Multiple sequence alignment - TraesCS5D01G252100

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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 TraesCS5D01G252100 chr5D 100.000 2840 0 0 1 2840 357888382 357885543 0.000000e+00 5245.0
1 TraesCS5D01G252100 chr2D 97.406 1966 31 2 895 2840 536080964 536082929 0.000000e+00 3330.0
2 TraesCS5D01G252100 chr2D 96.490 1966 49 2 895 2840 8949043 8947078 0.000000e+00 3230.0
3 TraesCS5D01G252100 chr2D 96.562 1949 39 16 894 2840 616991308 616989386 0.000000e+00 3203.0
4 TraesCS5D01G252100 chr2D 95.270 1353 23 2 1529 2840 577707060 577708412 0.000000e+00 2106.0
5 TraesCS5D01G252100 chr2D 96.880 641 18 2 895 1534 577689359 577689998 0.000000e+00 1072.0
6 TraesCS5D01G252100 chr2D 97.619 42 1 0 2000 2041 616990159 616990118 3.920000e-09 73.1
7 TraesCS5D01G252100 chr7A 91.902 1914 112 15 895 2768 483746927 483748837 0.000000e+00 2636.0
8 TraesCS5D01G252100 chr7A 84.348 230 18 10 664 880 119293054 119293278 2.870000e-50 209.0
9 TraesCS5D01G252100 chr3D 94.344 1715 50 11 891 2584 420461038 420459350 0.000000e+00 2586.0
10 TraesCS5D01G252100 chr3D 98.634 366 5 0 2475 2840 420459519 420459154 0.000000e+00 649.0
11 TraesCS5D01G252100 chr7B 91.456 1896 113 19 894 2752 659923966 659925849 0.000000e+00 2558.0
12 TraesCS5D01G252100 chr7B 85.600 125 4 4 2730 2840 659925886 659926010 4.970000e-23 119.0
13 TraesCS5D01G252100 chr2B 97.309 892 23 1 3 894 29541802 29540912 0.000000e+00 1513.0
14 TraesCS5D01G252100 chr2B 89.083 458 49 1 2196 2652 679646811 679647268 4.110000e-158 568.0
15 TraesCS5D01G252100 chr6B 90.186 1019 68 17 894 1910 671647801 671648789 0.000000e+00 1299.0
16 TraesCS5D01G252100 chr6B 95.170 704 32 2 895 1597 638986383 638985681 0.000000e+00 1110.0
17 TraesCS5D01G252100 chr6B 84.299 777 85 17 1944 2701 671648788 671649546 0.000000e+00 725.0
18 TraesCS5D01G252100 chr1A 89.417 463 35 7 65 523 45831066 45831518 3.170000e-159 571.0
19 TraesCS5D01G252100 chr1A 82.192 365 29 12 546 876 45833713 45834075 5.990000e-72 281.0
20 TraesCS5D01G252100 chr1A 86.207 58 8 0 1 58 45830964 45831021 2.360000e-06 63.9
21 TraesCS5D01G252100 chr3B 86.902 481 36 11 65 528 42180534 42181004 5.430000e-142 514.0
22 TraesCS5D01G252100 chr3B 82.114 369 25 13 546 876 42181906 42182271 7.750000e-71 278.0
23 TraesCS5D01G252100 chr3B 96.078 51 2 0 8 58 42180439 42180489 1.810000e-12 84.2
24 TraesCS5D01G252100 chr3A 86.966 468 46 8 65 528 354811268 354811724 1.950000e-141 512.0
25 TraesCS5D01G252100 chr6A 88.291 316 29 3 213 528 35442130 35442437 3.460000e-99 372.0
26 TraesCS5D01G252100 chr6A 89.655 58 6 0 1 58 35442037 35442094 1.090000e-09 75.0
27 TraesCS5D01G252100 chr7D 94.712 208 9 2 882 1089 25851067 25851272 3.530000e-84 322.0


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 TraesCS5D01G252100 chr5D 357885543 357888382 2839 True 5245.000000 5245 100.000000 1 2840 1 chr5D.!!$R1 2839
1 TraesCS5D01G252100 chr2D 536080964 536082929 1965 False 3330.000000 3330 97.406000 895 2840 1 chr2D.!!$F1 1945
2 TraesCS5D01G252100 chr2D 8947078 8949043 1965 True 3230.000000 3230 96.490000 895 2840 1 chr2D.!!$R1 1945
