Multiple sequence alignment - TraesCS3D01G438700

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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 TraesCS3D01G438700 chr3D 100.000 3197 0 0 1 3197 549376703 549373507 0.000000e+00 5904.0
1 TraesCS3D01G438700 chr3D 89.820 167 15 2 152 316 537154697 537154863 2.500000e-51 213.0
2 TraesCS3D01G438700 chr3B 96.676 2407 52 9 804 3195 728813218 728810825 0.000000e+00 3976.0
3 TraesCS3D01G438700 chr3B 90.876 274 19 5 533 806 728813690 728813423 2.340000e-96 363.0
4 TraesCS3D01G438700 chr3B 89.222 167 16 2 156 321 23408570 23408405 1.160000e-49 207.0
5 TraesCS3D01G438700 chr3B 79.200 125 16 5 10 124 729460692 729460568 9.510000e-11 78.7
6 TraesCS3D01G438700 chr3A 92.587 2064 60 30 316 2375 686731371 686729397 0.000000e+00 2878.0
7 TraesCS3D01G438700 chr3A 98.201 834 14 1 2362 3195 686728100 686727268 0.000000e+00 1456.0
8 TraesCS3D01G438700 chr5D 73.761 2138 507 48 1077 3183 560010915 560008801 0.000000e+00 791.0
9 TraesCS3D01G438700 chr2B 72.324 2121 535 45 1082 3174 694893482 694891386 4.530000e-173 617.0
10 TraesCS3D01G438700 chr4A 73.844 1449 337 37 1758 3183 604670056 604671485 3.630000e-149 538.0
11 TraesCS3D01G438700 chr4A 78.425 292 61 2 1079 1369 714099828 714100118 4.210000e-44 189.0
12 TraesCS3D01G438700 chr4A 79.592 98 12 7 286 377 663298969 663299064 2.660000e-06 63.9
13 TraesCS3D01G438700 chr1B 76.160 474 81 25 155 612 669708580 669708123 1.490000e-53 220.0
14 TraesCS3D01G438700 chr7D 86.735 196 23 3 139 333 500775441 500775634 6.950000e-52 215.0
15 TraesCS3D01G438700 chr7D 88.953 172 18 1 150 320 296507850 296507679 8.990000e-51 211.0
16 TraesCS3D01G438700 chr7D 81.061 132 14 5 1 122 553822062 553821932 9.440000e-16 95.3
17 TraesCS3D01G438700 chr6B 90.303 165 15 1 153 316 132353413 132353577 6.950000e-52 215.0
18 TraesCS3D01G438700 chr4D 89.881 168 16 1 153 319 87570451 87570618 6.950000e-52 215.0
19 TraesCS3D01G438700 chr4D 87.222 180 21 2 156 333 3590635 3590456 1.500000e-48 204.0
20 TraesCS3D01G438700 chr1D 89.474 171 16 2 150 319 463382071 463381902 6.950000e-52 215.0
21 TraesCS3D01G438700 chr6D 78.676 272 57 1 1071 1342 469066904 469067174 2.530000e-41 180.0
22 TraesCS3D01G438700 chr2D 93.651 63 4 0 1 63 539155882 539155944 9.440000e-16 95.3


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 TraesCS3D01G438700 chr3D 549373507 549376703 3196 True 5904.0 5904 100.000 1 3197 1 chr3D.!!$R1 3196
1 TraesCS3D01G438700 chr3B 728810825 728813690 2865 True 2169.5 3976 93.776 533 3195 2 chr3B.!!$R3 2662
2 TraesCS3D01G438700 chr3A 686727268 686731371 4103 True 2167.0 2878 95.394 316 3195 2 chr3A.!!$R1 2879
3 TraesCS3D01G438700 chr5D 560008801 560010915 2114 True 791.0 791 73.761 1077 3183 1 chr5D.!!$R1 2106
4 TraesCS3D01G438700 chr2B 694891386 694893482 2096 True 617.0 617 72.324 1082 3174 1 chr2B.!!$R1 2092
5 TraesCS3D01G438700 chr4A 604670056 604671485 1429 False 538.0 538 73.844 1758 3183 1 chr4A.!!$F1 1425

