Multiple sequence alignment - TraesCS4D01G165600

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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 TraesCS4D01G165600 chr4D 100.000 1716 0 0 681 2396 275208802 275207087 0.000000e+00 3169
1 TraesCS4D01G165600 chr4D 100.000 316 0 0 1 316 275209482 275209167 3.430000e-163 584
2 TraesCS4D01G165600 chr4D 95.732 328 2 1 1 316 268604408 268604735 3.530000e-143 518
3 TraesCS4D01G165600 chr4D 88.433 268 29 2 1392 1657 457888186 457887919 2.970000e-84 322
4 TraesCS4D01G165600 chr6D 93.943 1717 82 8 681 2396 242110855 242112550 0.000000e+00 2575
5 TraesCS4D01G165600 chr4B 93.655 1702 79 17 696 2392 341931328 341933005 0.000000e+00 2518
6 TraesCS4D01G165600 chr3A 95.559 1261 49 5 1137 2396 146690862 146689608 0.000000e+00 2012
7 TraesCS4D01G165600 chr7A 95.325 1262 53 4 1137 2396 512888332 512889589 0.000000e+00 1999
8 TraesCS4D01G165600 chr7A 87.072 526 60 5 1139 1657 224165766 224165242 2.650000e-164 588
9 TraesCS4D01G165600 chr7A 93.939 231 13 1 1 230 188323265 188323495 4.900000e-92 348
10 TraesCS4D01G165600 chr7A 93.088 217 12 3 16 230 188323532 188323747 4.970000e-82 315
11 TraesCS4D01G165600 chr2A 92.660 940 64 3 681 1619 319220512 319221447 0.000000e+00 1349
12 TraesCS4D01G165600 chr2A 95.385 65 3 0 245 309 319220320 319220384 1.170000e-18 104
13 TraesCS4D01G165600 chr5D 87.195 1023 115 12 1383 2396 192751642 192752657 0.000000e+00 1149
14 TraesCS4D01G165600 chr3B 97.680 431 8 2 1605 2035 461847360 461846932 0.000000e+00 739
15 TraesCS4D01G165600 chr3B 95.238 147 7 0 2250 2396 461846934 461846788 1.430000e-57 233
16 TraesCS4D01G165600 chr4A 86.767 529 62 5 1136 1657 603207455 603207982 1.230000e-162 582
17 TraesCS4D01G165600 chr4A 91.845 233 15 3 1 230 516776929 516776698 2.970000e-84 322
18 TraesCS4D01G165600 chr4A 86.286 175 20 4 60 232 677846759 677846931 1.130000e-43 187
19 TraesCS4D01G165600 chr1A 92.609 230 17 0 1 230 56431567 56431338 4.940000e-87 331
20 TraesCS4D01G165600 chr1A 92.641 231 15 2 1 230 121470847 121471076 4.940000e-87 331
21 TraesCS4D01G165600 chr7D 91.064 235 9 6 1 230 71768368 71768595 8.320000e-80 307
22 TraesCS4D01G165600 chr7B 91.266 229 15 2 2 230 252821460 252821683 8.320000e-80 307


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 TraesCS4D01G165600 chr4D 275207087 275209482 2395 True 1876.5 3169 100.0000 1 2396 2 chr4D.!!$R2 2395
1 TraesCS4D01G165600 chr6D 242110855 242112550 1695 False 2575.0 2575 93.9430 681 2396 1 chr6D.!!$F1 1715
2 TraesCS4D01G165600 chr4B 341931328 341933005 1677 False 2518.0 2518 93.6550 696 2392 1 chr4B.!!$F1 1696
3 TraesCS4D01G165600 chr3A 146689608 146690862 1254 True 2012.0 2012 95.5590 1137 2396 1 chr3A.!!$R1 1259
4 TraesCS4D01G165600 chr7A 512888332 512889589 1257 False 1999.0 1999 95.3250 1137 2396 1 chr7A.!!$F1 1259
5 TraesCS4D01G165600 chr7A 224165242 224165766 524 True 588.0 588 87.0720 1139 1657 1 chr7A.!!$R1 518
6 TraesCS4D01G165600 chr2A 319220320 319221447 1127 False 726.5 1349 94.0225 245 1619 2 chr2A.!!$F1 1374
7 TraesCS4D01G165600 chr5D 192751642 192752657 1015 False 1149.0 1149 87.1950 1383 2396 1 chr5D.!!$F1 1013
8 TraesCS4D01G165600 chr3B 461846788 461847360 572 True 486.0 739 96.4590 1605 2396 2 chr3B.!!$R1 791
