0.00 0.00 3.84
772 851 8.141268 TGTGCTAAATACATATCTCAACATCGA 58.859 33.333 0.00 0.00 0.00 3.59
773 852 9.144747 GTGCTAAATACATATCTCAACATCGAT 57.855 33.333 0.00 0.00 0.00 3.59
774 853 9.358872 TGCTAAATACATATCTCAACATCGATC 57.641 33.333 0.00 0.00 0.00 3.69
775 854 8.812329 GCTAAATACATATCTCAACATCGATCC 58.188 37.037 0.00 0.00 0.00 3.36
776 855 9.860898 CTAAATACATATCTCAACATCGATCCA 57.139 33.333 0.00 0.00 0.00 3.41
778 857 9.559732 AAATACATATCTCAACATCGATCCAAA 57.440 29.630 0.00 0.00 0.00 3.28
779 858 6.851222 ACATATCTCAACATCGATCCAAAC 57.149 37.500 0.00 0.00 0.00 2.93
780 859 6.348498 ACATATCTCAACATCGATCCAAACA 58.652 36.000 0.00 0.00 0.00 2.83
781 860 6.823182 ACATATCTCAACATCGATCCAAACAA 59.177 34.615 0.00 0.00 0.00 2.83
782 861 7.336679 ACATATCTCAACATCGATCCAAACAAA 59.663 33.333 0.00 0.00 0.00 2.83
783 862 6.573664 ATCTCAACATCGATCCAAACAAAA 57.426 33.333 0.00 0.00 0.00 2.44
784 863 5.757886 TCTCAACATCGATCCAAACAAAAC 58.242 37.500 0.00 0.00 0.00 2.43
785 864 4.532276 TCAACATCGATCCAAACAAAACG 58.468 39.130 0.00 0.00 0.00 3.60
786 865 2.928694 ACATCGATCCAAACAAAACGC 58.071 42.857 0.00 0.00 0.00 4.84
787 866 1.904412 CATCGATCCAAACAAAACGCG 59.096 47.619 3.53 3.53 0.00 6.01
788 867 0.236187 TCGATCCAAACAAAACGCGG 59.764 50.000 12.47 0.00 0.00 6.46
789 868 0.236187 CGATCCAAACAAAACGCGGA 59.764 50.000 12.47 0.00 0.00 5.54
790 869 1.681825 GATCCAAACAAAACGCGGAC 58.318 50.000 12.47 0.00 0.00 4.79
791 870 1.002251 GATCCAAACAAAACGCGGACA 60.002 47.619 12.47 0.00 0.00 4.02
792 871 1.025812 TCCAAACAAAACGCGGACAT 58.974 45.000 12.47 0.00 0.00 3.06
793 872 1.002251 TCCAAACAAAACGCGGACATC 60.002 47.619 12.47 0.00 0.00 3.06
794 873 1.041726 CAAACAAAACGCGGACATCG 58.958 50.000 12.47 0.00 42.76 3.84
795 874 0.938713 AAACAAAACGCGGACATCGA 59.061 45.000 12.47 0.00 42.43 3.59
796 875 0.233848 AACAAAACGCGGACATCGAC 59.766 50.000 12.47 0.00 42.43 4.20
797 876 1.131826 CAAAACGCGGACATCGACC 59.868 57.895 12.47 0.00 42.43 4.79
803 882 2.102357 CGGACATCGACCGGACAG 59.898 66.667 9.46 0.00 45.65 3.51
804 883 2.404186 CGGACATCGACCGGACAGA 61.404 63.158 9.46 4.32 45.65 3.41
805 884 1.139095 GGACATCGACCGGACAGAC 59.861 63.158 9.46 0.00 0.00 3.51
806 885 1.226323 GACATCGACCGGACAGACG 60.226 63.158 9.46 5.93 0.00 4.18
807 886 1.642037 GACATCGACCGGACAGACGA 61.642 60.000 9.46 11.46 39.01 4.20
808 887 1.226323 CATCGACCGGACAGACGAC 60.226 63.158 9.46 0.00 37.58 4.34
809 888 1.673337 ATCGACCGGACAGACGACA 60.673 57.895 9.46 0.00 37.58 4.35
810 889 1.919956 ATCGACCGGACAGACGACAC 61.920 60.000 9.46 0.00 37.58 3.67
811 890 2.900167 CGACCGGACAGACGACACA 61.900 63.158 9.46 0.00 35.47 3.72
812 891 1.361271 GACCGGACAGACGACACAA 59.639 57.895 9.46 0.00 35.47 3.33
813 892 0.249155 GACCGGACAGACGACACAAA 60.249 55.000 9.46 0.00 35.47 2.83
814 893 0.529119 ACCGGACAGACGACACAAAC 60.529 55.000 9.46 0.00 35.47 2.93
