Multiple sequence alignment - TraesCS2D01G397600

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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 TraesCS2D01G397600 chr2D 100.000 5156 0 0 1 5156 509730918 509736073 0.000000e+00 9522
1 TraesCS2D01G397600 chr2D 93.524 664 34 7 1 658 498511229 498511889 0.000000e+00 979
2 TraesCS2D01G397600 chr2D 93.062 663 38 6 1 658 377088530 377087871 0.000000e+00 963
3 TraesCS2D01G397600 chr2D 92.911 663 39 7 1 658 275211335 275210676 0.000000e+00 957
4 TraesCS2D01G397600 chr2D 92.447 662 44 4 1 658 72339773 72340432 0.000000e+00 941
5 TraesCS2D01G397600 chr2D 93.523 633 34 5 29 656 70792243 70792873 0.000000e+00 935
6 TraesCS2D01G397600 chr2D 90.991 222 15 3 682 899 72340516 72340736 1.400000e-75 294
7 TraesCS2D01G397600 chr2D 90.541 222 16 4 681 897 6365973 6366194 6.530000e-74 289
8 TraesCS2D01G397600 chr2D 89.474 228 20 2 678 901 377087793 377087566 8.450000e-73 285
9 TraesCS2D01G397600 chr2A 93.801 4162 147 30 1038 5156 653362858 653366951 0.000000e+00 6154
10 TraesCS2D01G397600 chr2B 90.162 1850 104 34 1857 3687 598957398 598959188 0.000000e+00 2337
11 TraesCS2D01G397600 chr2B 91.786 1254 58 21 3663 4881 598959281 598960524 0.000000e+00 1703
12 TraesCS2D01G397600 chr2B 90.594 893 48 18 944 1830 598956390 598957252 0.000000e+00 1151
13 TraesCS2D01G397600 chr2B 93.574 249 12 3 4910 5154 598960523 598960771 8.160000e-98 368
14 TraesCS2D01G397600 chr2B 89.381 226 19 3 678 899 109056019 109056243 3.930000e-71 279
15 TraesCS2D01G397600 chr6D 93.179 689 37 7 1 682 200497393 200496708 0.000000e+00 1003
16 TraesCS2D01G397600 chr7B 93.223 664 35 7 1 658 579853623 579852964 0.000000e+00 968
17 TraesCS2D01G397600 chr7B 88.511 235 21 5 678 907 579852885 579852652 3.930000e-71 279
18 TraesCS2D01G397600 chr4A 92.133 661 43 7 1 658 317056534 317055880 0.000000e+00 924
19 TraesCS2D01G397600 chr7A 91.867 664 43 9 1 658 412891029 412891687 0.000000e+00 917
20 TraesCS2D01G397600 chr1B 90.351 228 16 4 678 901 288463215 288463440 1.400000e-75 294
21 TraesCS2D01G397600 chr4B 90.541 222 14 5 682 897 105472746 105472526 2.350000e-73 287
22 TraesCS2D01G397600 chr3D 89.381 226 20 4 678 899 484748886 484748661 1.090000e-71 281
23 TraesCS2D01G397600 chr1D 87.712 236 24 4 678 908 276753647 276753412 2.370000e-68 270


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 TraesCS2D01G397600 chr2D 509730918 509736073 5155 False 9522.00 9522 100.000 1 5156 1 chr2D.!!$F4 5155
1 TraesCS2D01G397600 chr2D 498511229 498511889 660 False 979.00 979 93.524 1 658 1 chr2D.!!$F3 657
2 TraesCS2D01G397600 chr2D 275210676 275211335 659 True 957.00 957 92.911 1 658 1 chr2D.!!$R1 657
3 TraesCS2D01G397600 chr2D 70792243 70792873 630 False 935.00 935 93.523 29 656 1 chr2D.!!$F2 627
4 TraesCS2D01G397600 chr2D 377087566 377088530 964 True 624.00 963 91.268 1 901 2 chr2D.!!$R2 900
5 TraesCS2D01G397600 chr2D 72339773 72340736 963 False 617.50 941 91.719 1 899 2 chr2D.!!$F5 898
6 TraesCS2D01G397600 chr2A 653362858 653366951 4093 False 6154.00 6154 93.801 1038 5156 1 chr2A.!!$F1 4118
7 TraesCS2D01G397600 chr2B 598956390 598960771 4381 False 1389.75 2337 91.529 944 5154 4 chr2B.!!$F2 4210
8 TraesCS2D01G397600 chr6D 200496708 200497393 685 True 1003.00 1003 93.179 1 682 1 chr6D.!!$R1 681