9 TraesCS4D01G165600 chr4A 603207455 603207982 527 False 582.0 582 86.7670 1136 1657 1 chr4A.!!$F1 521

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
57 58 0.246635 TGACGCTTCCTTGCCTAGTC 59.753 55.0 0.0 0.0 0.0 2.59 F
89 90 0.247736 CTGACGCTTCCTTGCCTAGT 59.752 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 1031 3.461773 CGGCGGAGTGTGGGATCT 61.462 66.667 0.0 0.0 0.0 2.75 R
1397 1411 6.208599 TGAACTTCTGTCCAAAACTTTTCTGT 59.791 34.615 0.0 0.0 0.0 3.41 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
21 22 4.780275 GTACGTGAACCTAACTCTTCCT 57.220 45.455 0.00 0.00 0.00 3.36
22 23 5.886960 GTACGTGAACCTAACTCTTCCTA 57.113 43.478 0.00 0.00 0.00 2.94
23 24 4.780275 ACGTGAACCTAACTCTTCCTAC 57.220 45.455 0.00 0.00 0.00 3.18
24 25 3.509184 ACGTGAACCTAACTCTTCCTACC 59.491 47.826 0.00 0.00 0.00 3.18
25 26 3.762823 CGTGAACCTAACTCTTCCTACCT 59.237 47.826 0.00 0.00 0.00 3.08
26 27 4.220163 CGTGAACCTAACTCTTCCTACCTT 59.780 45.833 0.00 0.00 0.00 3.50
27 28 5.279356 CGTGAACCTAACTCTTCCTACCTTT 60.279 44.000 0.00 0.00 0.00 3.11
28 29 6.531923 GTGAACCTAACTCTTCCTACCTTTT 58.468 40.000 0.00 0.00 0.00 2.27
29 30 6.996879 GTGAACCTAACTCTTCCTACCTTTTT 59.003 38.462 0.00 0.00 0.00 1.94
50 51 2.856032 CGTGCTGACGCTTCCTTG 59.144 61.111 0.00 0.00 39.10 3.61
51 52 2.558313 GTGCTGACGCTTCCTTGC 59.442 61.111 0.00 0.00 36.97 4.01
52 53 2.669569 TGCTGACGCTTCCTTGCC 60.670 61.111 0.00 0.00 36.97 4.52
53 54 2.359230 GCTGACGCTTCCTTGCCT 60.359 61.111 0.00 0.00 0.00 4.75
54 55 1.079127 GCTGACGCTTCCTTGCCTA 60.079 57.895 0.00 0.00 0.00 3.93
55 56 1.086634 GCTGACGCTTCCTTGCCTAG 61.087 60.000 0.00 0.00 0.00 3.02
56 57 0.247736 CTGACGCTTCCTTGCCTAGT 59.752 55.000 0.00 0.00 0.00 2.57
57 58 0.246635 TGACGCTTCCTTGCCTAGTC 59.753 55.000 0.00 0.00 0.00 2.59
58 59 0.802607 GACGCTTCCTTGCCTAGTCG 60.803 60.000 0.00 0.00 0.00 4.18
59 60 1.215647 CGCTTCCTTGCCTAGTCGT 59.784 57.895 0.00 0.00 0.00 4.34
60 61 0.389948 CGCTTCCTTGCCTAGTCGTT 60.390 55.000 0.00 0.00 0.00 3.85
61 62 1.809684 GCTTCCTTGCCTAGTCGTTT 58.190 50.000 0.00 0.00 0.00 3.60
62 63 2.152016 GCTTCCTTGCCTAGTCGTTTT 58.848 47.619 0.00 0.00 0.00 2.43
63 64 2.552743 GCTTCCTTGCCTAGTCGTTTTT 59.447 45.455 0.00 0.00 0.00 1.94
80 81 3.552604 TTTTTATGTGCTGACGCTTCC 57.447 42.857 0.00 0.00 36.97 3.46
81 82 2.472695 TTTATGTGCTGACGCTTCCT 57.527 45.000 0.00 0.00 36.97 3.36
82 83 2.472695 TTATGTGCTGACGCTTCCTT 57.527 45.000 0.00 0.00 36.97 3.36
83 84 1.725641 TATGTGCTGACGCTTCCTTG 58.274 50.000 0.00 0.00 36.97 3.61
84 85 1.580845 ATGTGCTGACGCTTCCTTGC 61.581 55.000 0.00 0.00 36.97 4.01
85 86 2.669569 TGCTGACGCTTCCTTGCC 60.670 61.111 0.00 0.00 36.97 4.52
86 87 2.359230 GCTGACGCTTCCTTGCCT 60.359 61.111 0.00 0.00 0.00 4.75
87 88 1.079127 GCTGACGCTTCCTTGCCTA 60.079 57.895 0.00 0.00 0.00 3.93
88 89 1.086634 GCTGACGCTTCCTTGCCTAG 61.087 60.000 0.00 0.00 0.00 3.02
89 90 0.247736 CTGACGCTTCCTTGCCTAGT 59.752 55.000 0.00 0.00 0.00 2.57
90 91 0.246635 TGACGCTTCCTTGCCTAGTC 59.753 55.000 0.00 0.00 0.00 2.59
91 92 0.533032 GACGCTTCCTTGCCTAGTCT 59.467 55.000 0.00 0.00 0.00 3.24
92 93 1.749634 GACGCTTCCTTGCCTAGTCTA 59.250 52.381 0.00 0.00 0.00 2.59
93 94 2.165845 GACGCTTCCTTGCCTAGTCTAA 59.834 50.000 0.00 0.00 0.00 2.10
94 95 2.766828 ACGCTTCCTTGCCTAGTCTAAT 59.233 45.455 0.00 0.00 0.00 1.73
95 96 3.197983 ACGCTTCCTTGCCTAGTCTAATT 59.802 43.478 0.00 0.00 0.00 1.40