3 TraesCS5D01G252100 chr2D 577707060 577708412 1352 False 2106.000000 2106 95.270000 1529 2840 1 chr2D.!!$F3 1311
4 TraesCS5D01G252100 chr2D 616989386 616991308 1922 True 1638.050000 3203 97.090500 894 2840 2 chr2D.!!$R2 1946
5 TraesCS5D01G252100 chr2D 577689359 577689998 639 False 1072.000000 1072 96.880000 895 1534 1 chr2D.!!$F2 639
6 TraesCS5D01G252100 chr7A 483746927 483748837 1910 False 2636.000000 2636 91.902000 895 2768 1 chr7A.!!$F2 1873
7 TraesCS5D01G252100 chr3D 420459154 420461038 1884 True 1617.500000 2586 96.489000 891 2840 2 chr3D.!!$R1 1949
8 TraesCS5D01G252100 chr7B 659923966 659926010 2044 False 1338.500000 2558 88.528000 894 2840 2 chr7B.!!$F1 1946
9 TraesCS5D01G252100 chr2B 29540912 29541802 890 True 1513.000000 1513 97.309000 3 894 1 chr2B.!!$R1 891
10 TraesCS5D01G252100 chr6B 638985681 638986383 702 True 1110.000000 1110 95.170000 895 1597 1 chr6B.!!$R1 702
11 TraesCS5D01G252100 chr6B 671647801 671649546 1745 False 1012.000000 1299 87.242500 894 2701 2 chr6B.!!$F1 1807
12 TraesCS5D01G252100 chr1A 45830964 45834075 3111 False 305.300000 571 85.938667 1 876 3 chr1A.!!$F1 875
13 TraesCS5D01G252100 chr3B 42180439 42182271 1832 False 292.066667 514 88.364667 8 876 3 chr3B.!!$F1 868

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
816 3074 0.029834 GCAATTATGGTGGCGAGCAG 59.97 55.0 6.77 0.0 31.77 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 4759 0.175531 GGCCAAACAAGTGCACAACT 59.824 50.0 21.04 0.0 42.6 3.16 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
143 182 2.249413 CTTCCACAGCGGCTCCATCT 62.249 60.000 0.00 0.00 33.14 2.90
736 2994 4.518278 TTTTGCAGGGATATTCTAGCCA 57.482 40.909 0.00 0.00 35.47 4.75
737 2995 3.777106 TTGCAGGGATATTCTAGCCAG 57.223 47.619 0.00 0.00 35.47 4.85
738 2996 2.694397 TGCAGGGATATTCTAGCCAGT 58.306 47.619 0.00 0.00 35.47 4.00
739 2997 2.369860 TGCAGGGATATTCTAGCCAGTG 59.630 50.000 0.00 0.00 35.47 3.66
740 2998 2.289945 GCAGGGATATTCTAGCCAGTGG 60.290 54.545 4.20 4.20 35.47 4.00
741 2999 2.304180 CAGGGATATTCTAGCCAGTGGG 59.696 54.545 12.15 0.00 35.47 4.61
742 3000 1.630878 GGGATATTCTAGCCAGTGGGG 59.369 57.143 12.15 0.00 35.47 4.96
744 3002 2.039084 GGATATTCTAGCCAGTGGGGTG 59.961 54.545 12.15 0.00 46.52 4.61
745 3003 2.561209 TATTCTAGCCAGTGGGGTGA 57.439 50.000 12.15 0.00 46.52 4.02
746 3004 1.898863 ATTCTAGCCAGTGGGGTGAT 58.101 50.000 12.15 0.00 46.52 3.06
747 3005 0.911769 TTCTAGCCAGTGGGGTGATG 59.088 55.000 12.15 0.00 46.52 3.07
748 3006 1.153086 CTAGCCAGTGGGGTGATGC 60.153 63.158 12.15 0.00 46.52 3.91
749 3007 1.616327 TAGCCAGTGGGGTGATGCT 60.616 57.895 12.15 1.98 46.52 3.79
750 3008 0.326143 TAGCCAGTGGGGTGATGCTA 60.326 55.000 12.15 0.92 46.52 3.49
751 3009 1.452108 GCCAGTGGGGTGATGCTAC 60.452 63.158 12.15 0.00 39.65 3.58
752 3010 1.990424 CCAGTGGGGTGATGCTACA 59.010 57.895 0.00 0.00 0.00 2.74
753 3011 0.548031 CCAGTGGGGTGATGCTACAT 59.452 55.000 0.00 0.00 0.00 2.29
754 3012 1.064463 CCAGTGGGGTGATGCTACATT 60.064 52.381 0.00 0.00 0.00 2.71
755 3013 2.172505 CCAGTGGGGTGATGCTACATTA 59.827 50.000 0.00 0.00 0.00 1.90
756 3014 3.371487 CCAGTGGGGTGATGCTACATTAA 60.371 47.826 0.00 0.00 0.00 1.40
757 3015 4.464008 CAGTGGGGTGATGCTACATTAAT 58.536 43.478 0.00 0.00 0.00 1.40
