Multiple sequence alignment - TraesCS7D01G515200

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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 TraesCS7D01G515200 chr7D 100.000 3457 0 0 1 3457 615778230 615781686 0.000000e+00 6384
1 TraesCS7D01G515200 chr2D 99.190 3209 23 2 252 3457 46693766 46690558 0.000000e+00 5779
2 TraesCS7D01G515200 chr5D 98.699 2921 34 2 249 3167 41776632 41779550 0.000000e+00 5180
3 TraesCS7D01G515200 chr6B 94.631 3222 143 22 252 3455 712151898 712155107 0.000000e+00 4964
4 TraesCS7D01G515200 chr6B 94.415 3223 149 16 252 3457 366596284 366593076 0.000000e+00 4926
5 TraesCS7D01G515200 chr6B 82.969 1556 156 42 754 2259 409295371 409293875 0.000000e+00 1304
6 TraesCS7D01G515200 chr1B 94.039 3221 153 21 252 3455 6396360 6399558 0.000000e+00 4848
7 TraesCS7D01G515200 chr4A 93.973 3219 160 19 252 3455 58507671 58510870 0.000000e+00 4839
8 TraesCS7D01G515200 chr7A 93.773 3228 163 23 245 3455 11051452 11048246 0.000000e+00 4813
9 TraesCS7D01G515200 chr7A 92.520 254 14 3 1 253 708436917 708436668 3.280000e-95 359
10 TraesCS7D01G515200 chr7A 94.845 194 5 3 63 253 708331029 708331220 7.250000e-77 298
11 TraesCS7D01G515200 chr3B 93.265 3222 170 25 253 3457 465857842 465861033 0.000000e+00 4704
12 TraesCS7D01G515200 chr6D 99.205 2390 17 1 252 2639 429473821 429476210 0.000000e+00 4307
13 TraesCS7D01G515200 chr7B 92.126 254 16 2 2 253 708581236 708580985 4.240000e-94 355
14 TraesCS7D01G515200 chrUn 89.655 174 13 3 1 173 392921414 392921245 2.090000e-52 217


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 TraesCS7D01G515200 chr7D 615778230 615781686 3456 False 6384 6384 100.000 1 3457 1 chr7D.!!$F1 3456
1 TraesCS7D01G515200 chr2D 46690558 46693766 3208 True 5779 5779 99.190 252 3457 1 chr2D.!!$R1 3205
2 TraesCS7D01G515200 chr5D 41776632 41779550 2918 False 5180 5180 98.699 249 3167 1 chr5D.!!$F1 2918
3 TraesCS7D01G515200 chr6B 712151898 712155107 3209 False 4964 4964 94.631 252 3455 1 chr6B.!!$F1 3203
4 TraesCS7D01G515200 chr6B 366593076 366596284 3208 True 4926 4926 94.415 252 3457 1 chr6B.!!$R1 3205
5 TraesCS7D01G515200 chr6B 409293875 409295371 1496 True 1304 1304 82.969 754 2259 1 chr6B.!!$R2 1505
6 TraesCS7D01G515200 chr1B 6396360 6399558 3198 False 4848 4848 94.039 252 3455 1 chr1B.!!$F1 3203
7 TraesCS7D01G515200 chr4A 58507671 58510870 3199 False 4839 4839 93.973 252 3455 1 chr4A.!!$F1 3203
8 TraesCS7D01G515200 chr7A 11048246 11051452 3206 True 4813 4813 93.773 245 3455 1 chr7A.!!$R1 3210
9 TraesCS7D01G515200 chr3B 465857842 465861033 3191 False 4704 4704 93.265 253 3457 1 chr3B.!!$F1 3204
10 TraesCS7D01G515200 chr6D 429473821 429476210 2389 False 4307 4307 99.205 252 2639 1 chr6D.!!$F1 2387

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
179 180 0.036164 CACGGGGTTGAACATGGAGA 59.964 55.0 0.0 0.0 0.00 3.71 F
180 181 0.036306 ACGGGGTTGAACATGGAGAC 59.964 55.0 0.0 0.0 0.00 3.36 F
214 215 0.179189 GCAGCTTAATGCACCACGTC 60.179 55.0 0.0 0.0 45.77 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1628 4.934356 TCAAACTCCTGATTTAGGCCATT 58.066 39.130 5.01 0.0 46.87 3.16 R
1667 1698 7.255035 CCTCAATCACACTGGAAATGATATCAC 60.255 40.741 7.78 0.0 32.74 3.06 R