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
118 119 0.036732 TGGGTGTCTGTTGGAGATGC 59.963 55.0 0.00 0.0 31.63 3.91 F
604 609 0.099436 CTAATTCCCGCAGCAGCAAC 59.901 55.0 0.82 0.0 42.27 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1225 1.383523 GAGGATGGAAAAGAAGGCGG 58.616 55.0 0.0 0.0 0.00 6.13 R
2262 2495 2.505819 AGTTGACATCCCCATGTAGGTC 59.494 50.0 0.0 0.0 43.79 3.85 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
19 20 2.806198 CGGTTCGGACGCGCTTTA 60.806 61.111 5.73 0.00 0.00 1.85
20 21 2.162754 CGGTTCGGACGCGCTTTAT 61.163 57.895 5.73 0.00 0.00 1.40
21 22 1.689352 CGGTTCGGACGCGCTTTATT 61.689 55.000 5.73 0.00 0.00 1.40
22 23 0.445043 GGTTCGGACGCGCTTTATTT 59.555 50.000 5.73 0.00 0.00 1.40
23 24 1.135888 GGTTCGGACGCGCTTTATTTT 60.136 47.619 5.73 0.00 0.00 1.82
24 25 1.902504 GTTCGGACGCGCTTTATTTTG 59.097 47.619 5.73 0.00 0.00 2.44
25 26 0.179210 TCGGACGCGCTTTATTTTGC 60.179 50.000 5.73 0.00 0.00 3.68
31 32 3.383861 GCTTTATTTTGCGGCGGC 58.616 55.556 9.78 9.68 40.52 6.53
32 33 2.164663 GCTTTATTTTGCGGCGGCC 61.165 57.895 14.25 9.54 38.85 6.13
75 76 2.806288 CGTAAAAGCTGCGCTGTATT 57.194 45.000 16.05 8.41 39.62 1.89
76 77 3.918258 CGTAAAAGCTGCGCTGTATTA 57.082 42.857 16.05 9.64 39.62 0.98
77 78 4.452890 CGTAAAAGCTGCGCTGTATTAT 57.547 40.909 16.05 2.13 39.62 1.28
78 79 4.203828 CGTAAAAGCTGCGCTGTATTATG 58.796 43.478 16.05 12.83 39.62 1.90
79 80 4.026062 CGTAAAAGCTGCGCTGTATTATGA 60.026 41.667 16.05 0.00 39.62 2.15
80 81 5.333339 CGTAAAAGCTGCGCTGTATTATGAT 60.333 40.000 16.05 0.00 39.62 2.45
81 82 5.505173 AAAAGCTGCGCTGTATTATGATT 57.495 34.783 16.05 0.80 39.62 2.57
82 83 5.505173 AAAGCTGCGCTGTATTATGATTT 57.495 34.783 16.05 1.35 39.62 2.17
83 84 5.505173 AAGCTGCGCTGTATTATGATTTT 57.495 34.783 16.05 0.00 39.62 1.82
84 85 5.505173 AGCTGCGCTGTATTATGATTTTT 57.495 34.783 16.05 0.00 37.57 1.94
85 86 6.618287 AGCTGCGCTGTATTATGATTTTTA 57.382 33.333 16.05 0.00 37.57 1.52
86 87 6.662616 AGCTGCGCTGTATTATGATTTTTAG 58.337 36.000 16.05 0.00 37.57 1.85
87 88 5.340667 GCTGCGCTGTATTATGATTTTTAGC 59.659 40.000 16.05 2.40 0.00 3.09
89 90 5.957976 CGCTGTATTATGATTTTTAGCGC 57.042 39.130 0.00 0.00 44.65 5.92
90 91 4.545807 CGCTGTATTATGATTTTTAGCGCG 59.454 41.667 0.00 0.00 44.65 6.86
91 92 4.318332 GCTGTATTATGATTTTTAGCGCGC 59.682 41.667 26.66 26.66 0.00 6.86
92 93 4.778904 TGTATTATGATTTTTAGCGCGCC 58.221 39.130 30.33 11.28 0.00 6.53
93 94 2.376915 TTATGATTTTTAGCGCGCCG 57.623 45.000 30.33 0.00 0.00 6.46
110 111 3.276846 GCGCGTTGGGTGTCTGTT 61.277 61.111 8.43 0.00 0.00 3.16
111 112 2.631428 CGCGTTGGGTGTCTGTTG 59.369 61.111 0.00 0.00 0.00 3.33
112 113 2.892334 CGCGTTGGGTGTCTGTTGG 61.892 63.158 0.00 0.00 0.00 3.77
113 114 1.525077 GCGTTGGGTGTCTGTTGGA 60.525 57.895 0.00 0.00 0.00 3.53
114 115 1.507141 GCGTTGGGTGTCTGTTGGAG 61.507 60.000 0.00 0.00 0.00 3.86
115 116 0.105964 CGTTGGGTGTCTGTTGGAGA 59.894 55.000 0.00 0.00 0.00 3.71