758 3016 4.889409 CAGTGGGGTGATGCTACATTAATT 59.111 41.667 0.00 0.00 0.00 1.40
759 3017 6.061441 CAGTGGGGTGATGCTACATTAATTA 58.939 40.000 0.00 0.00 0.00 1.40
760 3018 6.017109 CAGTGGGGTGATGCTACATTAATTAC 60.017 42.308 0.00 0.00 0.00 1.89
761 3019 6.062095 GTGGGGTGATGCTACATTAATTACT 58.938 40.000 0.00 0.00 0.00 2.24
762 3020 6.017109 GTGGGGTGATGCTACATTAATTACTG 60.017 42.308 1.51 1.51 0.00 2.74
763 3021 5.473504 GGGGTGATGCTACATTAATTACTGG 59.526 44.000 7.63 0.00 0.00 4.00
764 3022 5.473504 GGGTGATGCTACATTAATTACTGGG 59.526 44.000 7.63 1.94 0.00 4.45
765 3023 5.473504 GGTGATGCTACATTAATTACTGGGG 59.526 44.000 7.63 1.64 0.00 4.96
766 3024 6.296026 GTGATGCTACATTAATTACTGGGGA 58.704 40.000 7.63 2.34 0.00 4.81
767 3025 6.942576 GTGATGCTACATTAATTACTGGGGAT 59.057 38.462 7.63 6.35 0.00 3.85
768 3026 6.942005 TGATGCTACATTAATTACTGGGGATG 59.058 38.462 7.63 0.32 0.00 3.51
769 3027 6.260700 TGCTACATTAATTACTGGGGATGT 57.739 37.500 7.63 5.79 0.00 3.06
770 3028 6.061441 TGCTACATTAATTACTGGGGATGTG 58.939 40.000 7.63 1.31 0.00 3.21
771 3029 5.473504 GCTACATTAATTACTGGGGATGTGG 59.526 44.000 7.63 6.32 0.00 4.17
772 3030 4.215109 ACATTAATTACTGGGGATGTGGC 58.785 43.478 7.63 0.00 0.00 5.01
773 3031 4.079212 ACATTAATTACTGGGGATGTGGCT 60.079 41.667 7.63 0.00 0.00 4.75
774 3032 5.133660 ACATTAATTACTGGGGATGTGGCTA 59.866 40.000 7.63 0.00 0.00 3.93
775 3033 3.864789 AATTACTGGGGATGTGGCTAG 57.135 47.619 0.00 0.00 0.00 3.42
776 3034 1.507140 TTACTGGGGATGTGGCTAGG 58.493 55.000 0.00 0.00 0.00 3.02
777 3035 0.341961 TACTGGGGATGTGGCTAGGT 59.658 55.000 0.00 0.00 0.00 3.08
778 3036 1.274703 ACTGGGGATGTGGCTAGGTG 61.275 60.000 0.00 0.00 0.00 4.00
779 3037 2.193248 GGGGATGTGGCTAGGTGC 59.807 66.667 0.00 0.00 41.94 5.01
780 3038 2.679342 GGGGATGTGGCTAGGTGCA 61.679 63.158 0.00 0.00 45.15 4.57
781 3039 1.533711 GGGATGTGGCTAGGTGCAT 59.466 57.895 0.00 0.00 45.15 3.96
782 3040 0.106519 GGGATGTGGCTAGGTGCATT 60.107 55.000 0.00 0.00 45.15 3.56
783 3041 1.686115 GGGATGTGGCTAGGTGCATTT 60.686 52.381 0.00 0.00 45.15 2.32
784 3042 2.102578 GGATGTGGCTAGGTGCATTTT 58.897 47.619 0.00 0.00 45.15 1.82
785 3043 3.287222 GGATGTGGCTAGGTGCATTTTA 58.713 45.455 0.00 0.00 45.15 1.52
786 3044 3.316308 GGATGTGGCTAGGTGCATTTTAG 59.684 47.826 0.00 0.00 45.15 1.85
787 3045 2.722094 TGTGGCTAGGTGCATTTTAGG 58.278 47.619 0.00 0.00 45.15 2.69
788 3046 2.024414 GTGGCTAGGTGCATTTTAGGG 58.976 52.381 0.00 0.00 45.15 3.53
789 3047 1.032794 GGCTAGGTGCATTTTAGGGC 58.967 55.000 0.00 0.00 45.15 5.19
790 3048 0.663153 GCTAGGTGCATTTTAGGGCG 59.337 55.000 0.00 0.00 42.31 6.13
791 3049 1.308998 CTAGGTGCATTTTAGGGCGG 58.691 55.000 0.00 0.00 0.00 6.13
792 3050 0.913205 TAGGTGCATTTTAGGGCGGA 59.087 50.000 0.00 0.00 0.00 5.54
793 3051 0.258774 AGGTGCATTTTAGGGCGGAT 59.741 50.000 0.00 0.00 0.00 4.18
794 3052 0.668535 GGTGCATTTTAGGGCGGATC 59.331 55.000 0.00 0.00 0.00 3.36
795 3053 1.680338 GTGCATTTTAGGGCGGATCT 58.320 50.000 0.00 0.00 0.00 2.75
796 3054 2.024414 GTGCATTTTAGGGCGGATCTT 58.976 47.619 0.00 0.00 0.00 2.40
797 3055 2.023673 TGCATTTTAGGGCGGATCTTG 58.976 47.619 0.00 0.00 0.00 3.02
798 3056 1.269257 GCATTTTAGGGCGGATCTTGC 60.269 52.381 0.00 0.00 0.00 4.01