9 TraesCS2D01G397600 chr7B 579852652 579853623 971 True 623.50 968 90.867 1 907 2 chr7B.!!$R1 906
10 TraesCS2D01G397600 chr4A 317055880 317056534 654 True 924.00 924 92.133 1 658 1 chr4A.!!$R1 657
11 TraesCS2D01G397600 chr7A 412891029 412891687 658 False 917.00 917 91.867 1 658 1 chr7A.!!$F1 657

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
662 676 0.034863 TGGGGGAGTAATGAAACCGC 60.035 55.0 0.00 0.0 35.02 5.68 F
879 958 0.037232 AGTTGGAGAAGTGCTACCGC 60.037 55.0 0.00 0.0 0.00 5.68 F
892 971 0.109597 CTACCGCGTGGACGTTAGTT 60.110 55.0 24.59 0.0 42.22 2.24 F
1017 1096 0.537143 ATTTGCAAGTCACCTCGGCA 60.537 50.0 0.00 0.0 0.00 5.69 F
2389 2619 0.301687 CGCGAAGTGCACATGGTATC 59.698 55.0 21.04 6.2 46.97 2.24 F
4071 4432 0.532862 CCAGTGGAAGCGTTGTGTCT 60.533 55.0 1.68 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1774 1.122227 CCCAATACCATGCCCCAAAG 58.878 55.00 0.00 0.00 0.00 2.77 R
2371 2601 1.656652 AGATACCATGTGCACTTCGC 58.343 50.00 19.41 1.18 42.89 4.70 R
2389 2619 5.610982 GCGCTCAAACATTTCATGAAACAAG 60.611 40.00 22.71 16.95 32.51 3.16 R
2959 3196 5.984725 TGGCGAATTTCCTAGTTGAGATAA 58.015 37.50 0.00 0.00 0.00 1.75 R
4096 4457 0.119155 TCCACCACCTCTCCATCCTT 59.881 55.00 0.00 0.00 0.00 3.36 R
4987 5376 3.966665 AGCAAGGGTTTGAGGAATGAAAA 59.033 39.13 0.00 0.00 36.36 2.29 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
284 287 2.102578 AGGCAAAATACAGATGTGGCC 58.897 47.619 0.00 0.00 40.41 5.36
450 454 1.177401 GGGGAAATTGACCACAGAGC 58.823 55.000 4.67 0.00 0.00 4.09
493 500 2.185310 GAATGTGGCACGGAGGGAGT 62.185 60.000 13.77 0.00 0.00 3.85
658 671 2.074579 TGGGTTGGGGGAGTAATGAAA 58.925 47.619 0.00 0.00 0.00 2.69
662 676 0.034863 TGGGGGAGTAATGAAACCGC 60.035 55.000 0.00 0.00 35.02 5.68
664 678 0.108041 GGGGAGTAATGAAACCGCGA 60.108 55.000 8.23 0.00 0.00 5.87
667 681 2.194271 GGAGTAATGAAACCGCGAGAG 58.806 52.381 8.23 0.00 0.00 3.20
700 774 4.980805 GCGACGGCAGTTCCACCA 62.981 66.667 0.00 0.00 39.62 4.17
845 923 4.219033 GCAAAAGACAATCAACGACGATT 58.781 39.130 0.00 0.00 36.00 3.34
874 952 1.004440 GGCGAGTTGGAGAAGTGCT 60.004 57.895 0.00 0.00 0.00 4.40
879 958 0.037232 AGTTGGAGAAGTGCTACCGC 60.037 55.000 0.00 0.00 0.00 5.68
884 963 2.209064 GAGAAGTGCTACCGCGTGGA 62.209 60.000 24.59 4.37 39.65 4.02
892 971 0.109597 CTACCGCGTGGACGTTAGTT 60.110 55.000 24.59 0.00 42.22 2.24
902 981 4.274069 GTGGACGTTAGTTTTTCCGAAAC 58.726 43.478 0.00 0.00 0.00 2.78
907 986 5.707931 ACGTTAGTTTTTCCGAAACCAAAA 58.292 33.333 0.00 0.00 0.00 2.44
908 987 5.572511 ACGTTAGTTTTTCCGAAACCAAAAC 59.427 36.000 0.00 0.00 39.63 2.43
909 988 5.572126 CGTTAGTTTTTCCGAAACCAAAACA 59.428 36.000 8.89 0.00 41.09 2.83
910 989 6.452741 CGTTAGTTTTTCCGAAACCAAAACAC 60.453 38.462 8.89 0.34 41.09 3.32
911 990 4.247258 AGTTTTTCCGAAACCAAAACACC 58.753 39.130 8.89 0.00 41.09 4.16
912 991 3.955650 TTTTCCGAAACCAAAACACCA 57.044 38.095 0.00 0.00 0.00 4.17
913 992 3.955650 TTTCCGAAACCAAAACACCAA 57.044 38.095 0.00 0.00 0.00 3.67
914 993 3.955650 TTCCGAAACCAAAACACCAAA 57.044 38.095 0.00 0.00 0.00 3.28
915 994 3.512033 TCCGAAACCAAAACACCAAAG 57.488 42.857 0.00 0.00 0.00 2.77
916 995 2.166664 TCCGAAACCAAAACACCAAAGG 59.833 45.455 0.00 0.00 0.00 3.11
917 996 2.166664 CCGAAACCAAAACACCAAAGGA 59.833 45.455 0.00 0.00 0.00 3.36