2894 2960 5.242171 TCTGTACCATTGTCTGAACGTAAGA 59.758 40.000 0.00 0.0 43.62 2.10 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
32 33 9.627123 ACATACAATAACATATGCTTAACACCT 57.373 29.630 1.58 0.00 32.92 4.00
34 35 9.845740 ATACAATAACATATGCTTAACACCTCA 57.154 29.630 1.58 0.00 0.00 3.86
35 36 8.752005 ACAATAACATATGCTTAACACCTCAT 57.248 30.769 1.58 0.00 0.00 2.90
36 37 9.189156 ACAATAACATATGCTTAACACCTCATT 57.811 29.630 1.58 0.00 0.00 2.57
37 38 9.454585 CAATAACATATGCTTAACACCTCATTG 57.545 33.333 1.58 0.00 0.00 2.82
38 39 8.978874 ATAACATATGCTTAACACCTCATTGA 57.021 30.769 1.58 0.00 0.00 2.57
39 40 7.886629 AACATATGCTTAACACCTCATTGAT 57.113 32.000 1.58 0.00 0.00 2.57
40 41 7.502120 ACATATGCTTAACACCTCATTGATC 57.498 36.000 1.58 0.00 0.00 2.92
41 42 7.285566 ACATATGCTTAACACCTCATTGATCT 58.714 34.615 1.58 0.00 0.00 2.75
42 43 7.443575 ACATATGCTTAACACCTCATTGATCTC 59.556 37.037 1.58 0.00 0.00 2.75
43 44 4.517285 TGCTTAACACCTCATTGATCTCC 58.483 43.478 0.00 0.00 0.00 3.71
44 45 4.225942 TGCTTAACACCTCATTGATCTCCT 59.774 41.667 0.00 0.00 0.00 3.69
45 46 5.425217 TGCTTAACACCTCATTGATCTCCTA 59.575 40.000 0.00 0.00 0.00 2.94
46 47 6.070251 TGCTTAACACCTCATTGATCTCCTAA 60.070 38.462 0.00 0.00 0.00 2.69
47 48 6.823689 GCTTAACACCTCATTGATCTCCTAAA 59.176 38.462 0.00 0.00 0.00 1.85
48 49 7.011857 GCTTAACACCTCATTGATCTCCTAAAG 59.988 40.741 0.00 0.00 0.00 1.85
49 50 4.775236 ACACCTCATTGATCTCCTAAAGC 58.225 43.478 0.00 0.00 0.00 3.51
50 51 4.472833 ACACCTCATTGATCTCCTAAAGCT 59.527 41.667 0.00 0.00 0.00 3.74
51 52 5.055812 CACCTCATTGATCTCCTAAAGCTC 58.944 45.833 0.00 0.00 0.00 4.09
52 53 4.718774 ACCTCATTGATCTCCTAAAGCTCA 59.281 41.667 0.00 0.00 0.00 4.26
53 54 5.163322 ACCTCATTGATCTCCTAAAGCTCAG 60.163 44.000 0.00 0.00 32.02 3.35
54 55 5.070180 CCTCATTGATCTCCTAAAGCTCAGA 59.930 44.000 0.00 0.00 32.02 3.27
55 56 5.911752 TCATTGATCTCCTAAAGCTCAGAC 58.088 41.667 0.00 0.00 32.02 3.51
56 57 4.744795 TTGATCTCCTAAAGCTCAGACC 57.255 45.455 0.00 0.00 32.02 3.85
57 58 3.713003 TGATCTCCTAAAGCTCAGACCA 58.287 45.455 0.00 0.00 0.00 4.02
58 59 4.293494 TGATCTCCTAAAGCTCAGACCAT 58.707 43.478 0.00 0.00 0.00 3.55
59 60 4.100653 TGATCTCCTAAAGCTCAGACCATG 59.899 45.833 0.00 0.00 0.00 3.66
60 61 3.445008 TCTCCTAAAGCTCAGACCATGT 58.555 45.455 0.00 0.00 0.00 3.21
61 62 3.840666 TCTCCTAAAGCTCAGACCATGTT 59.159 43.478 0.00 0.00 0.00 2.71
62 63 4.287067 TCTCCTAAAGCTCAGACCATGTTT 59.713 41.667 0.00 0.00 0.00 2.83
63 64 5.483937 TCTCCTAAAGCTCAGACCATGTTTA 59.516 40.000 0.00 0.00 0.00 2.01
64 65 6.156949 TCTCCTAAAGCTCAGACCATGTTTAT 59.843 38.462 0.00 0.00 0.00 1.40
65 66 6.115446 TCCTAAAGCTCAGACCATGTTTATG 58.885 40.000 0.00 0.00 0.00 1.90
66 67 5.882557 CCTAAAGCTCAGACCATGTTTATGT 59.117 40.000 0.00 0.00 32.21 2.29
67 68 6.375455 CCTAAAGCTCAGACCATGTTTATGTT 59.625 38.462 0.00 0.00 32.21 2.71
68 69 7.552687 CCTAAAGCTCAGACCATGTTTATGTTA 59.447 37.037 0.00 0.00 32.21 2.41
69 70 7.759489 AAAGCTCAGACCATGTTTATGTTAA 57.241 32.000 0.00 0.00 32.21 2.01
70 71 7.759489 AAGCTCAGACCATGTTTATGTTAAA 57.241 32.000 0.00 0.00 32.21 1.52
71 72 7.383102 AGCTCAGACCATGTTTATGTTAAAG 57.617 36.000 0.00 0.00 32.21 1.85
72 73 7.168219 AGCTCAGACCATGTTTATGTTAAAGA 58.832 34.615 0.00 0.00 32.21 2.52
73 74 7.665559 AGCTCAGACCATGTTTATGTTAAAGAA 59.334 33.333 0.00 0.00 32.21 2.52