116 117 1.270839 CGTTGGGTGTCTGTTGGAGAT 60.271 52.381 0.00 0.00 31.63 2.75
117 118 2.154462 GTTGGGTGTCTGTTGGAGATG 58.846 52.381 0.00 0.00 31.63 2.90
118 119 0.036732 TGGGTGTCTGTTGGAGATGC 59.963 55.000 0.00 0.00 31.63 3.91
119 120 0.326264 GGGTGTCTGTTGGAGATGCT 59.674 55.000 0.00 0.00 31.63 3.79
120 121 1.677217 GGGTGTCTGTTGGAGATGCTC 60.677 57.143 0.00 0.00 31.63 4.26
121 122 1.277557 GGTGTCTGTTGGAGATGCTCT 59.722 52.381 0.00 0.00 31.63 4.09
122 123 2.289945 GGTGTCTGTTGGAGATGCTCTT 60.290 50.000 0.00 0.00 31.63 2.85
123 124 3.055819 GGTGTCTGTTGGAGATGCTCTTA 60.056 47.826 0.00 0.00 31.63 2.10
124 125 4.383552 GGTGTCTGTTGGAGATGCTCTTAT 60.384 45.833 0.00 0.00 31.63 1.73
125 126 4.569966 GTGTCTGTTGGAGATGCTCTTATG 59.430 45.833 0.00 0.00 31.63 1.90
126 127 4.467438 TGTCTGTTGGAGATGCTCTTATGA 59.533 41.667 0.00 0.00 31.63 2.15
127 128 5.046376 TGTCTGTTGGAGATGCTCTTATGAA 60.046 40.000 0.00 0.00 31.63 2.57
128 129 6.054295 GTCTGTTGGAGATGCTCTTATGAAT 58.946 40.000 0.00 0.00 31.63 2.57
129 130 6.541641 GTCTGTTGGAGATGCTCTTATGAATT 59.458 38.462 0.00 0.00 31.63 2.17
130 131 7.712639 GTCTGTTGGAGATGCTCTTATGAATTA 59.287 37.037 0.00 0.00 31.63 1.40
131 132 7.712639 TCTGTTGGAGATGCTCTTATGAATTAC 59.287 37.037 0.00 0.00 0.00 1.89
132 133 7.568349 TGTTGGAGATGCTCTTATGAATTACT 58.432 34.615 0.00 0.00 0.00 2.24
133 134 7.496920 TGTTGGAGATGCTCTTATGAATTACTG 59.503 37.037 0.00 0.00 0.00 2.74
134 135 7.129457 TGGAGATGCTCTTATGAATTACTGT 57.871 36.000 0.00 0.00 0.00 3.55
135 136 8.250143 TGGAGATGCTCTTATGAATTACTGTA 57.750 34.615 0.00 0.00 0.00 2.74
136 137 8.874156 TGGAGATGCTCTTATGAATTACTGTAT 58.126 33.333 0.00 0.00 0.00 2.29
165 166 8.847444 ACGTACTTTGTATTATACTTTCTCCG 57.153 34.615 3.92 3.06 0.00 4.63
166 167 8.462016 ACGTACTTTGTATTATACTTTCTCCGT 58.538 33.333 3.92 3.60 0.00 4.69
167 168 9.294030 CGTACTTTGTATTATACTTTCTCCGTT 57.706 33.333 3.92 0.00 0.00 4.44
169 170 8.713737 ACTTTGTATTATACTTTCTCCGTTCC 57.286 34.615 3.92 0.00 0.00 3.62
170 171 8.537858 ACTTTGTATTATACTTTCTCCGTTCCT 58.462 33.333 3.92 0.00 0.00 3.36
173 174 8.985315 TGTATTATACTTTCTCCGTTCCTAGA 57.015 34.615 3.92 0.00 0.00 2.43
174 175 9.584008 TGTATTATACTTTCTCCGTTCCTAGAT 57.416 33.333 3.92 0.00 0.00 1.98
180 181 9.810870 ATACTTTCTCCGTTCCTAGATATAAGT 57.189 33.333 0.00 0.00 29.86 2.24
181 182 8.536340 ACTTTCTCCGTTCCTAGATATAAGTT 57.464 34.615 0.00 0.00 0.00 2.66
182 183 8.979534 ACTTTCTCCGTTCCTAGATATAAGTTT 58.020 33.333 0.00 0.00 0.00 2.66
183 184 9.819267 CTTTCTCCGTTCCTAGATATAAGTTTT 57.181 33.333 0.00 0.00 0.00 2.43
206 207 8.976986 TTTTTAGAGATTCCACTACGAAGTAC 57.023 34.615 0.00 0.00 45.11 2.73
207 208 7.692460 TTTAGAGATTCCACTACGAAGTACA 57.308 36.000 0.00 0.00 45.11 2.90
208 209 5.564048 AGAGATTCCACTACGAAGTACAC 57.436 43.478 0.00 0.00 45.11 2.90
209 210 5.008331 AGAGATTCCACTACGAAGTACACA 58.992 41.667 0.00 0.00 45.11 3.72
210 211 5.056894 AGATTCCACTACGAAGTACACAC 57.943 43.478 0.00 0.00 45.11 3.82
211 212 4.765856 AGATTCCACTACGAAGTACACACT 59.234 41.667 0.00 0.00 45.11 3.55