918 997 3.368531 CCGAAACCAAAACACCAAAGGAA 60.369 43.478 0.00 0.00 0.00 3.36
919 998 3.862845 CGAAACCAAAACACCAAAGGAAG 59.137 43.478 0.00 0.00 0.00 3.46
920 999 4.381079 CGAAACCAAAACACCAAAGGAAGA 60.381 41.667 0.00 0.00 0.00 2.87
921 1000 5.483811 GAAACCAAAACACCAAAGGAAGAA 58.516 37.500 0.00 0.00 0.00 2.52
922 1001 5.491323 AACCAAAACACCAAAGGAAGAAA 57.509 34.783 0.00 0.00 0.00 2.52
923 1002 5.084818 ACCAAAACACCAAAGGAAGAAAG 57.915 39.130 0.00 0.00 0.00 2.62
924 1003 4.775253 ACCAAAACACCAAAGGAAGAAAGA 59.225 37.500 0.00 0.00 0.00 2.52
925 1004 5.247337 ACCAAAACACCAAAGGAAGAAAGAA 59.753 36.000 0.00 0.00 0.00 2.52
926 1005 6.169800 CCAAAACACCAAAGGAAGAAAGAAA 58.830 36.000 0.00 0.00 0.00 2.52
927 1006 6.823182 CCAAAACACCAAAGGAAGAAAGAAAT 59.177 34.615 0.00 0.00 0.00 2.17
928 1007 7.201635 CCAAAACACCAAAGGAAGAAAGAAATG 60.202 37.037 0.00 0.00 0.00 2.32
929 1008 6.790232 AACACCAAAGGAAGAAAGAAATGA 57.210 33.333 0.00 0.00 0.00 2.57
930 1009 6.790232 ACACCAAAGGAAGAAAGAAATGAA 57.210 33.333 0.00 0.00 0.00 2.57
931 1010 6.809869 ACACCAAAGGAAGAAAGAAATGAAG 58.190 36.000 0.00 0.00 0.00 3.02
932 1011 6.607198 ACACCAAAGGAAGAAAGAAATGAAGA 59.393 34.615 0.00 0.00 0.00 2.87
933 1012 7.124147 ACACCAAAGGAAGAAAGAAATGAAGAA 59.876 33.333 0.00 0.00 0.00 2.52
934 1013 7.981225 CACCAAAGGAAGAAAGAAATGAAGAAA 59.019 33.333 0.00 0.00 0.00 2.52
935 1014 8.539544 ACCAAAGGAAGAAAGAAATGAAGAAAA 58.460 29.630 0.00 0.00 0.00 2.29
936 1015 9.038803 CCAAAGGAAGAAAGAAATGAAGAAAAG 57.961 33.333 0.00 0.00 0.00 2.27
937 1016 9.807649 CAAAGGAAGAAAGAAATGAAGAAAAGA 57.192 29.630 0.00 0.00 0.00 2.52
939 1018 9.978044 AAGGAAGAAAGAAATGAAGAAAAGATG 57.022 29.630 0.00 0.00 0.00 2.90
940 1019 9.140874 AGGAAGAAAGAAATGAAGAAAAGATGT 57.859 29.630 0.00 0.00 0.00 3.06
941 1020 9.189723 GGAAGAAAGAAATGAAGAAAAGATGTG 57.810 33.333 0.00 0.00 0.00 3.21
942 1021 9.189723 GAAGAAAGAAATGAAGAAAAGATGTGG 57.810 33.333 0.00 0.00 0.00 4.17
971 1050 7.550906 AGCCAGTATGAAGAAGACTATGTTTTC 59.449 37.037 0.00 0.00 39.69 2.29
972 1051 7.201652 GCCAGTATGAAGAAGACTATGTTTTCC 60.202 40.741 0.00 0.00 39.69 3.13
973 1052 8.043710 CCAGTATGAAGAAGACTATGTTTTCCT 58.956 37.037 0.00 0.00 39.69 3.36
1001 1080 5.611374 TCGTGGAAAGAAGACTCTGAATTT 58.389 37.500 0.00 0.00 30.03 1.82
1003 1082 5.456265 GTGGAAAGAAGACTCTGAATTTGC 58.544 41.667 0.00 0.00 30.03 3.68
1005 1084 5.593909 TGGAAAGAAGACTCTGAATTTGCAA 59.406 36.000 0.00 0.00 30.03 4.08
1006 1085 6.148264 GGAAAGAAGACTCTGAATTTGCAAG 58.852 40.000 0.00 0.00 30.03 4.01
1007 1086 6.238869 GGAAAGAAGACTCTGAATTTGCAAGT 60.239 38.462 0.00 0.00 30.03 3.16
1008 1087 5.938438 AGAAGACTCTGAATTTGCAAGTC 57.062 39.130 0.00 1.43 37.27 3.01
1009 1088 5.371526 AGAAGACTCTGAATTTGCAAGTCA 58.628 37.500 13.40 13.05 39.02 3.41
1010 1089 5.238214 AGAAGACTCTGAATTTGCAAGTCAC 59.762 40.000 13.40 7.89 39.02 3.67
1011 1090 3.817647 AGACTCTGAATTTGCAAGTCACC 59.182 43.478 13.40 0.02 39.02 4.02
1012 1091 3.817647 GACTCTGAATTTGCAAGTCACCT 59.182 43.478 10.05 0.00 37.04 4.00
1013 1092 3.817647 ACTCTGAATTTGCAAGTCACCTC 59.182 43.478 10.05 0.00 31.49 3.85
1014 1093 2.807967 TCTGAATTTGCAAGTCACCTCG 59.192 45.455 10.05 2.97 31.49 4.63
1015 1094 1.879380 TGAATTTGCAAGTCACCTCGG 59.121 47.619 10.05 0.00 29.45 4.63