799 3057 2.023673 CATTTTAGGGCGGATCTTGCA 58.976 47.619 11.61 0.00 0.00 4.08
800 3058 2.208132 TTTTAGGGCGGATCTTGCAA 57.792 45.000 0.00 0.00 0.00 4.08
801 3059 2.435372 TTTAGGGCGGATCTTGCAAT 57.565 45.000 0.00 0.00 0.00 3.56
802 3060 2.435372 TTAGGGCGGATCTTGCAATT 57.565 45.000 0.00 0.00 0.00 2.32
803 3061 3.569194 TTAGGGCGGATCTTGCAATTA 57.431 42.857 0.00 0.00 0.00 1.40
804 3062 2.664402 AGGGCGGATCTTGCAATTAT 57.336 45.000 0.00 0.00 0.00 1.28
805 3063 2.233271 AGGGCGGATCTTGCAATTATG 58.767 47.619 0.00 0.00 0.00 1.90
806 3064 1.270550 GGGCGGATCTTGCAATTATGG 59.729 52.381 0.00 0.00 0.00 2.74
807 3065 1.956477 GGCGGATCTTGCAATTATGGT 59.044 47.619 0.00 0.00 0.00 3.55
808 3066 2.287788 GGCGGATCTTGCAATTATGGTG 60.288 50.000 0.00 0.00 0.00 4.17
809 3067 2.287788 GCGGATCTTGCAATTATGGTGG 60.288 50.000 0.00 0.00 0.00 4.61
810 3068 2.287788 CGGATCTTGCAATTATGGTGGC 60.288 50.000 0.00 0.00 0.00 5.01
811 3069 2.287788 GGATCTTGCAATTATGGTGGCG 60.288 50.000 0.00 0.00 0.00 5.69
812 3070 2.121291 TCTTGCAATTATGGTGGCGA 57.879 45.000 0.00 0.00 0.00 5.54
813 3071 2.016318 TCTTGCAATTATGGTGGCGAG 58.984 47.619 0.00 0.00 38.78 5.03
814 3072 0.455410 TTGCAATTATGGTGGCGAGC 59.545 50.000 0.00 0.00 0.00 5.03
815 3073 0.679321 TGCAATTATGGTGGCGAGCA 60.679 50.000 2.25 2.25 0.00 4.26
816 3074 0.029834 GCAATTATGGTGGCGAGCAG 59.970 55.000 6.77 0.00 31.77 4.24
817 3075 1.382522 CAATTATGGTGGCGAGCAGT 58.617 50.000 6.77 0.00 31.77 4.40
818 3076 1.745087 CAATTATGGTGGCGAGCAGTT 59.255 47.619 6.77 0.00 31.77 3.16
819 3077 1.668419 ATTATGGTGGCGAGCAGTTC 58.332 50.000 6.77 0.00 31.77 3.01
820 3078 0.613260 TTATGGTGGCGAGCAGTTCT 59.387 50.000 6.77 0.00 31.77 3.01
821 3079 0.613260 TATGGTGGCGAGCAGTTCTT 59.387 50.000 6.77 0.00 31.77 2.52
822 3080 0.957395 ATGGTGGCGAGCAGTTCTTG 60.957 55.000 6.77 0.00 31.77 3.02
823 3081 2.328099 GGTGGCGAGCAGTTCTTGG 61.328 63.158 0.00 0.00 0.00 3.61
824 3082 1.598130 GTGGCGAGCAGTTCTTGGT 60.598 57.895 0.00 0.00 41.02 3.67
825 3083 1.148273 TGGCGAGCAGTTCTTGGTT 59.852 52.632 0.00 0.00 37.72 3.67
826 3084 0.394938 TGGCGAGCAGTTCTTGGTTA 59.605 50.000 0.00 0.00 37.72 2.85
827 3085 1.202710 TGGCGAGCAGTTCTTGGTTAA 60.203 47.619 0.00 0.00 37.72 2.01
828 3086 1.197036 GGCGAGCAGTTCTTGGTTAAC 59.803 52.381 0.00 0.00 37.72 2.01
829 3087 1.197036 GCGAGCAGTTCTTGGTTAACC 59.803 52.381 18.27 18.27 37.72 2.85
830 3088 2.489971 CGAGCAGTTCTTGGTTAACCA 58.510 47.619 23.69 23.69 45.94 3.67
852 3110 3.004024 GCATGGCGGTGATATTCTTTG 57.996 47.619 0.00 0.00 0.00 2.77
853 3111 2.358898 GCATGGCGGTGATATTCTTTGT 59.641 45.455 0.00 0.00 0.00 2.83
854 3112 3.548818 GCATGGCGGTGATATTCTTTGTC 60.549 47.826 0.00 0.00 0.00 3.18
855 3113 2.639065 TGGCGGTGATATTCTTTGTCC 58.361 47.619 0.00 0.00 0.00 4.02
856 3114 1.597663 GGCGGTGATATTCTTTGTCCG 59.402 52.381 0.00 0.00 39.52 4.79
858 3116 2.276201 CGGTGATATTCTTTGTCCGCA 58.724 47.619 0.00 0.00 0.00 5.69
859 3117 2.285220 CGGTGATATTCTTTGTCCGCAG 59.715 50.000 0.00 0.00 0.00 5.18
860 3118 2.032178 GGTGATATTCTTTGTCCGCAGC 59.968 50.000 0.00 0.00 0.00 5.25
861 3119 2.677836 GTGATATTCTTTGTCCGCAGCA 59.322 45.455 0.00 0.00 0.00 4.41
862 3120 2.938451 TGATATTCTTTGTCCGCAGCAG 59.062 45.455 0.00 0.00 0.00 4.24