815 894 0.528901 CCGGACAGACGACACAAACA 60.529 55.000 0.00 0.00 35.47 2.83
816 895 0.852777 CGGACAGACGACACAAACAG 59.147 55.000 0.00 0.00 35.47 3.16
817 896 1.535226 CGGACAGACGACACAAACAGA 60.535 52.381 0.00 0.00 35.47 3.41
818 897 2.755650 GGACAGACGACACAAACAGAT 58.244 47.619 0.00 0.00 0.00 2.90
819 898 3.610821 CGGACAGACGACACAAACAGATA 60.611 47.826 0.00 0.00 35.47 1.98
820 899 4.304110 GGACAGACGACACAAACAGATAA 58.696 43.478 0.00 0.00 0.00 1.75
821 900 4.748102 GGACAGACGACACAAACAGATAAA 59.252 41.667 0.00 0.00 0.00 1.40
822 901 5.235616 GGACAGACGACACAAACAGATAAAA 59.764 40.000 0.00 0.00 0.00 1.52
823 902 6.238266 GGACAGACGACACAAACAGATAAAAA 60.238 38.462 0.00 0.00 0.00 1.94
839 918 1.995376 AAAAACGGACAGAATGGGCT 58.005 45.000 0.00 0.00 43.62 5.19
840 919 1.995376 AAAACGGACAGAATGGGCTT 58.005 45.000 0.00 0.00 43.62 4.35
841 920 1.995376 AAACGGACAGAATGGGCTTT 58.005 45.000 0.00 0.00 43.62 3.51
842 921 1.247567 AACGGACAGAATGGGCTTTG 58.752 50.000 0.00 0.00 43.62 2.77
843 922 0.609131 ACGGACAGAATGGGCTTTGG 60.609 55.000 0.00 0.00 43.62 3.28
844 923 0.609131 CGGACAGAATGGGCTTTGGT 60.609 55.000 0.00 0.00 43.62 3.67
845 924 1.177401 GGACAGAATGGGCTTTGGTC 58.823 55.000 0.00 0.00 43.62 4.02
846 925 0.804989 GACAGAATGGGCTTTGGTCG 59.195 55.000 0.00 0.00 43.62 4.79
847 926 0.609131 ACAGAATGGGCTTTGGTCGG 60.609 55.000 0.00 0.00 43.62 4.79
848 927 1.678970 AGAATGGGCTTTGGTCGGC 60.679 57.895 0.00 0.00 0.00 5.54
849 928 1.678970 GAATGGGCTTTGGTCGGCT 60.679 57.895 0.00 0.00 0.00 5.52
850 929 1.228862 AATGGGCTTTGGTCGGCTT 60.229 52.632 0.00 0.00 0.00 4.35
851 930 1.535204 AATGGGCTTTGGTCGGCTTG 61.535 55.000 0.00 0.00 0.00 4.01
852 931 2.597510 GGGCTTTGGTCGGCTTGT 60.598 61.111 0.00 0.00 0.00 3.16
853 932 2.200337 GGGCTTTGGTCGGCTTGTT 61.200 57.895 0.00 0.00 0.00 2.83
854 933 1.285950 GGCTTTGGTCGGCTTGTTC 59.714 57.895 0.00 0.00 0.00 3.18
855 934 1.082104 GCTTTGGTCGGCTTGTTCG 60.082 57.895 0.00 0.00 0.00 3.95
856 935 1.503818 GCTTTGGTCGGCTTGTTCGA 61.504 55.000 0.00 0.00 0.00 3.71
857 936 0.512952 CTTTGGTCGGCTTGTTCGAG 59.487 55.000 0.00 0.00 37.31 4.04
858 937 0.179067 TTTGGTCGGCTTGTTCGAGT 60.179 50.000 0.00 0.00 37.31 4.18
859 938 0.179067 TTGGTCGGCTTGTTCGAGTT 60.179 50.000 0.00 0.00 37.31 3.01
860 939 0.878523 TGGTCGGCTTGTTCGAGTTG 60.879 55.000 0.00 0.00 37.31 3.16
861 940 1.204312 GTCGGCTTGTTCGAGTTGC 59.796 57.895 0.00 0.00 37.31 4.17
862 941 1.069090 TCGGCTTGTTCGAGTTGCT 59.931 52.632 0.00 0.00 32.51 3.91
863 942 0.944311 TCGGCTTGTTCGAGTTGCTC 60.944 55.000 0.00 0.00 32.51 4.26
864 943 0.946221 CGGCTTGTTCGAGTTGCTCT 60.946 55.000 0.00 0.00 0.00 4.09
870 949 4.670221 GCTTGTTCGAGTTGCTCTTATTGG 60.670 45.833 0.00 0.00 0.00 3.16
923 1003 2.180204 GCATTGCCAGTCGCGGTAT 61.180 57.895 6.13 0.00 42.08 2.73
940 1021 2.030805 GGTATCCAAATTCGCCATGCTC 60.031 50.000 0.00 0.00 0.00 4.26
1322 1403 0.100682 TTCGAGAGAATTCCGAGCCG 59.899 55.000 0.65 0.00 46.92 5.52