212 213 3.909776 TCCACTACGAAGTACACACTG 57.090 47.619 0.00 0.00 45.11 3.66
213 214 3.479489 TCCACTACGAAGTACACACTGA 58.521 45.455 0.00 0.00 45.11 3.41
214 215 4.077108 TCCACTACGAAGTACACACTGAT 58.923 43.478 0.00 0.00 45.11 2.90
215 216 4.082949 TCCACTACGAAGTACACACTGATG 60.083 45.833 0.00 0.00 45.11 3.07
216 217 4.321008 CCACTACGAAGTACACACTGATGT 60.321 45.833 0.00 0.00 45.11 3.06
217 218 5.106436 CCACTACGAAGTACACACTGATGTA 60.106 44.000 0.00 0.00 45.11 2.29
218 219 6.404403 CCACTACGAAGTACACACTGATGTAT 60.404 42.308 0.00 0.00 45.11 2.29
219 220 7.201670 CCACTACGAAGTACACACTGATGTATA 60.202 40.741 0.00 0.00 45.11 1.47
220 221 8.343366 CACTACGAAGTACACACTGATGTATAT 58.657 37.037 0.00 0.00 45.11 0.86
221 222 9.551734 ACTACGAAGTACACACTGATGTATATA 57.448 33.333 0.00 0.00 45.11 0.86
223 224 8.672823 ACGAAGTACACACTGATGTATATAGA 57.327 34.615 0.00 0.00 41.94 1.98
224 225 8.557864 ACGAAGTACACACTGATGTATATAGAC 58.442 37.037 0.00 0.00 41.94 2.59
225 226 8.557029 CGAAGTACACACTGATGTATATAGACA 58.443 37.037 2.07 2.07 36.72 3.41
258 259 7.617041 AGTGTAGATTCACTTATTTTGCTCC 57.383 36.000 0.00 0.00 44.92 4.70
259 260 6.313905 AGTGTAGATTCACTTATTTTGCTCCG 59.686 38.462 0.00 0.00 44.92 4.63
260 261 6.092259 GTGTAGATTCACTTATTTTGCTCCGT 59.908 38.462 0.00 0.00 35.68 4.69
261 262 7.277098 GTGTAGATTCACTTATTTTGCTCCGTA 59.723 37.037 0.00 0.00 35.68 4.02
262 263 7.985184 TGTAGATTCACTTATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
263 264 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
264 265 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
265 266 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
266 267 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
267 268 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
268 269 7.101054 TCACTTATTTTGCTCCGTATGTAGTT 58.899 34.615 0.00 0.00 0.00 2.24
269 270 7.604927 TCACTTATTTTGCTCCGTATGTAGTTT 59.395 33.333 0.00 0.00 0.00 2.66
270 271 7.692291 CACTTATTTTGCTCCGTATGTAGTTTG 59.308 37.037 0.00 0.00 0.00 2.93
271 272 7.389607 ACTTATTTTGCTCCGTATGTAGTTTGT 59.610 33.333 0.00 0.00 0.00 2.83
272 273 8.774890 TTATTTTGCTCCGTATGTAGTTTGTA 57.225 30.769 0.00 0.00 0.00 2.41
273 274 6.715344 TTTTGCTCCGTATGTAGTTTGTAG 57.285 37.500 0.00 0.00 0.00 2.74
274 275 5.395682 TTGCTCCGTATGTAGTTTGTAGT 57.604 39.130 0.00 0.00 0.00 2.73
275 276 6.513806 TTGCTCCGTATGTAGTTTGTAGTA 57.486 37.500 0.00 0.00 0.00 1.82
276 277 5.883661 TGCTCCGTATGTAGTTTGTAGTAC 58.116 41.667 0.00 0.00 0.00 2.73
277 278 5.415389 TGCTCCGTATGTAGTTTGTAGTACA 59.585 40.000 0.00 0.00 42.71 2.90
278 279 6.072008 TGCTCCGTATGTAGTTTGTAGTACAA 60.072 38.462 11.75 11.75 42.03 2.41
279 280 6.976925 GCTCCGTATGTAGTTTGTAGTACAAT 59.023 38.462 16.26 5.54 42.03 2.71
280 281 7.167136 GCTCCGTATGTAGTTTGTAGTACAATC 59.833 40.741 16.26 14.95 42.03 2.67
281 282 8.284945 TCCGTATGTAGTTTGTAGTACAATCT 57.715 34.615 23.47 23.47 42.03 2.40
282 283 8.400947 TCCGTATGTAGTTTGTAGTACAATCTC 58.599 37.037 23.59 17.08 42.03 2.75