1016 1095 0.598065 AATTTGCAAGTCACCTCGGC 59.402 50.000 0.00 0.00 0.00 5.54
1017 1096 0.537143 ATTTGCAAGTCACCTCGGCA 60.537 50.000 0.00 0.00 0.00 5.69
1018 1097 1.165907 TTTGCAAGTCACCTCGGCAG 61.166 55.000 0.00 0.00 33.91 4.85
1019 1098 3.426568 GCAAGTCACCTCGGCAGC 61.427 66.667 0.00 0.00 0.00 5.25
1020 1099 2.743928 CAAGTCACCTCGGCAGCC 60.744 66.667 0.00 0.00 0.00 4.85
1021 1100 2.925170 AAGTCACCTCGGCAGCCT 60.925 61.111 10.54 0.00 0.00 4.58
1022 1101 2.948720 AAGTCACCTCGGCAGCCTC 61.949 63.158 10.54 0.00 0.00 4.70
1023 1102 3.386237 GTCACCTCGGCAGCCTCT 61.386 66.667 10.54 0.00 0.00 3.69
1024 1103 2.052690 GTCACCTCGGCAGCCTCTA 61.053 63.158 10.54 0.00 0.00 2.43
1025 1104 2.052690 TCACCTCGGCAGCCTCTAC 61.053 63.158 10.54 0.00 0.00 2.59
1027 1106 2.443016 CCTCGGCAGCCTCTACCT 60.443 66.667 10.54 0.00 0.00 3.08
1028 1107 2.790791 CCTCGGCAGCCTCTACCTG 61.791 68.421 10.54 0.00 0.00 4.00
1029 1108 2.037367 TCGGCAGCCTCTACCTGT 59.963 61.111 10.54 0.00 32.93 4.00
1030 1109 2.010582 CTCGGCAGCCTCTACCTGTC 62.011 65.000 10.54 0.00 32.93 3.51
1031 1110 2.496817 GGCAGCCTCTACCTGTCG 59.503 66.667 3.29 0.00 32.93 4.35
1032 1111 2.352032 GGCAGCCTCTACCTGTCGT 61.352 63.158 3.29 0.00 32.93 4.34
1033 1112 1.035932 GGCAGCCTCTACCTGTCGTA 61.036 60.000 3.29 0.00 32.93 3.43
1034 1113 1.033574 GCAGCCTCTACCTGTCGTAT 58.966 55.000 0.00 0.00 32.93 3.06
1035 1114 2.228059 GCAGCCTCTACCTGTCGTATA 58.772 52.381 0.00 0.00 32.93 1.47
1054 1133 5.066117 CGTATACCAGAGTTGCTCTCAGTTA 59.934 44.000 10.92 0.00 44.98 2.24
1361 1440 2.974698 GCCGCAACTGTGAGCACT 60.975 61.111 1.99 0.00 0.00 4.40
1362 1441 1.667830 GCCGCAACTGTGAGCACTA 60.668 57.895 1.99 0.00 0.00 2.74
1363 1442 1.227999 GCCGCAACTGTGAGCACTAA 61.228 55.000 1.99 0.00 0.00 2.24
1374 1453 2.540101 GTGAGCACTAATAAAGCGCGAT 59.460 45.455 12.10 0.00 38.35 4.58
1427 1506 3.612247 ATGTGCTCTGACCGGTGGC 62.612 63.158 14.63 11.75 0.00 5.01
1612 1691 5.798125 GATGTGAGATCTACATCCCTTGA 57.202 43.478 22.13 0.00 45.40 3.02
1625 1704 6.780457 ACATCCCTTGATCAATTTTACCAG 57.220 37.500 8.96 0.00 0.00 4.00
1722 1803 2.028996 GCATGGTATTGGGGAACTGGG 61.029 57.143 0.00 0.00 0.00 4.45
1791 1872 3.117131 ACCACTTTATTGGGGATGGATCC 60.117 47.826 4.20 4.20 46.41 3.36
1929 2146 1.067749 GCTGCAATGCAACACCACA 59.932 52.632 9.92 0.00 38.41 4.17
1962 2179 3.124128 GCTTAACCTACAAACGGTACAGC 59.876 47.826 0.00 0.00 34.48 4.40
1995 2212 8.472007 ACACTATGGAAATTCAAGGTGTTTTA 57.528 30.769 6.22 0.00 34.99 1.52
2295 2524 7.456253 CGTGACAATGTCTGTTCTTAAATAGG 58.544 38.462 14.97 0.00 38.84 2.57
2330 2560 8.279970 ACTTATGCTGCACAAGATATACAAAA 57.720 30.769 25.86 0.00 0.00 2.44
2371 2601 7.142680 ACACAAAAGTTGGTACCAAATATTCG 58.857 34.615 28.67 17.86 37.70 3.34
2385 2615 1.006086 TATTCGCGAAGTGCACATGG 58.994 50.000 27.20 9.95 46.97 3.66
2389 2619 0.301687 CGCGAAGTGCACATGGTATC 59.698 55.000 21.04 6.20 46.97 2.24
2568 2800 2.235891 GTACCCAAAGTCCCAAAGTGG 58.764 52.381 0.00 0.00 37.25 4.00
2572 2804 1.410932 CCAAAGTCCCAAAGTGGTCCA 60.411 52.381 0.00 0.00 35.17 4.02
2791 3025 9.061435 CAAAGAATCAGAGGGATAAATAGTTCC 57.939 37.037 0.00 0.00 34.28 3.62
2959 3196 3.896888 TGATGTTCAATTGAAAGGCAGGT 59.103 39.130 22.07 3.16 35.58 4.00
2979 3216 6.018669 GCAGGTTATCTCAACTAGGAAATTCG 60.019 42.308 0.00 0.00 0.00 3.34
