Multiple sequence alignment - TraesCS2D01G350500

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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 TraesCS2D01G350500 chr2D 100.000 2887 0 0 1 2887 448500118 448503004 0.000000e+00 5332
1 TraesCS2D01G350500 chr2B 91.864 2237 92 26 264 2463 529768730 529766547 0.000000e+00 3040
2 TraesCS2D01G350500 chr2B 95.399 326 10 3 2564 2886 529766384 529766061 5.520000e-142 514
3 TraesCS2D01G350500 chr2A 88.003 2634 168 66 160 2709 594125625 594123056 0.000000e+00 2977
4 TraesCS2D01G350500 chr2A 91.971 137 4 1 2757 2886 594123045 594122909 4.910000e-43 185


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 TraesCS2D01G350500 chr2D 448500118 448503004 2886 False 5332 5332 100.0000 1 2887 1 chr2D.!!$F1 2886
1 TraesCS2D01G350500 chr2B 529766061 529768730 2669 True 1777 3040 93.6315 264 2886 2 chr2B.!!$R1 2622
2 TraesCS2D01G350500 chr2A 594122909 594125625 2716 True 1581 2977 89.9870 160 2886 2 chr2A.!!$R1 2726

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
117 118 0.036952 AGTGAGATGGTGGTGCTTCG 60.037 55.0 0.0 0.0 0.00 3.79 F
477 478 0.179026 CCCTCAGGCATGATGTCCAG 60.179 60.0 0.0 0.0 34.12 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1199 0.179145 GCATGCAAGCCATCACTCAC 60.179 55.0 14.21 0.00 29.71 3.51 R
2274 2363 0.107214 TTAAATGCCTGGCCGAGGAG 60.107 55.0 21.37 3.22 46.33 3.69 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
38 39 3.361158 CGCGGATGGGTGTTGCAA 61.361 61.111 0.00 0.00 0.00 4.08
39 40 2.568090 GCGGATGGGTGTTGCAAG 59.432 61.111 0.00 0.00 0.00 4.01
40 41 2.568090 CGGATGGGTGTTGCAAGC 59.432 61.111 0.00 0.00 0.00 4.01
41 42 1.973281 CGGATGGGTGTTGCAAGCT 60.973 57.895 0.00 0.00 0.00 3.74
42 43 1.885871 GGATGGGTGTTGCAAGCTC 59.114 57.895 0.00 0.00 0.00 4.09
43 44 1.598701 GGATGGGTGTTGCAAGCTCC 61.599 60.000 0.00 5.53 0.00 4.70
44 45 0.895100 GATGGGTGTTGCAAGCTCCA 60.895 55.000 14.43 14.43 0.00 3.86
45 46 0.896940 ATGGGTGTTGCAAGCTCCAG 60.897 55.000 16.39 0.00 0.00 3.86
46 47 2.270986 GGGTGTTGCAAGCTCCAGG 61.271 63.158 0.00 0.00 0.00 4.45
47 48 2.270986 GGTGTTGCAAGCTCCAGGG 61.271 63.158 0.00 0.00 0.00 4.45
48 49 1.228245 GTGTTGCAAGCTCCAGGGA 60.228 57.895 0.00 0.00 0.00 4.20
49 50 1.073722 TGTTGCAAGCTCCAGGGAG 59.926 57.895 11.06 11.06 44.56 4.30
57 58 4.285851 CTCCAGGGAGCGTTGTTC 57.714 61.111 1.73 0.00 35.31 3.18
58 59 1.674057 CTCCAGGGAGCGTTGTTCT 59.326 57.895 1.73 0.00 35.31 3.01
59 60 0.390472 CTCCAGGGAGCGTTGTTCTC 60.390 60.000 1.73 0.00 35.31 2.87
60 61 1.118965 TCCAGGGAGCGTTGTTCTCA 61.119 55.000 0.00 0.00 32.38 3.27
61 62 0.250295 CCAGGGAGCGTTGTTCTCAA 60.250 55.000 0.00 0.00 32.38 3.02
62 63 1.151668 CAGGGAGCGTTGTTCTCAAG 58.848 55.000 0.00 0.00 33.97 3.02
63 64 0.603975 AGGGAGCGTTGTTCTCAAGC 60.604 55.000 0.00 0.00 33.97 4.01
64 65 1.493311 GGAGCGTTGTTCTCAAGCG 59.507 57.895 0.00 0.00 34.98 4.68
65 66 1.154580 GAGCGTTGTTCTCAAGCGC 60.155 57.895 0.00 0.00 45.05 5.92
66 67 2.497628 GCGTTGTTCTCAAGCGCG 60.498 61.111 0.00 0.00 40.70 6.86
67 68 2.170985 CGTTGTTCTCAAGCGCGG 59.829 61.111 8.83 0.00 33.97 6.46
68 69 2.556287 GTTGTTCTCAAGCGCGGG 59.444 61.111 8.83 0.00 33.97 6.13
69 70 1.959226 GTTGTTCTCAAGCGCGGGA 60.959 57.895 8.83 2.27 33.97 5.14
70 71 1.003839 TTGTTCTCAAGCGCGGGAT 60.004 52.632 8.83 0.00 0.00 3.85
71 72 1.298157 TTGTTCTCAAGCGCGGGATG 61.298 55.000 8.83 1.05 0.00 3.51
72 73 1.741770 GTTCTCAAGCGCGGGATGT 60.742 57.895 8.83 0.00 0.00 3.06