283 284 8.404000 CCGTATGTAGTTTGTAGTACAATCTCT 58.596 37.037 23.59 18.98 42.03 3.10
310 311 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
311 312 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
312 313 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
313 314 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
314 315 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
340 341 6.919775 ATATCTAAGAGGTTTATCCACGCT 57.080 37.500 0.00 0.00 39.02 5.07
373 374 8.800370 TTATCTTAAGATGCAAACATACCACA 57.200 30.769 25.22 0.00 36.35 4.17
374 375 7.886629 ATCTTAAGATGCAAACATACCACAT 57.113 32.000 17.26 0.00 36.35 3.21
375 376 7.320443 TCTTAAGATGCAAACATACCACATC 57.680 36.000 0.00 0.00 36.35 3.06
376 377 6.883756 TCTTAAGATGCAAACATACCACATCA 59.116 34.615 0.00 0.00 39.64 3.07
377 378 7.557358 TCTTAAGATGCAAACATACCACATCAT 59.443 33.333 0.00 0.00 39.64 2.45
378 379 5.762825 AGATGCAAACATACCACATCATC 57.237 39.130 0.00 0.00 39.64 2.92
379 380 5.195185 AGATGCAAACATACCACATCATCA 58.805 37.500 0.00 0.00 39.64 3.07
380 381 5.831525 AGATGCAAACATACCACATCATCAT 59.168 36.000 0.00 0.00 39.64 2.45
381 382 6.999871 AGATGCAAACATACCACATCATCATA 59.000 34.615 0.00 0.00 39.64 2.15
382 383 6.375945 TGCAAACATACCACATCATCATAC 57.624 37.500 0.00 0.00 0.00 2.39
383 384 5.884792 TGCAAACATACCACATCATCATACA 59.115 36.000 0.00 0.00 0.00 2.29
384 385 6.038492 TGCAAACATACCACATCATCATACAG 59.962 38.462 0.00 0.00 0.00 2.74
454 455 8.880878 AAAAACTACCACAACAATTAACCATC 57.119 30.769 0.00 0.00 0.00 3.51
478 479 8.116651 TCCATGGAAAAATATCTTCGTTCAAA 57.883 30.769 13.46 0.00 0.00 2.69
484 485 9.528847 GGAAAAATATCTTCGTTCAAATTTTGC 57.471 29.630 4.19 0.00 29.60 3.68
600 605 1.398390 GTCAACTAATTCCCGCAGCAG 59.602 52.381 0.00 0.00 0.00 4.24
603 608 0.322456 ACTAATTCCCGCAGCAGCAA 60.322 50.000 0.82 0.00 42.27 3.91
604 609 0.099436 CTAATTCCCGCAGCAGCAAC 59.901 55.000 0.82 0.00 42.27 4.17
605 610 0.607762 TAATTCCCGCAGCAGCAACA 60.608 50.000 0.82 0.00 42.27 3.33
618 623 0.249398 AGCAACACACGGGTATCCTC 59.751 55.000 0.00 0.00 0.00 3.71
635 640 7.363617 GGGTATCCTCTAGTTTATACATTCGGG 60.364 44.444 10.87 0.00 0.00 5.14
654 659 4.058817 CGGGTATTAGATTCTTCCTGCAC 58.941 47.826 0.00 0.00 0.00 4.57
686 692 2.490115 GTCTAGACGAGATATGCCCCAG 59.510 54.545 7.22 0.00 36.29 4.45
690 696 1.122019 ACGAGATATGCCCCAGTCCC 61.122 60.000 0.00 0.00 0.00 4.46
691 697 1.831652 CGAGATATGCCCCAGTCCCC 61.832 65.000 0.00 0.00 0.00 4.81
692 698 0.768221 GAGATATGCCCCAGTCCCCA 60.768 60.000 0.00 0.00 0.00 4.96
718 724 4.263018 AGGTACCGAAGTTTGACTAACC 57.737 45.455 6.18 0.00 37.46 2.85
725 731 4.319549 CCGAAGTTTGACTAACCTTTCTGC 60.320 45.833 0.00 0.00 37.46 4.26
791 797 1.266718 CGTGCAATACAAACAGCCAGT 59.733 47.619 0.00 0.00 0.00 4.00
859 1077 2.221055 GCTTTCTTTGTCATCGTCACGT 59.779 45.455 0.00 0.00 0.00 4.49
863 1081 0.579630 TTTGTCATCGTCACGTGTGC 59.420 50.000 16.51 9.01 0.00 4.57
888 1106 4.745351 AGCTCCTTCCTTCCAAGAAAAAT 58.255 39.130 0.00 0.00 0.00 1.82