74 75 8.296713 GCTCAGACCATGTTTATGTTAAAGAAA 58.703 33.333 0.00 0.00 32.21 2.52
78 79 9.927668 AGACCATGTTTATGTTAAAGAAAATGG 57.072 29.630 3.25 3.25 32.21 3.16
79 80 9.921637 GACCATGTTTATGTTAAAGAAAATGGA 57.078 29.630 10.29 0.00 32.21 3.41
88 89 8.635765 ATGTTAAAGAAAATGGAACTAGAGCA 57.364 30.769 0.00 0.00 0.00 4.26
89 90 8.458573 TGTTAAAGAAAATGGAACTAGAGCAA 57.541 30.769 0.00 0.00 0.00 3.91
90 91 8.908903 TGTTAAAGAAAATGGAACTAGAGCAAA 58.091 29.630 0.00 0.00 0.00 3.68
91 92 9.181805 GTTAAAGAAAATGGAACTAGAGCAAAC 57.818 33.333 0.00 0.00 0.00 2.93
92 93 6.959639 AAGAAAATGGAACTAGAGCAAACA 57.040 33.333 0.00 0.00 0.00 2.83
93 94 6.319141 AGAAAATGGAACTAGAGCAAACAC 57.681 37.500 0.00 0.00 0.00 3.32
94 95 6.064717 AGAAAATGGAACTAGAGCAAACACT 58.935 36.000 0.00 0.00 0.00 3.55
95 96 6.547510 AGAAAATGGAACTAGAGCAAACACTT 59.452 34.615 0.00 0.00 0.00 3.16
96 97 7.719633 AGAAAATGGAACTAGAGCAAACACTTA 59.280 33.333 0.00 0.00 0.00 2.24
97 98 6.803154 AATGGAACTAGAGCAAACACTTAC 57.197 37.500 0.00 0.00 0.00 2.34
98 99 5.546621 TGGAACTAGAGCAAACACTTACT 57.453 39.130 0.00 0.00 0.00 2.24
99 100 5.539048 TGGAACTAGAGCAAACACTTACTC 58.461 41.667 0.00 0.00 0.00 2.59
100 101 5.304614 TGGAACTAGAGCAAACACTTACTCT 59.695 40.000 0.00 0.00 42.08 3.24
101 102 5.865013 GGAACTAGAGCAAACACTTACTCTC 59.135 44.000 0.00 0.00 40.01 3.20
102 103 5.394224 ACTAGAGCAAACACTTACTCTCC 57.606 43.478 0.00 0.00 40.01 3.71
103 104 4.833380 ACTAGAGCAAACACTTACTCTCCA 59.167 41.667 0.00 0.00 40.01 3.86
104 105 4.689612 AGAGCAAACACTTACTCTCCAA 57.310 40.909 0.00 0.00 34.42 3.53
105 106 4.636249 AGAGCAAACACTTACTCTCCAAG 58.364 43.478 0.00 0.00 34.42 3.61
106 107 3.744660 AGCAAACACTTACTCTCCAAGG 58.255 45.455 0.00 0.00 0.00 3.61
107 108 3.136626 AGCAAACACTTACTCTCCAAGGT 59.863 43.478 0.00 0.00 0.00 3.50
108 109 3.251004 GCAAACACTTACTCTCCAAGGTG 59.749 47.826 0.00 0.00 0.00 4.00
109 110 4.451900 CAAACACTTACTCTCCAAGGTGT 58.548 43.478 0.00 0.00 0.00 4.16
110 111 5.607477 CAAACACTTACTCTCCAAGGTGTA 58.393 41.667 0.00 0.00 0.00 2.90
111 112 6.231211 CAAACACTTACTCTCCAAGGTGTAT 58.769 40.000 0.00 0.00 0.00 2.29
112 113 5.662674 ACACTTACTCTCCAAGGTGTATC 57.337 43.478 0.00 0.00 0.00 2.24
113 114 5.334421 ACACTTACTCTCCAAGGTGTATCT 58.666 41.667 0.00 0.00 0.00 1.98
114 115 5.780793 ACACTTACTCTCCAAGGTGTATCTT 59.219 40.000 0.00 0.00 0.00 2.40
115 116 6.270231 ACACTTACTCTCCAAGGTGTATCTTT 59.730 38.462 0.00 0.00 0.00 2.52
116 117 7.162082 CACTTACTCTCCAAGGTGTATCTTTT 58.838 38.462 0.00 0.00 0.00 2.27
117 118 7.332182 CACTTACTCTCCAAGGTGTATCTTTTC 59.668 40.741 0.00 0.00 0.00 2.29
118 119 4.822026 ACTCTCCAAGGTGTATCTTTTCG 58.178 43.478 0.00 0.00 0.00 3.46
119 120 3.596214 TCTCCAAGGTGTATCTTTTCGC 58.404 45.455 0.00 0.00 0.00 4.70
120 121 2.678336 CTCCAAGGTGTATCTTTTCGCC 59.322 50.000 0.00 0.00 34.80 5.54
121 122 1.396996 CCAAGGTGTATCTTTTCGCCG 59.603 52.381 0.00 0.00 38.99 6.46
122 123 2.343101 CAAGGTGTATCTTTTCGCCGA 58.657 47.619 0.00 0.00 38.99 5.54
123 124 2.295253 AGGTGTATCTTTTCGCCGAG 57.705 50.000 0.00 0.00 38.99 4.63
124 125 1.134788 AGGTGTATCTTTTCGCCGAGG 60.135 52.381 0.00 0.00 38.99 4.63
125 126 1.134907 GGTGTATCTTTTCGCCGAGGA 60.135 52.381 0.00 0.00 0.00 3.71
126 127 2.613691 GTGTATCTTTTCGCCGAGGAA 58.386 47.619 0.00 0.00 0.00 3.36
127 128 2.347755 GTGTATCTTTTCGCCGAGGAAC 59.652 50.000 0.00 0.00 0.00 3.62