73 74 1.741401 TTCTCAAGCGCGGGATGTG 60.741 57.895 8.83 2.63 0.00 3.21
74 75 3.197790 CTCAAGCGCGGGATGTGG 61.198 66.667 8.83 0.00 0.00 4.17
75 76 3.958147 CTCAAGCGCGGGATGTGGT 62.958 63.158 8.83 0.00 41.39 4.16
77 78 1.743623 CAAGCGCGGGATGTGGTTA 60.744 57.895 8.83 0.00 46.37 2.85
78 79 1.095228 CAAGCGCGGGATGTGGTTAT 61.095 55.000 8.83 0.00 46.37 1.89
79 80 1.095228 AAGCGCGGGATGTGGTTATG 61.095 55.000 8.83 0.00 46.25 1.90
80 81 3.022287 CGCGGGATGTGGTTATGC 58.978 61.111 0.00 0.00 0.00 3.14
81 82 1.817520 CGCGGGATGTGGTTATGCA 60.818 57.895 0.00 0.00 0.00 3.96
82 83 1.372838 CGCGGGATGTGGTTATGCAA 61.373 55.000 0.00 0.00 0.00 4.08
83 84 0.381801 GCGGGATGTGGTTATGCAAG 59.618 55.000 0.00 0.00 0.00 4.01
84 85 1.024271 CGGGATGTGGTTATGCAAGG 58.976 55.000 0.00 0.00 0.00 3.61
85 86 1.402787 GGGATGTGGTTATGCAAGGG 58.597 55.000 0.00 0.00 0.00 3.95
86 87 1.341976 GGGATGTGGTTATGCAAGGGT 60.342 52.381 0.00 0.00 0.00 4.34
87 88 2.024414 GGATGTGGTTATGCAAGGGTC 58.976 52.381 0.00 0.00 0.00 4.46
88 89 1.670811 GATGTGGTTATGCAAGGGTCG 59.329 52.381 0.00 0.00 0.00 4.79
89 90 0.687920 TGTGGTTATGCAAGGGTCGA 59.312 50.000 0.00 0.00 0.00 4.20
90 91 1.084289 GTGGTTATGCAAGGGTCGAC 58.916 55.000 7.13 7.13 0.00 4.20
91 92 0.390603 TGGTTATGCAAGGGTCGACG 60.391 55.000 9.92 0.00 0.00 5.12
92 93 0.108520 GGTTATGCAAGGGTCGACGA 60.109 55.000 9.92 0.00 0.00 4.20
93 94 0.997196 GTTATGCAAGGGTCGACGAC 59.003 55.000 19.70 19.70 0.00 4.34
94 95 0.892755 TTATGCAAGGGTCGACGACT 59.107 50.000 25.87 7.55 32.47 4.18
95 96 0.172578 TATGCAAGGGTCGACGACTG 59.827 55.000 25.87 17.73 32.47 3.51
96 97 2.432628 GCAAGGGTCGACGACTGG 60.433 66.667 25.87 14.26 32.47 4.00
97 98 2.432628 CAAGGGTCGACGACTGGC 60.433 66.667 25.87 10.70 32.47 4.85
98 99 2.915659 AAGGGTCGACGACTGGCA 60.916 61.111 25.87 0.00 32.47 4.92
99 100 2.932234 AAGGGTCGACGACTGGCAG 61.932 63.158 25.87 14.16 32.47 4.85
100 101 3.681835 GGGTCGACGACTGGCAGT 61.682 66.667 25.87 22.26 32.47 4.40
101 102 2.430921 GGTCGACGACTGGCAGTG 60.431 66.667 27.45 18.86 32.47 3.66
102 103 2.643272 GTCGACGACTGGCAGTGA 59.357 61.111 27.45 13.30 0.00 3.41
103 104 1.442857 GTCGACGACTGGCAGTGAG 60.443 63.158 27.45 20.36 0.00 3.51
104 105 1.599797 TCGACGACTGGCAGTGAGA 60.600 57.895 27.45 15.02 0.00 3.27
105 106 0.960861 TCGACGACTGGCAGTGAGAT 60.961 55.000 27.45 7.08 0.00 2.75
106 107 0.799917 CGACGACTGGCAGTGAGATG 60.800 60.000 27.45 11.46 0.00 2.90
107 108 0.459237 GACGACTGGCAGTGAGATGG 60.459 60.000 27.45 9.13 0.00 3.51
108 109 1.188219 ACGACTGGCAGTGAGATGGT 61.188 55.000 27.45 9.77 0.00 3.55
109 110 0.738762 CGACTGGCAGTGAGATGGTG 60.739 60.000 27.45 0.31 0.00 4.17
110 111 0.392193 GACTGGCAGTGAGATGGTGG 60.392 60.000 27.45 0.00 0.00 4.61
111 112 1.130054 ACTGGCAGTGAGATGGTGGT 61.130 55.000 21.37 0.00 0.00 4.16
112 113 0.675837 CTGGCAGTGAGATGGTGGTG 60.676 60.000 6.28 0.00 0.00 4.17
113 114 2.042831 GGCAGTGAGATGGTGGTGC 61.043 63.158 0.00 0.00 0.00 5.01
114 115 1.002868 GCAGTGAGATGGTGGTGCT 60.003 57.895 0.00 0.00 0.00 4.40
115 116 0.607489 GCAGTGAGATGGTGGTGCTT 60.607 55.000 0.00 0.00 0.00 3.91
116 117 1.446907 CAGTGAGATGGTGGTGCTTC 58.553 55.000 0.00 0.00 0.00 3.86
117 118 0.036952 AGTGAGATGGTGGTGCTTCG 60.037 55.000 0.00 0.00 0.00 3.79
118 119 0.320771 GTGAGATGGTGGTGCTTCGT 60.321 55.000 0.00 0.00 0.00 3.85
119 120 0.320683 TGAGATGGTGGTGCTTCGTG 60.321 55.000 0.00 0.00 0.00 4.35
120 121 1.003355 AGATGGTGGTGCTTCGTGG 60.003 57.895 0.00 0.00 0.00 4.94
121 122 1.302511 GATGGTGGTGCTTCGTGGT 60.303 57.895 0.00 0.00 0.00 4.16