96 97 4.404715 ACGCTTCCTTGCCTAGTCTAATTA 59.595 41.667 0.00 0.00 0.00 1.40
97 98 4.745620 CGCTTCCTTGCCTAGTCTAATTAC 59.254 45.833 0.00 0.00 0.00 1.89
98 99 5.671493 GCTTCCTTGCCTAGTCTAATTACA 58.329 41.667 0.00 0.00 0.00 2.41
99 100 6.292150 GCTTCCTTGCCTAGTCTAATTACAT 58.708 40.000 0.00 0.00 0.00 2.29
100 101 6.768381 GCTTCCTTGCCTAGTCTAATTACATT 59.232 38.462 0.00 0.00 0.00 2.71
101 102 7.254932 GCTTCCTTGCCTAGTCTAATTACATTG 60.255 40.741 0.00 0.00 0.00 2.82
102 103 6.591935 TCCTTGCCTAGTCTAATTACATTGG 58.408 40.000 0.00 0.00 0.00 3.16
103 104 6.385759 TCCTTGCCTAGTCTAATTACATTGGA 59.614 38.462 0.00 0.00 0.00 3.53
104 105 7.072454 TCCTTGCCTAGTCTAATTACATTGGAT 59.928 37.037 0.00 0.00 32.27 3.41
105 106 7.173907 CCTTGCCTAGTCTAATTACATTGGATG 59.826 40.741 0.00 0.00 32.27 3.51
106 107 6.533730 TGCCTAGTCTAATTACATTGGATGG 58.466 40.000 0.00 0.00 32.27 3.51
107 108 5.940470 GCCTAGTCTAATTACATTGGATGGG 59.060 44.000 0.00 0.00 32.27 4.00
108 109 5.940470 CCTAGTCTAATTACATTGGATGGGC 59.060 44.000 0.00 0.00 32.27 5.36
109 110 5.653255 AGTCTAATTACATTGGATGGGCT 57.347 39.130 0.00 0.00 32.27 5.19
110 111 5.380043 AGTCTAATTACATTGGATGGGCTG 58.620 41.667 0.00 0.00 32.27 4.85
111 112 5.103940 AGTCTAATTACATTGGATGGGCTGT 60.104 40.000 0.00 0.00 32.27 4.40
112 113 6.101150 AGTCTAATTACATTGGATGGGCTGTA 59.899 38.462 0.00 0.00 32.27 2.74
113 114 6.942576 GTCTAATTACATTGGATGGGCTGTAT 59.057 38.462 0.00 0.00 32.27 2.29
114 115 8.100791 GTCTAATTACATTGGATGGGCTGTATA 58.899 37.037 0.00 0.00 32.27 1.47
115 116 8.835734 TCTAATTACATTGGATGGGCTGTATAT 58.164 33.333 0.00 0.00 33.60 0.86
116 117 7.707624 AATTACATTGGATGGGCTGTATATG 57.292 36.000 0.00 0.00 33.60 1.78
117 118 4.729552 ACATTGGATGGGCTGTATATGT 57.270 40.909 0.00 0.00 33.60 2.29
118 119 4.401022 ACATTGGATGGGCTGTATATGTG 58.599 43.478 0.00 0.00 33.60 3.21
119 120 4.104579 ACATTGGATGGGCTGTATATGTGA 59.895 41.667 0.00 0.00 33.60 3.58
120 121 3.769739 TGGATGGGCTGTATATGTGAC 57.230 47.619 0.00 0.00 0.00 3.67
121 122 3.044894 TGGATGGGCTGTATATGTGACA 58.955 45.455 0.00 0.00 0.00 3.58
122 123 3.457749 TGGATGGGCTGTATATGTGACAA 59.542 43.478 0.00 0.00 0.00 3.18
123 124 3.815401 GGATGGGCTGTATATGTGACAAC 59.185 47.826 0.00 0.00 0.00 3.32
124 125 2.899976 TGGGCTGTATATGTGACAACG 58.100 47.619 0.00 0.00 0.00 4.10
125 126 2.235155 TGGGCTGTATATGTGACAACGT 59.765 45.455 0.00 0.00 0.00 3.99
126 127 2.607635 GGGCTGTATATGTGACAACGTG 59.392 50.000 0.00 0.00 0.00 4.49
127 128 3.517602 GGCTGTATATGTGACAACGTGA 58.482 45.455 0.00 0.00 0.00 4.35
128 129 4.119862 GGCTGTATATGTGACAACGTGAT 58.880 43.478 0.00 0.00 0.00 3.06
129 130 5.286438 GGCTGTATATGTGACAACGTGATA 58.714 41.667 0.00 0.00 0.00 2.15
130 131 5.402568 GGCTGTATATGTGACAACGTGATAG 59.597 44.000 0.00 0.00 0.00 2.08
131 132 5.977725 GCTGTATATGTGACAACGTGATAGT 59.022 40.000 0.00 0.00 0.00 2.12
132 133 6.475727 GCTGTATATGTGACAACGTGATAGTT 59.524 38.462 0.00 0.00 34.15 2.24
133 134 7.306051 GCTGTATATGTGACAACGTGATAGTTC 60.306 40.741 0.00 0.00 30.96 3.01
134 135 7.540299 TGTATATGTGACAACGTGATAGTTCA 58.460 34.615 0.00 0.00 30.96 3.18
135 136 8.030106 TGTATATGTGACAACGTGATAGTTCAA 58.970 33.333 0.00 0.00 32.48 2.69
136 137 9.031360 GTATATGTGACAACGTGATAGTTCAAT 57.969 33.333 0.00 0.00 32.48 2.57