128 129 1.587034 GTATCTTTTCGCCGAGGAACG 59.413 52.381 0.00 0.00 42.18 3.95
129 130 1.359459 ATCTTTTCGCCGAGGAACGC 61.359 55.000 0.00 0.00 41.07 4.84
130 131 3.023591 CTTTTCGCCGAGGAACGCC 62.024 63.158 0.00 0.00 41.07 5.68
138 139 4.785453 GAGGAACGCCCAGCCCAG 62.785 72.222 0.00 0.00 37.41 4.45
159 160 3.660111 GGCGCAGACCACCAACAC 61.660 66.667 10.83 0.00 0.00 3.32
160 161 3.660111 GCGCAGACCACCAACACC 61.660 66.667 0.30 0.00 0.00 4.16
161 162 2.203139 CGCAGACCACCAACACCA 60.203 61.111 0.00 0.00 0.00 4.17
162 163 2.542907 CGCAGACCACCAACACCAC 61.543 63.158 0.00 0.00 0.00 4.16
163 164 2.542907 GCAGACCACCAACACCACG 61.543 63.158 0.00 0.00 0.00 4.94
164 165 1.891919 CAGACCACCAACACCACGG 60.892 63.158 0.00 0.00 0.00 4.94
165 166 2.593436 GACCACCAACACCACGGG 60.593 66.667 0.00 0.00 0.00 5.28
166 167 4.198224 ACCACCAACACCACGGGG 62.198 66.667 0.00 0.00 41.29 5.73
176 177 3.680156 CCACGGGGTTGAACATGG 58.320 61.111 0.00 0.00 0.00 3.66
177 178 1.074072 CCACGGGGTTGAACATGGA 59.926 57.895 0.00 0.00 0.00 3.41
178 179 0.960364 CCACGGGGTTGAACATGGAG 60.960 60.000 0.00 0.00 0.00 3.86
179 180 0.036164 CACGGGGTTGAACATGGAGA 59.964 55.000 0.00 0.00 0.00 3.71
180 181 0.036306 ACGGGGTTGAACATGGAGAC 59.964 55.000 0.00 0.00 0.00 3.36
181 182 1.019278 CGGGGTTGAACATGGAGACG 61.019 60.000 0.00 0.00 0.00 4.18
182 183 0.323629 GGGGTTGAACATGGAGACGA 59.676 55.000 0.00 0.00 0.00 4.20
183 184 1.271163 GGGGTTGAACATGGAGACGAA 60.271 52.381 0.00 0.00 0.00 3.85
184 185 1.804748 GGGTTGAACATGGAGACGAAC 59.195 52.381 0.00 0.00 0.00 3.95
185 186 2.489971 GGTTGAACATGGAGACGAACA 58.510 47.619 0.00 0.00 0.00 3.18
186 187 2.480419 GGTTGAACATGGAGACGAACAG 59.520 50.000 0.00 0.00 0.00 3.16
187 188 3.131396 GTTGAACATGGAGACGAACAGT 58.869 45.455 0.00 0.00 0.00 3.55
188 189 2.754472 TGAACATGGAGACGAACAGTG 58.246 47.619 0.00 0.00 0.00 3.66
189 190 2.069273 GAACATGGAGACGAACAGTGG 58.931 52.381 0.00 0.00 0.00 4.00
190 191 0.321671 ACATGGAGACGAACAGTGGG 59.678 55.000 0.00 0.00 0.00 4.61
191 192 1.021390 CATGGAGACGAACAGTGGGC 61.021 60.000 0.00 0.00 0.00 5.36
192 193 2.047179 GGAGACGAACAGTGGGCC 60.047 66.667 0.00 0.00 0.00 5.80
193 194 2.741092 GAGACGAACAGTGGGCCA 59.259 61.111 0.00 0.00 0.00 5.36
194 195 1.668151 GAGACGAACAGTGGGCCAC 60.668 63.158 29.32 29.32 34.10 5.01
195 196 3.041940 GACGAACAGTGGGCCACG 61.042 66.667 29.76 25.06 39.64 4.94
198 199 3.357079 GAACAGTGGGCCACGCAG 61.357 66.667 29.76 24.38 39.64 5.18
202 203 3.636231 AGTGGGCCACGCAGCTTA 61.636 61.111 29.76 0.00 39.64 3.09
203 204 2.671619 GTGGGCCACGCAGCTTAA 60.672 61.111 22.83 0.00 0.00 1.85
204 205 2.046285 GTGGGCCACGCAGCTTAAT 61.046 57.895 22.83 0.00 0.00 1.40
205 206 2.045708 TGGGCCACGCAGCTTAATG 61.046 57.895 0.00 0.00 0.00 1.90
206 207 2.102946 GGCCACGCAGCTTAATGC 59.897 61.111 0.00 0.00 42.95 3.56
207 208 2.699768 GGCCACGCAGCTTAATGCA 61.700 57.895 0.00 0.00 46.87 3.96
208 209 1.514873 GCCACGCAGCTTAATGCAC 60.515 57.895 0.00 0.00 46.87 4.57
209 210 1.137404 CCACGCAGCTTAATGCACC 59.863 57.895 0.00 0.00 46.87 5.01
210 211 1.585267 CCACGCAGCTTAATGCACCA 61.585 55.000 0.00 0.00 46.87 4.17
211 212 0.454957 CACGCAGCTTAATGCACCAC 60.455 55.000 0.00 0.00 46.87 4.16
212 213 1.226101 CGCAGCTTAATGCACCACG 60.226 57.895 0.00 0.00 46.87 4.94
