Multiple sequence alignment - TraesCS5D01G440300

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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 TraesCS5D01G440300 chr5D 100.000 2591 0 0 1 2591 493521564 493524154 0.000000e+00 4785
1 TraesCS5D01G440300 chr5D 78.086 972 136 42 659 1593 493777198 493778129 6.310000e-151 544
2 TraesCS5D01G440300 chr5D 85.041 488 71 2 1107 1593 493810589 493811075 1.790000e-136 496
3 TraesCS5D01G440300 chr5D 88.476 269 24 6 1 263 537327540 537327273 4.160000e-83 318
4 TraesCS5D01G440300 chr5D 85.047 107 11 3 1808 1914 416418431 416418532 1.270000e-18 104
5 TraesCS5D01G440300 chr5A 92.880 1573 81 11 272 1842 616648005 616649548 0.000000e+00 2255
6 TraesCS5D01G440300 chr5A 94.518 529 26 3 2065 2591 616654804 616655331 0.000000e+00 813
7 TraesCS5D01G440300 chr5A 90.000 270 23 4 1 266 632197181 632197450 1.910000e-91 346
8 TraesCS5D01G440300 chr5A 90.204 245 20 3 1825 2065 616649566 616649810 1.500000e-82 316
9 TraesCS5D01G440300 chr5B 90.922 1454 76 18 467 1908 609258671 609260080 0.000000e+00 1903
10 TraesCS5D01G440300 chr5B 87.621 517 54 8 1930 2438 609260205 609260719 2.220000e-165 592
11 TraesCS5D01G440300 chr5B 79.627 805 111 29 830 1593 609430087 609430879 1.770000e-146 529
12 TraesCS5D01G440300 chr5B 77.732 979 139 35 659 1593 609419849 609420792 6.350000e-146 527
13 TraesCS5D01G440300 chr5B 79.455 808 107 28 830 1593 609412429 609413221 3.820000e-143 518
14 TraesCS5D01G440300 chr5B 93.564 202 13 0 268 469 609258236 609258437 4.190000e-78 302
15 TraesCS5D01G440300 chr7B 82.677 635 90 13 978 1593 584186052 584185419 1.750000e-151 545
16 TraesCS5D01G440300 chr7A 81.295 695 102 12 917 1593 622742279 622741595 2.930000e-149 538
17 TraesCS5D01G440300 chr7A 89.630 270 22 5 1 266 223265839 223266106 3.190000e-89 339
18 TraesCS5D01G440300 chr2D 91.852 270 17 4 1 266 542136662 542136394 3.150000e-99 372
19 TraesCS5D01G440300 chr2D 89.668 271 19 8 1 266 189837098 189837364 1.150000e-88 337
20 TraesCS5D01G440300 chr6D 91.078 269 21 2 1 266 102989527 102989259 6.820000e-96 361
21 TraesCS5D01G440300 chr6D 82.394 142 16 6 1794 1934 303060005 303059872 5.860000e-22 115
22 TraesCS5D01G440300 chr4A 90.775 271 21 4 1 267 377591442 377591172 2.450000e-95 359
23 TraesCS5D01G440300 chr4A 89.362 94 8 2 1841 1934 55964872 55964781 1.630000e-22 117
24 TraesCS5D01G440300 chr3D 90.741 270 20 4 1 266 582108928 582108660 3.170000e-94 355
25 TraesCS5D01G440300 chr7D 89.455 275 21 7 1 269 605183429 605183701 8.880000e-90 340
26 TraesCS5D01G440300 chr2A 82.979 141 13 8 1794 1934 568285919 568285790 1.630000e-22 117
27 TraesCS5D01G440300 chr6A 83.471 121 14 4 1794 1914 498584380 498584494 9.800000e-20 108
28 TraesCS5D01G440300 chr6B 84.685 111 11 5 1803 1913 568575316 568575420 3.530000e-19 106
29 TraesCS5D01G440300 chr4D 84.762 105 9 5 1810 1913 338024505 338024407 5.900000e-17 99


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 TraesCS5D01G440300 chr5D 493521564 493524154 2590 False 4785.000000 4785 100.000000 1 2591 1 chr5D.!!$F2 2590
1 TraesCS5D01G440300 chr5D 493777198 493778129 931 False 544.000000 544 78.086000 659 1593 1 chr5D.!!$F3 934
2 TraesCS5D01G440300 chr5A 616648005 616649810 1805 False 1285.500000 2255 91.542000 272 2065 2 chr5A.!!$F3 1793
3 TraesCS5D01G440300 chr5A 616654804 616655331 527 False 813.000000 813 94.518000 2065 2591 1 chr5A.!!$F1 526
4 TraesCS5D01G440300 chr5B 609258236 609260719 2483 False 932.333333 1903 90.702333 268 2438 3 chr5B.!!$F4 2170