2985 3222 1.401905 CAACTAGGAAATTCGCCAGGC 59.598 52.381 0.00 0.00 0.00 4.85
3117 3354 1.860676 TATGCATTTCCGAGTACCGC 58.139 50.000 3.54 0.00 36.84 5.68
3153 3390 1.614903 CCTGCAGAAGTTCAATTGGCA 59.385 47.619 17.39 4.44 0.00 4.92
3223 3460 5.082425 ACAGATTGGAATTCTTTGCCTCTT 58.918 37.500 5.23 0.00 0.00 2.85
3251 3488 9.443323 TTTTCAGAATATTTCATAACCTGTCGA 57.557 29.630 0.00 0.00 0.00 4.20
3458 3695 2.363680 CACATCTCGAGCCACCTTCTAT 59.636 50.000 7.81 0.00 0.00 1.98
3467 3704 2.027745 AGCCACCTTCTATATCATGCCG 60.028 50.000 0.00 0.00 0.00 5.69
3533 3770 4.475028 TCGTATTTGCACAATCAAAGCTG 58.525 39.130 0.00 0.00 39.06 4.24
3658 3898 6.403866 TGAACTGCAATAAGGTGTTCAAAT 57.596 33.333 11.65 0.00 42.32 2.32
3735 4089 4.142730 GGCAGTGAGAAACATTCATCTGAC 60.143 45.833 0.00 6.43 31.37 3.51
3842 4197 2.431057 ACCACATAGCTTAGGAAGTCCG 59.569 50.000 0.00 0.00 42.08 4.79
4002 4357 3.270877 CGTTGCTTAGTGGGCTTATTCT 58.729 45.455 0.00 0.00 0.00 2.40
4011 4366 1.284785 TGGGCTTATTCTGGGTTCAGG 59.715 52.381 0.00 0.00 41.23 3.86
4013 4368 2.291605 GGGCTTATTCTGGGTTCAGGTT 60.292 50.000 0.00 0.00 41.23 3.50
4014 4369 2.755103 GGCTTATTCTGGGTTCAGGTTG 59.245 50.000 0.00 0.00 41.23 3.77
4015 4370 3.421844 GCTTATTCTGGGTTCAGGTTGT 58.578 45.455 0.00 0.00 41.23 3.32
4071 4432 0.532862 CCAGTGGAAGCGTTGTGTCT 60.533 55.000 1.68 0.00 0.00 3.41
4109 4470 0.261991 TAGCGGAAGGATGGAGAGGT 59.738 55.000 0.00 0.00 0.00 3.85
4147 4508 0.467474 GCATTAGGTGGGGTTAGGCC 60.467 60.000 0.00 0.00 0.00 5.19
4148 4509 0.923358 CATTAGGTGGGGTTAGGCCA 59.077 55.000 5.01 0.00 39.65 5.36
4208 4582 1.153349 GGGGAATCTGTGGAGCGAC 60.153 63.158 0.00 0.00 0.00 5.19
4232 4606 1.599606 GCTGTCTTCGAGCAGGAGGA 61.600 60.000 13.14 0.00 36.40 3.71
4468 4857 2.173519 CTTTGCCCATTCCATGTCTGT 58.826 47.619 0.00 0.00 0.00 3.41
4535 4924 2.613133 ACGATAGAGGAGAGTTACGTGC 59.387 50.000 0.00 0.00 41.38 5.34
4558 4947 5.900242 GCGTCTTTTACTGTGTGTTTTAGTC 59.100 40.000 0.00 0.00 0.00 2.59
4559 4948 6.455913 GCGTCTTTTACTGTGTGTTTTAGTCA 60.456 38.462 0.00 0.00 0.00 3.41
4560 4949 6.898189 CGTCTTTTACTGTGTGTTTTAGTCAC 59.102 38.462 0.00 0.00 36.48 3.67
4561 4950 7.201496 CGTCTTTTACTGTGTGTTTTAGTCACT 60.201 37.037 0.00 0.00 36.83 3.41
4562 4951 7.903431 GTCTTTTACTGTGTGTTTTAGTCACTG 59.097 37.037 0.00 0.00 36.83 3.66
4581 4970 7.222611 AGTCACTGTTCATATTTGTTTTGTTGC 59.777 33.333 0.00 0.00 0.00 4.17
4590 4979 0.177604 TGTTTTGTTGCAGGCTTGGG 59.822 50.000 0.00 0.00 0.00 4.12
4611 5000 1.664016 GCACGACCTGCAAGTTTGATG 60.664 52.381 0.00 0.00 46.29 3.07
4832 5221 7.066043 AGTCTCTCATTTGTACCTAGTTAGTCG 59.934 40.741 0.00 0.00 0.00 4.18
4937 5326 7.393234 TCTCCAGTGTTTATATTCCCTTGTTTG 59.607 37.037 0.00 0.00 0.00 2.93
5002 5391 9.541724 GTTTTCTTTGTTTTTCATTCCTCAAAC 57.458 29.630 0.00 0.00 0.00 2.93
5087 5478 4.018324 TCCCTCTGCTAGTTACTCTTCAGA 60.018 45.833 9.53 9.53 35.20 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.744202 GTTGCCATGTCAGTTGTAGGAG 59.256 50.000 0.00 0.00 0.00 3.69
200 201 2.880268 CTCGAAATGCTATGGCCATCAA 59.120 45.455 24.80 9.62 37.74 2.57
398 402 4.215742 ATTCCGGCCGATTCGCGA 62.216 61.111 30.73 11.67 44.57 5.87
450 454 2.897350 GCGATTTCTGCCCCCTCG 60.897 66.667 0.00 0.00 0.00 4.63
493 500 1.555075 AGCCGCAGATTGAAGGTAAGA 59.445 47.619 0.00 0.00 0.00 2.10