213 214 1.875963 GCAGCTTAATGCACCACGT 59.124 52.632 0.00 0.00 45.77 4.49
214 215 0.179189 GCAGCTTAATGCACCACGTC 60.179 55.000 0.00 0.00 45.77 4.34
215 216 1.155889 CAGCTTAATGCACCACGTCA 58.844 50.000 0.00 0.00 45.94 4.35
216 217 1.739466 CAGCTTAATGCACCACGTCAT 59.261 47.619 0.00 0.00 45.94 3.06
217 218 2.009774 AGCTTAATGCACCACGTCATC 58.990 47.619 0.00 0.00 45.94 2.92
218 219 1.737236 GCTTAATGCACCACGTCATCA 59.263 47.619 0.00 0.00 42.31 3.07
219 220 2.476185 GCTTAATGCACCACGTCATCAC 60.476 50.000 0.00 0.00 42.31 3.06
220 221 1.732941 TAATGCACCACGTCATCACC 58.267 50.000 0.00 0.00 0.00 4.02
221 222 0.250684 AATGCACCACGTCATCACCA 60.251 50.000 0.00 0.00 0.00 4.17
222 223 0.955428 ATGCACCACGTCATCACCAC 60.955 55.000 0.00 0.00 0.00 4.16
223 224 1.596752 GCACCACGTCATCACCACA 60.597 57.895 0.00 0.00 0.00 4.17
224 225 1.163420 GCACCACGTCATCACCACAA 61.163 55.000 0.00 0.00 0.00 3.33
225 226 1.304254 CACCACGTCATCACCACAAA 58.696 50.000 0.00 0.00 0.00 2.83
226 227 1.264020 CACCACGTCATCACCACAAAG 59.736 52.381 0.00 0.00 0.00 2.77
227 228 0.874390 CCACGTCATCACCACAAAGG 59.126 55.000 0.00 0.00 45.67 3.11
474 476 4.819105 ATCCTGTGTGATTTCGACCTTA 57.181 40.909 0.00 0.00 0.00 2.69
628 630 1.626825 GGTAACCTGTTGGACTGCCTA 59.373 52.381 0.00 0.00 37.04 3.93
1218 1242 3.510388 TTGAGTTCTCATGGCTACGAG 57.490 47.619 3.28 0.00 0.00 4.18
1415 1446 7.342799 AGGAAAATCAAATAAGATGCAGGCTAA 59.657 33.333 0.00 0.00 0.00 3.09
1422 1453 3.407424 AAGATGCAGGCTAATCGCATA 57.593 42.857 9.70 0.00 46.01 3.14
1597 1628 1.064003 TGTGGGCAAGCTCTTCCTTA 58.936 50.000 0.00 0.00 0.00 2.69
2894 2960 6.865834 TCAACATGGGGCAACTATTAAAAT 57.134 33.333 0.00 0.00 0.00 1.82
3167 3233 2.695666 GCCATAAGACTCCTGCTCAGTA 59.304 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.845740 TGAGGTGTTAAGCATATGTTATTGTAT 57.154 29.630 4.29 0.00 0.00 2.29
9 10 9.845740 ATGAGGTGTTAAGCATATGTTATTGTA 57.154 29.630 4.29 0.00 0.00 2.41
10 11 8.752005 ATGAGGTGTTAAGCATATGTTATTGT 57.248 30.769 4.29 0.00 0.00 2.71
11 12 9.454585 CAATGAGGTGTTAAGCATATGTTATTG 57.545 33.333 4.29 0.00 0.00 1.90
12 13 9.407380 TCAATGAGGTGTTAAGCATATGTTATT 57.593 29.630 4.29 0.31 0.00 1.40
13 14 8.978874 TCAATGAGGTGTTAAGCATATGTTAT 57.021 30.769 4.29 0.00 0.00 1.89
14 15 8.978874 ATCAATGAGGTGTTAAGCATATGTTA 57.021 30.769 4.29 0.00 0.00 2.41
15 16 7.776969 AGATCAATGAGGTGTTAAGCATATGTT 59.223 33.333 4.29 0.00 0.00 2.71
16 17 7.285566 AGATCAATGAGGTGTTAAGCATATGT 58.714 34.615 4.29 0.00 0.00 2.29
17 18 7.094890 GGAGATCAATGAGGTGTTAAGCATATG 60.095 40.741 0.00 0.00 0.00 1.78
18 19 6.939163 GGAGATCAATGAGGTGTTAAGCATAT 59.061 38.462 0.00 0.00 0.00 1.78
19 20 6.100279 AGGAGATCAATGAGGTGTTAAGCATA 59.900 38.462 0.00 0.00 0.00 3.14
20 21 5.104193 AGGAGATCAATGAGGTGTTAAGCAT 60.104 40.000 0.00 0.00 0.00 3.79
21 22 4.225942 AGGAGATCAATGAGGTGTTAAGCA 59.774 41.667 0.00 0.00 0.00 3.91
22 23 4.775236 AGGAGATCAATGAGGTGTTAAGC 58.225 43.478 0.00 0.00 0.00 3.09
23 24 7.011857 GCTTTAGGAGATCAATGAGGTGTTAAG 59.988 40.741 0.00 0.00 0.00 1.85
24 25 6.823689 GCTTTAGGAGATCAATGAGGTGTTAA 59.176 38.462 0.00 0.00 0.00 2.01
25 26 6.156949 AGCTTTAGGAGATCAATGAGGTGTTA 59.843 38.462 0.00 0.00 0.00 2.41
26 27 5.045286 AGCTTTAGGAGATCAATGAGGTGTT 60.045 40.000 0.00 0.00 0.00 3.32
27 28 4.472833 AGCTTTAGGAGATCAATGAGGTGT 59.527 41.667 0.00 0.00 0.00 4.16
