Multiple sequence alignment - TraesCS1A01G188000

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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 TraesCS1A01G188000 chr1A 100.000 3197 0 0 1 3197 339482296 339485492 0.000000e+00 5904
1 TraesCS1A01G188000 chr1B 90.777 2960 90 62 328 3185 351439083 351441961 0.000000e+00 3784
2 TraesCS1A01G188000 chr1D 92.554 2713 81 42 328 2947 260980065 260977381 0.000000e+00 3779
3 TraesCS1A01G188000 chr1D 85.338 266 13 11 2931 3195 260972078 260971838 5.290000e-63 252
4 TraesCS1A01G188000 chr1D 93.023 172 6 4 151 319 260980338 260980170 2.460000e-61 246
5 TraesCS1A01G188000 chr6D 79.348 184 17 11 2506 2676 16011425 16011600 3.370000e-20 110


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 TraesCS1A01G188000 chr1A 339482296 339485492 3196 False 5904.0 5904 100.0000 1 3197 1 chr1A.!!$F1 3196
1 TraesCS1A01G188000 chr1B 351439083 351441961 2878 False 3784.0 3784 90.7770 328 3185 1 chr1B.!!$F1 2857
2 TraesCS1A01G188000 chr1D 260977381 260980338 2957 True 2012.5 3779 92.7885 151 2947 2 chr1D.!!$R2 2796

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
380 482 0.106708 TCTTATCGCATGGAGCCACC 59.893 55.0 0.0 0.0 41.38 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2471 0.318441 AGTTGCAGCTGCTCGAGTTA 59.682 50.0 36.61 14.44 42.66 2.24 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
40 41 7.681939 AAATTATACCCGTTAGCATGTATGG 57.318 36.000 0.00 0.00 0.00 2.74
41 42 3.695830 ATACCCGTTAGCATGTATGGG 57.304 47.619 15.99 15.99 44.70 4.00
42 43 1.502690 ACCCGTTAGCATGTATGGGA 58.497 50.000 21.49 0.00 42.26 4.37
43 44 1.841277 ACCCGTTAGCATGTATGGGAA 59.159 47.619 21.49 0.00 42.26 3.97
44 45 2.158813 ACCCGTTAGCATGTATGGGAAG 60.159 50.000 21.49 3.74 42.26 3.46
45 46 2.104111 CCCGTTAGCATGTATGGGAAGA 59.896 50.000 13.59 0.00 42.26 2.87
46 47 3.433031 CCCGTTAGCATGTATGGGAAGAA 60.433 47.826 13.59 0.00 42.26 2.52
47 48 4.389374 CCGTTAGCATGTATGGGAAGAAT 58.611 43.478 0.00 0.00 0.00 2.40
48 49 4.821805 CCGTTAGCATGTATGGGAAGAATT 59.178 41.667 0.00 0.00 0.00 2.17
49 50 5.995282 CCGTTAGCATGTATGGGAAGAATTA 59.005 40.000 0.00 0.00 0.00 1.40
50 51 6.655003 CCGTTAGCATGTATGGGAAGAATTAT 59.345 38.462 0.00 0.00 0.00 1.28
51 52 7.822334 CCGTTAGCATGTATGGGAAGAATTATA 59.178 37.037 0.00 0.00 0.00 0.98
52 53 8.656849 CGTTAGCATGTATGGGAAGAATTATAC 58.343 37.037 0.00 0.00 0.00 1.47
53 54 8.947115 GTTAGCATGTATGGGAAGAATTATACC 58.053 37.037 0.00 0.00 0.00 2.73
54 55 6.485171 AGCATGTATGGGAAGAATTATACCC 58.515 40.000 0.00 0.00 42.37 3.69
55 56 5.354234 GCATGTATGGGAAGAATTATACCCG 59.646 44.000 0.00 0.00 44.70 5.28
56 57 6.472887 CATGTATGGGAAGAATTATACCCGT 58.527 40.000 11.19 11.19 44.70 5.28
57 58 6.503560 TGTATGGGAAGAATTATACCCGTT 57.496 37.500 11.55 4.50 44.70 4.44
58 59 7.615039 TGTATGGGAAGAATTATACCCGTTA 57.385 36.000 11.55 3.77 44.70 3.18
59 60 8.209802 TGTATGGGAAGAATTATACCCGTTAT 57.790 34.615 11.55 3.09 44.70 1.89
60 61 9.324008 TGTATGGGAAGAATTATACCCGTTATA 57.676 33.333 11.55 2.37 44.70 0.98
61 62 9.813446 GTATGGGAAGAATTATACCCGTTATAG 57.187 37.037 11.55 0.00 44.70 1.31
62 63 7.248743 TGGGAAGAATTATACCCGTTATAGG 57.751 40.000 0.00 0.00 44.70 2.57
75 76 5.974108 CCCGTTATAGGGTATGAGTAATGG 58.026 45.833 0.00 0.00 46.38 3.16
76 77 5.416947 CCGTTATAGGGTATGAGTAATGGC 58.583 45.833 0.00 0.00 0.00 4.40
77 78 5.100259 CGTTATAGGGTATGAGTAATGGCG 58.900 45.833 0.00 0.00 0.00 5.69
78 79 5.106038 CGTTATAGGGTATGAGTAATGGCGA 60.106 44.000 0.00 0.00 0.00 5.54