1480 1561 2.659610 GGCTTGACGAGGACAGCT 59.340 61.111 0.00 0.00 0.00 4.24
1560 1641 1.889105 CGTGTTCAGGTGCTGTGCT 60.889 57.895 0.00 0.00 32.61 4.40
1677 1758 3.208594 CATGTACATGTGGTCTGGATGG 58.791 50.000 24.91 0.00 34.23 3.51
1698 1779 2.172483 TTGCAGAAGGAGAGGCCGTC 62.172 60.000 0.00 0.00 44.48 4.79
1746 1827 7.446931 ACAGTTGTGTCATTCAATACCACAATA 59.553 33.333 14.04 0.00 44.81 1.90
1756 1837 4.966168 TCAATACCACAATAGCTGGTAGGA 59.034 41.667 7.72 5.42 45.47 2.94
1762 1843 1.409064 CAATAGCTGGTAGGACGCAGA 59.591 52.381 0.00 0.00 0.00 4.26
1794 1875 2.874701 CGAGGGAGCATTGGAGTATTTG 59.125 50.000 0.00 0.00 0.00 2.32
1824 1905 2.040009 GAGGTATTGGGCTAGCGGCA 62.040 60.000 9.00 0.00 44.01 5.69
1867 1948 9.982651 TTAGTATTATTACCTGTTGCTCAGATC 57.017 33.333 10.22 0.00 46.27 2.75
1933 2014 2.054799 AGGCTGGAGTTGACAAGGTTA 58.945 47.619 0.00 0.00 0.00 2.85
2021 2102 9.533831 AAGAGTTTATTCTGGTTATTGTGGATT 57.466 29.630 0.00 0.00 0.00 3.01
2226 2307 5.041191 AGCTTATGACCAAGACTTATGGG 57.959 43.478 0.00 0.00 42.48 4.00
2271 2352 7.276658 CACTACACTTGTATTGTGGATCTTCTC 59.723 40.741 0.00 0.00 39.52 2.87
2399 2480 1.202114 GAATTTTGACATGGCCGAGCA 59.798 47.619 0.00 0.00 0.00 4.26
2746 2827 4.131596 GGTTAGTTTAACTCACCACAGCA 58.868 43.478 19.99 0.00 41.11 4.41
2826 2907 7.009265 CGAATAATGAAGAATCTACGTGTGTGT 59.991 37.037 0.00 0.00 0.00 3.72
3040 3124 6.018751 GGAATTTTTGAAGTCAGCAGGTTTTC 60.019 38.462 0.00 0.00 0.00 2.29
3041 3125 5.398603 TTTTTGAAGTCAGCAGGTTTTCA 57.601 34.783 0.00 0.00 0.00 2.69
3042 3126 5.596836 TTTTGAAGTCAGCAGGTTTTCAT 57.403 34.783 0.00 0.00 0.00 2.57
3043 3127 4.572985 TTGAAGTCAGCAGGTTTTCATG 57.427 40.909 0.00 0.00 34.46 3.07
3044 3128 2.886523 TGAAGTCAGCAGGTTTTCATGG 59.113 45.455 0.00 0.00 31.73 3.66
3045 3129 2.957402 AGTCAGCAGGTTTTCATGGA 57.043 45.000 0.00 0.00 31.73 3.41
3046 3130 2.787994 AGTCAGCAGGTTTTCATGGAG 58.212 47.619 0.00 0.00 31.73 3.86
3047 3131 2.107204 AGTCAGCAGGTTTTCATGGAGT 59.893 45.455 0.00 0.00 31.73 3.85
3048 3132 2.887152 GTCAGCAGGTTTTCATGGAGTT 59.113 45.455 0.00 0.00 31.73 3.01
3049 3133 3.319122 GTCAGCAGGTTTTCATGGAGTTT 59.681 43.478 0.00 0.00 31.73 2.66
3050 3134 3.960102 TCAGCAGGTTTTCATGGAGTTTT 59.040 39.130 0.00 0.00 31.73 2.43
3051 3135 4.405358 TCAGCAGGTTTTCATGGAGTTTTT 59.595 37.500 0.00 0.00 31.73 1.94
3052 3136 4.508861 CAGCAGGTTTTCATGGAGTTTTTG 59.491 41.667 0.00 0.00 31.73 2.44
3053 3137 4.405358 AGCAGGTTTTCATGGAGTTTTTGA 59.595 37.500 0.00 0.00 31.73 2.69
3054 3138 5.104982 AGCAGGTTTTCATGGAGTTTTTGAA 60.105 36.000 0.00 0.00 31.73 2.69
3055 3139 5.234972 GCAGGTTTTCATGGAGTTTTTGAAG 59.765 40.000 0.00 0.00 31.54 3.02
3056 3140 6.340522 CAGGTTTTCATGGAGTTTTTGAAGT 58.659 36.000 0.00 0.00 31.54 3.01
3057 3141 6.476706 CAGGTTTTCATGGAGTTTTTGAAGTC 59.523 38.462 0.00 0.00 31.54 3.01
3058 3142 6.154363 AGGTTTTCATGGAGTTTTTGAAGTCA 59.846 34.615 0.00 0.00 31.54 3.41