5 TraesCS5D01G440300 chr5B 609430087 609430879 792 False 529.000000 529 79.627000 830 1593 1 chr5B.!!$F3 763
6 TraesCS5D01G440300 chr5B 609419849 609420792 943 False 527.000000 527 77.732000 659 1593 1 chr5B.!!$F2 934
7 TraesCS5D01G440300 chr5B 609412429 609413221 792 False 518.000000 518 79.455000 830 1593 1 chr5B.!!$F1 763
8 TraesCS5D01G440300 chr7B 584185419 584186052 633 True 545.000000 545 82.677000 978 1593 1 chr7B.!!$R1 615
9 TraesCS5D01G440300 chr7A 622741595 622742279 684 True 538.000000 538 81.295000 917 1593 1 chr7A.!!$R1 676

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
294 295 0.24912 TGGTGACGGCAGATTAGTGG 59.751 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1938 0.60813 CCCTACGGCAGCTGCATATA 59.392 55.0 37.63 24.26 44.36 0.86 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
55 56 9.191995 GTAAATAGTATGCAATTTATGTTGGGC 57.808 33.333 4.96 0.00 31.99 5.36
56 57 7.601705 AATAGTATGCAATTTATGTTGGGCT 57.398 32.000 0.00 0.00 0.00 5.19
57 58 5.937975 AGTATGCAATTTATGTTGGGCTT 57.062 34.783 0.00 0.00 0.00 4.35
58 59 6.298441 AGTATGCAATTTATGTTGGGCTTT 57.702 33.333 0.00 0.00 0.00 3.51
59 60 7.416964 AGTATGCAATTTATGTTGGGCTTTA 57.583 32.000 0.00 0.00 0.00 1.85
60 61 7.491682 AGTATGCAATTTATGTTGGGCTTTAG 58.508 34.615 0.00 0.00 0.00 1.85
61 62 5.991933 TGCAATTTATGTTGGGCTTTAGA 57.008 34.783 0.00 0.00 0.00 2.10
62 63 6.543430 TGCAATTTATGTTGGGCTTTAGAT 57.457 33.333 0.00 0.00 0.00 1.98
63 64 6.945218 TGCAATTTATGTTGGGCTTTAGATT 58.055 32.000 0.00 0.00 0.00 2.40
64 65 8.072321 TGCAATTTATGTTGGGCTTTAGATTA 57.928 30.769 0.00 0.00 0.00 1.75
65 66 8.196771 TGCAATTTATGTTGGGCTTTAGATTAG 58.803 33.333 0.00 0.00 0.00 1.73
66 67 7.653311 GCAATTTATGTTGGGCTTTAGATTAGG 59.347 37.037 0.00 0.00 0.00 2.69
67 68 6.709018 TTTATGTTGGGCTTTAGATTAGGC 57.291 37.500 0.00 0.00 37.45 3.93
77 78 7.392494 GGCTTTAGATTAGGCCCATTATTAC 57.608 40.000 0.00 0.00 38.77 1.89
78 79 7.175797 GGCTTTAGATTAGGCCCATTATTACT 58.824 38.462 0.00 0.00 38.77 2.24
79 80 7.121315 GGCTTTAGATTAGGCCCATTATTACTG 59.879 40.741 0.00 0.00 38.77 2.74
80 81 7.883311 GCTTTAGATTAGGCCCATTATTACTGA 59.117 37.037 0.00 0.00 0.00 3.41
81 82 9.965902 CTTTAGATTAGGCCCATTATTACTGAT 57.034 33.333 0.00 0.00 0.00 2.90
82 83 9.739276 TTTAGATTAGGCCCATTATTACTGATG 57.261 33.333 0.00 0.00 0.00 3.07
83 84 7.335127 AGATTAGGCCCATTATTACTGATGT 57.665 36.000 0.00 0.00 0.00 3.06
84 85 7.398024 AGATTAGGCCCATTATTACTGATGTC 58.602 38.462 0.00 0.00 0.00 3.06
85 86 4.373156 AGGCCCATTATTACTGATGTCC 57.627 45.455 0.00 0.00 0.00 4.02
86 87 3.721575 AGGCCCATTATTACTGATGTCCA 59.278 43.478 0.00 0.00 0.00 4.02
87 88 4.354987 AGGCCCATTATTACTGATGTCCAT 59.645 41.667 0.00 0.00 0.00 3.41
88 89 5.079643 GGCCCATTATTACTGATGTCCATT 58.920 41.667 0.00 0.00 0.00 3.16
89 90 5.539955 GGCCCATTATTACTGATGTCCATTT 59.460 40.000 0.00 0.00 0.00 2.32
90 91 6.041979 GGCCCATTATTACTGATGTCCATTTT 59.958 38.462 0.00 0.00 0.00 1.82
91 92 6.925165 GCCCATTATTACTGATGTCCATTTTG 59.075 38.462 0.00 0.00 0.00 2.44
92 93 7.417797 GCCCATTATTACTGATGTCCATTTTGT 60.418 37.037 0.00 0.00 0.00 2.83
93 94 8.137437 CCCATTATTACTGATGTCCATTTTGTC 58.863 37.037 0.00 0.00 0.00 3.18
94 95 8.685427 CCATTATTACTGATGTCCATTTTGTCA 58.315 33.333 0.00 0.00 0.00 3.58
100 101 7.718272 ACTGATGTCCATTTTGTCATTTTTG 57.282 32.000 0.00 0.00 0.00 2.44
101 102 7.274447 ACTGATGTCCATTTTGTCATTTTTGT 58.726 30.769 0.00 0.00 0.00 2.83
102 103 8.420222 ACTGATGTCCATTTTGTCATTTTTGTA 58.580 29.630 0.00 0.00 0.00 2.41
103 104 9.426837 CTGATGTCCATTTTGTCATTTTTGTAT 57.573 29.630 0.00 0.00 0.00 2.29