28 29 5.033589 AGCTTTAGGAGATCAATGAGGTG 57.966 43.478 0.00 0.00 0.00 4.00
29 30 5.289083 GAGCTTTAGGAGATCAATGAGGT 57.711 43.478 0.00 0.00 40.53 3.85
37 38 4.100808 ACATGGTCTGAGCTTTAGGAGATC 59.899 45.833 8.47 0.00 41.21 2.75
38 39 4.036518 ACATGGTCTGAGCTTTAGGAGAT 58.963 43.478 8.47 0.00 0.00 2.75
39 40 3.445008 ACATGGTCTGAGCTTTAGGAGA 58.555 45.455 8.47 0.00 0.00 3.71
40 41 3.902881 ACATGGTCTGAGCTTTAGGAG 57.097 47.619 8.47 0.00 0.00 3.69
41 42 4.640771 AAACATGGTCTGAGCTTTAGGA 57.359 40.909 8.47 0.00 0.00 2.94
42 43 5.882557 ACATAAACATGGTCTGAGCTTTAGG 59.117 40.000 8.47 8.77 0.00 2.69
43 44 6.992063 ACATAAACATGGTCTGAGCTTTAG 57.008 37.500 8.47 0.00 0.00 1.85
44 45 8.856153 TTAACATAAACATGGTCTGAGCTTTA 57.144 30.769 8.47 5.50 0.00 1.85
45 46 7.759489 TTAACATAAACATGGTCTGAGCTTT 57.241 32.000 8.47 3.47 0.00 3.51
46 47 7.665559 TCTTTAACATAAACATGGTCTGAGCTT 59.334 33.333 8.47 0.00 0.00 3.74
47 48 7.168219 TCTTTAACATAAACATGGTCTGAGCT 58.832 34.615 8.47 0.00 0.00 4.09
48 49 7.377766 TCTTTAACATAAACATGGTCTGAGC 57.622 36.000 0.00 0.00 0.00 4.26
52 53 9.927668 CCATTTTCTTTAACATAAACATGGTCT 57.072 29.630 0.00 0.00 0.00 3.85
53 54 9.921637 TCCATTTTCTTTAACATAAACATGGTC 57.078 29.630 0.00 0.00 30.85 4.02
62 63 9.733556 TGCTCTAGTTCCATTTTCTTTAACATA 57.266 29.630 0.00 0.00 0.00 2.29
63 64 8.635765 TGCTCTAGTTCCATTTTCTTTAACAT 57.364 30.769 0.00 0.00 0.00 2.71
64 65 8.458573 TTGCTCTAGTTCCATTTTCTTTAACA 57.541 30.769 0.00 0.00 0.00 2.41
65 66 9.181805 GTTTGCTCTAGTTCCATTTTCTTTAAC 57.818 33.333 0.00 0.00 0.00 2.01
66 67 8.908903 TGTTTGCTCTAGTTCCATTTTCTTTAA 58.091 29.630 0.00 0.00 0.00 1.52
67 68 8.349983 GTGTTTGCTCTAGTTCCATTTTCTTTA 58.650 33.333 0.00 0.00 0.00 1.85
68 69 7.068716 AGTGTTTGCTCTAGTTCCATTTTCTTT 59.931 33.333 0.00 0.00 0.00 2.52
69 70 6.547510 AGTGTTTGCTCTAGTTCCATTTTCTT 59.452 34.615 0.00 0.00 0.00 2.52
70 71 6.064717 AGTGTTTGCTCTAGTTCCATTTTCT 58.935 36.000 0.00 0.00 0.00 2.52
71 72 6.319141 AGTGTTTGCTCTAGTTCCATTTTC 57.681 37.500 0.00 0.00 0.00 2.29
72 73 6.715347 AAGTGTTTGCTCTAGTTCCATTTT 57.285 33.333 0.00 0.00 0.00 1.82
73 74 6.998673 AGTAAGTGTTTGCTCTAGTTCCATTT 59.001 34.615 0.00 0.00 0.00 2.32
74 75 6.534634 AGTAAGTGTTTGCTCTAGTTCCATT 58.465 36.000 0.00 0.00 0.00 3.16
75 76 6.115448 AGTAAGTGTTTGCTCTAGTTCCAT 57.885 37.500 0.00 0.00 0.00 3.41
76 77 5.539048 GAGTAAGTGTTTGCTCTAGTTCCA 58.461 41.667 0.00 0.00 41.27 3.53
84 85 3.748568 CCTTGGAGAGTAAGTGTTTGCTC 59.251 47.826 0.00 0.00 43.79 4.26
85 86 3.136626 ACCTTGGAGAGTAAGTGTTTGCT 59.863 43.478 0.00 0.00 31.45 3.91
86 87 3.251004 CACCTTGGAGAGTAAGTGTTTGC 59.749 47.826 0.00 0.00 0.00 3.68
87 88 4.451900 ACACCTTGGAGAGTAAGTGTTTG 58.548 43.478 0.00 0.00 0.00 2.93
88 89 4.772886 ACACCTTGGAGAGTAAGTGTTT 57.227 40.909 0.00 0.00 0.00 2.83
89 90 5.780793 AGATACACCTTGGAGAGTAAGTGTT 59.219 40.000 0.00 0.00 0.00 3.32
90 91 5.334421 AGATACACCTTGGAGAGTAAGTGT 58.666 41.667 0.00 0.00 0.00 3.55
91 92 5.923733 AGATACACCTTGGAGAGTAAGTG 57.076 43.478 0.00 0.00 0.00 3.16
92 93 6.936968 AAAGATACACCTTGGAGAGTAAGT 57.063 37.500 0.00 0.00 0.00 2.24
93 94 6.531948 CGAAAAGATACACCTTGGAGAGTAAG 59.468 42.308 0.00 0.00 0.00 2.34
94 95 6.395629 CGAAAAGATACACCTTGGAGAGTAA 58.604 40.000 0.00 0.00 0.00 2.24
95 96 5.623824 GCGAAAAGATACACCTTGGAGAGTA 60.624 44.000 0.00 0.00 0.00 2.59