79 80 6.405508 CGTTATAGGGTATGAGTAATGGCGAT 60.406 42.308 0.00 0.00 0.00 4.58
80 81 3.685139 AGGGTATGAGTAATGGCGATG 57.315 47.619 0.00 0.00 0.00 3.84
81 82 2.303022 AGGGTATGAGTAATGGCGATGG 59.697 50.000 0.00 0.00 0.00 3.51
82 83 2.615493 GGGTATGAGTAATGGCGATGGG 60.615 54.545 0.00 0.00 0.00 4.00
83 84 2.038557 GGTATGAGTAATGGCGATGGGT 59.961 50.000 0.00 0.00 0.00 4.51
84 85 3.259876 GGTATGAGTAATGGCGATGGGTA 59.740 47.826 0.00 0.00 0.00 3.69
85 86 4.262721 GGTATGAGTAATGGCGATGGGTAA 60.263 45.833 0.00 0.00 0.00 2.85
86 87 3.469008 TGAGTAATGGCGATGGGTAAG 57.531 47.619 0.00 0.00 0.00 2.34
87 88 2.143925 GAGTAATGGCGATGGGTAAGC 58.856 52.381 0.00 0.00 0.00 3.09
88 89 1.768870 AGTAATGGCGATGGGTAAGCT 59.231 47.619 0.00 0.00 0.00 3.74
89 90 2.143925 GTAATGGCGATGGGTAAGCTC 58.856 52.381 0.00 0.00 0.00 4.09
90 91 0.546122 AATGGCGATGGGTAAGCTCA 59.454 50.000 0.00 0.00 0.00 4.26
91 92 0.179045 ATGGCGATGGGTAAGCTCAC 60.179 55.000 0.00 0.00 0.00 3.51
92 93 1.883084 GGCGATGGGTAAGCTCACG 60.883 63.158 0.00 0.00 0.00 4.35
93 94 2.526120 GCGATGGGTAAGCTCACGC 61.526 63.158 0.00 0.00 38.00 5.34
94 95 2.230940 CGATGGGTAAGCTCACGCG 61.231 63.158 3.53 3.53 42.32 6.01
95 96 1.883084 GATGGGTAAGCTCACGCGG 60.883 63.158 12.47 0.00 42.32 6.46
96 97 3.385749 ATGGGTAAGCTCACGCGGG 62.386 63.158 12.47 6.51 42.32 6.13
97 98 4.832608 GGGTAAGCTCACGCGGGG 62.833 72.222 9.32 0.00 42.32 5.73
98 99 4.078516 GGTAAGCTCACGCGGGGT 62.079 66.667 9.32 1.03 42.32 4.95
100 101 4.077184 TAAGCTCACGCGGGGTGG 62.077 66.667 22.77 15.07 46.96 4.61
110 111 3.416880 CGGGGTGGGCAAGGGTAT 61.417 66.667 0.00 0.00 0.00 2.73
111 112 2.278738 GGGGTGGGCAAGGGTATG 59.721 66.667 0.00 0.00 0.00 2.39
112 113 2.313427 GGGGTGGGCAAGGGTATGA 61.313 63.158 0.00 0.00 0.00 2.15
113 114 1.227383 GGGTGGGCAAGGGTATGAG 59.773 63.158 0.00 0.00 0.00 2.90
114 115 1.227383 GGTGGGCAAGGGTATGAGG 59.773 63.158 0.00 0.00 0.00 3.86
115 116 1.571773 GGTGGGCAAGGGTATGAGGT 61.572 60.000 0.00 0.00 0.00 3.85
116 117 0.394352 GTGGGCAAGGGTATGAGGTG 60.394 60.000 0.00 0.00 0.00 4.00
117 118 1.227383 GGGCAAGGGTATGAGGTGG 59.773 63.158 0.00 0.00 0.00 4.61
118 119 1.453928 GGCAAGGGTATGAGGTGGC 60.454 63.158 0.00 0.00 0.00 5.01
119 120 1.609783 GCAAGGGTATGAGGTGGCT 59.390 57.895 0.00 0.00 0.00 4.75
120 121 0.464554 GCAAGGGTATGAGGTGGCTC 60.465 60.000 0.00 0.00 0.00 4.70
121 122 0.181350 CAAGGGTATGAGGTGGCTCC 59.819 60.000 0.00 0.00 0.00 4.70
122 123 0.253160 AAGGGTATGAGGTGGCTCCA 60.253 55.000 8.51 0.00 39.02 3.86
123 124 0.983378 AGGGTATGAGGTGGCTCCAC 60.983 60.000 10.49 10.49 45.49 4.02
133 134 2.664402 GTGGCTCCACCCATATTCAT 57.336 50.000 7.82 0.00 40.79 2.57
134 135 3.788227 GTGGCTCCACCCATATTCATA 57.212 47.619 7.82 0.00 40.79 2.15
135 136 3.412386 GTGGCTCCACCCATATTCATAC 58.588 50.000 7.82 0.00 40.79 2.39
136 137 2.375174 TGGCTCCACCCATATTCATACC 59.625 50.000 0.00 0.00 37.83 2.73
137 138 2.375174 GGCTCCACCCATATTCATACCA 59.625 50.000 0.00 0.00 0.00 3.25
138 139 3.010584 GGCTCCACCCATATTCATACCAT 59.989 47.826 0.00 0.00 0.00 3.55
139 140 4.012374 GCTCCACCCATATTCATACCATG 58.988 47.826 0.00 0.00 0.00 3.66
140 141 4.012374 CTCCACCCATATTCATACCATGC 58.988 47.826 0.00 0.00 0.00 4.06
141 142 2.749076 CCACCCATATTCATACCATGCG 59.251 50.000 0.00 0.00 0.00 4.73
142 143 2.749076 CACCCATATTCATACCATGCGG 59.251 50.000 0.00 0.00 38.77 5.69
143 144 2.290896 ACCCATATTCATACCATGCGGG 60.291 50.000 0.00 0.00 44.81 6.13
187 189 4.729868 AGGAGGTGTTAGCAATGAGTTTT 58.270 39.130 0.00 0.00 0.00 2.43
188 190 5.876357 AGGAGGTGTTAGCAATGAGTTTTA 58.124 37.500 0.00 0.00 0.00 1.52