3059 3143 6.476706 GGTTTTCATGGAGTTTTTGAAGTCAG 59.523 38.462 0.00 0.00 31.54 3.51
3060 3144 4.836125 TCATGGAGTTTTTGAAGTCAGC 57.164 40.909 0.00 0.00 0.00 4.26
3061 3145 4.206375 TCATGGAGTTTTTGAAGTCAGCA 58.794 39.130 0.00 0.00 0.00 4.41
3062 3146 4.276678 TCATGGAGTTTTTGAAGTCAGCAG 59.723 41.667 0.00 0.00 0.00 4.24
3063 3147 2.951642 TGGAGTTTTTGAAGTCAGCAGG 59.048 45.455 0.00 0.00 0.00 4.85
3064 3148 2.952310 GGAGTTTTTGAAGTCAGCAGGT 59.048 45.455 0.00 0.00 0.00 4.00
3065 3149 3.381590 GGAGTTTTTGAAGTCAGCAGGTT 59.618 43.478 0.00 0.00 0.00 3.50
3066 3150 4.142160 GGAGTTTTTGAAGTCAGCAGGTTT 60.142 41.667 0.00 0.00 0.00 3.27
3067 3151 5.405935 AGTTTTTGAAGTCAGCAGGTTTT 57.594 34.783 0.00 0.00 0.00 2.43
3153 3237 2.600790 TCCGACCTGTACTCTGGAAAA 58.399 47.619 7.04 0.00 36.65 2.29
3241 3327 6.528321 TCATTGCCTTCTATAAGTGATGGAG 58.472 40.000 0.00 0.00 32.46 3.86
3322 3408 9.002600 GTATGATATGAATATTTGTGGACAGCA 57.997 33.333 0.00 0.00 0.00 4.41
3331 3417 7.886629 ATATTTGTGGACAGCACTGAAATAT 57.113 32.000 4.31 6.56 0.00 1.28
3339 3425 8.462016 GTGGACAGCACTGAAATATAAGATTTT 58.538 33.333 4.31 0.00 0.00 1.82
3371 3457 5.796350 ACAACTAATTATCTGGTTGTCGC 57.204 39.130 12.68 0.00 45.80 5.19
3392 3478 4.442052 CGCTGTCCCATCTTTCATCTCTTA 60.442 45.833 0.00 0.00 0.00 2.10
3395 3481 4.782691 TGTCCCATCTTTCATCTCTTACCA 59.217 41.667 0.00 0.00 0.00 3.25
3396 3482 5.250543 TGTCCCATCTTTCATCTCTTACCAA 59.749 40.000 0.00 0.00 0.00 3.67
3397 3483 6.069440 TGTCCCATCTTTCATCTCTTACCAAT 60.069 38.462 0.00 0.00 0.00 3.16
3398 3484 7.127186 TGTCCCATCTTTCATCTCTTACCAATA 59.873 37.037 0.00 0.00 0.00 1.90
3399 3485 8.160106 GTCCCATCTTTCATCTCTTACCAATAT 58.840 37.037 0.00 0.00 0.00 1.28
3452 3538 3.776969 TCTGCTCAGGATGGTCATAAAGT 59.223 43.478 0.00 0.00 36.16 2.66
3460 3546 5.297776 CAGGATGGTCATAAAGTTGGATCAC 59.702 44.000 0.00 0.00 0.00 3.06
3510 3597 3.181477 CCTTCTGAGAGCATGACAGTAGG 60.181 52.174 14.94 14.94 40.65 3.18
3544 3631 5.163530 TGCAATTATACCTGGAGCAACAATG 60.164 40.000 0.00 0.00 0.00 2.82
3548 3635 0.185901 ACCTGGAGCAACAATGGTGT 59.814 50.000 0.00 0.00 40.75 4.16
3549 3636 0.599558 CCTGGAGCAACAATGGTGTG 59.400 55.000 0.00 0.00 38.27 3.82
3657 3745 8.854979 TTTTCATTTCGCTGGATGTATATTTG 57.145 30.769 0.00 0.00 0.00 2.32
3659 3747 4.829064 TTTCGCTGGATGTATATTTGGC 57.171 40.909 0.00 0.00 0.00 4.52
3733 3822 5.810587 GCAATAGTTCCACTGAATCTCGTTA 59.189 40.000 0.00 0.00 31.98 3.18
3754 3843 8.877779 TCGTTATGCATTGAAATTAATTTTGGG 58.122 29.630 14.45 6.66 0.00 4.12
3787 3876 0.901124 TTGGCTGTGCTTGGTTTTGT 59.099 45.000 0.00 0.00 0.00 2.83
3832 3921 3.254657 CCTTTTTGAGGTCATGGCGTTTA 59.745 43.478 0.00 0.00 40.95 2.01
3892 3981 3.004839 GGTTTCTTTCTGTTCCCTCTTGC 59.995 47.826 0.00 0.00 0.00 4.01
3917 4006 5.763698 TGCTCATCCATTTGATCTCTTGATC 59.236 40.000 0.00 0.00 46.89 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.101399 CTCTCCGGACATCTTCCACG 59.899 60.000 0.00 0.00 46.29 4.94