863 3121 1.737838 TATTCTTTGTCCGCAGCAGG 58.262 50.000 0.00 0.00 0.00 4.85
864 3122 0.250901 ATTCTTTGTCCGCAGCAGGT 60.251 50.000 0.00 0.00 0.00 4.00
865 3123 1.165907 TTCTTTGTCCGCAGCAGGTG 61.166 55.000 0.00 0.00 0.00 4.00
874 3132 4.994471 CAGCAGGTGGAGCACGCA 62.994 66.667 0.00 0.00 34.83 5.24
875 3133 4.254709 AGCAGGTGGAGCACGCAA 62.255 61.111 0.00 0.00 34.83 4.85
876 3134 3.286751 GCAGGTGGAGCACGCAAA 61.287 61.111 0.00 0.00 34.83 3.68
877 3135 2.949106 CAGGTGGAGCACGCAAAG 59.051 61.111 0.00 0.00 34.83 2.77
878 3136 2.281761 AGGTGGAGCACGCAAAGG 60.282 61.111 0.00 0.00 34.83 3.11
879 3137 2.594592 GGTGGAGCACGCAAAGGT 60.595 61.111 0.00 0.00 34.83 3.50
880 3138 2.639286 GTGGAGCACGCAAAGGTG 59.361 61.111 0.00 0.00 40.89 4.00
881 3139 2.186826 GTGGAGCACGCAAAGGTGT 61.187 57.895 0.00 0.00 40.08 4.16
887 3145 3.840437 ACGCAAAGGTGTGCATGT 58.160 50.000 0.00 0.00 45.19 3.21
888 3146 1.359833 ACGCAAAGGTGTGCATGTG 59.640 52.632 0.00 0.00 45.19 3.21
889 3147 2.017783 CGCAAAGGTGTGCATGTGC 61.018 57.895 0.00 0.00 45.19 4.57
890 3148 1.665599 GCAAAGGTGTGCATGTGCC 60.666 57.895 2.07 0.00 44.29 5.01
891 3149 1.372004 CAAAGGTGTGCATGTGCCG 60.372 57.895 2.07 0.00 41.18 5.69
892 3150 1.528076 AAAGGTGTGCATGTGCCGA 60.528 52.632 2.07 0.00 41.18 5.54
968 3226 4.102681 CCTCAACTCCTAATCCCGGTAATT 59.897 45.833 0.00 2.34 0.00 1.40
1472 3740 5.125578 GCCCCGATTTTTCTACTCATTCTTT 59.874 40.000 0.00 0.00 0.00 2.52
1549 3828 2.295070 GGTGGTTGTGGGTATGTTGAAC 59.705 50.000 0.00 0.00 0.00 3.18
2008 4312 4.107622 GGAATGAAATTTGTGATCTGGCG 58.892 43.478 0.00 0.00 36.07 5.69
2129 4494 3.391965 TGAGCATTTGCAAACAACATCC 58.608 40.909 15.41 1.28 45.16 3.51
2222 4587 8.213518 TGCAAATAGATTACAAAAGCTAGGAG 57.786 34.615 0.00 0.00 37.04 3.69
2442 4807 1.753073 CTCTTGGGGGCTTAAATGCAG 59.247 52.381 0.00 0.00 34.04 4.41
2506 4946 1.002990 CAGTGGCTGGTGCAGATGA 60.003 57.895 0.00 0.00 41.91 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 218 0.325203 GAGGAGGACTGGAGAAGGCT 60.325 60.000 0.00 0.00 32.61 4.58
414 464 0.035458 CTTGCAAGGACCTCCGAAGT 59.965 55.000 19.14 0.00 42.08 3.01
510 567 3.818787 CCAATGCCGCTGCCAGAC 61.819 66.667 0.00 0.00 36.33 3.51
727 2985 1.492176 CATCACCCCACTGGCTAGAAT 59.508 52.381 3.17 0.00 37.83 2.40
728 2986 0.911769 CATCACCCCACTGGCTAGAA 59.088 55.000 3.17 0.00 37.83 2.10
729 2987 1.626356 GCATCACCCCACTGGCTAGA 61.626 60.000 3.17 0.00 37.83 2.43
730 2988 1.153086 GCATCACCCCACTGGCTAG 60.153 63.158 0.00 0.00 37.83 3.42
731 2989 0.326143 TAGCATCACCCCACTGGCTA 60.326 55.000 0.00 0.00 37.83 3.93
732 2990 1.616327 TAGCATCACCCCACTGGCT 60.616 57.895 0.00 0.00 37.83 4.75
733 2991 1.452108 GTAGCATCACCCCACTGGC 60.452 63.158 0.00 0.00 37.83 4.85
734 2992 0.548031 ATGTAGCATCACCCCACTGG 59.452 55.000 0.00 0.00 41.37 4.00
735 2993 2.425143 AATGTAGCATCACCCCACTG 57.575 50.000 0.00 0.00 0.00 3.66
736 2994 4.796110 ATTAATGTAGCATCACCCCACT 57.204 40.909 0.00 0.00 0.00 4.00
737 2995 6.017109 CAGTAATTAATGTAGCATCACCCCAC 60.017 42.308 4.75 0.00 0.00 4.61
738 2996 6.061441 CAGTAATTAATGTAGCATCACCCCA 58.939 40.000 4.75 0.00 0.00 4.96
739 2997 5.473504 CCAGTAATTAATGTAGCATCACCCC 59.526 44.000 11.63 0.00 0.00 4.95