189 191 6.485171 AGGAGGTGTTAGCAATGAGTTTTAT 58.515 36.000 0.00 0.00 0.00 1.40
191 193 8.107095 AGGAGGTGTTAGCAATGAGTTTTATAA 58.893 33.333 0.00 0.00 0.00 0.98
192 194 8.398665 GGAGGTGTTAGCAATGAGTTTTATAAG 58.601 37.037 0.00 0.00 0.00 1.73
193 195 8.281212 AGGTGTTAGCAATGAGTTTTATAAGG 57.719 34.615 0.00 0.00 0.00 2.69
223 225 3.381272 CCATGTTCCGCTGGATTGTATTT 59.619 43.478 0.00 0.00 34.24 1.40
235 237 4.979197 TGGATTGTATTTTGCACGTTGTTC 59.021 37.500 0.00 0.00 0.00 3.18
236 238 4.384547 GGATTGTATTTTGCACGTTGTTCC 59.615 41.667 0.00 0.00 0.00 3.62
237 239 2.988343 TGTATTTTGCACGTTGTTCCG 58.012 42.857 0.00 0.00 0.00 4.30
238 240 1.711824 GTATTTTGCACGTTGTTCCGC 59.288 47.619 0.00 0.00 0.00 5.54
239 241 0.383949 ATTTTGCACGTTGTTCCGCT 59.616 45.000 0.00 0.00 0.00 5.52
345 445 5.238583 ACTAGGCTGTCATCACTTTTGTAC 58.761 41.667 0.00 0.00 0.00 2.90
346 446 4.357918 AGGCTGTCATCACTTTTGTACT 57.642 40.909 0.00 0.00 0.00 2.73
347 447 5.483685 AGGCTGTCATCACTTTTGTACTA 57.516 39.130 0.00 0.00 0.00 1.82
380 482 0.106708 TCTTATCGCATGGAGCCACC 59.893 55.000 0.00 0.00 41.38 4.61
381 483 1.224069 CTTATCGCATGGAGCCACCG 61.224 60.000 0.00 0.00 42.61 4.94
382 484 2.658679 TTATCGCATGGAGCCACCGG 62.659 60.000 0.00 0.00 42.61 5.28
466 569 0.182537 AACAGCCACTACAGCCACAA 59.817 50.000 0.00 0.00 0.00 3.33
472 575 2.146342 CCACTACAGCCACAAGACAAG 58.854 52.381 0.00 0.00 0.00 3.16
544 647 1.340114 GCCAACCCGGAAAGAGAAGAT 60.340 52.381 0.73 0.00 36.56 2.40
545 648 2.880167 GCCAACCCGGAAAGAGAAGATT 60.880 50.000 0.73 0.00 36.56 2.40
826 948 6.590234 ATTTCCACACCAAAGAATAACCTC 57.410 37.500 0.00 0.00 0.00 3.85
872 994 6.037786 TGCGGTAGAATTATATAAGCAGCT 57.962 37.500 1.02 0.00 0.00 4.24
873 995 6.464222 TGCGGTAGAATTATATAAGCAGCTT 58.536 36.000 13.46 13.46 0.00 3.74
874 996 6.368791 TGCGGTAGAATTATATAAGCAGCTTG 59.631 38.462 18.54 0.00 0.00 4.01
896 1018 2.749441 GCCAAGCCACTCTGGAGC 60.749 66.667 0.00 0.00 40.96 4.70
900 1022 0.954449 CAAGCCACTCTGGAGCAGTG 60.954 60.000 0.00 0.00 40.96 3.66
958 1080 1.268625 TCTCGACGCTTGTTAGCTCAA 59.731 47.619 0.00 0.00 45.51 3.02
959 1081 2.058798 CTCGACGCTTGTTAGCTCAAA 58.941 47.619 0.00 0.00 45.51 2.69
972 1094 3.228188 AGCTCAAATCCAACTCCAACA 57.772 42.857 0.00 0.00 0.00 3.33
2082 2241 3.701604 CTACGTGGACTGCGAGGGC 62.702 68.421 0.00 0.00 40.52 5.19
2208 2367 3.935315 TCTGCAATGAGGAGAACAGAAG 58.065 45.455 0.00 0.00 42.19 2.85
2210 2369 4.040829 TCTGCAATGAGGAGAACAGAAGAA 59.959 41.667 0.00 0.00 42.19 2.52
2268 2436 2.351726 GCTAGTTCGGCACAATCGAATT 59.648 45.455 2.34 1.41 41.47 2.17
2269 2437 2.900122 AGTTCGGCACAATCGAATTG 57.100 45.000 2.34 0.00 45.59 2.32
2270 2438 1.468520 AGTTCGGCACAATCGAATTGG 59.531 47.619 10.82 0.00 44.42 3.16
2271 2439 1.466950 GTTCGGCACAATCGAATTGGA 59.533 47.619 10.82 0.00 44.42 3.53
2272 2440 1.814793 TCGGCACAATCGAATTGGAA 58.185 45.000 10.82 0.00 44.42 3.53
2319 2487 0.389037 CTGTAACTCGAGCAGCTGCA 60.389 55.000 38.24 18.87 45.16 4.41
2320 2488 0.033366 TGTAACTCGAGCAGCTGCAA 59.967 50.000 38.24 22.48 45.16 4.08
2330 2498 1.816835 AGCAGCTGCAACTACGTACTA 59.183 47.619 38.24 0.00 45.16 1.82
2331 2499 1.918609 GCAGCTGCAACTACGTACTAC 59.081 52.381 33.36 0.00 41.59 2.73
2332 2500 3.596967 GCAGCTGCAACTACGTACTACG 61.597 54.545 33.36 7.07 43.78 3.51
2381 2551 3.736740 GCTCTTTCTACTACTCTGCTGGC 60.737 52.174 0.00 0.00 0.00 4.85
2488 2660 6.030228 GCTGTAATTTTGTTGTGCTAGATCC 58.970 40.000 0.00 0.00 0.00 3.36
2489 2661 6.349280 GCTGTAATTTTGTTGTGCTAGATCCA 60.349 38.462 0.00 0.00 0.00 3.41