935 1153 2.358247 TTGAGCGGAAGTTCGGCC 60.358 61.111 26.40 19.30 45.05 6.13
988 1206 1.078567 CTTGGTGAGCAGAGGAGCC 60.079 63.158 0.00 0.00 34.23 4.70
1007 1225 1.577328 CGGAGCACCACAATGACCAC 61.577 60.000 0.00 0.00 35.59 4.16
1011 1229 2.282180 ACCACAATGACCACCGCC 60.282 61.111 0.00 0.00 0.00 6.13
1263 1490 3.498841 CGGATACACCTCTCTATGGACCT 60.499 52.174 0.00 0.00 36.31 3.85
1495 1722 2.102588 GGTTCAATCCCGCTAGAGCTAA 59.897 50.000 0.00 0.00 39.32 3.09
2262 2495 9.045223 TGATGATCCTTGATATTTCAACTAACG 57.955 33.333 0.00 0.00 36.94 3.18
2341 2574 8.562892 CCAATACCTTAGCATCAAGTCAAATAG 58.437 37.037 0.00 0.00 0.00 1.73
2506 4053 6.655078 AAACCAACTTCATAGTGCAATTCT 57.345 33.333 0.00 0.00 34.01 2.40
2741 4288 3.243234 TGCCACCAAGTTTGTTTCATACG 60.243 43.478 0.00 0.00 0.00 3.06
2756 4303 8.405418 TGTTTCATACGGATAGCTTAGTAGAT 57.595 34.615 0.00 0.00 0.00 1.98
2840 4387 8.985315 AACAAATTATTAGCATGGATCTCTCA 57.015 30.769 0.00 0.00 0.00 3.27
3104 4651 4.801164 CCAATGGAGGGATCTTCTCAAAT 58.199 43.478 15.04 7.90 33.18 2.32
3135 4682 3.270433 ACAATCCTTGATGGGGAACTCAT 59.730 43.478 0.00 0.00 36.37 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.689352 AATAAAGCGCGTCCGAACCG 61.689 55.000 8.43 0.00 36.29 4.44
3 4 0.445043 AAATAAAGCGCGTCCGAACC 59.555 50.000 8.43 0.00 36.29 3.62
4 5 1.902504 CAAAATAAAGCGCGTCCGAAC 59.097 47.619 8.43 0.00 36.29 3.95
5 6 1.726571 GCAAAATAAAGCGCGTCCGAA 60.727 47.619 8.43 0.00 36.29 4.30
6 7 0.179210 GCAAAATAAAGCGCGTCCGA 60.179 50.000 8.43 0.00 36.29 4.55
7 8 2.265446 GCAAAATAAAGCGCGTCCG 58.735 52.632 8.43 0.00 37.57 4.79
14 15 2.164663 GGCCGCCGCAAAATAAAGC 61.165 57.895 0.00 0.00 36.38 3.51
15 16 1.871789 CGGCCGCCGCAAAATAAAG 60.872 57.895 20.79 0.00 41.17 1.85
16 17 2.179517 CGGCCGCCGCAAAATAAA 59.820 55.556 20.79 0.00 41.17 1.40
64 65 5.561499 CGCTAAAAATCATAATACAGCGCAG 59.439 40.000 11.47 3.33 43.22 5.18
65 66 5.439828 CGCTAAAAATCATAATACAGCGCA 58.560 37.500 11.47 0.00 43.22 6.09
66 67 5.957976 CGCTAAAAATCATAATACAGCGC 57.042 39.130 0.00 0.00 43.22 5.92
68 69 4.318332 GCGCGCTAAAAATCATAATACAGC 59.682 41.667 26.67 0.00 0.00 4.40
69 70 4.846137 GGCGCGCTAAAAATCATAATACAG 59.154 41.667 32.29 0.00 0.00 2.74
70 71 4.609559 CGGCGCGCTAAAAATCATAATACA 60.610 41.667 32.29 0.00 0.00 2.29
71 72 3.838550 CGGCGCGCTAAAAATCATAATAC 59.161 43.478 32.29 6.92 0.00 1.89
72 73 4.060288 CGGCGCGCTAAAAATCATAATA 57.940 40.909 32.29 0.00 0.00 0.98
73 74 2.916111 CGGCGCGCTAAAAATCATAAT 58.084 42.857 32.29 0.00 0.00 1.28
74 75 2.376915 CGGCGCGCTAAAAATCATAA 57.623 45.000 32.29 0.00 0.00 1.90
76 77 4.996113 CGGCGCGCTAAAAATCAT 57.004 50.000 32.29 0.00 0.00 2.45
93 94 3.276846 AACAGACACCCAACGCGC 61.277 61.111 5.73 0.00 0.00 6.86
94 95 2.631428 CAACAGACACCCAACGCG 59.369 61.111 3.53 3.53 0.00 6.01
95 96 1.507141 CTCCAACAGACACCCAACGC 61.507 60.000 0.00 0.00 0.00 4.84
96 97 0.105964 TCTCCAACAGACACCCAACG 59.894 55.000 0.00 0.00 0.00 4.10