547 554 3.192230 CATTCGCGGCCGTTGCTA 61.192 61.111 28.70 11.29 37.74 3.49
662 676 4.544689 CGCCACTCGCTCCTCTCG 62.545 72.222 0.00 0.00 34.21 4.04
664 678 3.137459 CTCGCCACTCGCTCCTCT 61.137 66.667 0.00 0.00 38.27 3.69
874 952 0.313672 AAACTAACGTCCACGCGGTA 59.686 50.000 12.47 0.00 44.43 4.02
879 958 2.126467 TCGGAAAAACTAACGTCCACG 58.874 47.619 0.00 0.00 46.33 4.94
884 963 4.961435 TTGGTTTCGGAAAAACTAACGT 57.039 36.364 4.46 0.00 33.01 3.99
892 971 3.955650 TGGTGTTTTGGTTTCGGAAAA 57.044 38.095 4.46 0.00 0.00 2.29
902 981 5.337578 TCTTTCTTCCTTTGGTGTTTTGG 57.662 39.130 0.00 0.00 0.00 3.28
907 986 6.607198 TCTTCATTTCTTTCTTCCTTTGGTGT 59.393 34.615 0.00 0.00 0.00 4.16
908 987 7.042797 TCTTCATTTCTTTCTTCCTTTGGTG 57.957 36.000 0.00 0.00 0.00 4.17
909 988 7.660030 TTCTTCATTTCTTTCTTCCTTTGGT 57.340 32.000 0.00 0.00 0.00 3.67
910 989 8.947055 TTTTCTTCATTTCTTTCTTCCTTTGG 57.053 30.769 0.00 0.00 0.00 3.28
911 990 9.807649 TCTTTTCTTCATTTCTTTCTTCCTTTG 57.192 29.630 0.00 0.00 0.00 2.77
913 992 9.978044 CATCTTTTCTTCATTTCTTTCTTCCTT 57.022 29.630 0.00 0.00 0.00 3.36
914 993 9.140874 ACATCTTTTCTTCATTTCTTTCTTCCT 57.859 29.630 0.00 0.00 0.00 3.36
915 994 9.189723 CACATCTTTTCTTCATTTCTTTCTTCC 57.810 33.333 0.00 0.00 0.00 3.46
916 995 9.189723 CCACATCTTTTCTTCATTTCTTTCTTC 57.810 33.333 0.00 0.00 0.00 2.87
917 996 8.146412 CCCACATCTTTTCTTCATTTCTTTCTT 58.854 33.333 0.00 0.00 0.00 2.52
918 997 7.664758 CCCACATCTTTTCTTCATTTCTTTCT 58.335 34.615 0.00 0.00 0.00 2.52
919 998 6.367149 GCCCACATCTTTTCTTCATTTCTTTC 59.633 38.462 0.00 0.00 0.00 2.62
920 999 6.183360 TGCCCACATCTTTTCTTCATTTCTTT 60.183 34.615 0.00 0.00 0.00 2.52
921 1000 5.305128 TGCCCACATCTTTTCTTCATTTCTT 59.695 36.000 0.00 0.00 0.00 2.52
922 1001 4.834496 TGCCCACATCTTTTCTTCATTTCT 59.166 37.500 0.00 0.00 0.00 2.52
923 1002 5.138125 TGCCCACATCTTTTCTTCATTTC 57.862 39.130 0.00 0.00 0.00 2.17
924 1003 4.562143 GCTGCCCACATCTTTTCTTCATTT 60.562 41.667 0.00 0.00 0.00 2.32
925 1004 3.056322 GCTGCCCACATCTTTTCTTCATT 60.056 43.478 0.00 0.00 0.00 2.57
926 1005 2.494870 GCTGCCCACATCTTTTCTTCAT 59.505 45.455 0.00 0.00 0.00 2.57
927 1006 1.888512 GCTGCCCACATCTTTTCTTCA 59.111 47.619 0.00 0.00 0.00 3.02
928 1007 1.203287 GGCTGCCCACATCTTTTCTTC 59.797 52.381 7.66 0.00 0.00 2.87
929 1008 1.260544 GGCTGCCCACATCTTTTCTT 58.739 50.000 7.66 0.00 0.00 2.52
930 1009 0.112995 TGGCTGCCCACATCTTTTCT 59.887 50.000 17.53 0.00 35.79 2.52
931 1010 0.529378 CTGGCTGCCCACATCTTTTC 59.471 55.000 17.53 0.00 35.79 2.29
932 1011 0.178953 ACTGGCTGCCCACATCTTTT 60.179 50.000 17.53 0.00 35.79 2.27
933 1012 0.698238 TACTGGCTGCCCACATCTTT 59.302 50.000 17.53 0.00 35.79 2.52
934 1013 0.921896 ATACTGGCTGCCCACATCTT 59.078 50.000 17.53 0.00 35.79 2.40
935 1014 0.182061 CATACTGGCTGCCCACATCT 59.818 55.000 17.53 0.00 35.79 2.90
936 1015 0.181114 TCATACTGGCTGCCCACATC 59.819 55.000 17.53 0.00 35.79 3.06
937 1016 0.625316 TTCATACTGGCTGCCCACAT 59.375 50.000 17.53 3.10 35.79 3.21
938 1017 0.035152 CTTCATACTGGCTGCCCACA 60.035 55.000 17.53 0.42 35.79 4.17
939 1018 0.253044 TCTTCATACTGGCTGCCCAC 59.747 55.000 17.53 0.00 35.79 4.61
940 1019 0.991146 TTCTTCATACTGGCTGCCCA 59.009 50.000 17.53 1.24 39.32 5.36
941 1020 1.210478 TCTTCTTCATACTGGCTGCCC 59.790 52.381 17.53 0.00 0.00 5.36
942 1021 2.093235 AGTCTTCTTCATACTGGCTGCC 60.093 50.000 12.87 12.87 0.00 4.85