2508 2680 4.684724 TCCAAGGGTAGAGTATGTCTTGT 58.315 43.478 0.00 0.00 36.64 3.16
2642 2838 7.224753 ACGATACTGGAATTTGTGCAATACTAG 59.775 37.037 0.00 0.00 0.00 2.57
2643 2839 5.567138 ACTGGAATTTGTGCAATACTAGC 57.433 39.130 0.00 0.00 0.00 3.42
2644 2840 5.009631 ACTGGAATTTGTGCAATACTAGCA 58.990 37.500 0.00 0.00 40.19 3.49
2645 2841 5.124457 ACTGGAATTTGTGCAATACTAGCAG 59.876 40.000 0.00 0.00 43.63 4.24
2648 2844 5.123820 GGAATTTGTGCAATACTAGCAGTGA 59.876 40.000 0.00 0.00 43.63 3.41
2652 2848 4.578871 TGTGCAATACTAGCAGTGAATGT 58.421 39.130 0.00 0.00 43.63 2.71
2679 2875 3.534554 TCTGTATACGAGCTGAACCGTA 58.465 45.455 7.72 7.72 43.97 4.02
2701 2922 8.266682 CCGTATACAAATATGTCTTGTTCTTCG 58.733 37.037 3.32 0.03 41.05 3.79
2723 2944 9.302345 CTTCGTTATACTCTTGCTAATCTTCAA 57.698 33.333 0.00 0.00 0.00 2.69
2740 2961 6.525578 TCTTCAATACTCAACGACATAGGT 57.474 37.500 0.00 0.00 0.00 3.08
2744 2965 6.124340 TCAATACTCAACGACATAGGTAGGA 58.876 40.000 0.00 0.00 0.00 2.94
2791 3012 6.582677 TTGTTCTGTTTGTTTCTCTTGGAA 57.417 33.333 0.00 0.00 0.00 3.53
2874 3095 0.248289 TCCGACAAGGGAATCCGAAC 59.752 55.000 0.00 0.00 41.52 3.95
2950 3171 5.450274 GGTTGAATTGCCATTTTTGCAGTTT 60.450 36.000 0.00 0.00 38.56 2.66
2959 3180 4.094590 CCATTTTTGCAGTTTCAAGTTGCA 59.905 37.500 0.00 0.00 45.28 4.08
2965 3186 5.219226 TGCAGTTTCAAGTTGCAAAAATG 57.781 34.783 0.00 11.17 44.13 2.32
2966 3187 4.094590 TGCAGTTTCAAGTTGCAAAAATGG 59.905 37.500 15.15 0.00 44.13 3.16
2967 3188 4.094739 GCAGTTTCAAGTTGCAAAAATGGT 59.905 37.500 15.15 0.00 37.75 3.55
2968 3189 5.293079 GCAGTTTCAAGTTGCAAAAATGGTA 59.707 36.000 15.15 0.00 37.75 3.25
2969 3190 6.509997 GCAGTTTCAAGTTGCAAAAATGGTAG 60.510 38.462 15.15 0.00 37.75 3.18
2971 3192 4.662468 TCAAGTTGCAAAAATGGTAGCA 57.338 36.364 0.00 0.00 34.79 3.49
2972 3193 5.016051 TCAAGTTGCAAAAATGGTAGCAA 57.984 34.783 0.00 0.00 43.90 3.91
3020 3241 2.784596 CCAGTGGCGCATGTTACG 59.215 61.111 10.83 0.00 0.00 3.18
3081 3303 1.261238 GCGAGGGCCCTGATATAGCT 61.261 60.000 34.59 0.00 0.00 3.32
3082 3304 1.960471 GCGAGGGCCCTGATATAGCTA 60.960 57.143 34.59 0.00 0.00 3.32
3083 3305 2.028130 CGAGGGCCCTGATATAGCTAG 58.972 57.143 34.59 0.00 0.00 3.42
3084 3306 1.760029 GAGGGCCCTGATATAGCTAGC 59.240 57.143 34.59 6.62 0.00 3.42
3086 3308 0.833949 GGCCCTGATATAGCTAGCCC 59.166 60.000 12.13 0.00 32.45 5.19
3087 3309 1.623834 GGCCCTGATATAGCTAGCCCT 60.624 57.143 12.13 0.92 32.45 5.19
3088 3310 2.359355 GGCCCTGATATAGCTAGCCCTA 60.359 54.545 12.13 3.52 32.45 3.53
3090 3312 3.628769 GCCCTGATATAGCTAGCCCTACT 60.629 52.174 12.13 0.00 0.00 2.57
3091 3313 4.386536 GCCCTGATATAGCTAGCCCTACTA 60.387 50.000 12.13 0.00 0.00 1.82
3092 3314 5.694405 GCCCTGATATAGCTAGCCCTACTAT 60.694 48.000 12.13 4.88 0.00 2.12
3093 3315 6.007703 CCCTGATATAGCTAGCCCTACTATC 58.992 48.000 12.13 10.98 0.00 2.08
3094 3316 6.410970 CCCTGATATAGCTAGCCCTACTATCA 60.411 46.154 12.13 14.46 0.00 2.15
3116 3338 3.890147 ACATGAACCGGGAGAGATACTAC 59.110 47.826 6.32 0.00 0.00 2.73
3117 3339 3.947612 TGAACCGGGAGAGATACTACT 57.052 47.619 6.32 0.00 0.00 2.57
3118 3340 3.818180 TGAACCGGGAGAGATACTACTC 58.182 50.000 6.32 0.00 37.19 2.59
3128 3350 6.817765 GAGAGATACTACTCCAAGGATCAG 57.182 45.833 0.00 0.00 39.04 2.90
3146 3375 2.106338 TCAGATTCACCTGTGGCTGAAA 59.894 45.455 12.58 0.00 33.91 2.69
3150 3379 1.227823 CACCTGTGGCTGAAACGGA 60.228 57.895 0.00 0.00 0.00 4.69
3168 3397 2.165030 CGGACCTATTTGTACGACTGGT 59.835 50.000 0.00 1.66 45.53 4.00
3180 3409 1.670083 GACTGGTTGTACGCCCCAC 60.670 63.158 4.15 0.00 0.00 4.61