97 98 2.154462 CATCTCCAACAGACACCCAAC 58.846 52.381 0.00 0.00 32.26 3.77
98 99 1.545428 GCATCTCCAACAGACACCCAA 60.545 52.381 0.00 0.00 32.26 4.12
99 100 0.036732 GCATCTCCAACAGACACCCA 59.963 55.000 0.00 0.00 32.26 4.51
100 101 0.326264 AGCATCTCCAACAGACACCC 59.674 55.000 0.00 0.00 32.26 4.61
101 102 1.731720 GAGCATCTCCAACAGACACC 58.268 55.000 0.00 0.00 32.26 4.16
139 140 9.935682 CGGAGAAAGTATAATACAAAGTACGTA 57.064 33.333 0.00 0.00 0.00 3.57
140 141 8.462016 ACGGAGAAAGTATAATACAAAGTACGT 58.538 33.333 0.00 0.00 0.00 3.57
141 142 8.847444 ACGGAGAAAGTATAATACAAAGTACG 57.153 34.615 0.00 0.00 0.00 3.67
143 144 9.807649 GGAACGGAGAAAGTATAATACAAAGTA 57.192 33.333 0.00 0.00 0.00 2.24
144 145 8.537858 AGGAACGGAGAAAGTATAATACAAAGT 58.462 33.333 0.00 0.00 0.00 2.66
145 146 8.943909 AGGAACGGAGAAAGTATAATACAAAG 57.056 34.615 0.00 0.00 0.00 2.77
147 148 9.412460 TCTAGGAACGGAGAAAGTATAATACAA 57.588 33.333 0.00 0.00 0.00 2.41
148 149 8.985315 TCTAGGAACGGAGAAAGTATAATACA 57.015 34.615 0.00 0.00 0.00 2.29
154 155 9.810870 ACTTATATCTAGGAACGGAGAAAGTAT 57.189 33.333 0.00 0.00 0.00 2.12
155 156 9.638176 AACTTATATCTAGGAACGGAGAAAGTA 57.362 33.333 0.00 0.00 0.00 2.24
156 157 8.536340 AACTTATATCTAGGAACGGAGAAAGT 57.464 34.615 0.00 0.00 0.00 2.66
157 158 9.819267 AAAACTTATATCTAGGAACGGAGAAAG 57.181 33.333 0.00 0.00 0.00 2.62
181 182 8.579006 TGTACTTCGTAGTGGAATCTCTAAAAA 58.421 33.333 4.78 0.00 35.78 1.94
182 183 8.025445 GTGTACTTCGTAGTGGAATCTCTAAAA 58.975 37.037 4.78 0.00 35.78 1.52
183 184 7.175467 TGTGTACTTCGTAGTGGAATCTCTAAA 59.825 37.037 4.78 0.00 35.78 1.85
184 185 6.656270 TGTGTACTTCGTAGTGGAATCTCTAA 59.344 38.462 4.78 0.00 35.78 2.10
185 186 6.093219 GTGTGTACTTCGTAGTGGAATCTCTA 59.907 42.308 4.78 0.00 35.78 2.43
186 187 5.008331 TGTGTACTTCGTAGTGGAATCTCT 58.992 41.667 4.78 0.00 35.78 3.10
187 188 5.094134 GTGTGTACTTCGTAGTGGAATCTC 58.906 45.833 4.78 0.00 35.78 2.75
188 189 4.765856 AGTGTGTACTTCGTAGTGGAATCT 59.234 41.667 4.78 0.00 35.78 2.40
189 190 4.857588 CAGTGTGTACTTCGTAGTGGAATC 59.142 45.833 4.78 0.00 34.07 2.52
190 191 4.521639 TCAGTGTGTACTTCGTAGTGGAAT 59.478 41.667 4.78 0.00 34.07 3.01
191 192 3.884693 TCAGTGTGTACTTCGTAGTGGAA 59.115 43.478 4.78 0.00 34.07 3.53
192 193 3.479489 TCAGTGTGTACTTCGTAGTGGA 58.521 45.455 4.78 0.00 34.07 4.02
193 194 3.909776 TCAGTGTGTACTTCGTAGTGG 57.090 47.619 4.78 0.00 34.07 4.00
194 195 4.795268 ACATCAGTGTGTACTTCGTAGTG 58.205 43.478 4.78 0.00 37.14 2.74
195 196 6.754702 ATACATCAGTGTGTACTTCGTAGT 57.245 37.500 0.00 0.00 39.39 2.73
197 198 9.768662 TCTATATACATCAGTGTGTACTTCGTA 57.231 33.333 7.45 0.00 39.39 3.43
198 199 8.557864 GTCTATATACATCAGTGTGTACTTCGT 58.442 37.037 7.45 0.00 39.39 3.85
199 200 8.557029 TGTCTATATACATCAGTGTGTACTTCG 58.443 37.037 7.45 0.00 39.39 3.79
235 236 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
236 237 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
237 238 6.663944 ACGGAGCAAAATAAGTGAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