991 1070 3.817647 GAGGTGACTTGCAAATTCAGAGT 59.182 43.478 10.05 0.00 44.43 3.24
1001 1080 2.031012 CTGCCGAGGTGACTTGCA 59.969 61.111 0.00 0.00 44.43 4.08
1003 1082 2.743928 GGCTGCCGAGGTGACTTG 60.744 66.667 1.35 0.00 44.43 3.16
1006 1085 2.052690 TAGAGGCTGCCGAGGTGAC 61.053 63.158 13.96 0.58 0.00 3.67
1007 1086 2.052690 GTAGAGGCTGCCGAGGTGA 61.053 63.158 13.96 0.00 0.00 4.02
1008 1087 2.496817 GTAGAGGCTGCCGAGGTG 59.503 66.667 13.96 0.00 0.00 4.00
1009 1088 2.760385 GGTAGAGGCTGCCGAGGT 60.760 66.667 13.96 0.00 0.00 3.85
1010 1089 2.443016 AGGTAGAGGCTGCCGAGG 60.443 66.667 13.96 0.00 41.15 4.63
1011 1090 2.010582 GACAGGTAGAGGCTGCCGAG 62.011 65.000 13.96 2.03 41.15 4.63
1012 1091 2.037367 ACAGGTAGAGGCTGCCGA 59.963 61.111 13.96 0.00 41.15 5.54
1013 1092 2.496817 GACAGGTAGAGGCTGCCG 59.503 66.667 13.96 0.00 41.15 5.69
1014 1093 1.035932 TACGACAGGTAGAGGCTGCC 61.036 60.000 11.65 11.65 36.48 4.85
1015 1094 1.033574 ATACGACAGGTAGAGGCTGC 58.966 55.000 0.00 0.00 33.84 5.25
1016 1095 2.553172 GGTATACGACAGGTAGAGGCTG 59.447 54.545 0.00 0.00 33.84 4.85
1017 1096 2.174210 TGGTATACGACAGGTAGAGGCT 59.826 50.000 0.00 0.00 33.84 4.58
1018 1097 2.553172 CTGGTATACGACAGGTAGAGGC 59.447 54.545 0.00 0.00 33.84 4.70
1019 1098 4.066490 CTCTGGTATACGACAGGTAGAGG 58.934 52.174 8.67 0.00 33.84 3.69
1020 1099 4.706035 ACTCTGGTATACGACAGGTAGAG 58.294 47.826 8.67 0.00 33.84 2.43
1021 1100 4.767578 ACTCTGGTATACGACAGGTAGA 57.232 45.455 8.67 0.00 33.84 2.59
1022 1101 4.497674 GCAACTCTGGTATACGACAGGTAG 60.498 50.000 8.67 3.86 33.84 3.18
1023 1102 3.379372 GCAACTCTGGTATACGACAGGTA 59.621 47.826 8.67 0.00 35.47 3.08
1024 1103 2.165845 GCAACTCTGGTATACGACAGGT 59.834 50.000 8.67 4.32 35.47 4.00
1025 1104 2.427453 AGCAACTCTGGTATACGACAGG 59.573 50.000 8.67 3.85 35.47 4.00
1027 1106 3.353557 AGAGCAACTCTGGTATACGACA 58.646 45.455 0.00 0.00 39.62 4.35
1028 1107 3.377485 TGAGAGCAACTCTGGTATACGAC 59.623 47.826 0.98 0.00 41.35 4.34
1029 1108 3.617284 TGAGAGCAACTCTGGTATACGA 58.383 45.455 0.98 0.00 41.35 3.43
1030 1109 3.378742 ACTGAGAGCAACTCTGGTATACG 59.621 47.826 16.99 0.00 41.35 3.06
1031 1110 4.993029 ACTGAGAGCAACTCTGGTATAC 57.007 45.455 16.99 0.00 41.35 1.47
1032 1111 5.360144 GGTAACTGAGAGCAACTCTGGTATA 59.640 44.000 14.66 7.16 44.36 1.47
1033 1112 4.160626 GGTAACTGAGAGCAACTCTGGTAT 59.839 45.833 14.66 7.82 44.36 2.73
1034 1113 3.510360 GGTAACTGAGAGCAACTCTGGTA 59.490 47.826 16.99 13.62 41.35 3.25
1035 1114 2.300437 GGTAACTGAGAGCAACTCTGGT 59.700 50.000 16.99 14.37 41.35 4.00
1054 1133 3.311110 TCGCTGGCGAGAAAGGGT 61.311 61.111 13.78 0.00 44.01 4.34
1288 1367 2.359404 GGGAGGAGGAGACGGTGA 59.641 66.667 0.00 0.00 0.00 4.02
1361 1440 1.493772 CCGACCATCGCGCTTTATTA 58.506 50.000 5.56 0.00 38.82 0.98
1362 1441 1.772063 GCCGACCATCGCGCTTTATT 61.772 55.000 5.56 0.00 38.82 1.40
1363 1442 2.244651 GCCGACCATCGCGCTTTAT 61.245 57.895 5.56 0.00 38.82 1.40
1374 1453 0.174845 CATAAAGGAGACGCCGACCA 59.825 55.000 0.00 0.00 43.43 4.02
1625 1704 2.640346 AAACAACACAAACCACGGTC 57.360 45.000 0.00 0.00 0.00 4.79
1695 1774 1.122227 CCCAATACCATGCCCCAAAG 58.878 55.000 0.00 0.00 0.00 2.77
1722 1803 7.308049 GCTTCCGATTATTAGGGAGTTCATTTC 60.308 40.741 0.00 0.00 35.53 2.17