104 105 9.421806 TGATGTCCATTTTGTCATTTTTGTATC 57.578 29.630 0.00 0.00 0.00 2.24
105 106 9.643693 GATGTCCATTTTGTCATTTTTGTATCT 57.356 29.630 0.00 0.00 0.00 1.98
106 107 9.643693 ATGTCCATTTTGTCATTTTTGTATCTC 57.356 29.630 0.00 0.00 0.00 2.75
107 108 7.807433 TGTCCATTTTGTCATTTTTGTATCTCG 59.193 33.333 0.00 0.00 0.00 4.04
108 109 8.020819 GTCCATTTTGTCATTTTTGTATCTCGA 58.979 33.333 0.00 0.00 0.00 4.04
109 110 8.236586 TCCATTTTGTCATTTTTGTATCTCGAG 58.763 33.333 5.93 5.93 0.00 4.04
110 111 7.008628 CCATTTTGTCATTTTTGTATCTCGAGC 59.991 37.037 7.81 0.00 0.00 5.03
111 112 6.552859 TTTGTCATTTTTGTATCTCGAGCA 57.447 33.333 7.81 0.00 0.00 4.26
112 113 6.552859 TTGTCATTTTTGTATCTCGAGCAA 57.447 33.333 7.81 3.53 0.00 3.91
113 114 6.741992 TGTCATTTTTGTATCTCGAGCAAT 57.258 33.333 7.81 0.00 0.00 3.56
114 115 6.545508 TGTCATTTTTGTATCTCGAGCAATG 58.454 36.000 7.81 7.21 0.00 2.82
115 116 6.149308 TGTCATTTTTGTATCTCGAGCAATGT 59.851 34.615 7.81 0.00 0.00 2.71
116 117 7.023575 GTCATTTTTGTATCTCGAGCAATGTT 58.976 34.615 7.81 0.00 0.00 2.71
117 118 7.538678 GTCATTTTTGTATCTCGAGCAATGTTT 59.461 33.333 7.81 0.00 0.00 2.83
118 119 8.081633 TCATTTTTGTATCTCGAGCAATGTTTT 58.918 29.630 7.81 0.00 0.00 2.43
119 120 9.340695 CATTTTTGTATCTCGAGCAATGTTTTA 57.659 29.630 7.81 0.00 0.00 1.52
120 121 9.906660 ATTTTTGTATCTCGAGCAATGTTTTAA 57.093 25.926 7.81 0.00 0.00 1.52
121 122 9.737427 TTTTTGTATCTCGAGCAATGTTTTAAA 57.263 25.926 7.81 0.75 0.00 1.52
122 123 9.906660 TTTTGTATCTCGAGCAATGTTTTAAAT 57.093 25.926 7.81 0.00 0.00 1.40
123 124 9.906660 TTTGTATCTCGAGCAATGTTTTAAATT 57.093 25.926 7.81 0.00 0.00 1.82
124 125 9.906660 TTGTATCTCGAGCAATGTTTTAAATTT 57.093 25.926 7.81 0.00 0.00 1.82
125 126 9.906660 TGTATCTCGAGCAATGTTTTAAATTTT 57.093 25.926 7.81 0.00 0.00 1.82
128 129 9.643693 ATCTCGAGCAATGTTTTAAATTTTGAT 57.356 25.926 7.81 3.65 0.00 2.57
129 130 9.474920 TCTCGAGCAATGTTTTAAATTTTGATT 57.525 25.926 7.81 0.00 0.00 2.57
131 132 9.861138 TCGAGCAATGTTTTAAATTTTGATTTG 57.139 25.926 0.00 0.00 0.00 2.32
132 133 9.861138 CGAGCAATGTTTTAAATTTTGATTTGA 57.139 25.926 0.00 0.00 0.00 2.69
170 171 3.715618 CATTGATGTTGTGCAATGTGC 57.284 42.857 0.00 0.00 43.81 4.57
171 172 3.322369 CATTGATGTTGTGCAATGTGCT 58.678 40.909 0.00 0.00 45.31 4.40
172 173 2.425578 TGATGTTGTGCAATGTGCTG 57.574 45.000 1.43 0.00 45.31 4.41
173 174 1.000052 TGATGTTGTGCAATGTGCTGG 60.000 47.619 1.43 0.00 45.31 4.85
174 175 1.270274 GATGTTGTGCAATGTGCTGGA 59.730 47.619 1.43 0.00 45.31 3.86
175 176 1.330234 TGTTGTGCAATGTGCTGGAT 58.670 45.000 1.43 0.00 45.31 3.41
176 177 1.687660 TGTTGTGCAATGTGCTGGATT 59.312 42.857 1.43 0.00 45.31 3.01
177 178 2.102757 TGTTGTGCAATGTGCTGGATTT 59.897 40.909 1.43 0.00 45.31 2.17
178 179 3.132925 GTTGTGCAATGTGCTGGATTTT 58.867 40.909 1.43 0.00 45.31 1.82
179 180 3.472283 TGTGCAATGTGCTGGATTTTT 57.528 38.095 1.43 0.00 45.31 1.94
214 215 8.522178 TTTTACCATTTTAAAATGTGCTACCG 57.478 30.769 29.82 19.09 43.24 4.02
215 216 5.968528 ACCATTTTAAAATGTGCTACCGA 57.031 34.783 29.82 0.00 43.24 4.69
216 217 5.949735 ACCATTTTAAAATGTGCTACCGAG 58.050 37.500 29.82 18.00 43.24 4.63
217 218 5.475564 ACCATTTTAAAATGTGCTACCGAGT 59.524 36.000 29.82 18.49 43.24 4.18
218 219 6.015772 ACCATTTTAAAATGTGCTACCGAGTT 60.016 34.615 29.82 8.13 43.24 3.01
219 220 6.866248 CCATTTTAAAATGTGCTACCGAGTTT 59.134 34.615 29.82 0.00 43.24 2.66
220 221 7.148820 CCATTTTAAAATGTGCTACCGAGTTTG 60.149 37.037 29.82 12.53 43.24 2.93
221 222 3.915437 AAAATGTGCTACCGAGTTTGG 57.085 42.857 0.00 0.00 0.00 3.28
222 223 2.851263 AATGTGCTACCGAGTTTGGA 57.149 45.000 0.00 0.00 0.00 3.53