138 139 9.764363 ATATGTGACAACGTGATAGTTCAATAT 57.236 29.630 0.00 0.00 32.48 1.28
139 140 7.289587 TGTGACAACGTGATAGTTCAATATG 57.710 36.000 0.00 0.00 32.48 1.78
140 141 6.871492 TGTGACAACGTGATAGTTCAATATGT 59.129 34.615 0.00 0.00 32.48 2.29
141 142 7.386573 TGTGACAACGTGATAGTTCAATATGTT 59.613 33.333 0.00 0.00 32.48 2.71
142 143 7.688167 GTGACAACGTGATAGTTCAATATGTTG 59.312 37.037 0.00 0.00 38.10 3.33
143 144 7.072177 ACAACGTGATAGTTCAATATGTTGG 57.928 36.000 2.06 0.00 37.33 3.77
144 145 6.653320 ACAACGTGATAGTTCAATATGTTGGT 59.347 34.615 2.06 0.00 37.33 3.67
145 146 7.820386 ACAACGTGATAGTTCAATATGTTGGTA 59.180 33.333 2.06 0.00 37.33 3.25
146 147 8.826710 CAACGTGATAGTTCAATATGTTGGTAT 58.173 33.333 2.06 0.00 35.99 2.73
147 148 8.365399 ACGTGATAGTTCAATATGTTGGTATG 57.635 34.615 2.06 0.00 35.99 2.39
148 149 7.985184 ACGTGATAGTTCAATATGTTGGTATGT 59.015 33.333 2.06 0.00 35.99 2.29
149 150 9.471084 CGTGATAGTTCAATATGTTGGTATGTA 57.529 33.333 2.06 0.00 35.99 2.29
154 155 8.263940 AGTTCAATATGTTGGTATGTACACAC 57.736 34.615 0.00 0.00 35.99 3.82
155 156 8.100791 AGTTCAATATGTTGGTATGTACACACT 58.899 33.333 3.95 0.00 35.99 3.55
156 157 9.373603 GTTCAATATGTTGGTATGTACACACTA 57.626 33.333 3.95 0.00 35.99 2.74
157 158 9.945904 TTCAATATGTTGGTATGTACACACTAA 57.054 29.630 3.95 1.02 35.99 2.24
163 164 9.899661 ATGTTGGTATGTACACACTAATATGTT 57.100 29.630 10.97 0.00 0.00 2.71
166 167 9.518906 TTGGTATGTACACACTAATATGTTACG 57.481 33.333 3.95 0.00 0.00 3.18
167 168 8.136800 TGGTATGTACACACTAATATGTTACGG 58.863 37.037 3.95 0.00 0.00 4.02
168 169 8.352201 GGTATGTACACACTAATATGTTACGGA 58.648 37.037 3.95 0.00 0.00 4.69
169 170 9.734620 GTATGTACACACTAATATGTTACGGAA 57.265 33.333 0.00 0.00 0.00 4.30
171 172 9.656040 ATGTACACACTAATATGTTACGGAAAA 57.344 29.630 0.00 0.00 0.00 2.29
172 173 9.486497 TGTACACACTAATATGTTACGGAAAAA 57.514 29.630 0.00 0.00 0.00 1.94
173 174 9.745323 GTACACACTAATATGTTACGGAAAAAC 57.255 33.333 0.00 0.00 0.00 2.43
174 175 7.809665 ACACACTAATATGTTACGGAAAAACC 58.190 34.615 0.00 0.00 0.00 3.27
175 176 7.662669 ACACACTAATATGTTACGGAAAAACCT 59.337 33.333 0.00 0.00 36.31 3.50
176 177 8.508875 CACACTAATATGTTACGGAAAAACCTT 58.491 33.333 0.00 0.00 36.31 3.50
177 178 9.070179 ACACTAATATGTTACGGAAAAACCTTT 57.930 29.630 0.00 0.00 36.31 3.11
185 186 8.223177 TGTTACGGAAAAACCTTTAAATCTCA 57.777 30.769 0.00 0.00 36.31 3.27
186 187 8.347035 TGTTACGGAAAAACCTTTAAATCTCAG 58.653 33.333 0.00 0.00 36.31 3.35
187 188 5.769367 ACGGAAAAACCTTTAAATCTCAGC 58.231 37.500 0.00 0.00 36.31 4.26
188 189 5.161358 CGGAAAAACCTTTAAATCTCAGCC 58.839 41.667 0.00 0.00 36.31 4.85
189 190 5.278758 CGGAAAAACCTTTAAATCTCAGCCA 60.279 40.000 0.00 0.00 36.31 4.75
190 191 6.572314 CGGAAAAACCTTTAAATCTCAGCCAT 60.572 38.462 0.00 0.00 36.31 4.40
191 192 7.161404 GGAAAAACCTTTAAATCTCAGCCATT 58.839 34.615 0.00 0.00 35.41 3.16
192 193 8.311109 GGAAAAACCTTTAAATCTCAGCCATTA 58.689 33.333 0.00 0.00 35.41 1.90
193 194 9.875691 GAAAAACCTTTAAATCTCAGCCATTAT 57.124 29.630 0.00 0.00 0.00 1.28
204 205 9.903682 AAATCTCAGCCATTATTATTTTGATCG 57.096 29.630 0.00 0.00 0.00 3.69
205 206 7.439157 TCTCAGCCATTATTATTTTGATCGG 57.561 36.000 0.00 0.00 0.00 4.18
206 207 7.223584 TCTCAGCCATTATTATTTTGATCGGA 58.776 34.615 0.00 0.00 0.00 4.55
207 208 7.173218 TCTCAGCCATTATTATTTTGATCGGAC 59.827 37.037 0.00 0.00 0.00 4.79