122 123 1.298859 GATGGTGGTGCTTCGTGGTC 61.299 60.000 0.00 0.00 0.00 4.02
123 124 2.050836 ATGGTGGTGCTTCGTGGTCA 62.051 55.000 0.00 0.00 0.00 4.02
124 125 1.961277 GGTGGTGCTTCGTGGTCAG 60.961 63.158 0.00 0.00 0.00 3.51
125 126 1.961277 GTGGTGCTTCGTGGTCAGG 60.961 63.158 0.00 0.00 0.00 3.86
126 127 2.358737 GGTGCTTCGTGGTCAGGG 60.359 66.667 0.00 0.00 0.00 4.45
127 128 3.050275 GTGCTTCGTGGTCAGGGC 61.050 66.667 0.00 0.00 0.00 5.19
128 129 4.680237 TGCTTCGTGGTCAGGGCG 62.680 66.667 0.00 0.00 0.00 6.13
129 130 4.681978 GCTTCGTGGTCAGGGCGT 62.682 66.667 0.00 0.00 0.00 5.68
130 131 2.967397 CTTCGTGGTCAGGGCGTA 59.033 61.111 0.00 0.00 0.00 4.42
131 132 1.515954 CTTCGTGGTCAGGGCGTAT 59.484 57.895 0.00 0.00 0.00 3.06
132 133 0.527817 CTTCGTGGTCAGGGCGTATC 60.528 60.000 0.00 0.00 0.00 2.24
133 134 1.252215 TTCGTGGTCAGGGCGTATCA 61.252 55.000 0.00 0.00 0.00 2.15
134 135 1.518572 CGTGGTCAGGGCGTATCAC 60.519 63.158 0.00 0.00 0.00 3.06
135 136 1.518572 GTGGTCAGGGCGTATCACG 60.519 63.158 0.00 0.00 45.88 4.35
136 137 2.106332 GGTCAGGGCGTATCACGG 59.894 66.667 0.44 0.00 42.82 4.94
137 138 2.106332 GTCAGGGCGTATCACGGG 59.894 66.667 0.44 0.00 42.82 5.28
138 139 2.363276 TCAGGGCGTATCACGGGT 60.363 61.111 0.44 0.00 42.82 5.28
139 140 1.985662 TCAGGGCGTATCACGGGTT 60.986 57.895 0.44 0.00 42.82 4.11
140 141 1.520787 CAGGGCGTATCACGGGTTC 60.521 63.158 0.44 0.00 42.82 3.62
141 142 1.684734 AGGGCGTATCACGGGTTCT 60.685 57.895 0.44 0.00 42.82 3.01
142 143 1.520787 GGGCGTATCACGGGTTCTG 60.521 63.158 0.44 0.00 42.82 3.02
143 144 2.171725 GGCGTATCACGGGTTCTGC 61.172 63.158 0.44 0.00 42.82 4.26
144 145 2.171725 GCGTATCACGGGTTCTGCC 61.172 63.158 0.44 0.00 42.82 4.85
173 174 4.505217 GCGATGGTGCTCGTTGCG 62.505 66.667 0.00 0.00 46.63 4.85
174 175 3.853330 CGATGGTGCTCGTTGCGG 61.853 66.667 0.00 0.00 46.63 5.69
211 212 0.454600 GAGTTGATGCGACCGACCTA 59.545 55.000 0.00 0.00 0.00 3.08
217 218 3.834799 GCGACCGACCTAGGTGGG 61.835 72.222 34.51 34.51 46.09 4.61
239 240 3.376078 TTTCGACCGGCGCCTAGT 61.376 61.111 26.68 21.90 40.61 2.57
243 244 3.142838 GACCGGCGCCTAGTGGTA 61.143 66.667 26.68 0.00 34.12 3.25
244 245 3.421687 GACCGGCGCCTAGTGGTAC 62.422 68.421 26.68 13.64 34.12 3.34
251 252 1.883209 GCGCCTAGTGGTACCCAAAAA 60.883 52.381 10.07 0.00 34.18 1.94
252 253 2.081462 CGCCTAGTGGTACCCAAAAAG 58.919 52.381 10.07 0.00 34.18 2.27
259 260 5.061721 AGTGGTACCCAAAAAGAATCAGT 57.938 39.130 10.07 0.00 34.18 3.41
261 262 4.583073 GTGGTACCCAAAAAGAATCAGTGT 59.417 41.667 10.07 0.00 34.18 3.55
262 263 4.582656 TGGTACCCAAAAAGAATCAGTGTG 59.417 41.667 10.07 0.00 0.00 3.82
285 286 4.558860 GTCTTGTTGCTTTGTGAAGTTGTC 59.441 41.667 0.00 0.00 35.25 3.18
311 312 7.461182 TGAAACCAAATCTGGACGAAATATT 57.539 32.000 0.00 0.00 46.92 1.28
435 436 3.375647 AATAGCCCCTCGCCTTAAAAA 57.624 42.857 0.00 0.00 38.78 1.94
477 478 0.179026 CCCTCAGGCATGATGTCCAG 60.179 60.000 0.00 0.00 34.12 3.86
490 491 3.118075 TGATGTCCAGGACACTGTCAAAA 60.118 43.478 25.35 0.47 45.65 2.44
505 507 9.174166 ACACTGTCAAAACTGAACTTAAGTAAT 57.826 29.630 8.92 0.00 0.00 1.89
549 551 5.116069 TGAAGTTAAAAATTGACGGCTCC 57.884 39.130 0.00 0.00 0.00 4.70
591 593 7.116376 CAGGGTACATCAATCGTATGTATGTTC 59.884 40.741 0.00 0.00 40.80 3.18
660 662 7.755591 TCATCAAATCTTCAGTAGCAATTCAC 58.244 34.615 0.00 0.00 0.00 3.18
702 704 2.567615 CCAGGCCCCAGAGTACATATAC 59.432 54.545 0.00 0.00 0.00 1.47
722 724 3.077617 GCTTGATCAGCTGGGTCTC 57.922 57.895 15.13 6.71 46.27 3.36
835 866 0.395586 AAGTGCAACCCAGAGCAACA 60.396 50.000 0.00 0.00 43.20 3.33