223 224 2.386661 ATGTGCTACCGAGTTTGGAG 57.613 50.000 0.00 0.00 0.00 3.86
224 225 0.320421 TGTGCTACCGAGTTTGGAGC 60.320 55.000 0.00 0.00 34.65 4.70
225 226 0.320421 GTGCTACCGAGTTTGGAGCA 60.320 55.000 0.00 0.00 38.77 4.26
226 227 0.320421 TGCTACCGAGTTTGGAGCAC 60.320 55.000 0.00 0.00 37.30 4.40
227 228 1.019805 GCTACCGAGTTTGGAGCACC 61.020 60.000 0.00 0.00 34.40 5.01
228 229 0.736325 CTACCGAGTTTGGAGCACCG 60.736 60.000 0.00 0.00 39.42 4.94
229 230 2.162338 TACCGAGTTTGGAGCACCGG 62.162 60.000 0.00 0.00 42.30 5.28
230 231 2.742372 CGAGTTTGGAGCACCGGG 60.742 66.667 6.32 0.00 39.42 5.73
231 232 2.747686 GAGTTTGGAGCACCGGGA 59.252 61.111 6.32 0.00 39.42 5.14
232 233 1.072505 GAGTTTGGAGCACCGGGAA 59.927 57.895 6.32 0.00 39.42 3.97
233 234 1.228154 AGTTTGGAGCACCGGGAAC 60.228 57.895 6.32 1.08 39.42 3.62
234 235 1.527380 GTTTGGAGCACCGGGAACA 60.527 57.895 6.32 0.00 39.42 3.18
235 236 1.527380 TTTGGAGCACCGGGAACAC 60.527 57.895 6.32 0.00 39.42 3.32
236 237 2.969300 TTTGGAGCACCGGGAACACC 62.969 60.000 6.32 3.05 39.42 4.16
237 238 4.717313 GGAGCACCGGGAACACCC 62.717 72.222 6.32 0.00 40.27 4.61
238 239 3.637273 GAGCACCGGGAACACCCT 61.637 66.667 6.32 0.00 41.43 4.34
239 240 2.203877 AGCACCGGGAACACCCTA 60.204 61.111 6.32 0.00 41.43 3.53
240 241 2.240162 GAGCACCGGGAACACCCTAG 62.240 65.000 6.32 0.00 41.43 3.02
241 242 2.288025 GCACCGGGAACACCCTAGA 61.288 63.158 6.32 0.00 41.43 2.43
242 243 1.898154 CACCGGGAACACCCTAGAG 59.102 63.158 6.32 0.00 41.43 2.43
243 244 0.613853 CACCGGGAACACCCTAGAGA 60.614 60.000 6.32 0.00 41.43 3.10
244 245 0.338814 ACCGGGAACACCCTAGAGAT 59.661 55.000 6.32 0.00 41.43 2.75
245 246 0.753262 CCGGGAACACCCTAGAGATG 59.247 60.000 0.00 0.00 41.43 2.90
246 247 0.753262 CGGGAACACCCTAGAGATGG 59.247 60.000 0.00 0.00 41.43 3.51
247 248 1.688311 CGGGAACACCCTAGAGATGGA 60.688 57.143 0.00 0.00 41.43 3.41
248 249 2.478292 GGGAACACCCTAGAGATGGAA 58.522 52.381 0.00 0.00 40.49 3.53
249 250 2.436173 GGGAACACCCTAGAGATGGAAG 59.564 54.545 0.00 0.00 40.49 3.46
250 251 3.108376 GGAACACCCTAGAGATGGAAGT 58.892 50.000 0.00 0.00 0.00 3.01
251 252 4.287552 GGAACACCCTAGAGATGGAAGTA 58.712 47.826 0.00 0.00 0.00 2.24
252 253 4.099727 GGAACACCCTAGAGATGGAAGTAC 59.900 50.000 0.00 0.00 0.00 2.73
253 254 4.611564 ACACCCTAGAGATGGAAGTACT 57.388 45.455 0.00 0.00 0.00 2.73
254 255 5.728937 ACACCCTAGAGATGGAAGTACTA 57.271 43.478 0.00 0.00 0.00 1.82
255 256 5.697067 ACACCCTAGAGATGGAAGTACTAG 58.303 45.833 0.00 0.00 0.00 2.57
256 257 5.432390 ACACCCTAGAGATGGAAGTACTAGA 59.568 44.000 0.00 0.00 34.36 2.43
257 258 6.103501 ACACCCTAGAGATGGAAGTACTAGAT 59.896 42.308 0.00 0.00 34.36 1.98
258 259 7.295196 ACACCCTAGAGATGGAAGTACTAGATA 59.705 40.741 0.00 0.00 34.36 1.98
259 260 8.333235 CACCCTAGAGATGGAAGTACTAGATAT 58.667 40.741 0.00 0.00 34.36 1.63
260 261 8.907050 ACCCTAGAGATGGAAGTACTAGATATT 58.093 37.037 0.00 0.00 34.36 1.28
261 262 9.762381 CCCTAGAGATGGAAGTACTAGATATTT 57.238 37.037 0.00 0.00 34.36 1.40
264 265 8.658840 AGAGATGGAAGTACTAGATATTTCCC 57.341 38.462 16.62 8.24 45.12 3.97
265 266 7.676468 AGAGATGGAAGTACTAGATATTTCCCC 59.324 40.741 16.62 11.73 45.12 4.81
266 267 6.437793 AGATGGAAGTACTAGATATTTCCCCG 59.562 42.308 16.62 0.00 45.12 5.73
288 289 2.108514 CGCATTGGTGACGGCAGAT 61.109 57.895 0.00 0.00 0.00 2.90
294 295 0.249120 TGGTGACGGCAGATTAGTGG 59.751 55.000 0.00 0.00 0.00 4.00
500 737 6.874664 TGCACAGTTTTAATCCGTCTGTATAA 59.125 34.615 0.00 0.00 37.27 0.98
609 846 1.819288 ACACCTGATACGGACAGTCTG 59.181 52.381 7.94 7.94 34.04 3.51