1791 1872 3.390639 AGCATCTCCAGTAATCCTCCAAG 59.609 47.826 0.00 0.00 0.00 3.61
1896 2113 6.769341 TGCATTGCAGCCCTGATATAATATAG 59.231 38.462 7.38 0.00 33.32 1.31
1929 2146 8.715088 CGTTTGTAGGTTAAGCAAATAGTAACT 58.285 33.333 7.52 0.00 35.08 2.24
1995 2212 5.212532 TGCCAGTTGCTTCAAATGTATTT 57.787 34.783 6.31 0.00 37.68 1.40
2114 2335 6.426937 TGGCAATCTTGTCTTGTACTAACTTC 59.573 38.462 0.00 0.00 33.01 3.01
2295 2524 6.662414 TGTGCAGCATAAGTAGTTGAATAC 57.338 37.500 0.00 0.00 0.00 1.89
2351 2581 4.696402 TCGCGAATATTTGGTACCAACTTT 59.304 37.500 27.08 18.98 35.46 2.66
2371 2601 1.656652 AGATACCATGTGCACTTCGC 58.343 50.000 19.41 1.18 42.89 4.70
2385 2615 8.642020 GCTCAAACATTTCATGAAACAAGATAC 58.358 33.333 22.71 6.39 32.51 2.24
2389 2619 5.610982 GCGCTCAAACATTTCATGAAACAAG 60.611 40.000 22.71 16.95 32.51 3.16
2568 2800 6.308371 TGAAAGAGAAAAATAACGGTGGAC 57.692 37.500 0.00 0.00 0.00 4.02
2572 2804 7.329588 ACACTTGAAAGAGAAAAATAACGGT 57.670 32.000 0.00 0.00 0.00 4.83
2791 3025 6.238211 GGTGTGAATGGATCTTACTCAAATCG 60.238 42.308 0.00 0.00 0.00 3.34
2959 3196 5.984725 TGGCGAATTTCCTAGTTGAGATAA 58.015 37.500 0.00 0.00 0.00 1.75
3040 3277 3.200605 TCAACATCATGAGCCTACATGGT 59.799 43.478 0.09 6.28 45.10 3.55
3117 3354 0.523072 CAGGCAGTTCATTTGGGTCG 59.477 55.000 0.00 0.00 0.00 4.79
3153 3390 6.554334 AGCGTGTGTTTGAATAACTACATT 57.446 33.333 0.00 0.00 0.00 2.71
3241 3478 5.244402 TGAAGGATTGTACTTCGACAGGTTA 59.756 40.000 0.00 0.00 45.59 2.85
3251 3488 7.390718 GGAATACTTGTGTGAAGGATTGTACTT 59.609 37.037 0.00 0.00 31.24 2.24
3467 3704 1.544724 TGATTTACAGGCTTGCCACC 58.455 50.000 14.54 0.00 0.00 4.61
3735 4089 3.181461 ACCTAAAGATCCTCTCATTGCCG 60.181 47.826 0.00 0.00 0.00 5.69
4002 4357 5.389520 TGAAATAATCACAACCTGAACCCA 58.610 37.500 0.00 0.00 31.50 4.51
4015 4370 3.624707 GCCCAGACCAGGTGAAATAATCA 60.625 47.826 0.00 0.00 35.05 2.57
4065 4426 1.340248 GGGACAAGACGAAGAGACACA 59.660 52.381 0.00 0.00 0.00 3.72
4071 4432 1.541310 ATGCGGGGACAAGACGAAGA 61.541 55.000 0.00 0.00 0.00 2.87
4096 4457 0.119155 TCCACCACCTCTCCATCCTT 59.881 55.000 0.00 0.00 0.00 3.36
4130 4491 1.499007 CATGGCCTAACCCCACCTAAT 59.501 52.381 3.32 0.00 37.83 1.73
4159 4520 3.123620 GCAGCTCGCCTGACAAGG 61.124 66.667 7.04 0.00 44.64 3.61
4161 4522 2.357881 CAGCAGCTCGCCTGACAA 60.358 61.111 0.00 0.00 44.64 3.18
4208 4582 3.243892 GCTCGAAGACAGCTCGCG 61.244 66.667 0.00 0.00 33.75 5.87
4324 4712 4.157105 ACAAAAAGCACTACCAAAACTCGT 59.843 37.500 0.00 0.00 0.00 4.18
4422 4811 3.053291 CCGCGGGCTAGCAAAACA 61.053 61.111 20.10 0.00 36.85 2.83
4535 4924 6.898189 GTGACTAAAACACACAGTAAAAGACG 59.102 38.462 0.00 0.00 38.05 4.18
4558 4947 7.231705 TGCAACAAAACAAATATGAACAGTG 57.768 32.000 0.00 0.00 0.00 3.66
4559 4948 6.479660 CCTGCAACAAAACAAATATGAACAGT 59.520 34.615 0.00 0.00 0.00 3.55
4560 4949 6.564499 GCCTGCAACAAAACAAATATGAACAG 60.564 38.462 0.00 0.00 0.00 3.16
4561 4950 5.236047 GCCTGCAACAAAACAAATATGAACA 59.764 36.000 0.00 0.00 0.00 3.18
4562 4951 5.466393 AGCCTGCAACAAAACAAATATGAAC 59.534 36.000 0.00 0.00 0.00 3.18
4611 5000 5.294552 GTGGGCAACAGTATTATTCAGACTC 59.705 44.000 0.00 0.00 39.74 3.36
4987 5376 3.966665 AGCAAGGGTTTGAGGAATGAAAA 59.033 39.130 0.00 0.00 36.36 2.29
5087 5478 9.927081 ATAAAAAGATAATGATGACTGAAGGGT 57.073 29.630 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.