1062 1097 0.941542 CACACCAACCAAGGTACACG 59.058 55.000 0.00 0.00 40.77 4.49
1070 1105 1.671742 CAAGGTACACGCACCCTCT 59.328 57.895 0.00 0.00 39.62 3.69
1082 1117 1.504912 CACCCTCTCATGTCCCATCT 58.495 55.000 0.00 0.00 0.00 2.90
1083 1118 1.415659 CACCCTCTCATGTCCCATCTC 59.584 57.143 0.00 0.00 0.00 2.75
1084 1119 1.055040 CCCTCTCATGTCCCATCTCC 58.945 60.000 0.00 0.00 0.00 3.71
1086 1121 1.693726 CCTCTCATGTCCCATCTCCCA 60.694 57.143 0.00 0.00 0.00 4.37
1090 1125 1.770658 TCATGTCCCATCTCCCATGTC 59.229 52.381 0.00 0.00 36.81 3.06
1091 1126 1.143813 ATGTCCCATCTCCCATGTCC 58.856 55.000 0.00 0.00 0.00 4.02
1092 1127 0.988145 TGTCCCATCTCCCATGTCCC 60.988 60.000 0.00 0.00 0.00 4.46
1950 2017 2.937519 TCACTCACTCACTCACTCACT 58.062 47.619 0.00 0.00 0.00 3.41
1951 2018 2.881513 TCACTCACTCACTCACTCACTC 59.118 50.000 0.00 0.00 0.00 3.51
1952 2019 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1953 2020 2.621055 ACTCACTCACTCACTCACTCAC 59.379 50.000 0.00 0.00 0.00 3.51
1954 2021 2.884012 CTCACTCACTCACTCACTCACT 59.116 50.000 0.00 0.00 0.00 3.41
1955 2022 2.881513 TCACTCACTCACTCACTCACTC 59.118 50.000 0.00 0.00 0.00 3.51
1956 2023 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1957 2024 2.621055 ACTCACTCACTCACTCACTCAC 59.379 50.000 0.00 0.00 0.00 3.51
1958 2025 2.884012 CTCACTCACTCACTCACTCACT 59.116 50.000 0.00 0.00 0.00 3.41
1959 2026 2.881513 TCACTCACTCACTCACTCACTC 59.118 50.000 0.00 0.00 0.00 3.51
1960 2027 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1961 2028 2.621055 ACTCACTCACTCACTCACTCAC 59.379 50.000 0.00 0.00 0.00 3.51
1962 2029 2.884012 CTCACTCACTCACTCACTCACT 59.116 50.000 0.00 0.00 0.00 3.41
1963 2030 2.881513 TCACTCACTCACTCACTCACTC 59.118 50.000 0.00 0.00 0.00 3.51
1964 2031 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1965 2032 2.621055 ACTCACTCACTCACTCACTCAC 59.379 50.000 0.00 0.00 0.00 3.51
1981 2048 0.249996 TCACCCCTCGTCGTTTTTCC 60.250 55.000 0.00 0.00 0.00 3.13
2074 2152 4.084433 TGCGATGTTTTTACTGGTACGTTC 60.084 41.667 0.00 0.00 0.00 3.95
2098 2177 1.336240 GGATTGTGTCCTTTGCTGTGC 60.336 52.381 0.00 0.00 44.16 4.57
2106 2185 0.100325 CCTTTGCTGTGCGTGTTTCA 59.900 50.000 0.00 0.00 0.00 2.69
2227 2316 1.227556 AAGAGCAACCGACGCAACT 60.228 52.632 0.00 0.00 0.00 3.16
2276 2365 3.535962 CGAGGGAGCCAGAGCCTC 61.536 72.222 0.00 0.00 41.25 4.70
2277 2366 3.160748 GAGGGAGCCAGAGCCTCC 61.161 72.222 0.00 0.00 41.25 4.30
2278 2367 3.693572 AGGGAGCCAGAGCCTCCT 61.694 66.667 7.32 0.00 41.25 3.69
2279 2368 3.160748 GGGAGCCAGAGCCTCCTC 61.161 72.222 7.32 0.00 41.25 3.71
2280 2369 3.535962 GGAGCCAGAGCCTCCTCG 61.536 72.222 0.33 0.00 43.05 4.63
2281 2370 3.535962 GAGCCAGAGCCTCCTCGG 61.536 72.222 0.00 0.00 43.05 4.63
2304 2412 2.224079 CAGGCATTTAATCGGATCGGTG 59.776 50.000 0.00 0.00 0.00 4.94
2357 2473 5.008019 GTGATCGGCATCAAGTATGAACAAT 59.992 40.000 1.98 0.00 40.90 2.71
2363 2479 4.335315 GCATCAAGTATGAACAATCGGGAA 59.665 41.667 0.00 0.00 39.49 3.97
2426 2542 0.704076 AGCAGCCCAATTAAGGACCA 59.296 50.000 0.00 0.00 0.00 4.02
2427 2543 1.106285 GCAGCCCAATTAAGGACCAG 58.894 55.000 0.00 0.00 0.00 4.00
2433 2549 2.747446 CCCAATTAAGGACCAGACGTTG 59.253 50.000 0.00 0.00 0.00 4.10
2443 2564 0.246635 CCAGACGTTGAGAACCCGAT 59.753 55.000 0.00 0.00 0.00 4.18
2444 2565 1.350193 CAGACGTTGAGAACCCGATG 58.650 55.000 0.00 0.00 0.00 3.84
2517 2662 2.874694 CGAACGGGCTCATCATGCG 61.875 63.158 0.00 0.00 0.00 4.73
2518 2663 3.173390 GAACGGGCTCATCATGCGC 62.173 63.158 0.00 0.00 39.52 6.09