740 2998 5.473504 CCCAGTAATTAATGTAGCATCACCC 59.526 44.000 11.63 0.00 0.00 4.61
741 2999 5.473504 CCCCAGTAATTAATGTAGCATCACC 59.526 44.000 11.63 0.00 0.00 4.02
742 3000 6.296026 TCCCCAGTAATTAATGTAGCATCAC 58.704 40.000 11.63 0.00 0.00 3.06
743 3001 6.508030 TCCCCAGTAATTAATGTAGCATCA 57.492 37.500 11.63 0.00 0.00 3.07
744 3002 6.942576 ACATCCCCAGTAATTAATGTAGCATC 59.057 38.462 11.63 0.00 0.00 3.91
745 3003 6.716628 CACATCCCCAGTAATTAATGTAGCAT 59.283 38.462 11.63 0.00 0.00 3.79
746 3004 6.061441 CACATCCCCAGTAATTAATGTAGCA 58.939 40.000 11.63 0.00 0.00 3.49
747 3005 5.473504 CCACATCCCCAGTAATTAATGTAGC 59.526 44.000 11.63 0.00 0.00 3.58
748 3006 5.473504 GCCACATCCCCAGTAATTAATGTAG 59.526 44.000 11.63 3.16 0.00 2.74
749 3007 5.133660 AGCCACATCCCCAGTAATTAATGTA 59.866 40.000 11.63 0.00 0.00 2.29
750 3008 4.079212 AGCCACATCCCCAGTAATTAATGT 60.079 41.667 11.63 2.76 0.00 2.71
751 3009 4.473444 AGCCACATCCCCAGTAATTAATG 58.527 43.478 5.94 5.94 0.00 1.90
752 3010 4.814224 AGCCACATCCCCAGTAATTAAT 57.186 40.909 0.00 0.00 0.00 1.40
753 3011 4.104102 CCTAGCCACATCCCCAGTAATTAA 59.896 45.833 0.00 0.00 0.00 1.40
754 3012 3.650942 CCTAGCCACATCCCCAGTAATTA 59.349 47.826 0.00 0.00 0.00 1.40
755 3013 2.443255 CCTAGCCACATCCCCAGTAATT 59.557 50.000 0.00 0.00 0.00 1.40
756 3014 2.057922 CCTAGCCACATCCCCAGTAAT 58.942 52.381 0.00 0.00 0.00 1.89
757 3015 1.274184 ACCTAGCCACATCCCCAGTAA 60.274 52.381 0.00 0.00 0.00 2.24
758 3016 0.341961 ACCTAGCCACATCCCCAGTA 59.658 55.000 0.00 0.00 0.00 2.74
759 3017 1.082954 ACCTAGCCACATCCCCAGT 59.917 57.895 0.00 0.00 0.00 4.00
760 3018 1.528824 CACCTAGCCACATCCCCAG 59.471 63.158 0.00 0.00 0.00 4.45
761 3019 2.679342 GCACCTAGCCACATCCCCA 61.679 63.158 0.00 0.00 37.23 4.96
762 3020 1.999634 ATGCACCTAGCCACATCCCC 62.000 60.000 0.00 0.00 44.83 4.81
763 3021 0.106519 AATGCACCTAGCCACATCCC 60.107 55.000 0.00 0.00 44.83 3.85
764 3022 1.767759 AAATGCACCTAGCCACATCC 58.232 50.000 0.00 0.00 44.83 3.51
765 3023 3.316308 CCTAAAATGCACCTAGCCACATC 59.684 47.826 0.00 0.00 44.83 3.06
766 3024 3.290710 CCTAAAATGCACCTAGCCACAT 58.709 45.455 0.00 0.00 44.83 3.21
767 3025 2.620367 CCCTAAAATGCACCTAGCCACA 60.620 50.000 0.00 0.00 44.83 4.17
768 3026 2.024414 CCCTAAAATGCACCTAGCCAC 58.976 52.381 0.00 0.00 44.83 5.01
769 3027 1.684869 GCCCTAAAATGCACCTAGCCA 60.685 52.381 0.00 0.00 44.83 4.75
770 3028 1.032794 GCCCTAAAATGCACCTAGCC 58.967 55.000 0.00 0.00 44.83 3.93
771 3029 0.663153 CGCCCTAAAATGCACCTAGC 59.337 55.000 0.00 0.00 45.96 3.42
772 3030 1.134220 TCCGCCCTAAAATGCACCTAG 60.134 52.381 0.00 0.00 0.00 3.02
773 3031 0.913205 TCCGCCCTAAAATGCACCTA 59.087 50.000 0.00 0.00 0.00 3.08
774 3032 0.258774 ATCCGCCCTAAAATGCACCT 59.741 50.000 0.00 0.00 0.00 4.00
775 3033 0.668535 GATCCGCCCTAAAATGCACC 59.331 55.000 0.00 0.00 0.00 5.01
776 3034 1.680338 AGATCCGCCCTAAAATGCAC 58.320 50.000 0.00 0.00 0.00 4.57
777 3035 2.023673 CAAGATCCGCCCTAAAATGCA 58.976 47.619 0.00 0.00 0.00 3.96
778 3036 1.269257 GCAAGATCCGCCCTAAAATGC 60.269 52.381 0.00 0.00 0.00 3.56
779 3037 2.023673 TGCAAGATCCGCCCTAAAATG 58.976 47.619 2.49 0.00 0.00 2.32
780 3038 2.435372 TGCAAGATCCGCCCTAAAAT 57.565 45.000 2.49 0.00 0.00 1.82
781 3039 2.208132 TTGCAAGATCCGCCCTAAAA 57.792 45.000 0.00 0.00 0.00 1.52