184 185 3.262420 CACCTTCGCAAACTACTATGCT 58.738 45.455 0.00 0.00 40.39 3.79
224 225 1.690893 ACATCCACCTCTCCGATCATG 59.309 52.381 0.00 0.00 0.00 3.07
225 226 2.094100 ACATCCACCTCTCCGATCAT 57.906 50.000 0.00 0.00 0.00 2.45
462 470 4.270153 TGCCTCCACCCTCCCAGT 62.270 66.667 0.00 0.00 0.00 4.00
769 848 0.236187 CCGCGTTTTGTTTGGATCGA 59.764 50.000 4.92 0.00 0.00 3.59
770 849 0.236187 TCCGCGTTTTGTTTGGATCG 59.764 50.000 4.92 0.00 0.00 3.69
771 850 1.002251 TGTCCGCGTTTTGTTTGGATC 60.002 47.619 4.92 0.00 0.00 3.36
772 851 1.025812 TGTCCGCGTTTTGTTTGGAT 58.974 45.000 4.92 0.00 0.00 3.41
773 852 1.002251 GATGTCCGCGTTTTGTTTGGA 60.002 47.619 4.92 0.00 0.00 3.53
774 853 1.404477 GATGTCCGCGTTTTGTTTGG 58.596 50.000 4.92 0.00 0.00 3.28
775 854 1.041726 CGATGTCCGCGTTTTGTTTG 58.958 50.000 4.92 0.00 0.00 2.93
776 855 0.938713 TCGATGTCCGCGTTTTGTTT 59.061 45.000 4.92 0.00 38.37 2.83
777 856 0.233848 GTCGATGTCCGCGTTTTGTT 59.766 50.000 4.92 0.00 38.37 2.83
778 857 1.562575 GGTCGATGTCCGCGTTTTGT 61.563 55.000 4.92 0.00 38.37 2.83
779 858 1.131826 GGTCGATGTCCGCGTTTTG 59.868 57.895 4.92 0.00 38.37 2.44
780 859 2.377310 CGGTCGATGTCCGCGTTTT 61.377 57.895 4.92 0.00 41.48 2.43
781 860 2.807895 CGGTCGATGTCCGCGTTT 60.808 61.111 4.92 0.00 41.48 3.60
782 861 4.789075 CCGGTCGATGTCCGCGTT 62.789 66.667 4.92 0.00 45.71 4.84
785 864 4.124351 TGTCCGGTCGATGTCCGC 62.124 66.667 7.40 0.00 45.71 5.54
786 865 2.102357 CTGTCCGGTCGATGTCCG 59.898 66.667 0.00 6.00 46.49 4.79
787 866 1.139095 GTCTGTCCGGTCGATGTCC 59.861 63.158 0.00 0.00 0.00 4.02
788 867 1.226323 CGTCTGTCCGGTCGATGTC 60.226 63.158 0.00 0.00 0.00 3.06
789 868 1.673337 TCGTCTGTCCGGTCGATGT 60.673 57.895 0.00 0.00 0.00 3.06
790 869 1.226323 GTCGTCTGTCCGGTCGATG 60.226 63.158 0.00 4.01 34.93 3.84
791 870 1.673337 TGTCGTCTGTCCGGTCGAT 60.673 57.895 0.00 0.00 34.93 3.59
792 871 2.281002 TGTCGTCTGTCCGGTCGA 60.281 61.111 0.00 2.91 0.00 4.20
793 872 2.126965 GTGTCGTCTGTCCGGTCG 60.127 66.667 0.00 0.34 0.00 4.79
794 873 0.249155 TTTGTGTCGTCTGTCCGGTC 60.249 55.000 0.00 0.00 0.00 4.79
795 874 0.529119 GTTTGTGTCGTCTGTCCGGT 60.529 55.000 0.00 0.00 0.00 5.28
796 875 0.528901 TGTTTGTGTCGTCTGTCCGG 60.529 55.000 0.00 0.00 0.00 5.14
797 876 0.852777 CTGTTTGTGTCGTCTGTCCG 59.147 55.000 0.00 0.00 0.00 4.79
798 877 2.218953 TCTGTTTGTGTCGTCTGTCC 57.781 50.000 0.00 0.00 0.00 4.02
799 878 5.900339 TTTATCTGTTTGTGTCGTCTGTC 57.100 39.130 0.00 0.00 0.00 3.51
800 879 6.671614 TTTTTATCTGTTTGTGTCGTCTGT 57.328 33.333 0.00 0.00 0.00 3.41
820 899 1.995376 AGCCCATTCTGTCCGTTTTT 58.005 45.000 0.00 0.00 0.00 1.94
821 900 1.995376 AAGCCCATTCTGTCCGTTTT 58.005 45.000 0.00 0.00 0.00 2.43
822 901 1.613437 CAAAGCCCATTCTGTCCGTTT 59.387 47.619 0.00 0.00 0.00 3.60
823 902 1.247567 CAAAGCCCATTCTGTCCGTT 58.752 50.000 0.00 0.00 0.00 4.44