3185 3414 0.035176 GGTTGTACGCCCCACAAGTA 59.965 55.000 0.00 0.00 36.61 2.24
3186 3415 1.435577 GTTGTACGCCCCACAAGTAG 58.564 55.000 0.00 0.00 36.61 2.57
3187 3416 1.050204 TTGTACGCCCCACAAGTAGT 58.950 50.000 0.00 0.00 32.32 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.573035 CCATACATGCTAACGGGTATAATTTTT 58.427 33.333 0.00 0.00 0.00 1.94
15 16 7.175990 CCCATACATGCTAACGGGTATAATTTT 59.824 37.037 0.00 0.00 0.00 1.82
16 17 6.657541 CCCATACATGCTAACGGGTATAATTT 59.342 38.462 0.00 0.00 0.00 1.82
17 18 6.013206 TCCCATACATGCTAACGGGTATAATT 60.013 38.462 0.00 0.00 35.08 1.40
18 19 5.486063 TCCCATACATGCTAACGGGTATAAT 59.514 40.000 0.00 0.00 35.08 1.28
19 20 4.839550 TCCCATACATGCTAACGGGTATAA 59.160 41.667 0.00 0.00 35.08 0.98
20 21 4.418359 TCCCATACATGCTAACGGGTATA 58.582 43.478 0.00 0.00 35.08 1.47
21 22 3.244582 TCCCATACATGCTAACGGGTAT 58.755 45.455 0.00 0.00 35.08 2.73
22 23 2.680251 TCCCATACATGCTAACGGGTA 58.320 47.619 0.00 0.00 35.08 3.69
23 24 1.502690 TCCCATACATGCTAACGGGT 58.497 50.000 0.00 0.00 35.08 5.28
24 25 2.104111 TCTTCCCATACATGCTAACGGG 59.896 50.000 0.00 0.00 34.81 5.28
25 26 3.469008 TCTTCCCATACATGCTAACGG 57.531 47.619 0.00 0.00 0.00 4.44
26 27 7.672983 ATAATTCTTCCCATACATGCTAACG 57.327 36.000 0.00 0.00 0.00 3.18
27 28 8.947115 GGTATAATTCTTCCCATACATGCTAAC 58.053 37.037 0.00 0.00 0.00 2.34
28 29 8.107095 GGGTATAATTCTTCCCATACATGCTAA 58.893 37.037 1.15 0.00 39.68 3.09
29 30 7.580688 CGGGTATAATTCTTCCCATACATGCTA 60.581 40.741 6.38 0.00 39.87 3.49
30 31 6.485171 GGGTATAATTCTTCCCATACATGCT 58.515 40.000 1.15 0.00 39.68 3.79
31 32 5.354234 CGGGTATAATTCTTCCCATACATGC 59.646 44.000 6.38 0.00 39.87 4.06
32 33 6.472887 ACGGGTATAATTCTTCCCATACATG 58.527 40.000 6.38 0.00 39.87 3.21
33 34 6.697641 ACGGGTATAATTCTTCCCATACAT 57.302 37.500 6.38 0.00 39.87 2.29
34 35 6.503560 AACGGGTATAATTCTTCCCATACA 57.496 37.500 6.38 0.00 39.87 2.29
35 36 9.813446 CTATAACGGGTATAATTCTTCCCATAC 57.187 37.037 6.38 0.00 39.87 2.39
36 37 8.984855 CCTATAACGGGTATAATTCTTCCCATA 58.015 37.037 6.38 0.19 39.87 2.74
37 38 7.092578 CCCTATAACGGGTATAATTCTTCCCAT 60.093 40.741 6.38 0.00 39.87 4.00
38 39 6.214005 CCCTATAACGGGTATAATTCTTCCCA 59.786 42.308 6.38 0.00 39.87 4.37
39 40 6.647229 CCCTATAACGGGTATAATTCTTCCC 58.353 44.000 0.00 0.00 39.51 3.97
53 54 5.416947 GCCATTACTCATACCCTATAACGG 58.583 45.833 0.00 0.00 0.00 4.44
54 55 5.100259 CGCCATTACTCATACCCTATAACG 58.900 45.833 0.00 0.00 0.00 3.18
55 56 6.276832 TCGCCATTACTCATACCCTATAAC 57.723 41.667 0.00 0.00 0.00 1.89
56 57 6.127168 CCATCGCCATTACTCATACCCTATAA 60.127 42.308 0.00 0.00 0.00 0.98
57 58 5.362717 CCATCGCCATTACTCATACCCTATA 59.637 44.000 0.00 0.00 0.00 1.31
58 59 4.162320 CCATCGCCATTACTCATACCCTAT 59.838 45.833 0.00 0.00 0.00 2.57
59 60 3.513912 CCATCGCCATTACTCATACCCTA 59.486 47.826 0.00 0.00 0.00 3.53
60 61 2.303022 CCATCGCCATTACTCATACCCT 59.697 50.000 0.00 0.00 0.00 4.34
61 62 2.615493 CCCATCGCCATTACTCATACCC 60.615 54.545 0.00 0.00 0.00 3.69
62 63 2.038557 ACCCATCGCCATTACTCATACC 59.961 50.000 0.00 0.00 0.00 2.73
63 64 3.402628 ACCCATCGCCATTACTCATAC 57.597 47.619 0.00 0.00 0.00 2.39
64 65 4.562757 GCTTACCCATCGCCATTACTCATA 60.563 45.833 0.00 0.00 0.00 2.15
65 66 3.807209 GCTTACCCATCGCCATTACTCAT 60.807 47.826 0.00 0.00 0.00 2.90
66 67 2.484770 GCTTACCCATCGCCATTACTCA 60.485 50.000 0.00 0.00 0.00 3.41
67 68 2.143925 GCTTACCCATCGCCATTACTC 58.856 52.381 0.00 0.00 0.00 2.59
68 69 1.768870 AGCTTACCCATCGCCATTACT 59.231 47.619 0.00 0.00 0.00 2.24