673 911 1.335182 GAGTCTCATTCGCTCGGATGA 59.665 52.381 12.16 12.16 0.00 2.92
700 938 0.733150 TGTCTGCACCTCGACTATCG 59.267 55.000 5.54 0.00 42.10 2.92
837 1085 0.696501 ACCGCCCAACTAACCATCTT 59.303 50.000 0.00 0.00 0.00 2.40
884 1132 3.421844 GCTGAGTTAACATCCCCAGTTT 58.578 45.455 8.61 0.00 0.00 2.66
929 1185 4.863491 TGTTCGTCGGGCTCTATATAAAC 58.137 43.478 0.00 0.00 0.00 2.01
1066 1346 2.509336 CACGCCTCCACGTCCATC 60.509 66.667 0.00 0.00 46.34 3.51
1191 1489 3.923864 ACCTGCTGCGTCAACGGA 61.924 61.111 4.54 0.02 40.23 4.69
1229 1527 4.643387 GTGCTCGCCCCCTGTGTT 62.643 66.667 0.00 0.00 0.00 3.32
1239 1537 1.302832 CCCTGTGTTGGCTGAGACC 60.303 63.158 0.00 0.00 0.00 3.85
1268 1566 5.505819 CGATCCTGACTATAAACAGCTTCGA 60.506 44.000 15.25 0.00 38.24 3.71
1404 1702 5.008019 GTGCAACAAGATGATCCGTATCAAT 59.992 40.000 0.00 0.00 40.53 2.57
1609 1907 3.308866 GTGAGCACAAATATGTACGGGAC 59.691 47.826 0.00 0.00 37.82 4.46
1621 1919 0.896940 TACGGGACAGTTCGCTCCTT 60.897 55.000 0.00 0.00 32.43 3.36
1640 1938 7.501844 GCTCCTTAGTCCTCACTTGTTATATT 58.498 38.462 0.00 0.00 33.62 1.28
1641 1939 8.639761 GCTCCTTAGTCCTCACTTGTTATATTA 58.360 37.037 0.00 0.00 33.62 0.98
1725 2023 7.921786 TGCTGCTATTTAAATAAGTCACTGT 57.078 32.000 9.15 0.00 0.00 3.55
1736 2034 9.772973 TTAAATAAGTCACTGTTCACATGTACT 57.227 29.630 0.00 0.00 0.00 2.73
1737 2035 7.891183 AATAAGTCACTGTTCACATGTACTC 57.109 36.000 0.00 0.00 0.00 2.59
1774 2072 6.279513 TCCCAAGTTTATGTATTTGCCTTG 57.720 37.500 0.00 0.00 0.00 3.61
1789 2087 6.865834 TTTGCCTTGTTTGGGTGATATATT 57.134 33.333 0.00 0.00 0.00 1.28
1900 2235 9.371136 CACACTAAAATGTGTCTACATACATCT 57.629 33.333 0.00 0.00 46.90 2.90
2013 2456 5.117584 GGCTAAAAGTTAGTAGAGGGCTTC 58.882 45.833 0.00 0.00 0.00 3.86
2028 2471 2.096496 GGGCTTCGTCTTCATTGACATG 59.904 50.000 0.00 0.00 36.82 3.21
2097 2540 3.572255 ACCGAACCATGCAAAATAGTGTT 59.428 39.130 0.00 0.00 0.00 3.32
2099 2542 4.320861 CCGAACCATGCAAAATAGTGTTCA 60.321 41.667 0.00 0.00 0.00 3.18
2111 2554 8.023128 GCAAAATAGTGTTCAGCTCTTCAAATA 58.977 33.333 0.00 0.00 0.00 1.40
2384 2835 5.346011 GGCAAAAAGAATAAGAAAAGCCTCG 59.654 40.000 0.00 0.00 35.63 4.63
2443 2895 3.243468 TGCACACGTAGTAAACACTAGCA 60.243 43.478 0.00 0.00 41.61 3.49
2452 2904 2.902705 AAACACTAGCACCGAAGACA 57.097 45.000 0.00 0.00 0.00 3.41
2453 2905 3.402628 AAACACTAGCACCGAAGACAT 57.597 42.857 0.00 0.00 0.00 3.06
2462 2914 4.505217 CGAAGACATGCGGCGCAC 62.505 66.667 38.84 24.69 43.04 5.34
2508 2960 5.841957 AGATGTTTTCATATTCTGCACCC 57.158 39.130 0.00 0.00 41.05 4.61
2525 2977 2.123597 CATGCATGGTGGGAGGGG 60.124 66.667 19.40 0.00 0.00 4.79
2576 3028 8.554490 AGAAGCCAGGAATAAGAATAGTTAGA 57.446 34.615 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.191995 GCCCAACATAAATTGCATACTATTTAC 57.808 33.333 3.94 0.00 36.67 2.01
30 31 9.142014 AGCCCAACATAAATTGCATACTATTTA 57.858 29.630 4.26 4.26 37.70 1.40
31 32 8.021898 AGCCCAACATAAATTGCATACTATTT 57.978 30.769 0.00 0.00 35.74 1.40
32 33 7.601705 AGCCCAACATAAATTGCATACTATT 57.398 32.000 0.00 0.00 0.00 1.73
33 34 7.601705 AAGCCCAACATAAATTGCATACTAT 57.398 32.000 0.00 0.00 0.00 2.12
34 35 7.416964 AAAGCCCAACATAAATTGCATACTA 57.583 32.000 0.00 0.00 0.00 1.82
35 36 5.937975 AAGCCCAACATAAATTGCATACT 57.062 34.783 0.00 0.00 0.00 2.12
36 37 7.488322 TCTAAAGCCCAACATAAATTGCATAC 58.512 34.615 0.00 0.00 0.00 2.39
37 38 7.652524 TCTAAAGCCCAACATAAATTGCATA 57.347 32.000 0.00 0.00 0.00 3.14
38 39 6.543430 TCTAAAGCCCAACATAAATTGCAT 57.457 33.333 0.00 0.00 0.00 3.96
39 40 5.991933 TCTAAAGCCCAACATAAATTGCA 57.008 34.783 0.00 0.00 0.00 4.08