208 209 6.073276 TCAGCCATTATTATTTTGATCGGACG 60.073 38.462 0.00 0.00 0.00 4.79
209 210 5.181245 AGCCATTATTATTTTGATCGGACGG 59.819 40.000 0.00 0.00 0.00 4.79
210 211 5.048991 GCCATTATTATTTTGATCGGACGGT 60.049 40.000 0.00 0.00 0.00 4.83
211 212 6.370593 CCATTATTATTTTGATCGGACGGTG 58.629 40.000 0.00 0.00 0.00 4.94
212 213 3.963383 ATTATTTTGATCGGACGGTGC 57.037 42.857 0.00 0.00 0.00 5.01
213 214 2.388310 TATTTTGATCGGACGGTGCA 57.612 45.000 0.00 0.00 0.00 4.57
214 215 1.529226 ATTTTGATCGGACGGTGCAA 58.471 45.000 0.00 0.00 0.00 4.08
215 216 1.309950 TTTTGATCGGACGGTGCAAA 58.690 45.000 0.00 0.00 0.00 3.68
216 217 1.529226 TTTGATCGGACGGTGCAAAT 58.471 45.000 0.00 0.00 0.00 2.32
217 218 2.388310 TTGATCGGACGGTGCAAATA 57.612 45.000 0.00 0.00 0.00 1.40
218 219 2.388310 TGATCGGACGGTGCAAATAA 57.612 45.000 0.00 0.00 0.00 1.40
219 220 2.912771 TGATCGGACGGTGCAAATAAT 58.087 42.857 0.00 0.00 0.00 1.28
220 221 4.061357 TGATCGGACGGTGCAAATAATA 57.939 40.909 0.00 0.00 0.00 0.98
221 222 4.637276 TGATCGGACGGTGCAAATAATAT 58.363 39.130 0.00 0.00 0.00 1.28
222 223 5.060506 TGATCGGACGGTGCAAATAATATT 58.939 37.500 0.00 0.00 0.00 1.28
223 224 6.224584 TGATCGGACGGTGCAAATAATATTA 58.775 36.000 0.00 0.00 0.00 0.98
224 225 6.706716 TGATCGGACGGTGCAAATAATATTAA 59.293 34.615 0.00 0.00 0.00 1.40
225 226 6.289745 TCGGACGGTGCAAATAATATTAAC 57.710 37.500 0.00 0.00 0.00 2.01
226 227 5.816258 TCGGACGGTGCAAATAATATTAACA 59.184 36.000 0.00 0.00 0.00 2.41
227 228 6.483974 TCGGACGGTGCAAATAATATTAACAT 59.516 34.615 0.00 0.00 0.00 2.71
228 229 7.656542 TCGGACGGTGCAAATAATATTAACATA 59.343 33.333 0.00 0.00 0.00 2.29
229 230 8.447833 CGGACGGTGCAAATAATATTAACATAT 58.552 33.333 0.00 0.00 0.00 1.78
873 874 1.406205 GCGCCTAAGCTCTCCTTCTTT 60.406 52.381 0.00 0.00 36.60 2.52
884 885 4.162131 GCTCTCCTTCTTTCTTCTCCTCAT 59.838 45.833 0.00 0.00 0.00 2.90
886 887 5.588845 TCTCCTTCTTTCTTCTCCTCATCT 58.411 41.667 0.00 0.00 0.00 2.90
894 895 6.666980 TCTTTCTTCTCCTCATCTTCTCATCA 59.333 38.462 0.00 0.00 0.00 3.07
1016 1017 3.585990 CATGGATTCCCGTGCGCC 61.586 66.667 4.18 0.00 42.08 6.53
1041 1042 1.762460 CGGCCCTAGATCCCACACT 60.762 63.158 0.00 0.00 0.00 3.55
1152 1156 1.708993 GCTGGATCCATGGTGGGCTA 61.709 60.000 16.63 0.00 38.32 3.93
1397 1411 7.728148 TGTTGTTGATTGTCTAGGTTGTAGTA 58.272 34.615 0.00 0.00 0.00 1.82
1512 1532 9.500785 AGTTGAAAGTTTGAATGAAAAGGAAAA 57.499 25.926 0.00 0.00 0.00 2.29
2196 2224 5.925969 GCACTACAAATGCATAGTTTTGGTT 59.074 36.000 13.50 0.00 42.88 3.67
2287 2316 1.175983 TGGGAAATTGTGACGCACCC 61.176 55.000 5.63 5.63 32.73 4.61
2328 2357 4.954118 AGTGTGCCCTCCCGTCCA 62.954 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.780275 AGGAAGAGTTAGGTTCACGTAC 57.220 45.455 0.00 0.00 0.00 3.67
1 2 4.702131 GGTAGGAAGAGTTAGGTTCACGTA 59.298 45.833 0.00 0.00 0.00 3.57
2 3 3.509184 GGTAGGAAGAGTTAGGTTCACGT 59.491 47.826 0.00 0.00 0.00 4.49
3 4 3.762823 AGGTAGGAAGAGTTAGGTTCACG 59.237 47.826 0.00 0.00 0.00 4.35
4 5 5.741962 AAGGTAGGAAGAGTTAGGTTCAC 57.258 43.478 0.00 0.00 0.00 3.18
5 6 6.758806 AAAAGGTAGGAAGAGTTAGGTTCA 57.241 37.500 0.00 0.00 0.00 3.18
36 37 1.079127 TAGGCAAGGAAGCGTCAGC 60.079 57.895 1.14 2.32 45.58 4.26
37 38 0.247736 ACTAGGCAAGGAAGCGTCAG 59.752 55.000 1.14 0.00 34.11 3.51
38 39 0.246635 GACTAGGCAAGGAAGCGTCA 59.753 55.000 1.14 0.00 34.11 4.35