69 70 2.143925 GAGCTTACCCATCGCCATTAC 58.856 52.381 0.00 0.00 0.00 1.89
70 71 1.765904 TGAGCTTACCCATCGCCATTA 59.234 47.619 0.00 0.00 0.00 1.90
71 72 0.546122 TGAGCTTACCCATCGCCATT 59.454 50.000 0.00 0.00 0.00 3.16
72 73 0.179045 GTGAGCTTACCCATCGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
73 74 1.220749 GTGAGCTTACCCATCGCCA 59.779 57.895 0.00 0.00 0.00 5.69
74 75 1.883084 CGTGAGCTTACCCATCGCC 60.883 63.158 2.62 0.00 0.00 5.54
75 76 3.706140 CGTGAGCTTACCCATCGC 58.294 61.111 2.62 0.00 0.00 4.58
93 94 3.416880 ATACCCTTGCCCACCCCG 61.417 66.667 0.00 0.00 0.00 5.73
94 95 2.278738 CATACCCTTGCCCACCCC 59.721 66.667 0.00 0.00 0.00 4.95
95 96 1.227383 CTCATACCCTTGCCCACCC 59.773 63.158 0.00 0.00 0.00 4.61
96 97 1.227383 CCTCATACCCTTGCCCACC 59.773 63.158 0.00 0.00 0.00 4.61
97 98 0.394352 CACCTCATACCCTTGCCCAC 60.394 60.000 0.00 0.00 0.00 4.61
98 99 1.570857 CCACCTCATACCCTTGCCCA 61.571 60.000 0.00 0.00 0.00 5.36
99 100 1.227383 CCACCTCATACCCTTGCCC 59.773 63.158 0.00 0.00 0.00 5.36
100 101 1.453928 GCCACCTCATACCCTTGCC 60.454 63.158 0.00 0.00 0.00 4.52
101 102 0.464554 GAGCCACCTCATACCCTTGC 60.465 60.000 0.00 0.00 38.03 4.01
102 103 0.181350 GGAGCCACCTCATACCCTTG 59.819 60.000 0.00 0.00 39.96 3.61
103 104 0.253160 TGGAGCCACCTCATACCCTT 60.253 55.000 0.00 0.00 39.96 3.95
104 105 0.983378 GTGGAGCCACCTCATACCCT 60.983 60.000 8.48 0.00 40.79 4.34
105 106 1.527370 GTGGAGCCACCTCATACCC 59.473 63.158 8.48 0.00 40.79 3.69
114 115 2.664402 ATGAATATGGGTGGAGCCAC 57.336 50.000 11.18 11.18 45.49 5.01
115 116 2.375174 GGTATGAATATGGGTGGAGCCA 59.625 50.000 0.00 0.00 39.65 4.75
116 117 2.375174 TGGTATGAATATGGGTGGAGCC 59.625 50.000 0.00 0.00 0.00 4.70
117 118 3.788227 TGGTATGAATATGGGTGGAGC 57.212 47.619 0.00 0.00 0.00 4.70
118 119 4.012374 GCATGGTATGAATATGGGTGGAG 58.988 47.826 0.00 0.00 0.00 3.86
119 120 3.558958 CGCATGGTATGAATATGGGTGGA 60.559 47.826 0.00 0.00 32.19 4.02
120 121 2.749076 CGCATGGTATGAATATGGGTGG 59.251 50.000 0.00 0.00 32.19 4.61
121 122 2.749076 CCGCATGGTATGAATATGGGTG 59.251 50.000 0.00 0.00 34.20 4.61
122 123 2.290896 CCCGCATGGTATGAATATGGGT 60.291 50.000 0.00 0.00 34.20 4.51
123 124 2.368439 CCCGCATGGTATGAATATGGG 58.632 52.381 0.00 0.00 35.34 4.00
142 143 0.819582 CAAGAATGTGGGATGGCACC 59.180 55.000 0.00 0.00 0.00 5.01
143 144 0.174162 GCAAGAATGTGGGATGGCAC 59.826 55.000 0.00 0.00 0.00 5.01
144 145 1.314534 CGCAAGAATGTGGGATGGCA 61.315 55.000 0.00 0.00 43.02 4.92
145 146 1.434696 CGCAAGAATGTGGGATGGC 59.565 57.895 0.00 0.00 43.02 4.40
187 189 5.803145 GCGGAACATGGAATCATCCCTTATA 60.803 44.000 0.00 0.00 45.95 0.98
188 190 4.655963 CGGAACATGGAATCATCCCTTAT 58.344 43.478 0.00 0.00 45.95 1.73
189 191 3.747388 GCGGAACATGGAATCATCCCTTA 60.747 47.826 0.00 0.00 45.95 2.69
191 193 1.477558 GCGGAACATGGAATCATCCCT 60.478 52.381 0.00 0.00 45.95 4.20
192 194 0.954452 GCGGAACATGGAATCATCCC 59.046 55.000 0.00 0.00 45.95 3.85
193 195 1.605710 CAGCGGAACATGGAATCATCC 59.394 52.381 0.00 0.00 46.76 3.51
223 225 2.712539 CAGCGGAACAACGTGCAA 59.287 55.556 0.00 0.00 35.98 4.08
235 237 4.670896 AATAATTGGGAATTTCCAGCGG 57.329 40.909 17.08 0.00 38.64 5.52
236 238 6.105333 TCAAAATAATTGGGAATTTCCAGCG 58.895 36.000 17.08 0.00 38.64 5.18
237 239 7.920160 TTCAAAATAATTGGGAATTTCCAGC 57.080 32.000 17.08 1.52 38.64 4.85
345 445 5.061064 GCGATAAGAACGTGCCAGATAATAG 59.939 44.000 0.00 0.00 0.00 1.73
346 446 4.921515 GCGATAAGAACGTGCCAGATAATA 59.078 41.667 0.00 0.00 0.00 0.98
347 447 3.741344 GCGATAAGAACGTGCCAGATAAT 59.259 43.478 0.00 0.00 0.00 1.28