824 903 0.609131 CCAAAGCCCATTCTGTCCGT 60.609 55.000 0.00 0.00 0.00 4.69
825 904 0.609131 ACCAAAGCCCATTCTGTCCG 60.609 55.000 0.00 0.00 0.00 4.79
826 905 1.177401 GACCAAAGCCCATTCTGTCC 58.823 55.000 0.00 0.00 0.00 4.02
827 906 0.804989 CGACCAAAGCCCATTCTGTC 59.195 55.000 0.00 0.00 0.00 3.51
828 907 0.609131 CCGACCAAAGCCCATTCTGT 60.609 55.000 0.00 0.00 0.00 3.41
829 908 1.937546 GCCGACCAAAGCCCATTCTG 61.938 60.000 0.00 0.00 0.00 3.02
830 909 1.678970 GCCGACCAAAGCCCATTCT 60.679 57.895 0.00 0.00 0.00 2.40
831 910 1.250840 AAGCCGACCAAAGCCCATTC 61.251 55.000 0.00 0.00 0.00 2.67
832 911 1.228862 AAGCCGACCAAAGCCCATT 60.229 52.632 0.00 0.00 0.00 3.16
833 912 1.978617 CAAGCCGACCAAAGCCCAT 60.979 57.895 0.00 0.00 0.00 4.00
834 913 2.597217 CAAGCCGACCAAAGCCCA 60.597 61.111 0.00 0.00 0.00 5.36
835 914 2.142357 GAACAAGCCGACCAAAGCCC 62.142 60.000 0.00 0.00 0.00 5.19
836 915 1.285950 GAACAAGCCGACCAAAGCC 59.714 57.895 0.00 0.00 0.00 4.35
837 916 1.082104 CGAACAAGCCGACCAAAGC 60.082 57.895 0.00 0.00 0.00 3.51
838 917 0.512952 CTCGAACAAGCCGACCAAAG 59.487 55.000 0.00 0.00 32.18 2.77
839 918 0.179067 ACTCGAACAAGCCGACCAAA 60.179 50.000 0.00 0.00 32.18 3.28
840 919 0.179067 AACTCGAACAAGCCGACCAA 60.179 50.000 0.00 0.00 32.18 3.67
841 920 0.878523 CAACTCGAACAAGCCGACCA 60.879 55.000 0.00 0.00 32.18 4.02
842 921 1.860078 CAACTCGAACAAGCCGACC 59.140 57.895 0.00 0.00 32.18 4.79
843 922 1.204312 GCAACTCGAACAAGCCGAC 59.796 57.895 0.00 0.00 32.18 4.79
844 923 0.944311 GAGCAACTCGAACAAGCCGA 60.944 55.000 0.00 0.00 34.61 5.54
845 924 0.946221 AGAGCAACTCGAACAAGCCG 60.946 55.000 0.00 0.00 35.36 5.52
846 925 1.230324 AAGAGCAACTCGAACAAGCC 58.770 50.000 0.00 0.00 35.36 4.35
847 926 4.398247 CAATAAGAGCAACTCGAACAAGC 58.602 43.478 0.00 0.00 35.36 4.01
848 927 4.452455 ACCAATAAGAGCAACTCGAACAAG 59.548 41.667 0.00 0.00 35.36 3.16
849 928 4.385825 ACCAATAAGAGCAACTCGAACAA 58.614 39.130 0.00 0.00 35.36 2.83
850 929 4.002906 ACCAATAAGAGCAACTCGAACA 57.997 40.909 0.00 0.00 35.36 3.18
851 930 4.927425 TGTACCAATAAGAGCAACTCGAAC 59.073 41.667 0.00 0.00 35.36 3.95
852 931 4.927425 GTGTACCAATAAGAGCAACTCGAA 59.073 41.667 0.00 0.00 35.36 3.71
853 932 4.491676 GTGTACCAATAAGAGCAACTCGA 58.508 43.478 0.00 0.00 35.36 4.04
854 933 3.303495 CGTGTACCAATAAGAGCAACTCG 59.697 47.826 0.00 0.00 35.36 4.18
855 934 4.243270 ACGTGTACCAATAAGAGCAACTC 58.757 43.478 0.00 0.00 0.00 3.01
856 935 4.267349 ACGTGTACCAATAAGAGCAACT 57.733 40.909 0.00 0.00 0.00 3.16
857 936 4.449743 TGAACGTGTACCAATAAGAGCAAC 59.550 41.667 0.00 0.00 0.00 4.17
858 937 4.633175 TGAACGTGTACCAATAAGAGCAA 58.367 39.130 0.00 0.00 0.00 3.91
859 938 4.260139 TGAACGTGTACCAATAAGAGCA 57.740 40.909 0.00 0.00 0.00 4.26
860 939 4.630069 ACATGAACGTGTACCAATAAGAGC 59.370 41.667 0.00 0.00 0.00 4.09
861 940 5.004440 CGACATGAACGTGTACCAATAAGAG 59.996 44.000 0.00 0.00 31.16 2.85