39 40 0.802607 CGACTAGGCAAGGAAGCGTC 60.803 60.000 0.00 0.00 34.11 5.19
40 41 1.215647 CGACTAGGCAAGGAAGCGT 59.784 57.895 0.00 0.00 36.48 5.07
41 42 0.389948 AACGACTAGGCAAGGAAGCG 60.390 55.000 0.00 0.00 34.64 4.68
42 43 1.809684 AAACGACTAGGCAAGGAAGC 58.190 50.000 0.00 0.00 0.00 3.86
69 70 1.079127 TAGGCAAGGAAGCGTCAGC 60.079 57.895 1.14 2.32 45.58 4.26
70 71 0.247736 ACTAGGCAAGGAAGCGTCAG 59.752 55.000 1.14 0.00 34.11 3.51
71 72 0.246635 GACTAGGCAAGGAAGCGTCA 59.753 55.000 1.14 0.00 34.11 4.35
72 73 0.533032 AGACTAGGCAAGGAAGCGTC 59.467 55.000 0.00 0.00 34.11 5.19
73 74 1.848652 TAGACTAGGCAAGGAAGCGT 58.151 50.000 0.00 0.00 36.48 5.07
74 75 2.961526 TTAGACTAGGCAAGGAAGCG 57.038 50.000 0.00 0.00 34.64 4.68
75 76 5.671493 TGTAATTAGACTAGGCAAGGAAGC 58.329 41.667 0.00 0.00 0.00 3.86
76 77 7.227512 CCAATGTAATTAGACTAGGCAAGGAAG 59.772 40.741 0.00 0.00 32.46 3.46
77 78 7.054124 CCAATGTAATTAGACTAGGCAAGGAA 58.946 38.462 0.00 0.00 32.46 3.36
78 79 6.385759 TCCAATGTAATTAGACTAGGCAAGGA 59.614 38.462 0.00 0.00 32.46 3.36
79 80 6.591935 TCCAATGTAATTAGACTAGGCAAGG 58.408 40.000 0.00 0.00 32.46 3.61
80 81 7.173907 CCATCCAATGTAATTAGACTAGGCAAG 59.826 40.741 0.00 0.00 32.46 4.01
81 82 6.998074 CCATCCAATGTAATTAGACTAGGCAA 59.002 38.462 0.00 0.00 32.46 4.52
82 83 6.465751 CCCATCCAATGTAATTAGACTAGGCA 60.466 42.308 0.00 0.00 32.46 4.75
83 84 5.940470 CCCATCCAATGTAATTAGACTAGGC 59.060 44.000 0.00 0.00 32.46 3.93
84 85 5.940470 GCCCATCCAATGTAATTAGACTAGG 59.060 44.000 0.00 0.00 32.46 3.02
85 86 6.652481 CAGCCCATCCAATGTAATTAGACTAG 59.348 42.308 0.00 0.00 32.46 2.57
86 87 6.101150 ACAGCCCATCCAATGTAATTAGACTA 59.899 38.462 0.00 0.00 32.46 2.59
87 88 5.103940 ACAGCCCATCCAATGTAATTAGACT 60.104 40.000 0.00 0.00 32.46 3.24
88 89 5.133221 ACAGCCCATCCAATGTAATTAGAC 58.867 41.667 0.00 0.00 32.46 2.59
89 90 5.387113 ACAGCCCATCCAATGTAATTAGA 57.613 39.130 0.00 0.00 32.46 2.10
90 91 8.896744 CATATACAGCCCATCCAATGTAATTAG 58.103 37.037 0.00 0.00 32.46 1.73
91 92 8.390143 ACATATACAGCCCATCCAATGTAATTA 58.610 33.333 0.00 0.00 32.46 1.40
92 93 7.177216 CACATATACAGCCCATCCAATGTAATT 59.823 37.037 0.00 0.00 36.63 1.40
93 94 6.660521 CACATATACAGCCCATCCAATGTAAT 59.339 38.462 0.00 0.00 32.31 1.89
94 95 6.003326 CACATATACAGCCCATCCAATGTAA 58.997 40.000 0.00 0.00 32.31 2.41
95 96 5.309282 TCACATATACAGCCCATCCAATGTA 59.691 40.000 0.00 0.00 33.04 2.29
96 97 4.104579 TCACATATACAGCCCATCCAATGT 59.895 41.667 0.00 0.00 0.00 2.71
97 98 4.456911 GTCACATATACAGCCCATCCAATG 59.543 45.833 0.00 0.00 0.00 2.82
98 99 4.104579 TGTCACATATACAGCCCATCCAAT 59.895 41.667 0.00 0.00 0.00 3.16
99 100 3.457749 TGTCACATATACAGCCCATCCAA 59.542 43.478 0.00 0.00 0.00 3.53
100 101 3.044894 TGTCACATATACAGCCCATCCA 58.955 45.455 0.00 0.00 0.00 3.41
101 102 3.769739 TGTCACATATACAGCCCATCC 57.230 47.619 0.00 0.00 0.00 3.51
102 103 3.494626 CGTTGTCACATATACAGCCCATC 59.505 47.826 0.00 0.00 0.00 3.51
103 104 3.118408 ACGTTGTCACATATACAGCCCAT 60.118 43.478 0.00 0.00 0.00 4.00
104 105 2.235155 ACGTTGTCACATATACAGCCCA 59.765 45.455 0.00 0.00 0.00 5.36
105 106 2.607635 CACGTTGTCACATATACAGCCC 59.392 50.000 0.00 0.00 0.00 5.19
106 107 3.517602 TCACGTTGTCACATATACAGCC 58.482 45.455 0.00 0.00 0.00 4.85
107 108 5.977725 ACTATCACGTTGTCACATATACAGC 59.022 40.000 0.00 0.00 0.00 4.40