782 3040 2.435372 ATTGCAAGATCCGCCCTAAA 57.565 45.000 4.94 0.00 0.00 1.85
783 3041 2.435372 AATTGCAAGATCCGCCCTAA 57.565 45.000 4.94 0.00 0.00 2.69
784 3042 3.411446 CATAATTGCAAGATCCGCCCTA 58.589 45.455 4.94 0.00 0.00 3.53
785 3043 2.233271 CATAATTGCAAGATCCGCCCT 58.767 47.619 4.94 0.00 0.00 5.19
786 3044 1.270550 CCATAATTGCAAGATCCGCCC 59.729 52.381 4.94 0.00 0.00 6.13
787 3045 1.956477 ACCATAATTGCAAGATCCGCC 59.044 47.619 4.94 0.00 0.00 6.13
788 3046 2.287788 CCACCATAATTGCAAGATCCGC 60.288 50.000 4.94 0.00 0.00 5.54
789 3047 2.287788 GCCACCATAATTGCAAGATCCG 60.288 50.000 4.94 0.00 0.00 4.18
790 3048 2.287788 CGCCACCATAATTGCAAGATCC 60.288 50.000 4.94 0.00 0.00 3.36
791 3049 2.618241 TCGCCACCATAATTGCAAGATC 59.382 45.455 4.94 0.00 0.00 2.75
792 3050 2.620115 CTCGCCACCATAATTGCAAGAT 59.380 45.455 4.94 0.00 0.00 2.40
793 3051 2.016318 CTCGCCACCATAATTGCAAGA 58.984 47.619 4.94 0.00 0.00 3.02
794 3052 1.534595 GCTCGCCACCATAATTGCAAG 60.535 52.381 4.94 0.00 0.00 4.01
795 3053 0.455410 GCTCGCCACCATAATTGCAA 59.545 50.000 0.00 0.00 0.00 4.08
796 3054 0.679321 TGCTCGCCACCATAATTGCA 60.679 50.000 0.00 0.00 0.00 4.08
797 3055 0.029834 CTGCTCGCCACCATAATTGC 59.970 55.000 0.00 0.00 0.00 3.56
798 3056 1.382522 ACTGCTCGCCACCATAATTG 58.617 50.000 0.00 0.00 0.00 2.32
799 3057 2.017049 GAACTGCTCGCCACCATAATT 58.983 47.619 0.00 0.00 0.00 1.40
800 3058 1.210478 AGAACTGCTCGCCACCATAAT 59.790 47.619 0.00 0.00 0.00 1.28
801 3059 0.613260 AGAACTGCTCGCCACCATAA 59.387 50.000 0.00 0.00 0.00 1.90
802 3060 0.613260 AAGAACTGCTCGCCACCATA 59.387 50.000 0.00 0.00 0.00 2.74
803 3061 0.957395 CAAGAACTGCTCGCCACCAT 60.957 55.000 0.00 0.00 0.00 3.55
804 3062 1.597854 CAAGAACTGCTCGCCACCA 60.598 57.895 0.00 0.00 0.00 4.17
805 3063 2.328099 CCAAGAACTGCTCGCCACC 61.328 63.158 0.00 0.00 0.00 4.61
806 3064 1.166531 AACCAAGAACTGCTCGCCAC 61.167 55.000 0.00 0.00 0.00 5.01
807 3065 0.394938 TAACCAAGAACTGCTCGCCA 59.605 50.000 0.00 0.00 0.00 5.69
808 3066 1.197036 GTTAACCAAGAACTGCTCGCC 59.803 52.381 0.00 0.00 0.00 5.54
809 3067 1.197036 GGTTAACCAAGAACTGCTCGC 59.803 52.381 20.12 0.00 35.64 5.03
810 3068 2.489971 TGGTTAACCAAGAACTGCTCG 58.510 47.619 25.19 0.00 44.35 5.03
832 3090 2.358898 ACAAAGAATATCACCGCCATGC 59.641 45.455 0.00 0.00 0.00 4.06
833 3091 3.003689 GGACAAAGAATATCACCGCCATG 59.996 47.826 0.00 0.00 0.00 3.66
834 3092 3.214328 GGACAAAGAATATCACCGCCAT 58.786 45.455 0.00 0.00 0.00 4.40
835 3093 2.639065 GGACAAAGAATATCACCGCCA 58.361 47.619 0.00 0.00 0.00 5.69
836 3094 1.597663 CGGACAAAGAATATCACCGCC 59.402 52.381 0.00 0.00 33.03 6.13
838 3096 2.276201 TGCGGACAAAGAATATCACCG 58.724 47.619 0.00 0.00 41.44 4.94
839 3097 2.032178 GCTGCGGACAAAGAATATCACC 59.968 50.000 0.00 0.00 0.00 4.02
840 3098 2.677836 TGCTGCGGACAAAGAATATCAC 59.322 45.455 0.00 0.00 0.00 3.06
841 3099 2.938451 CTGCTGCGGACAAAGAATATCA 59.062 45.455 1.17 0.00 0.00 2.15
842 3100 2.289002 CCTGCTGCGGACAAAGAATATC 59.711 50.000 10.70 0.00 0.00 1.63
843 3101 2.292267 CCTGCTGCGGACAAAGAATAT 58.708 47.619 10.70 0.00 0.00 1.28
844 3102 1.003118 ACCTGCTGCGGACAAAGAATA 59.997 47.619 10.70 0.00 0.00 1.75
845 3103 0.250901 ACCTGCTGCGGACAAAGAAT 60.251 50.000 10.70 0.00 0.00 2.40