2580 2763 2.447887 GCAGATCGTGTGCTGGACG 61.448 63.158 0.00 0.00 37.96 4.79
2667 2854 2.505405 TCGAGAGCGAGTTATATGCCT 58.495 47.619 0.00 0.00 42.51 4.75
2754 2941 1.808411 TGCGGGAAAGCAAGAACTAG 58.192 50.000 0.00 0.00 45.06 2.57
2808 2998 3.947612 ATCTGAACCAATCTGCCTCAT 57.052 42.857 0.00 0.00 0.00 2.90
2814 3004 5.324409 TGAACCAATCTGCCTCATTAAACT 58.676 37.500 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.326889 CTTGCAACACCCATCCGCG 62.327 63.158 0.00 0.00 0.00 6.46
22 23 2.568090 CTTGCAACACCCATCCGC 59.432 61.111 0.00 0.00 0.00 5.54
23 24 1.926511 GAGCTTGCAACACCCATCCG 61.927 60.000 0.00 0.00 0.00 4.18
24 25 1.598701 GGAGCTTGCAACACCCATCC 61.599 60.000 0.00 0.00 0.00 3.51
25 26 0.895100 TGGAGCTTGCAACACCCATC 60.895 55.000 0.00 0.00 0.00 3.51
26 27 0.896940 CTGGAGCTTGCAACACCCAT 60.897 55.000 0.00 0.00 0.00 4.00
27 28 1.529010 CTGGAGCTTGCAACACCCA 60.529 57.895 0.00 1.81 0.00 4.51
28 29 2.270986 CCTGGAGCTTGCAACACCC 61.271 63.158 0.00 0.00 0.00 4.61
29 30 2.270986 CCCTGGAGCTTGCAACACC 61.271 63.158 0.00 1.82 0.00 4.16
30 31 1.228245 TCCCTGGAGCTTGCAACAC 60.228 57.895 0.00 0.00 0.00 3.32
31 32 1.073722 CTCCCTGGAGCTTGCAACA 59.926 57.895 0.00 0.00 35.31 3.33
32 33 3.993535 CTCCCTGGAGCTTGCAAC 58.006 61.111 0.00 0.00 35.31 4.17
40 41 0.390472 GAGAACAACGCTCCCTGGAG 60.390 60.000 8.91 8.91 44.56 3.86
41 42 1.118965 TGAGAACAACGCTCCCTGGA 61.119 55.000 0.00 0.00 0.00 3.86
42 43 0.250295 TTGAGAACAACGCTCCCTGG 60.250 55.000 0.00 0.00 0.00 4.45
43 44 1.151668 CTTGAGAACAACGCTCCCTG 58.848 55.000 0.00 0.00 32.27 4.45
44 45 0.603975 GCTTGAGAACAACGCTCCCT 60.604 55.000 0.00 0.00 32.09 4.20
45 46 1.869690 GCTTGAGAACAACGCTCCC 59.130 57.895 0.00 0.00 32.09 4.30
46 47 1.493311 CGCTTGAGAACAACGCTCC 59.507 57.895 0.00 0.00 32.38 4.70
47 48 1.154580 GCGCTTGAGAACAACGCTC 60.155 57.895 0.00 0.00 44.42 5.03
48 49 2.939022 GCGCTTGAGAACAACGCT 59.061 55.556 0.00 0.00 44.42 5.07
49 50 2.497628 CGCGCTTGAGAACAACGC 60.498 61.111 5.56 0.34 44.39 4.84
50 51 2.170985 CCGCGCTTGAGAACAACG 59.829 61.111 5.56 0.00 35.44 4.10
51 52 1.298859 ATCCCGCGCTTGAGAACAAC 61.299 55.000 5.56 0.00 32.27 3.32
52 53 1.003839 ATCCCGCGCTTGAGAACAA 60.004 52.632 5.56 0.00 34.65 2.83
53 54 1.741401 CATCCCGCGCTTGAGAACA 60.741 57.895 5.56 0.00 0.00 3.18
54 55 1.741770 ACATCCCGCGCTTGAGAAC 60.742 57.895 5.56 0.00 0.00 3.01
55 56 1.741401 CACATCCCGCGCTTGAGAA 60.741 57.895 5.56 0.00 0.00 2.87
56 57 2.125552 CACATCCCGCGCTTGAGA 60.126 61.111 5.56 0.00 0.00 3.27
57 58 3.197790 CCACATCCCGCGCTTGAG 61.198 66.667 5.56 0.00 0.00 3.02
58 59 2.173758 TAACCACATCCCGCGCTTGA 62.174 55.000 5.56 1.22 0.00 3.02
59 60 1.095228 ATAACCACATCCCGCGCTTG 61.095 55.000 5.56 0.00 0.00 4.01
60 61 1.095228 CATAACCACATCCCGCGCTT 61.095 55.000 5.56 0.00 0.00 4.68
61 62 1.523711 CATAACCACATCCCGCGCT 60.524 57.895 5.56 0.00 0.00 5.92
62 63 3.022287 CATAACCACATCCCGCGC 58.978 61.111 0.00 0.00 0.00 6.86
63 64 1.372838 TTGCATAACCACATCCCGCG 61.373 55.000 0.00 0.00 0.00 6.46
64 65 0.381801 CTTGCATAACCACATCCCGC 59.618 55.000 0.00 0.00 0.00 6.13
65 66 1.024271 CCTTGCATAACCACATCCCG 58.976 55.000 0.00 0.00 0.00 5.14
66 67 1.341976 ACCCTTGCATAACCACATCCC 60.342 52.381 0.00 0.00 0.00 3.85
67 68 2.024414 GACCCTTGCATAACCACATCC 58.976 52.381 0.00 0.00 0.00 3.51
68 69 1.670811 CGACCCTTGCATAACCACATC 59.329 52.381 0.00 0.00 0.00 3.06
69 70 1.280710 TCGACCCTTGCATAACCACAT 59.719 47.619 0.00 0.00 0.00 3.21
70 71 0.687920 TCGACCCTTGCATAACCACA 59.312 50.000 0.00 0.00 0.00 4.17