108 109 7.700656 TGAACTATCACGTTGTCACATATACAG 59.299 37.037 0.00 0.00 0.00 2.74
109 110 7.540299 TGAACTATCACGTTGTCACATATACA 58.460 34.615 0.00 0.00 0.00 2.29
110 111 7.980742 TGAACTATCACGTTGTCACATATAC 57.019 36.000 0.00 0.00 0.00 1.47
112 113 9.764363 ATATTGAACTATCACGTTGTCACATAT 57.236 29.630 0.00 0.00 34.61 1.78
113 114 9.030301 CATATTGAACTATCACGTTGTCACATA 57.970 33.333 0.00 0.00 34.61 2.29
114 115 7.549134 ACATATTGAACTATCACGTTGTCACAT 59.451 33.333 0.00 0.00 34.61 3.21
115 116 6.871492 ACATATTGAACTATCACGTTGTCACA 59.129 34.615 0.00 0.00 34.61 3.58
116 117 7.290857 ACATATTGAACTATCACGTTGTCAC 57.709 36.000 0.00 0.00 34.61 3.67
117 118 7.148490 CCAACATATTGAACTATCACGTTGTCA 60.148 37.037 0.00 0.00 38.15 3.58
118 119 7.148474 ACCAACATATTGAACTATCACGTTGTC 60.148 37.037 0.00 0.00 38.15 3.18
119 120 6.653320 ACCAACATATTGAACTATCACGTTGT 59.347 34.615 0.00 0.00 38.15 3.32
120 121 7.072177 ACCAACATATTGAACTATCACGTTG 57.928 36.000 0.00 0.00 38.15 4.10
121 122 8.826710 CATACCAACATATTGAACTATCACGTT 58.173 33.333 0.00 0.00 38.15 3.99
122 123 7.985184 ACATACCAACATATTGAACTATCACGT 59.015 33.333 0.00 0.00 38.15 4.49
123 124 8.365399 ACATACCAACATATTGAACTATCACG 57.635 34.615 0.00 0.00 38.15 4.35
128 129 9.373603 GTGTGTACATACCAACATATTGAACTA 57.626 33.333 11.42 0.00 38.15 2.24
129 130 8.100791 AGTGTGTACATACCAACATATTGAACT 58.899 33.333 18.02 0.00 38.15 3.01
130 131 8.263940 AGTGTGTACATACCAACATATTGAAC 57.736 34.615 18.02 0.00 38.15 3.18
131 132 9.945904 TTAGTGTGTACATACCAACATATTGAA 57.054 29.630 18.02 0.00 38.15 2.69
137 138 9.899661 AACATATTAGTGTGTACATACCAACAT 57.100 29.630 18.02 4.14 31.49 2.71
140 141 9.518906 CGTAACATATTAGTGTGTACATACCAA 57.481 33.333 18.02 12.08 31.49 3.67
141 142 8.136800 CCGTAACATATTAGTGTGTACATACCA 58.863 37.037 18.02 2.83 31.49 3.25
142 143 8.352201 TCCGTAACATATTAGTGTGTACATACC 58.648 37.037 18.02 2.15 31.49 2.73
143 144 9.734620 TTCCGTAACATATTAGTGTGTACATAC 57.265 33.333 14.37 14.37 31.49 2.39
145 146 9.656040 TTTTCCGTAACATATTAGTGTGTACAT 57.344 29.630 0.00 0.00 31.49 2.29
146 147 9.486497 TTTTTCCGTAACATATTAGTGTGTACA 57.514 29.630 0.00 0.00 31.49 2.90
147 148 9.745323 GTTTTTCCGTAACATATTAGTGTGTAC 57.255 33.333 0.00 0.00 31.49 2.90
148 149 8.934825 GGTTTTTCCGTAACATATTAGTGTGTA 58.065 33.333 0.00 0.00 31.49 2.90
149 150 7.662669 AGGTTTTTCCGTAACATATTAGTGTGT 59.337 33.333 0.00 0.00 41.99 3.72
150 151 8.036273 AGGTTTTTCCGTAACATATTAGTGTG 57.964 34.615 0.00 0.00 41.99 3.82
151 152 8.625786 AAGGTTTTTCCGTAACATATTAGTGT 57.374 30.769 0.00 0.00 41.99 3.55
159 160 8.852135 TGAGATTTAAAGGTTTTTCCGTAACAT 58.148 29.630 0.00 0.00 41.99 2.71
160 161 8.223177 TGAGATTTAAAGGTTTTTCCGTAACA 57.777 30.769 0.00 0.00 41.99 2.41
161 162 7.325338 GCTGAGATTTAAAGGTTTTTCCGTAAC 59.675 37.037 0.00 0.00 41.99 2.50
162 163 7.364970 GCTGAGATTTAAAGGTTTTTCCGTAA 58.635 34.615 0.00 0.00 41.99 3.18
163 164 6.072342 GGCTGAGATTTAAAGGTTTTTCCGTA 60.072 38.462 0.00 0.00 41.99 4.02
164 165 5.278808 GGCTGAGATTTAAAGGTTTTTCCGT 60.279 40.000 0.00 0.00 41.99 4.69
165 166 5.161358 GGCTGAGATTTAAAGGTTTTTCCG 58.839 41.667 0.00 0.00 41.99 4.30
166 167 6.096673 TGGCTGAGATTTAAAGGTTTTTCC 57.903 37.500 0.00 0.00 0.00 3.13
167 168 9.875691 ATAATGGCTGAGATTTAAAGGTTTTTC 57.124 29.630 0.00 0.00 0.00 2.29
178 179 9.903682 CGATCAAAATAATAATGGCTGAGATTT 57.096 29.630 0.00 0.00 0.00 2.17