380 482 0.719465 CGAAAAGTCATTCCGGTCCG 59.281 55.000 3.60 3.60 0.00 4.79
381 483 2.000447 CTCGAAAAGTCATTCCGGTCC 59.000 52.381 0.00 0.00 0.00 4.46
382 484 1.393883 GCTCGAAAAGTCATTCCGGTC 59.606 52.381 0.00 0.00 0.00 4.79
383 485 1.002087 AGCTCGAAAAGTCATTCCGGT 59.998 47.619 0.00 0.00 0.00 5.28
384 486 1.726853 AGCTCGAAAAGTCATTCCGG 58.273 50.000 0.00 0.00 0.00 5.14
385 487 4.566759 TGATAAGCTCGAAAAGTCATTCCG 59.433 41.667 0.00 0.00 0.00 4.30
528 631 5.735766 CTCTTTAATCTTCTCTTTCCGGGT 58.264 41.667 0.00 0.00 0.00 5.28
538 641 2.501723 TGGGCTCGCTCTTTAATCTTCT 59.498 45.455 0.00 0.00 0.00 2.85
544 647 0.673644 GCTGTGGGCTCGCTCTTTAA 60.674 55.000 0.00 0.00 38.06 1.52
545 648 1.079127 GCTGTGGGCTCGCTCTTTA 60.079 57.895 0.00 0.00 38.06 1.85
826 948 3.127533 CTGCCGCCTTTTCTCCGG 61.128 66.667 0.00 0.00 44.58 5.14
896 1018 1.295357 TACACGCGGAAATGGCACTG 61.295 55.000 12.47 0.00 0.00 3.66
900 1022 3.408288 TTTTATACACGCGGAAATGGC 57.592 42.857 12.47 0.00 0.00 4.40
958 1080 0.958822 GCGGTTGTTGGAGTTGGATT 59.041 50.000 0.00 0.00 0.00 3.01
959 1081 0.893727 GGCGGTTGTTGGAGTTGGAT 60.894 55.000 0.00 0.00 0.00 3.41
2208 2367 3.744660 GTGTATGGTGGGAGGATCATTC 58.255 50.000 0.00 0.00 36.25 2.67
2210 2369 1.694150 CGTGTATGGTGGGAGGATCAT 59.306 52.381 0.00 0.00 36.25 2.45
2268 2436 2.381618 TCCAGGTCCAATTCCAATTCCA 59.618 45.455 0.00 0.00 0.00 3.53
2269 2437 3.100207 TCCAGGTCCAATTCCAATTCC 57.900 47.619 0.00 0.00 0.00 3.01
2270 2438 5.682234 ATTTCCAGGTCCAATTCCAATTC 57.318 39.130 0.00 0.00 0.00 2.17
2271 2439 6.452757 AAATTTCCAGGTCCAATTCCAATT 57.547 33.333 0.00 0.00 0.00 2.32
2272 2440 5.045651 GGAAATTTCCAGGTCCAATTCCAAT 60.046 40.000 28.76 0.00 46.76 3.16
2303 2471 0.318441 AGTTGCAGCTGCTCGAGTTA 59.682 50.000 36.61 14.44 42.66 2.24
2304 2472 0.318441 TAGTTGCAGCTGCTCGAGTT 59.682 50.000 36.61 19.05 42.66 3.01
2330 2498 5.716094 TGCATCTGTACACAAATACTACGT 58.284 37.500 0.00 0.00 0.00 3.57
2331 2499 6.641176 TTGCATCTGTACACAAATACTACG 57.359 37.500 0.00 0.00 0.00 3.51
2333 2501 9.325198 CCTTATTGCATCTGTACACAAATACTA 57.675 33.333 0.00 0.00 0.00 1.82
2381 2551 1.290203 CACCTATGCACACGGCTAAG 58.710 55.000 0.00 0.00 45.15 2.18
2387 2557 3.242413 GCAATCTTACACCTATGCACACG 60.242 47.826 0.00 0.00 34.10 4.49
2458 2628 6.225318 AGCACAACAAAATTACAGCAATCAT 58.775 32.000 0.00 0.00 0.00 2.45
2488 2660 7.171630 AGTAACAAGACATACTCTACCCTTG 57.828 40.000 0.00 0.00 37.57 3.61
2489 2661 7.341512 GGTAGTAACAAGACATACTCTACCCTT 59.658 40.741 0.00 0.00 39.77 3.95
2508 2680 2.712087 TGCACAAGAAAGGGGGTAGTAA 59.288 45.455 0.00 0.00 0.00 2.24
2642 2838 1.605710 ACAGAGCACAACATTCACTGC 59.394 47.619 0.00 0.00 0.00 4.40
2643 2839 5.220284 CGTATACAGAGCACAACATTCACTG 60.220 44.000 3.32 0.00 0.00 3.66
2644 2840 4.864806 CGTATACAGAGCACAACATTCACT 59.135 41.667 3.32 0.00 0.00 3.41
2645 2841 4.862574 TCGTATACAGAGCACAACATTCAC 59.137 41.667 3.32 0.00 0.00 3.18
2723 2944 6.039493 CACTTCCTACCTATGTCGTTGAGTAT 59.961 42.308 0.00 0.00 0.00 2.12
2791 3012 1.002134 CCTTGGACGAGGCCAATGT 60.002 57.895 11.29 0.00 46.19 2.71
2809 3030 4.005650 TCACAATCATGGTTCTCTTGAGC 58.994 43.478 0.00 0.00 33.81 4.26
2874 3095 3.129502 CGCAGTGCTCCACATGGG 61.130 66.667 14.33 0.00 36.74 4.00
2918 3139 5.859205 AATGGCAATTCAACCCTAGAATC 57.141 39.130 0.00 0.00 34.78 2.52
2950 3171 4.662468 TGCTACCATTTTTGCAACTTGA 57.338 36.364 0.00 0.00 32.12 3.02
2959 3180 7.125507 TCCACATATCCATTTGCTACCATTTTT 59.874 33.333 0.00 0.00 0.00 1.94
2961 3182 6.135454 TCCACATATCCATTTGCTACCATTT 58.865 36.000 0.00 0.00 0.00 2.32