96 97 4.822026 CGAAAAGATACACCTTGGAGAGT 58.178 43.478 0.00 0.00 0.00 3.24
97 98 3.619038 GCGAAAAGATACACCTTGGAGAG 59.381 47.826 0.00 0.00 0.00 3.20
98 99 3.596214 GCGAAAAGATACACCTTGGAGA 58.404 45.455 0.00 0.00 0.00 3.71
99 100 2.678336 GGCGAAAAGATACACCTTGGAG 59.322 50.000 0.00 0.00 0.00 3.86
100 101 2.706890 GGCGAAAAGATACACCTTGGA 58.293 47.619 0.00 0.00 0.00 3.53
101 102 1.396996 CGGCGAAAAGATACACCTTGG 59.603 52.381 0.00 0.00 0.00 3.61
102 103 2.343101 TCGGCGAAAAGATACACCTTG 58.657 47.619 7.35 0.00 0.00 3.61
103 104 2.618053 CTCGGCGAAAAGATACACCTT 58.382 47.619 12.13 0.00 0.00 3.50
104 105 1.134788 CCTCGGCGAAAAGATACACCT 60.135 52.381 12.13 0.00 0.00 4.00
105 106 1.134907 TCCTCGGCGAAAAGATACACC 60.135 52.381 12.13 0.00 0.00 4.16
106 107 2.288961 TCCTCGGCGAAAAGATACAC 57.711 50.000 12.13 0.00 0.00 2.90
107 108 2.613691 GTTCCTCGGCGAAAAGATACA 58.386 47.619 12.13 0.00 0.00 2.29
108 109 1.587034 CGTTCCTCGGCGAAAAGATAC 59.413 52.381 12.13 8.31 35.71 2.24
109 110 1.917273 CGTTCCTCGGCGAAAAGATA 58.083 50.000 12.13 0.00 35.71 1.98
110 111 1.359459 GCGTTCCTCGGCGAAAAGAT 61.359 55.000 12.13 0.00 40.26 2.40
111 112 2.025418 GCGTTCCTCGGCGAAAAGA 61.025 57.895 12.13 5.38 40.26 2.52
112 113 2.474712 GCGTTCCTCGGCGAAAAG 59.525 61.111 12.13 6.98 40.26 2.27
121 122 4.785453 CTGGGCTGGGCGTTCCTC 62.785 72.222 0.00 0.00 36.20 3.71
142 143 3.660111 GTGTTGGTGGTCTGCGCC 61.660 66.667 4.18 0.00 0.00 6.53
143 144 3.660111 GGTGTTGGTGGTCTGCGC 61.660 66.667 0.00 0.00 0.00 6.09
144 145 2.203139 TGGTGTTGGTGGTCTGCG 60.203 61.111 0.00 0.00 0.00 5.18
145 146 2.542907 CGTGGTGTTGGTGGTCTGC 61.543 63.158 0.00 0.00 0.00 4.26
146 147 1.891919 CCGTGGTGTTGGTGGTCTG 60.892 63.158 0.00 0.00 0.00 3.51
147 148 2.508928 CCGTGGTGTTGGTGGTCT 59.491 61.111 0.00 0.00 0.00 3.85
148 149 2.593436 CCCGTGGTGTTGGTGGTC 60.593 66.667 0.00 0.00 0.00 4.02
149 150 4.198224 CCCCGTGGTGTTGGTGGT 62.198 66.667 0.00 0.00 0.00 4.16
150 151 4.198224 ACCCCGTGGTGTTGGTGG 62.198 66.667 0.00 0.00 45.58 4.61
159 160 0.960364 CTCCATGTTCAACCCCGTGG 60.960 60.000 0.00 0.00 38.80 4.94
160 161 0.036164 TCTCCATGTTCAACCCCGTG 59.964 55.000 0.00 0.00 0.00 4.94
161 162 0.036306 GTCTCCATGTTCAACCCCGT 59.964 55.000 0.00 0.00 0.00 5.28
162 163 1.019278 CGTCTCCATGTTCAACCCCG 61.019 60.000 0.00 0.00 0.00 5.73
163 164 0.323629 TCGTCTCCATGTTCAACCCC 59.676 55.000 0.00 0.00 0.00 4.95
164 165 1.804748 GTTCGTCTCCATGTTCAACCC 59.195 52.381 0.00 0.00 0.00 4.11
165 166 2.480419 CTGTTCGTCTCCATGTTCAACC 59.520 50.000 0.00 0.00 0.00 3.77
166 167 3.059597 CACTGTTCGTCTCCATGTTCAAC 60.060 47.826 0.00 0.00 0.00 3.18
167 168 3.130633 CACTGTTCGTCTCCATGTTCAA 58.869 45.455 0.00 0.00 0.00 2.69
168 169 2.547855 CCACTGTTCGTCTCCATGTTCA 60.548 50.000 0.00 0.00 0.00 3.18
169 170 2.069273 CCACTGTTCGTCTCCATGTTC 58.931 52.381 0.00 0.00 0.00 3.18
170 171 1.270839 CCCACTGTTCGTCTCCATGTT 60.271 52.381 0.00 0.00 0.00 2.71
171 172 0.321671 CCCACTGTTCGTCTCCATGT 59.678 55.000 0.00 0.00 0.00 3.21
172 173 1.021390 GCCCACTGTTCGTCTCCATG 61.021 60.000 0.00 0.00 0.00 3.66
173 174 1.296715 GCCCACTGTTCGTCTCCAT 59.703 57.895 0.00 0.00 0.00 3.41
174 175 2.741092 GCCCACTGTTCGTCTCCA 59.259 61.111 0.00 0.00 0.00 3.86
175 176 2.047179 GGCCCACTGTTCGTCTCC 60.047 66.667 0.00 0.00 0.00 3.71