71 72 1.084289 GTCGACCCTTGCATAACCAC 58.916 55.000 3.51 0.00 0.00 4.16
72 73 0.390603 CGTCGACCCTTGCATAACCA 60.391 55.000 10.58 0.00 0.00 3.67
73 74 0.108520 TCGTCGACCCTTGCATAACC 60.109 55.000 10.58 0.00 0.00 2.85
74 75 0.997196 GTCGTCGACCCTTGCATAAC 59.003 55.000 14.60 0.00 0.00 1.89
75 76 0.892755 AGTCGTCGACCCTTGCATAA 59.107 50.000 21.40 0.00 32.18 1.90
76 77 0.172578 CAGTCGTCGACCCTTGCATA 59.827 55.000 21.40 0.00 32.18 3.14
77 78 1.079819 CAGTCGTCGACCCTTGCAT 60.080 57.895 21.40 0.00 32.18 3.96
78 79 2.338620 CAGTCGTCGACCCTTGCA 59.661 61.111 21.40 0.00 32.18 4.08
79 80 2.432628 CCAGTCGTCGACCCTTGC 60.433 66.667 21.40 0.00 32.18 4.01
80 81 2.432628 GCCAGTCGTCGACCCTTG 60.433 66.667 21.40 13.17 32.18 3.61
81 82 2.915659 TGCCAGTCGTCGACCCTT 60.916 61.111 21.40 0.39 32.18 3.95
82 83 3.374402 CTGCCAGTCGTCGACCCT 61.374 66.667 21.40 3.04 32.18 4.34
83 84 3.681835 ACTGCCAGTCGTCGACCC 61.682 66.667 21.40 10.95 32.18 4.46
84 85 2.430921 CACTGCCAGTCGTCGACC 60.431 66.667 21.40 7.42 32.18 4.79
85 86 1.442857 CTCACTGCCAGTCGTCGAC 60.443 63.158 17.70 17.70 0.00 4.20
86 87 0.960861 ATCTCACTGCCAGTCGTCGA 60.961 55.000 0.00 0.00 0.00 4.20
87 88 0.799917 CATCTCACTGCCAGTCGTCG 60.800 60.000 0.00 0.00 0.00 5.12
88 89 0.459237 CCATCTCACTGCCAGTCGTC 60.459 60.000 0.00 0.00 0.00 4.20
89 90 1.188219 ACCATCTCACTGCCAGTCGT 61.188 55.000 0.00 0.00 0.00 4.34
90 91 0.738762 CACCATCTCACTGCCAGTCG 60.739 60.000 0.00 0.00 0.00 4.18
91 92 0.392193 CCACCATCTCACTGCCAGTC 60.392 60.000 0.00 0.00 0.00 3.51
92 93 1.130054 ACCACCATCTCACTGCCAGT 61.130 55.000 0.00 0.00 0.00 4.00
93 94 0.675837 CACCACCATCTCACTGCCAG 60.676 60.000 0.00 0.00 0.00 4.85
94 95 1.376086 CACCACCATCTCACTGCCA 59.624 57.895 0.00 0.00 0.00 4.92
95 96 2.042831 GCACCACCATCTCACTGCC 61.043 63.158 0.00 0.00 0.00 4.85
96 97 0.607489 AAGCACCACCATCTCACTGC 60.607 55.000 0.00 0.00 0.00 4.40
97 98 1.446907 GAAGCACCACCATCTCACTG 58.553 55.000 0.00 0.00 0.00 3.66
98 99 0.036952 CGAAGCACCACCATCTCACT 60.037 55.000 0.00 0.00 0.00 3.41
99 100 0.320771 ACGAAGCACCACCATCTCAC 60.321 55.000 0.00 0.00 0.00 3.51
100 101 0.320683 CACGAAGCACCACCATCTCA 60.321 55.000 0.00 0.00 0.00 3.27
101 102 1.021390 CCACGAAGCACCACCATCTC 61.021 60.000 0.00 0.00 0.00 2.75
102 103 1.003355 CCACGAAGCACCACCATCT 60.003 57.895 0.00 0.00 0.00 2.90
103 104 1.298859 GACCACGAAGCACCACCATC 61.299 60.000 0.00 0.00 0.00 3.51
104 105 1.302511 GACCACGAAGCACCACCAT 60.303 57.895 0.00 0.00 0.00 3.55
105 106 2.110213 GACCACGAAGCACCACCA 59.890 61.111 0.00 0.00 0.00 4.17
106 107 1.961277 CTGACCACGAAGCACCACC 60.961 63.158 0.00 0.00 0.00 4.61
107 108 1.961277 CCTGACCACGAAGCACCAC 60.961 63.158 0.00 0.00 0.00 4.16
108 109 2.425592 CCTGACCACGAAGCACCA 59.574 61.111 0.00 0.00 0.00 4.17
109 110 2.358737 CCCTGACCACGAAGCACC 60.359 66.667 0.00 0.00 0.00 5.01
110 111 3.050275 GCCCTGACCACGAAGCAC 61.050 66.667 0.00 0.00 0.00 4.40
111 112 4.680237 CGCCCTGACCACGAAGCA 62.680 66.667 0.00 0.00 0.00 3.91
112 113 2.573609 ATACGCCCTGACCACGAAGC 62.574 60.000 0.00 0.00 0.00 3.86
113 114 0.527817 GATACGCCCTGACCACGAAG 60.528 60.000 0.00 0.00 0.00 3.79
114 115 1.252215 TGATACGCCCTGACCACGAA 61.252 55.000 0.00 0.00 0.00 3.85
115 116 1.679641 TGATACGCCCTGACCACGA 60.680 57.895 0.00 0.00 0.00 4.35
116 117 1.518572 GTGATACGCCCTGACCACG 60.519 63.158 0.00 0.00 0.00 4.94
117 118 1.518572 CGTGATACGCCCTGACCAC 60.519 63.158 0.00 0.00 33.65 4.16
118 119 2.717044 CCGTGATACGCCCTGACCA 61.717 63.158 0.00 0.00 40.91 4.02