40 41 7.653311 CCTAATCTAAAGCCCAACATAAATTGC 59.347 37.037 0.00 0.00 0.00 3.56
41 42 7.653311 GCCTAATCTAAAGCCCAACATAAATTG 59.347 37.037 0.00 0.00 0.00 2.32
42 43 7.202001 GGCCTAATCTAAAGCCCAACATAAATT 60.202 37.037 0.00 0.00 39.60 1.82
43 44 6.267699 GGCCTAATCTAAAGCCCAACATAAAT 59.732 38.462 0.00 0.00 39.60 1.40
44 45 5.596772 GGCCTAATCTAAAGCCCAACATAAA 59.403 40.000 0.00 0.00 39.60 1.40
45 46 5.137551 GGCCTAATCTAAAGCCCAACATAA 58.862 41.667 0.00 0.00 39.60 1.90
46 47 4.725490 GGCCTAATCTAAAGCCCAACATA 58.275 43.478 0.00 0.00 39.60 2.29
47 48 3.566351 GGCCTAATCTAAAGCCCAACAT 58.434 45.455 0.00 0.00 39.60 2.71
48 49 3.012934 GGCCTAATCTAAAGCCCAACA 57.987 47.619 0.00 0.00 39.60 3.33
53 54 7.121315 CAGTAATAATGGGCCTAATCTAAAGCC 59.879 40.741 4.53 0.00 44.99 4.35
54 55 7.883311 TCAGTAATAATGGGCCTAATCTAAAGC 59.117 37.037 4.53 0.00 0.00 3.51
55 56 9.965902 ATCAGTAATAATGGGCCTAATCTAAAG 57.034 33.333 4.53 0.00 0.00 1.85
56 57 9.739276 CATCAGTAATAATGGGCCTAATCTAAA 57.261 33.333 4.53 0.00 0.00 1.85
57 58 8.890472 ACATCAGTAATAATGGGCCTAATCTAA 58.110 33.333 4.53 0.00 0.00 2.10
58 59 8.449423 ACATCAGTAATAATGGGCCTAATCTA 57.551 34.615 4.53 0.00 0.00 1.98
59 60 7.335127 ACATCAGTAATAATGGGCCTAATCT 57.665 36.000 4.53 0.00 0.00 2.40
60 61 6.599638 GGACATCAGTAATAATGGGCCTAATC 59.400 42.308 4.53 0.00 0.00 1.75
61 62 6.045459 TGGACATCAGTAATAATGGGCCTAAT 59.955 38.462 4.53 0.00 0.00 1.73
62 63 5.371176 TGGACATCAGTAATAATGGGCCTAA 59.629 40.000 4.53 0.00 0.00 2.69
63 64 4.910913 TGGACATCAGTAATAATGGGCCTA 59.089 41.667 4.53 0.00 0.00 3.93
64 65 3.721575 TGGACATCAGTAATAATGGGCCT 59.278 43.478 4.53 0.00 0.00 5.19
65 66 4.098914 TGGACATCAGTAATAATGGGCC 57.901 45.455 0.00 0.00 0.00 5.80
66 67 6.655078 AAATGGACATCAGTAATAATGGGC 57.345 37.500 0.00 0.00 0.00 5.36
67 68 8.010733 ACAAAATGGACATCAGTAATAATGGG 57.989 34.615 0.00 0.00 0.00 4.00
68 69 8.685427 TGACAAAATGGACATCAGTAATAATGG 58.315 33.333 0.00 0.00 0.00 3.16
74 75 9.258826 CAAAAATGACAAAATGGACATCAGTAA 57.741 29.630 0.00 0.00 0.00 2.24
75 76 8.420222 ACAAAAATGACAAAATGGACATCAGTA 58.580 29.630 0.00 0.00 0.00 2.74
76 77 7.274447 ACAAAAATGACAAAATGGACATCAGT 58.726 30.769 0.00 0.00 0.00 3.41
77 78 7.718272 ACAAAAATGACAAAATGGACATCAG 57.282 32.000 0.00 0.00 0.00 2.90
78 79 9.421806 GATACAAAAATGACAAAATGGACATCA 57.578 29.630 0.00 0.00 0.00 3.07
79 80 9.643693 AGATACAAAAATGACAAAATGGACATC 57.356 29.630 0.00 0.00 0.00 3.06
80 81 9.643693 GAGATACAAAAATGACAAAATGGACAT 57.356 29.630 0.00 0.00 0.00 3.06
81 82 7.807433 CGAGATACAAAAATGACAAAATGGACA 59.193 33.333 0.00 0.00 0.00 4.02
82 83 8.020819 TCGAGATACAAAAATGACAAAATGGAC 58.979 33.333 0.00 0.00 0.00 4.02
83 84 8.105097 TCGAGATACAAAAATGACAAAATGGA 57.895 30.769 0.00 0.00 0.00 3.41
84 85 7.008628 GCTCGAGATACAAAAATGACAAAATGG 59.991 37.037 18.75 0.00 0.00 3.16
85 86 7.538334 TGCTCGAGATACAAAAATGACAAAATG 59.462 33.333 18.75 0.00 0.00 2.32
86 87 7.592938 TGCTCGAGATACAAAAATGACAAAAT 58.407 30.769 18.75 0.00 0.00 1.82
87 88 6.964908 TGCTCGAGATACAAAAATGACAAAA 58.035 32.000 18.75 0.00 0.00 2.44
88 89 6.552859 TGCTCGAGATACAAAAATGACAAA 57.447 33.333 18.75 0.00 0.00 2.83
89 90 6.552859 TTGCTCGAGATACAAAAATGACAA 57.447 33.333 18.75 2.82 0.00 3.18
90 91 6.149308 ACATTGCTCGAGATACAAAAATGACA 59.851 34.615 18.75 0.00 0.00 3.58
91 92 6.546395 ACATTGCTCGAGATACAAAAATGAC 58.454 36.000 18.75 0.00 0.00 3.06
92 93 6.741992 ACATTGCTCGAGATACAAAAATGA 57.258 33.333 18.75 0.00 0.00 2.57
93 94 7.801547 AAACATTGCTCGAGATACAAAAATG 57.198 32.000 18.75 14.25 0.00 2.32
94 95 9.906660 TTAAAACATTGCTCGAGATACAAAAAT 57.093 25.926 18.75 0.84 0.00 1.82