176 177 1.668151 GTGGCCCACTGTTCGTCTC 60.668 63.158 6.63 0.00 0.00 3.36
177 178 2.426023 GTGGCCCACTGTTCGTCT 59.574 61.111 6.63 0.00 0.00 4.18
178 179 3.041940 CGTGGCCCACTGTTCGTC 61.042 66.667 12.94 0.00 31.34 4.20
181 182 3.357079 CTGCGTGGCCCACTGTTC 61.357 66.667 12.94 0.00 31.34 3.18
184 185 3.899981 TAAGCTGCGTGGCCCACTG 62.900 63.158 12.94 6.83 31.34 3.66
185 186 2.484287 ATTAAGCTGCGTGGCCCACT 62.484 55.000 12.94 0.00 31.34 4.00
186 187 2.046285 ATTAAGCTGCGTGGCCCAC 61.046 57.895 2.98 2.98 0.00 4.61
187 188 2.045708 CATTAAGCTGCGTGGCCCA 61.046 57.895 0.00 0.00 0.00 5.36
188 189 2.800736 CATTAAGCTGCGTGGCCC 59.199 61.111 0.00 0.00 0.00 5.80
189 190 2.102946 GCATTAAGCTGCGTGGCC 59.897 61.111 0.00 0.00 41.15 5.36
190 191 1.514873 GTGCATTAAGCTGCGTGGC 60.515 57.895 0.00 0.33 45.30 5.01
191 192 1.137404 GGTGCATTAAGCTGCGTGG 59.863 57.895 0.00 0.00 45.30 4.94
192 193 0.454957 GTGGTGCATTAAGCTGCGTG 60.455 55.000 0.00 0.00 45.30 5.34
193 194 1.875963 GTGGTGCATTAAGCTGCGT 59.124 52.632 0.00 0.00 45.30 5.24
194 195 1.226101 CGTGGTGCATTAAGCTGCG 60.226 57.895 0.00 0.00 45.30 5.18
195 196 0.179189 GACGTGGTGCATTAAGCTGC 60.179 55.000 0.00 0.00 45.94 5.25
196 197 1.155889 TGACGTGGTGCATTAAGCTG 58.844 50.000 0.00 0.00 45.94 4.24
197 198 2.009774 GATGACGTGGTGCATTAAGCT 58.990 47.619 0.00 0.00 45.94 3.74
198 199 1.737236 TGATGACGTGGTGCATTAAGC 59.263 47.619 0.00 0.00 45.96 3.09
199 200 2.095853 GGTGATGACGTGGTGCATTAAG 59.904 50.000 0.00 0.00 0.00 1.85
200 201 2.080693 GGTGATGACGTGGTGCATTAA 58.919 47.619 0.00 0.00 0.00 1.40
201 202 1.002544 TGGTGATGACGTGGTGCATTA 59.997 47.619 0.00 0.00 0.00 1.90
202 203 0.250684 TGGTGATGACGTGGTGCATT 60.251 50.000 0.00 0.00 0.00 3.56
203 204 0.955428 GTGGTGATGACGTGGTGCAT 60.955 55.000 0.00 0.00 0.00 3.96
204 205 1.596752 GTGGTGATGACGTGGTGCA 60.597 57.895 0.00 0.00 0.00 4.57
205 206 1.163420 TTGTGGTGATGACGTGGTGC 61.163 55.000 0.00 0.00 0.00 5.01
206 207 1.264020 CTTTGTGGTGATGACGTGGTG 59.736 52.381 0.00 0.00 0.00 4.17
207 208 1.593196 CTTTGTGGTGATGACGTGGT 58.407 50.000 0.00 0.00 0.00 4.16
208 209 0.874390 CCTTTGTGGTGATGACGTGG 59.126 55.000 0.00 0.00 0.00 4.94
239 240 4.344865 CCAACAGGGGGTCGTGGG 62.345 72.222 0.00 0.00 33.45 4.61
240 241 3.566210 ACCAACAGGGGGTCGTGG 61.566 66.667 0.00 0.00 42.91 4.94
241 242 2.281484 CACCAACAGGGGGTCGTG 60.281 66.667 0.00 0.00 42.91 4.35
247 248 6.187727 ACATTATCTATACACCAACAGGGG 57.812 41.667 0.00 0.00 42.91 4.79
314 315 7.872993 CCCTTCTCTGCGTTCTGATTTATATTA 59.127 37.037 0.00 0.00 0.00 0.98
474 476 1.442769 CACCGCAATTAGCAGTCACT 58.557 50.000 0.00 0.00 46.13 3.41
628 630 0.673644 GTAATCACAGCTGCACCGGT 60.674 55.000 15.27 0.00 0.00 5.28
731 735 9.880157 GTACCACTATCAATTAACTACAGGAAA 57.120 33.333 0.00 0.00 0.00 3.13
1415 1446 9.728025 AGTTAGTCAACTCCTGCATTATGCGAT 62.728 40.741 12.78 0.00 43.30 4.58
1422 1453 4.973168 TCAAGTTAGTCAACTCCTGCATT 58.027 39.130 0.00 0.00 44.41 3.56
1597 1628 4.934356 TCAAACTCCTGATTTAGGCCATT 58.066 39.130 5.01 0.00 46.87 3.16
1667 1698 7.255035 CCTCAATCACACTGGAAATGATATCAC 60.255 40.741 7.78 0.00 32.74 3.06
2894 2960 5.242171 TCTGTACCATTGTCTGAACGTAAGA 59.758 40.000 0.00 0.00 43.62 2.10


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

AutoCloner maintained by Alex Coulton.