119 120 2.106332 CCGTGATACGCCCTGACC 59.894 66.667 0.00 0.00 40.91 4.02
120 121 2.106332 CCCGTGATACGCCCTGAC 59.894 66.667 0.00 0.00 40.91 3.51
121 122 1.952102 GAACCCGTGATACGCCCTGA 61.952 60.000 0.00 0.00 40.91 3.86
122 123 1.520787 GAACCCGTGATACGCCCTG 60.521 63.158 0.00 0.00 40.91 4.45
123 124 1.684734 AGAACCCGTGATACGCCCT 60.685 57.895 0.00 0.00 40.91 5.19
124 125 1.520787 CAGAACCCGTGATACGCCC 60.521 63.158 0.00 0.00 40.91 6.13
125 126 2.171725 GCAGAACCCGTGATACGCC 61.172 63.158 0.00 0.00 40.91 5.68
126 127 2.171725 GGCAGAACCCGTGATACGC 61.172 63.158 0.00 0.00 40.91 4.42
127 128 4.104143 GGCAGAACCCGTGATACG 57.896 61.111 0.00 0.00 42.11 3.06
149 150 4.431131 AGCACCATCGCCCCCTTG 62.431 66.667 0.00 0.00 0.00 3.61
150 151 4.115199 GAGCACCATCGCCCCCTT 62.115 66.667 0.00 0.00 0.00 3.95
153 154 4.778143 AACGAGCACCATCGCCCC 62.778 66.667 0.00 0.00 46.60 5.80
154 155 3.499737 CAACGAGCACCATCGCCC 61.500 66.667 0.00 0.00 46.60 6.13
155 156 4.166011 GCAACGAGCACCATCGCC 62.166 66.667 0.00 0.00 46.60 5.54
156 157 4.505217 CGCAACGAGCACCATCGC 62.505 66.667 0.00 0.00 46.60 4.58
158 159 4.166011 GCCGCAACGAGCACCATC 62.166 66.667 0.00 0.00 46.13 3.51
173 174 1.133325 TCATACAGGGAGAGGAGAGCC 60.133 57.143 0.00 0.00 0.00 4.70
174 175 2.238521 CTCATACAGGGAGAGGAGAGC 58.761 57.143 0.00 0.00 34.24 4.09
211 212 2.826003 GGTCGAAACCCACCCACCT 61.826 63.158 0.00 0.00 39.93 4.00
243 244 4.536765 AGACACACTGATTCTTTTTGGGT 58.463 39.130 0.00 0.00 0.00 4.51
244 245 5.163519 ACAAGACACACTGATTCTTTTTGGG 60.164 40.000 0.00 0.00 0.00 4.12
251 252 3.813443 AGCAACAAGACACACTGATTCT 58.187 40.909 0.00 0.00 0.00 2.40
252 253 4.558538 AAGCAACAAGACACACTGATTC 57.441 40.909 0.00 0.00 0.00 2.52
259 260 3.505680 ACTTCACAAAGCAACAAGACACA 59.494 39.130 0.00 0.00 35.81 3.72
261 262 4.022416 ACAACTTCACAAAGCAACAAGACA 60.022 37.500 0.00 0.00 35.81 3.41
262 263 4.485163 ACAACTTCACAAAGCAACAAGAC 58.515 39.130 0.00 0.00 35.81 3.01
285 286 4.764679 TTCGTCCAGATTTGGTTTCATG 57.235 40.909 1.59 0.00 45.26 3.07
327 328 9.048446 GGCGAATTAAGGAAACACATAACTATA 57.952 33.333 0.00 0.00 0.00 1.31
435 436 3.181455 TGCCTGATACGTTGATGCCTATT 60.181 43.478 0.00 0.00 0.00 1.73
477 478 4.965119 AAGTTCAGTTTTGACAGTGTCC 57.035 40.909 20.43 5.02 31.71 4.02
490 491 8.890410 TGGTAGGAGTATTACTTAAGTTCAGT 57.110 34.615 14.49 2.31 0.00 3.41
505 507 2.116238 GTCCAATGGCTGGTAGGAGTA 58.884 52.381 0.00 0.00 46.51 2.59
528 530 5.154222 CAGGAGCCGTCAATTTTTAACTTC 58.846 41.667 0.00 0.00 0.00 3.01
549 551 1.669115 CTGTCCACCAAGTCGGCAG 60.669 63.158 0.00 0.00 39.03 4.85
591 593 0.452987 AAAGTGTGTGTGCAGTGCAG 59.547 50.000 20.42 0.00 40.08 4.41
660 662 1.302511 CTGTGGTGGGGAACGGAAG 60.303 63.158 0.00 0.00 0.00 3.46
835 866 1.073199 CGAGGGGCAGTTTGGTCTT 59.927 57.895 0.00 0.00 0.00 3.01
1062 1097 3.403624 TGGGACATGAGAGGGTGC 58.596 61.111 0.00 0.00 0.00 5.01
1150 1199 0.179145 GCATGCAAGCCATCACTCAC 60.179 55.000 14.21 0.00 29.71 3.51
1205 1254 1.376037 CGACTTCTTGGACAGGCCC 60.376 63.158 0.00 0.00 34.97 5.80
1706 1761 1.473965 CGGATCACCTCCATCTGGTTG 60.474 57.143 0.00 0.00 45.24 3.77
1869 1924 2.322422 CTACGCTACCGACGACCG 59.678 66.667 0.00 0.00 38.29 4.79
1870 1925 2.023882 GCTACGCTACCGACGACC 59.976 66.667 0.00 0.00 38.29 4.79
1871 1926 1.582168 GTGCTACGCTACCGACGAC 60.582 63.158 0.00 0.00 38.29 4.34
1872 1927 1.742880 AGTGCTACGCTACCGACGA 60.743 57.895 0.00 0.00 38.29 4.20
1950 2017 0.188587 AGGGGTGAGTGAGTGAGTGA 59.811 55.000 0.00 0.00 0.00 3.41