862 941 4.860352 CGACATGAACGTGTACCAATAAGA 59.140 41.667 0.00 0.00 31.16 2.10
863 942 4.624024 ACGACATGAACGTGTACCAATAAG 59.376 41.667 17.93 0.00 42.37 1.73
864 943 4.558178 ACGACATGAACGTGTACCAATAA 58.442 39.130 17.93 0.00 42.37 1.40
870 949 1.903139 CTCGACGACATGAACGTGTAC 59.097 52.381 21.87 10.62 43.97 2.90
923 1003 1.037030 GGGAGCATGGCGAATTTGGA 61.037 55.000 0.00 0.00 0.00 3.53
1319 1400 2.100631 CAGGACATGACGTTCCGGC 61.101 63.158 0.00 0.00 34.27 6.13
1320 1401 1.447838 CCAGGACATGACGTTCCGG 60.448 63.158 0.00 0.00 0.00 5.14
1322 1403 1.270625 TGTTCCAGGACATGACGTTCC 60.271 52.381 0.00 0.00 0.00 3.62
1480 1561 0.486879 ATGGCAAGGAAGAACCCCAA 59.513 50.000 0.00 0.00 40.05 4.12
1560 1641 0.324738 AGACAAGATCGGAGAGGCCA 60.325 55.000 5.01 0.00 43.63 5.36
1666 1747 1.001764 CTGCAAGCCATCCAGACCA 60.002 57.895 0.00 0.00 0.00 4.02
1670 1751 0.034767 TCCTTCTGCAAGCCATCCAG 60.035 55.000 0.00 0.00 0.00 3.86
1674 1755 0.255318 CCTCTCCTTCTGCAAGCCAT 59.745 55.000 0.00 0.00 0.00 4.40
1677 1758 1.748500 GGCCTCTCCTTCTGCAAGC 60.749 63.158 0.00 0.00 0.00 4.01
1698 1779 1.082690 GAGAAGGAAGCGCTTTGAGG 58.917 55.000 25.84 0.00 0.00 3.86
1746 1827 0.176680 CATTCTGCGTCCTACCAGCT 59.823 55.000 0.00 0.00 0.00 4.24
1756 1837 0.965866 TCGGAGTCTCCATTCTGCGT 60.966 55.000 19.15 0.00 43.73 5.24
1762 1843 3.215671 CTCCCTCGGAGTCTCCATT 57.784 57.895 19.15 0.00 44.25 3.16
1794 1875 3.808618 GCCCAATACCTCTCATCATGGAC 60.809 52.174 0.00 0.00 0.00 4.02
1824 1905 2.295349 ACTAACGAATGTGACCACGTCT 59.705 45.455 0.00 0.00 38.00 4.18
2021 2102 7.879677 TCATTGCACTGAGAAGAAAAAGATCTA 59.120 33.333 2.07 0.00 0.00 1.98
2226 2307 1.135141 TGTTTCACACTTGGTTGCAGC 60.135 47.619 0.00 0.00 0.00 5.25
2271 2352 1.811266 CAGACAACCTGATCGCCCG 60.811 63.158 0.00 0.00 45.78 6.13
2399 2480 2.954989 TCAATGACTCGCTCTGCTATCT 59.045 45.455 0.00 0.00 0.00 1.98
2746 2827 4.114794 GCAAATGCTATCGCCAATTTCTT 58.885 39.130 0.00 0.00 38.21 2.52
2826 2907 2.785540 TAGCAACATGGCAGTCATCA 57.214 45.000 0.00 0.00 32.92 3.07
2877 2958 3.624861 GGCTTACATCTCTGACCACAATG 59.375 47.826 0.00 0.00 0.00 2.82
3040 3124 4.543692 CTGCTGACTTCAAAAACTCCATG 58.456 43.478 0.00 0.00 0.00 3.66
3041 3125 3.571401 CCTGCTGACTTCAAAAACTCCAT 59.429 43.478 0.00 0.00 0.00 3.41
3042 3126 2.951642 CCTGCTGACTTCAAAAACTCCA 59.048 45.455 0.00 0.00 0.00 3.86
3043 3127 2.952310 ACCTGCTGACTTCAAAAACTCC 59.048 45.455 0.00 0.00 0.00 3.85
3044 3128 4.639135 AACCTGCTGACTTCAAAAACTC 57.361 40.909 0.00 0.00 0.00 3.01
3045 3129 5.170748 CAAAACCTGCTGACTTCAAAAACT 58.829 37.500 0.00 0.00 0.00 2.66
3046 3130 4.329801 CCAAAACCTGCTGACTTCAAAAAC 59.670 41.667 0.00 0.00 0.00 2.43
3047 3131 4.020662 ACCAAAACCTGCTGACTTCAAAAA 60.021 37.500 0.00 0.00 0.00 1.94
3048 3132 3.513515 ACCAAAACCTGCTGACTTCAAAA 59.486 39.130 0.00 0.00 0.00 2.44
3049 3133 3.096092 ACCAAAACCTGCTGACTTCAAA 58.904 40.909 0.00 0.00 0.00 2.69