95 96 9.737427 TTTAAAACATTGCTCGAGATACAAAAA 57.263 25.926 18.75 4.80 0.00 1.94
96 97 9.906660 ATTTAAAACATTGCTCGAGATACAAAA 57.093 25.926 18.75 4.60 0.00 2.44
97 98 9.906660 AATTTAAAACATTGCTCGAGATACAAA 57.093 25.926 18.75 2.00 0.00 2.83
98 99 9.906660 AAATTTAAAACATTGCTCGAGATACAA 57.093 25.926 18.75 11.56 0.00 2.41
99 100 9.906660 AAAATTTAAAACATTGCTCGAGATACA 57.093 25.926 18.75 1.12 0.00 2.29
102 103 9.643693 ATCAAAATTTAAAACATTGCTCGAGAT 57.356 25.926 18.75 0.00 0.00 2.75
103 104 9.474920 AATCAAAATTTAAAACATTGCTCGAGA 57.525 25.926 18.75 0.00 0.00 4.04
105 106 9.861138 CAAATCAAAATTTAAAACATTGCTCGA 57.139 25.926 0.00 0.00 33.27 4.04
106 107 9.861138 TCAAATCAAAATTTAAAACATTGCTCG 57.139 25.926 0.00 0.00 33.27 5.03
196 197 6.866248 CCAAACTCGGTAGCACATTTTAAAAT 59.134 34.615 7.64 7.64 0.00 1.82
197 198 6.039493 TCCAAACTCGGTAGCACATTTTAAAA 59.961 34.615 2.51 2.51 0.00 1.52
198 199 5.531659 TCCAAACTCGGTAGCACATTTTAAA 59.468 36.000 0.00 0.00 0.00 1.52
199 200 5.064558 TCCAAACTCGGTAGCACATTTTAA 58.935 37.500 0.00 0.00 0.00 1.52
200 201 4.643463 TCCAAACTCGGTAGCACATTTTA 58.357 39.130 0.00 0.00 0.00 1.52
201 202 3.482436 TCCAAACTCGGTAGCACATTTT 58.518 40.909 0.00 0.00 0.00 1.82
202 203 3.074412 CTCCAAACTCGGTAGCACATTT 58.926 45.455 0.00 0.00 0.00 2.32
203 204 2.699954 CTCCAAACTCGGTAGCACATT 58.300 47.619 0.00 0.00 0.00 2.71
204 205 1.676014 GCTCCAAACTCGGTAGCACAT 60.676 52.381 0.00 0.00 32.61 3.21
205 206 0.320421 GCTCCAAACTCGGTAGCACA 60.320 55.000 0.00 0.00 32.61 4.57
206 207 0.320421 TGCTCCAAACTCGGTAGCAC 60.320 55.000 0.00 0.00 35.58 4.40
207 208 0.320421 GTGCTCCAAACTCGGTAGCA 60.320 55.000 0.00 0.00 37.07 3.49
208 209 1.019805 GGTGCTCCAAACTCGGTAGC 61.020 60.000 0.00 0.00 32.83 3.58
209 210 0.736325 CGGTGCTCCAAACTCGGTAG 60.736 60.000 5.52 0.00 0.00 3.18
210 211 1.290955 CGGTGCTCCAAACTCGGTA 59.709 57.895 5.52 0.00 0.00 4.02
211 212 2.030562 CGGTGCTCCAAACTCGGT 59.969 61.111 5.52 0.00 0.00 4.69
212 213 2.742372 CCGGTGCTCCAAACTCGG 60.742 66.667 5.52 0.00 0.00 4.63
213 214 2.725203 TTCCCGGTGCTCCAAACTCG 62.725 60.000 0.00 0.00 0.00 4.18
214 215 1.072505 TTCCCGGTGCTCCAAACTC 59.927 57.895 0.00 0.00 0.00 3.01
215 216 1.228154 GTTCCCGGTGCTCCAAACT 60.228 57.895 0.00 0.00 0.00 2.66
216 217 1.527380 TGTTCCCGGTGCTCCAAAC 60.527 57.895 0.00 6.68 0.00 2.93
217 218 1.527380 GTGTTCCCGGTGCTCCAAA 60.527 57.895 0.00 0.00 0.00 3.28
218 219 2.112297 GTGTTCCCGGTGCTCCAA 59.888 61.111 0.00 0.00 0.00 3.53
219 220 3.948719 GGTGTTCCCGGTGCTCCA 61.949 66.667 0.00 0.00 0.00 3.86
220 221 4.717313 GGGTGTTCCCGGTGCTCC 62.717 72.222 0.00 0.00 44.74 4.70
229 230 3.108376 ACTTCCATCTCTAGGGTGTTCC 58.892 50.000 0.00 0.00 0.00 3.62
230 231 4.957327 AGTACTTCCATCTCTAGGGTGTTC 59.043 45.833 0.00 0.00 0.00 3.18
231 232 4.949121 AGTACTTCCATCTCTAGGGTGTT 58.051 43.478 0.00 0.00 0.00 3.32
232 233 4.611564 AGTACTTCCATCTCTAGGGTGT 57.388 45.455 0.00 0.00 0.00 4.16
233 234 5.942961 TCTAGTACTTCCATCTCTAGGGTG 58.057 45.833 0.00 0.00 31.90 4.61
234 235 6.790177 ATCTAGTACTTCCATCTCTAGGGT 57.210 41.667 0.00 0.00 31.90 4.34
235 236 9.762381 AAATATCTAGTACTTCCATCTCTAGGG 57.238 37.037 0.00 0.00 31.90 3.53
238 239 9.756571 GGGAAATATCTAGTACTTCCATCTCTA 57.243 37.037 0.00 0.00 37.82 2.43
239 240 7.676468 GGGGAAATATCTAGTACTTCCATCTCT 59.324 40.741 0.00 0.00 37.82 3.10
240 241 7.363094 CGGGGAAATATCTAGTACTTCCATCTC 60.363 44.444 0.00 0.00 37.82 2.75
241 242 6.437793 CGGGGAAATATCTAGTACTTCCATCT 59.562 42.308 0.00 0.00 37.82 2.90
242 243 6.210984 ACGGGGAAATATCTAGTACTTCCATC 59.789 42.308 0.00 0.00 37.82 3.51