1951 2018 0.605589 GAGGGGTGAGTGAGTGAGTG 59.394 60.000 0.00 0.00 0.00 3.51
1952 2019 0.896019 CGAGGGGTGAGTGAGTGAGT 60.896 60.000 0.00 0.00 0.00 3.41
1953 2020 0.896019 ACGAGGGGTGAGTGAGTGAG 60.896 60.000 0.00 0.00 0.00 3.51
1954 2021 0.894184 GACGAGGGGTGAGTGAGTGA 60.894 60.000 0.00 0.00 0.00 3.41
1955 2022 1.587054 GACGAGGGGTGAGTGAGTG 59.413 63.158 0.00 0.00 0.00 3.51
1956 2023 1.972223 CGACGAGGGGTGAGTGAGT 60.972 63.158 0.00 0.00 0.00 3.41
1957 2024 1.524863 AACGACGAGGGGTGAGTGAG 61.525 60.000 0.00 0.00 0.00 3.51
1958 2025 1.111116 AAACGACGAGGGGTGAGTGA 61.111 55.000 0.00 0.00 0.00 3.41
1959 2026 0.249741 AAAACGACGAGGGGTGAGTG 60.250 55.000 0.00 0.00 0.00 3.51
1960 2027 0.466963 AAAAACGACGAGGGGTGAGT 59.533 50.000 0.00 0.00 0.00 3.41
1961 2028 1.145803 GAAAAACGACGAGGGGTGAG 58.854 55.000 0.00 0.00 0.00 3.51
1962 2029 0.249996 GGAAAAACGACGAGGGGTGA 60.250 55.000 0.00 0.00 0.00 4.02
1963 2030 0.250166 AGGAAAAACGACGAGGGGTG 60.250 55.000 0.00 0.00 0.00 4.61
1964 2031 0.471191 AAGGAAAAACGACGAGGGGT 59.529 50.000 0.00 0.00 0.00 4.95
1965 2032 1.265905 CAAAGGAAAAACGACGAGGGG 59.734 52.381 0.00 0.00 0.00 4.79
1981 2048 5.352569 ACAACACAAGTGAGAGAGAACAAAG 59.647 40.000 7.28 0.00 0.00 2.77
2098 2177 3.666374 GCAGAATCAGAAGCTGAAACACG 60.666 47.826 0.78 0.00 44.04 4.49
2106 2185 2.683867 GCAAGATGCAGAATCAGAAGCT 59.316 45.455 0.00 0.00 44.26 3.74
2194 2283 1.003839 TCTTGCTCGGCCATTCGTT 60.004 52.632 2.24 0.00 0.00 3.85
2200 2289 2.669569 GTTGCTCTTGCTCGGCCA 60.670 61.111 2.24 0.00 40.48 5.36
2273 2362 1.983119 TAAATGCCTGGCCGAGGAGG 61.983 60.000 21.37 13.15 46.33 4.30
2274 2363 0.107214 TTAAATGCCTGGCCGAGGAG 60.107 55.000 21.37 3.22 46.33 3.69
2275 2364 0.550914 ATTAAATGCCTGGCCGAGGA 59.449 50.000 21.37 6.94 46.33 3.71
2276 2365 0.954452 GATTAAATGCCTGGCCGAGG 59.046 55.000 17.53 14.87 46.13 4.63
2277 2366 0.588252 CGATTAAATGCCTGGCCGAG 59.412 55.000 17.53 0.00 0.00 4.63
2278 2367 0.817634 CCGATTAAATGCCTGGCCGA 60.818 55.000 17.53 0.00 0.00 5.54
2279 2368 0.817634 TCCGATTAAATGCCTGGCCG 60.818 55.000 17.53 10.19 0.00 6.13
2280 2369 1.541588 GATCCGATTAAATGCCTGGCC 59.458 52.381 17.53 0.00 0.00 5.36
2281 2370 1.197721 CGATCCGATTAAATGCCTGGC 59.802 52.381 12.87 12.87 0.00 4.85
2282 2371 1.806542 CCGATCCGATTAAATGCCTGG 59.193 52.381 0.00 0.00 0.00 4.45
2304 2412 1.678101 GCATTTACCTCCATCCACTGC 59.322 52.381 0.00 0.00 0.00 4.40
2357 2473 1.108776 CAGGGTTCGTATCTTCCCGA 58.891 55.000 0.00 0.00 44.13 5.14
2363 2479 1.522569 GCAGGCAGGGTTCGTATCT 59.477 57.895 0.00 0.00 0.00 1.98
2392 2508 0.446616 CTGCTCGTAGTACGTCTGCA 59.553 55.000 25.67 25.67 43.14 4.41
2426 2542 0.246635 CCATCGGGTTCTCAACGTCT 59.753 55.000 0.00 0.00 0.00 4.18
2427 2543 2.750815 CCATCGGGTTCTCAACGTC 58.249 57.895 0.00 0.00 0.00 4.34
2486 2630 4.742201 GTTCGCCAGCTCTCGCCA 62.742 66.667 0.00 0.00 36.60 5.69
2497 2642 2.203070 ATGATGAGCCCGTTCGCC 60.203 61.111 0.00 0.00 0.00 5.54
2510 2655 2.107750 CTCCCGAGTGCGCATGAT 59.892 61.111 15.91 2.08 35.83 2.45
2550 2709 0.179073 CGATCTGCCCTCGAAATGGT 60.179 55.000 0.00 0.00 38.38 3.55
2562 2721 2.447887 CGTCCAGCACACGATCTGC 61.448 63.158 0.00 0.00 39.75 4.26
2667 2854 3.208383 CAAGCGCACCACACACCA 61.208 61.111 11.47 0.00 0.00 4.17
2693 2880 1.961394 TCTTCATATTCTAGCCGCCGT 59.039 47.619 0.00 0.00 0.00 5.68
2754 2941 1.872679 GCGGCGTGTAGAGCTGTAC 60.873 63.158 13.92 13.92 42.62 2.90
2814 3004 4.561326 GCCTACTCGTACCACAAACCTTTA 60.561 45.833 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.