3050 3134 2.687935 GACCAAAACCTGCTGACTTCAA 59.312 45.455 0.00 0.00 0.00 2.69
3051 3135 2.092429 AGACCAAAACCTGCTGACTTCA 60.092 45.455 0.00 0.00 0.00 3.02
3052 3136 2.576615 AGACCAAAACCTGCTGACTTC 58.423 47.619 0.00 0.00 0.00 3.01
3053 3137 2.736670 AGACCAAAACCTGCTGACTT 57.263 45.000 0.00 0.00 0.00 3.01
3054 3138 2.706190 AGTAGACCAAAACCTGCTGACT 59.294 45.455 0.00 0.00 0.00 3.41
3055 3139 3.067833 GAGTAGACCAAAACCTGCTGAC 58.932 50.000 0.00 0.00 0.00 3.51
3056 3140 2.703536 TGAGTAGACCAAAACCTGCTGA 59.296 45.455 0.00 0.00 0.00 4.26
3057 3141 3.126001 TGAGTAGACCAAAACCTGCTG 57.874 47.619 0.00 0.00 0.00 4.41
3058 3142 3.136626 AGTTGAGTAGACCAAAACCTGCT 59.863 43.478 0.00 0.00 0.00 4.24
3059 3143 3.251004 CAGTTGAGTAGACCAAAACCTGC 59.749 47.826 0.00 0.00 0.00 4.85
3060 3144 4.703897 TCAGTTGAGTAGACCAAAACCTG 58.296 43.478 0.00 0.00 0.00 4.00
3061 3145 4.202367 CCTCAGTTGAGTAGACCAAAACCT 60.202 45.833 8.23 0.00 40.48 3.50
3062 3146 4.065789 CCTCAGTTGAGTAGACCAAAACC 58.934 47.826 8.23 0.00 40.48 3.27
3063 3147 4.065789 CCCTCAGTTGAGTAGACCAAAAC 58.934 47.826 8.23 0.00 40.48 2.43
3064 3148 3.971305 TCCCTCAGTTGAGTAGACCAAAA 59.029 43.478 8.23 0.00 40.48 2.44
3065 3149 3.583228 TCCCTCAGTTGAGTAGACCAAA 58.417 45.455 8.23 0.00 40.48 3.28
3066 3150 3.254093 TCCCTCAGTTGAGTAGACCAA 57.746 47.619 8.23 0.00 40.48 3.67
3067 3151 2.992847 TCCCTCAGTTGAGTAGACCA 57.007 50.000 8.23 0.00 40.48 4.02
3153 3237 7.983484 GGATCAAAGATCCAGCAAATTTTATGT 59.017 33.333 18.63 0.00 38.09 2.29
3241 3327 2.488153 AGACTTGGGCGAAAAATGCTAC 59.512 45.455 0.00 0.00 0.00 3.58
3452 3538 0.107643 TCCAGCAACACGTGATCCAA 59.892 50.000 25.01 0.00 0.00 3.53
3460 3546 3.052082 CCAGGCTCCAGCAACACG 61.052 66.667 0.03 0.00 44.36 4.49
3510 3597 5.408604 CCAGGTATAATTGCACCGATAGTTC 59.591 44.000 0.00 0.00 39.94 3.01
3544 3631 0.109319 CCATTTTGTAGCGCCACACC 60.109 55.000 8.55 0.00 0.00 4.16
3548 3635 1.173043 CCTTCCATTTTGTAGCGCCA 58.827 50.000 2.29 0.00 0.00 5.69
3549 3636 0.179137 GCCTTCCATTTTGTAGCGCC 60.179 55.000 2.29 0.00 0.00 6.53
3659 3747 2.094675 CCTGGCCACTGTTCTTATTGG 58.905 52.381 0.00 0.00 0.00 3.16
3721 3810 9.720667 TTAATTTCAATGCATAACGAGATTCAG 57.279 29.630 0.00 0.00 0.00 3.02
3733 3822 9.694137 CAAAACCCAAAATTAATTTCAATGCAT 57.306 25.926 13.68 0.00 0.00 3.96
3754 3843 4.260334 GCACAGCCAAATGAAAGACAAAAC 60.260 41.667 0.00 0.00 0.00 2.43
3767 3856 1.277557 ACAAAACCAAGCACAGCCAAA 59.722 42.857 0.00 0.00 0.00 3.28
3811 3900 3.369546 AAACGCCATGACCTCAAAAAG 57.630 42.857 0.00 0.00 0.00 2.27
3832 3921 8.336806 CAAACAATGCTGTCAATTTGTACAAAT 58.663 29.630 24.88 24.88 37.42 2.32
3869 3958 4.207165 CAAGAGGGAACAGAAAGAAACCA 58.793 43.478 0.00 0.00 0.00 3.67
3892 3981 5.123936 TCAAGAGATCAAATGGATGAGCAG 58.876 41.667 0.00 0.00 38.17 4.24


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

AutoCloner maintained by Alex Coulton.