2962 3183 5.704354 TCCACATATCCATTTGCTACCATT 58.296 37.500 0.00 0.00 0.00 3.16
2963 3184 5.319453 CTCCACATATCCATTTGCTACCAT 58.681 41.667 0.00 0.00 0.00 3.55
2964 3185 4.446167 CCTCCACATATCCATTTGCTACCA 60.446 45.833 0.00 0.00 0.00 3.25
2965 3186 4.074970 CCTCCACATATCCATTTGCTACC 58.925 47.826 0.00 0.00 0.00 3.18
2966 3187 3.503748 GCCTCCACATATCCATTTGCTAC 59.496 47.826 0.00 0.00 0.00 3.58
2967 3188 3.498481 GGCCTCCACATATCCATTTGCTA 60.498 47.826 0.00 0.00 0.00 3.49
2968 3189 2.590821 GCCTCCACATATCCATTTGCT 58.409 47.619 0.00 0.00 0.00 3.91
2969 3190 1.615392 GGCCTCCACATATCCATTTGC 59.385 52.381 0.00 0.00 0.00 3.68
2971 3192 2.146998 AGGGCCTCCACATATCCATTT 58.853 47.619 0.00 0.00 34.83 2.32
2972 3193 1.426598 CAGGGCCTCCACATATCCATT 59.573 52.381 0.95 0.00 34.83 3.16
2973 3194 1.070604 CAGGGCCTCCACATATCCAT 58.929 55.000 0.95 0.00 34.83 3.41
2974 3195 1.708993 GCAGGGCCTCCACATATCCA 61.709 60.000 0.95 0.00 34.83 3.41
3013 3234 1.466167 CTTTCTGCTGCTGCGTAACAT 59.534 47.619 11.21 0.00 43.34 2.71
3018 3239 0.036577 AGATCTTTCTGCTGCTGCGT 60.037 50.000 11.21 0.00 43.34 5.24
3020 3241 0.733729 CCAGATCTTTCTGCTGCTGC 59.266 55.000 8.89 8.89 46.76 5.25
3021 3242 1.380524 CCCAGATCTTTCTGCTGCTG 58.619 55.000 0.00 0.00 46.76 4.41
3022 3243 0.394080 GCCCAGATCTTTCTGCTGCT 60.394 55.000 0.00 0.00 46.76 4.24
3039 3260 6.490534 GCTTATCAGACAAGTTAAATCTGCC 58.509 40.000 6.22 0.00 39.80 4.85
3045 3266 5.175859 CCCTCGCTTATCAGACAAGTTAAA 58.824 41.667 0.00 0.00 0.00 1.52
3053 3274 1.069935 GGGCCCTCGCTTATCAGAC 59.930 63.158 17.04 0.00 34.44 3.51
3081 3303 3.572682 CGGTTCATGTGATAGTAGGGCTA 59.427 47.826 0.00 0.00 0.00 3.93
3082 3304 2.365617 CGGTTCATGTGATAGTAGGGCT 59.634 50.000 0.00 0.00 0.00 5.19
3083 3305 2.548067 CCGGTTCATGTGATAGTAGGGC 60.548 54.545 0.00 0.00 0.00 5.19
3084 3306 2.037251 CCCGGTTCATGTGATAGTAGGG 59.963 54.545 0.00 0.00 0.00 3.53
3086 3308 3.889538 TCTCCCGGTTCATGTGATAGTAG 59.110 47.826 0.00 0.00 0.00 2.57
3087 3309 3.889538 CTCTCCCGGTTCATGTGATAGTA 59.110 47.826 0.00 0.00 0.00 1.82
3088 3310 2.695666 CTCTCCCGGTTCATGTGATAGT 59.304 50.000 0.00 0.00 0.00 2.12
3090 3312 3.026707 TCTCTCCCGGTTCATGTGATA 57.973 47.619 0.00 0.00 0.00 2.15
3091 3313 1.866015 TCTCTCCCGGTTCATGTGAT 58.134 50.000 0.00 0.00 0.00 3.06
3092 3314 1.866015 ATCTCTCCCGGTTCATGTGA 58.134 50.000 0.00 0.00 0.00 3.58
3093 3315 2.695666 AGTATCTCTCCCGGTTCATGTG 59.304 50.000 0.00 0.00 0.00 3.21
3094 3316 3.033659 AGTATCTCTCCCGGTTCATGT 57.966 47.619 0.00 0.00 0.00 3.21
3116 3338 3.199508 ACAGGTGAATCTGATCCTTGGAG 59.800 47.826 0.00 0.00 38.11 3.86
3117 3339 3.054875 CACAGGTGAATCTGATCCTTGGA 60.055 47.826 0.00 0.00 38.11 3.53
3118 3340 3.276857 CACAGGTGAATCTGATCCTTGG 58.723 50.000 0.00 0.00 38.11 3.61
3119 3341 3.276857 CCACAGGTGAATCTGATCCTTG 58.723 50.000 0.00 0.00 38.11 3.61
3120 3342 2.356535 GCCACAGGTGAATCTGATCCTT 60.357 50.000 0.00 0.00 38.11 3.36
3121 3343 1.211457 GCCACAGGTGAATCTGATCCT 59.789 52.381 0.00 0.00 38.11 3.24
3122 3344 1.211457 AGCCACAGGTGAATCTGATCC 59.789 52.381 0.00 0.00 38.11 3.36
3123 3345 2.286872 CAGCCACAGGTGAATCTGATC 58.713 52.381 0.00 0.00 44.53 2.92
3124 3346 2.414994 CAGCCACAGGTGAATCTGAT 57.585 50.000 0.00 0.00 44.53 2.90
3146 3375 2.165030 CCAGTCGTACAAATAGGTCCGT 59.835 50.000 0.00 0.00 0.00 4.69
3150 3379 4.612264 ACAACCAGTCGTACAAATAGGT 57.388 40.909 0.00 0.00 0.00 3.08
3168 3397 1.050204 ACTACTTGTGGGGCGTACAA 58.950 50.000 5.31 5.31 36.66 2.41


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

AutoCloner maintained by Alex Coulton.