846 3104 1.148273 ACCTGCTGCGGACAAAGAA 59.852 52.632 10.70 0.00 0.00 2.52
847 3105 1.597854 CACCTGCTGCGGACAAAGA 60.598 57.895 10.70 0.00 0.00 2.52
848 3106 2.620112 CCACCTGCTGCGGACAAAG 61.620 63.158 10.70 0.00 0.00 2.77
849 3107 2.594303 CCACCTGCTGCGGACAAA 60.594 61.111 10.70 0.00 0.00 2.83
850 3108 3.535629 CTCCACCTGCTGCGGACAA 62.536 63.158 10.70 0.00 0.00 3.18
851 3109 4.007644 CTCCACCTGCTGCGGACA 62.008 66.667 10.70 0.00 0.00 4.02
857 3115 4.994471 TGCGTGCTCCACCTGCTG 62.994 66.667 0.00 0.00 0.00 4.41
858 3116 3.772853 TTTGCGTGCTCCACCTGCT 62.773 57.895 0.00 0.00 0.00 4.24
859 3117 3.259425 CTTTGCGTGCTCCACCTGC 62.259 63.158 0.00 0.00 0.00 4.85
860 3118 2.620112 CCTTTGCGTGCTCCACCTG 61.620 63.158 0.00 0.00 0.00 4.00
861 3119 2.281761 CCTTTGCGTGCTCCACCT 60.282 61.111 0.00 0.00 0.00 4.00
862 3120 2.594592 ACCTTTGCGTGCTCCACC 60.595 61.111 0.00 0.00 0.00 4.61
863 3121 2.186826 ACACCTTTGCGTGCTCCAC 61.187 57.895 0.00 0.00 37.25 4.02
864 3122 2.186160 CACACCTTTGCGTGCTCCA 61.186 57.895 0.00 0.00 37.25 3.86
865 3123 2.639286 CACACCTTTGCGTGCTCC 59.361 61.111 0.00 0.00 37.25 4.70
870 3128 1.359833 CACATGCACACCTTTGCGT 59.640 52.632 0.00 0.00 46.20 5.24
871 3129 2.017783 GCACATGCACACCTTTGCG 61.018 57.895 0.00 0.00 46.20 4.85
872 3130 1.665599 GGCACATGCACACCTTTGC 60.666 57.895 6.15 0.00 44.36 3.68
873 3131 1.372004 CGGCACATGCACACCTTTG 60.372 57.895 6.15 0.00 44.36 2.77
874 3132 1.528076 TCGGCACATGCACACCTTT 60.528 52.632 6.15 0.00 44.36 3.11
875 3133 2.112928 TCGGCACATGCACACCTT 59.887 55.556 6.15 0.00 44.36 3.50
876 3134 2.669569 GTCGGCACATGCACACCT 60.670 61.111 6.15 0.00 44.36 4.00
877 3135 4.088762 CGTCGGCACATGCACACC 62.089 66.667 6.15 0.00 44.36 4.16
878 3136 4.088762 CCGTCGGCACATGCACAC 62.089 66.667 6.15 0.48 44.36 3.82
879 3137 3.816367 TTCCGTCGGCACATGCACA 62.816 57.895 6.34 0.00 44.36 4.57
880 3138 2.123988 TTTTCCGTCGGCACATGCAC 62.124 55.000 6.34 0.00 44.36 4.57
881 3139 1.448119 TTTTTCCGTCGGCACATGCA 61.448 50.000 6.34 0.00 44.36 3.96
882 3140 0.729140 CTTTTTCCGTCGGCACATGC 60.729 55.000 6.34 0.00 41.14 4.06
883 3141 0.591170 ACTTTTTCCGTCGGCACATG 59.409 50.000 6.34 0.00 0.00 3.21
884 3142 0.872388 GACTTTTTCCGTCGGCACAT 59.128 50.000 6.34 0.00 0.00 3.21
885 3143 1.161563 GGACTTTTTCCGTCGGCACA 61.162 55.000 6.34 0.00 33.46 4.57
886 3144 1.572941 GGACTTTTTCCGTCGGCAC 59.427 57.895 6.34 0.00 33.46 5.01
887 3145 4.052519 GGACTTTTTCCGTCGGCA 57.947 55.556 6.34 0.00 33.46 5.69
968 3226 4.890581 GGGATTAGAGAGTTGAGAGTGCTA 59.109 45.833 0.00 0.00 0.00 3.49
1472 3740 2.631384 TGAGGGGATGAGGAAGAACAA 58.369 47.619 0.00 0.00 0.00 2.83
1549 3828 2.121564 GGCAACGGATCATCATGCCG 62.122 60.000 11.34 7.10 46.11 5.69
1678 3957 1.661463 TCACCTCCTGCTTCATCCTT 58.339 50.000 0.00 0.00 0.00 3.36
2222 4587 2.424956 GCCAGGCATATTAAGGCTATGC 59.575 50.000 6.55 10.78 46.92 3.14
2394 4759 0.175531 GGCCAAACAAGTGCACAACT 59.824 50.000 21.04 0.00 42.60 3.16
2442 4807 1.153005 CTGCCCCAGGAAGAGCATC 60.153 63.158 0.00 0.00 34.16 3.91
2506 4946 2.988839 GCCACTGCCCCAGGAAGAT 61.989 63.158 0.00 0.00 35.51 2.40


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

AutoCloner maintained by Alex Coulton.