179 180 8.517878 CCGATCAAAATAATAATGGCTGAGATT 58.482 33.333 0.00 0.00 0.00 2.40
180 181 7.884877 TCCGATCAAAATAATAATGGCTGAGAT 59.115 33.333 0.00 0.00 0.00 2.75
181 182 7.173218 GTCCGATCAAAATAATAATGGCTGAGA 59.827 37.037 0.00 0.00 0.00 3.27
182 183 7.301054 GTCCGATCAAAATAATAATGGCTGAG 58.699 38.462 0.00 0.00 0.00 3.35
183 184 6.073276 CGTCCGATCAAAATAATAATGGCTGA 60.073 38.462 0.00 0.00 0.00 4.26
184 185 6.079763 CGTCCGATCAAAATAATAATGGCTG 58.920 40.000 0.00 0.00 0.00 4.85
185 186 5.181245 CCGTCCGATCAAAATAATAATGGCT 59.819 40.000 0.00 0.00 0.00 4.75
186 187 5.048991 ACCGTCCGATCAAAATAATAATGGC 60.049 40.000 0.00 0.00 0.00 4.40
187 188 6.370593 CACCGTCCGATCAAAATAATAATGG 58.629 40.000 0.00 0.00 0.00 3.16
188 189 5.851177 GCACCGTCCGATCAAAATAATAATG 59.149 40.000 0.00 0.00 0.00 1.90
189 190 5.529430 TGCACCGTCCGATCAAAATAATAAT 59.471 36.000 0.00 0.00 0.00 1.28
190 191 4.876679 TGCACCGTCCGATCAAAATAATAA 59.123 37.500 0.00 0.00 0.00 1.40
191 192 4.443621 TGCACCGTCCGATCAAAATAATA 58.556 39.130 0.00 0.00 0.00 0.98
192 193 3.275143 TGCACCGTCCGATCAAAATAAT 58.725 40.909 0.00 0.00 0.00 1.28
193 194 2.701107 TGCACCGTCCGATCAAAATAA 58.299 42.857 0.00 0.00 0.00 1.40
194 195 2.388310 TGCACCGTCCGATCAAAATA 57.612 45.000 0.00 0.00 0.00 1.40
195 196 1.529226 TTGCACCGTCCGATCAAAAT 58.471 45.000 0.00 0.00 0.00 1.82
196 197 1.309950 TTTGCACCGTCCGATCAAAA 58.690 45.000 0.00 0.00 0.00 2.44
197 198 1.529226 ATTTGCACCGTCCGATCAAA 58.471 45.000 0.00 0.00 0.00 2.69
198 199 2.388310 TATTTGCACCGTCCGATCAA 57.612 45.000 0.00 0.00 0.00 2.57
199 200 2.388310 TTATTTGCACCGTCCGATCA 57.612 45.000 0.00 0.00 0.00 2.92
200 201 5.607119 AATATTATTTGCACCGTCCGATC 57.393 39.130 0.00 0.00 0.00 3.69
201 202 6.483974 TGTTAATATTATTTGCACCGTCCGAT 59.516 34.615 0.00 0.00 0.00 4.18
202 203 5.816258 TGTTAATATTATTTGCACCGTCCGA 59.184 36.000 0.00 0.00 0.00 4.55
203 204 6.050454 TGTTAATATTATTTGCACCGTCCG 57.950 37.500 0.00 0.00 0.00 4.79
235 236 9.993454 CTATATAGAGCCGGCCGTATATATATA 57.007 37.037 28.83 25.18 0.00 0.86
236 237 8.712103 TCTATATAGAGCCGGCCGTATATATAT 58.288 37.037 28.83 25.38 0.00 0.86
237 238 8.082672 TCTATATAGAGCCGGCCGTATATATA 57.917 38.462 28.83 24.67 0.00 0.86
238 239 6.955364 TCTATATAGAGCCGGCCGTATATAT 58.045 40.000 28.83 24.82 0.00 0.86
239 240 6.364568 TCTATATAGAGCCGGCCGTATATA 57.635 41.667 27.80 27.80 0.00 0.86
240 241 5.238624 TCTATATAGAGCCGGCCGTATAT 57.761 43.478 28.31 28.31 0.00 0.86
241 242 4.639334 CTCTATATAGAGCCGGCCGTATA 58.361 47.826 26.15 23.31 42.83 1.47
242 243 3.478509 CTCTATATAGAGCCGGCCGTAT 58.521 50.000 26.15 21.88 42.83 3.06
243 244 2.915349 CTCTATATAGAGCCGGCCGTA 58.085 52.381 26.15 15.89 42.83 4.02
271 272 4.082463 GGTTTTGCAAGTTCGGGAATATCA 60.082 41.667 0.00 0.00 0.00 2.15
873 874 4.341806 GCTGATGAGAAGATGAGGAGAAGA 59.658 45.833 0.00 0.00 0.00 2.87
884 885 0.459759 CTGCTGCGCTGATGAGAAGA 60.460 55.000 19.32 0.00 0.00 2.87
886 887 2.104859 GCTGCTGCGCTGATGAGAA 61.105 57.895 19.32 0.00 0.00 2.87
1016 1017 3.792053 GATCTAGGGCCGTGCGGTG 62.792 68.421 8.57 0.00 37.65 4.94
1030 1031 3.461773 CGGCGGAGTGTGGGATCT 61.462 66.667 0.00 0.00 0.00 2.75
1397 1411 6.208599 TGAACTTCTGTCCAAAACTTTTCTGT 59.791 34.615 0.00 0.00 0.00 3.41
2328 2357 1.522668 TGCGCACAGATAAAAGCAGT 58.477 45.000 5.66 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.