243 244 6.014499 CACGGGGAAATATCTAGTACTTCCAT 60.014 42.308 0.00 0.00 37.82 3.41
244 245 5.303589 CACGGGGAAATATCTAGTACTTCCA 59.696 44.000 0.00 0.00 37.82 3.53
245 246 5.780984 CACGGGGAAATATCTAGTACTTCC 58.219 45.833 0.00 0.00 35.76 3.46
246 247 5.228665 GCACGGGGAAATATCTAGTACTTC 58.771 45.833 0.00 0.00 0.00 3.01
247 248 4.040095 GGCACGGGGAAATATCTAGTACTT 59.960 45.833 0.00 0.00 0.00 2.24
248 249 3.577415 GGCACGGGGAAATATCTAGTACT 59.423 47.826 0.00 0.00 0.00 2.73
249 250 3.922910 GGCACGGGGAAATATCTAGTAC 58.077 50.000 0.00 0.00 0.00 2.73
266 267 4.101790 CCGTCACCAATGCGGCAC 62.102 66.667 4.03 0.00 38.22 5.01
288 289 1.138859 CATCTCCGGATGCACCACTAA 59.861 52.381 3.57 0.00 42.12 2.24
294 295 0.107456 ATGGTCATCTCCGGATGCAC 59.893 55.000 3.57 2.03 46.41 4.57
609 846 3.023591 GCACGGCGGCTAACTGTTC 62.024 63.158 13.24 0.00 0.00 3.18
651 889 1.298713 CCGAGCGAATGAGACTCCG 60.299 63.158 0.00 0.00 0.00 4.63
884 1132 4.431809 GCAATTGCTATGCATGTTGGTTA 58.568 39.130 23.21 0.00 43.29 2.85
929 1185 4.645535 AGGATATTGGTTGATCCATCGTG 58.354 43.478 3.87 0.00 46.60 4.35
1122 1420 2.138179 GCCCGGCAGGTATCCACTA 61.138 63.158 3.91 0.00 38.26 2.74
1233 1531 4.458829 AGGATCGCCGGGGTCTCA 62.459 66.667 19.13 0.00 39.96 3.27
1239 1537 1.254026 TTATAGTCAGGATCGCCGGG 58.746 55.000 2.18 0.00 39.96 5.73
1268 1566 1.575447 GCCCCCATCTCCACCTTCTT 61.575 60.000 0.00 0.00 0.00 2.52
1536 1834 2.528127 TTCCCGTTGAGGCCCAGA 60.528 61.111 0.00 0.00 39.21 3.86
1596 1894 2.429610 AGCGAACTGTCCCGTACATATT 59.570 45.455 0.00 0.00 37.50 1.28
1609 1907 1.819288 TGAGGACTAAGGAGCGAACTG 59.181 52.381 0.00 0.00 0.00 3.16
1640 1938 0.608130 CCCTACGGCAGCTGCATATA 59.392 55.000 37.63 24.26 44.36 0.86
1641 1939 1.372683 CCCTACGGCAGCTGCATAT 59.627 57.895 37.63 24.44 44.36 1.78
1642 1940 2.807107 CCCCTACGGCAGCTGCATA 61.807 63.158 37.63 26.92 44.36 3.14
1643 1941 4.181010 CCCCTACGGCAGCTGCAT 62.181 66.667 37.63 27.26 44.36 3.96
1725 2023 8.487313 AAATAGCAAATACGAGTACATGTGAA 57.513 30.769 9.11 0.00 0.00 3.18
1732 2030 6.913873 TGGGAAAATAGCAAATACGAGTAC 57.086 37.500 0.00 0.00 0.00 2.73
1733 2031 7.107542 ACTTGGGAAAATAGCAAATACGAGTA 58.892 34.615 0.00 0.00 0.00 2.59
1734 2032 5.944007 ACTTGGGAAAATAGCAAATACGAGT 59.056 36.000 0.00 0.00 0.00 4.18
1735 2033 6.436843 ACTTGGGAAAATAGCAAATACGAG 57.563 37.500 0.00 0.00 0.00 4.18
1736 2034 6.827586 AACTTGGGAAAATAGCAAATACGA 57.172 33.333 0.00 0.00 0.00 3.43
1737 2035 9.019764 CATAAACTTGGGAAAATAGCAAATACG 57.980 33.333 0.00 0.00 0.00 3.06
1774 2072 6.715347 AGGAGCAAAATATATCACCCAAAC 57.285 37.500 0.00 0.00 0.00 2.93
1789 2087 6.855763 ATATTTGTGAATGGAAGGAGCAAA 57.144 33.333 0.00 0.00 0.00 3.68
2013 2456 7.182361 AGTATAATGCATGTCAATGAAGACG 57.818 36.000 0.00 0.00 41.41 4.18
2060 2503 6.439675 TGGTTCGGTATTTAAAACTATGCC 57.560 37.500 0.00 0.00 0.00 4.40
2097 2540 6.226787 GGCTATAGCTTATTTGAAGAGCTGA 58.773 40.000 23.53 0.00 45.66 4.26
2111 2554 4.559862 ATGAAATAGCCGGCTATAGCTT 57.440 40.909 41.53 32.89 40.56 3.74
2360 2809 5.346011 CGAGGCTTTTCTTATTCTTTTTGCC 59.654 40.000 0.00 0.00 37.15 4.52
2384 2835 0.595310 GCCGACCTATGCGAGAGTTC 60.595 60.000 0.00 0.00 0.00 3.01
2462 2914 4.728102 TAAGTCACGGGCGCGGTG 62.728 66.667 27.52 20.36 36.29 4.94
2508 2960 2.015243 ATCCCCTCCCACCATGCATG 62.015 60.000 20.19 20.19 0.00 4.06
2516 2968 2.893489 GCAAAATATGATCCCCTCCCAC 59.107 50.000 0.00 0.00 0.00 4.61
2518 2970 2.893489 GTGCAAAATATGATCCCCTCCC 59.107 50.000 0.00 0.00 0.00 4.30
2525 2977 7.887996 TTGTTTTCTGGTGCAAAATATGATC 57.112 32.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.