238 239 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
239 240 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
240 241 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
241 242 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
242 243 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
243 244 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
244 245 6.903883 ACTACATACGGAGCAAAATAAGTG 57.096 37.500 0.00 0.00 0.00 3.16
245 246 7.389607 ACAAACTACATACGGAGCAAAATAAGT 59.610 33.333 0.00 0.00 0.00 2.24
246 247 7.748847 ACAAACTACATACGGAGCAAAATAAG 58.251 34.615 0.00 0.00 0.00 1.73
247 248 7.675962 ACAAACTACATACGGAGCAAAATAA 57.324 32.000 0.00 0.00 0.00 1.40
248 249 8.036575 ACTACAAACTACATACGGAGCAAAATA 58.963 33.333 0.00 0.00 0.00 1.40
249 250 6.877322 ACTACAAACTACATACGGAGCAAAAT 59.123 34.615 0.00 0.00 0.00 1.82
250 251 6.225318 ACTACAAACTACATACGGAGCAAAA 58.775 36.000 0.00 0.00 0.00 2.44
251 252 5.786311 ACTACAAACTACATACGGAGCAAA 58.214 37.500 0.00 0.00 0.00 3.68
252 253 5.395682 ACTACAAACTACATACGGAGCAA 57.604 39.130 0.00 0.00 0.00 3.91
253 254 5.415389 TGTACTACAAACTACATACGGAGCA 59.585 40.000 0.00 0.00 0.00 4.26
254 255 5.883661 TGTACTACAAACTACATACGGAGC 58.116 41.667 0.00 0.00 0.00 4.70
255 256 8.404000 AGATTGTACTACAAACTACATACGGAG 58.596 37.037 9.38 0.00 41.96 4.63
256 257 8.284945 AGATTGTACTACAAACTACATACGGA 57.715 34.615 9.38 0.00 41.96 4.69
257 258 8.404000 AGAGATTGTACTACAAACTACATACGG 58.596 37.037 10.75 0.00 40.59 4.02
284 285 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
285 286 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
286 287 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
287 288 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
288 289 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
289 290 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
290 291 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
291 292 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
295 296 9.638176 GATATATACTCCCTCCGTTCCTAAATA 57.362 37.037 0.00 0.00 0.00 1.40
296 297 8.345306 AGATATATACTCCCTCCGTTCCTAAAT 58.655 37.037 0.00 0.00 0.00 1.40
297 298 7.706674 AGATATATACTCCCTCCGTTCCTAAA 58.293 38.462 0.00 0.00 0.00 1.85
298 299 7.281366 AGATATATACTCCCTCCGTTCCTAA 57.719 40.000 0.00 0.00 0.00 2.69
299 300 6.905067 AGATATATACTCCCTCCGTTCCTA 57.095 41.667 0.00 0.00 0.00 2.94
300 301 5.799978 AGATATATACTCCCTCCGTTCCT 57.200 43.478 0.00 0.00 0.00 3.36
301 302 7.344913 TCTTAGATATATACTCCCTCCGTTCC 58.655 42.308 0.00 0.00 0.00 3.62
302 303 7.499895 CCTCTTAGATATATACTCCCTCCGTTC 59.500 44.444 0.00 0.00 0.00 3.95
303 304 7.036717 ACCTCTTAGATATATACTCCCTCCGTT 60.037 40.741 0.00 0.00 0.00 4.44
304 305 6.447735 ACCTCTTAGATATATACTCCCTCCGT 59.552 42.308 0.00 0.00 0.00 4.69
305 306 6.902408 ACCTCTTAGATATATACTCCCTCCG 58.098 44.000 0.00 0.00 0.00 4.63
313 314 9.733219 GCGTGGATAAACCTCTTAGATATATAC 57.267 37.037 0.00 0.00 39.86 1.47
314 315 9.696572 AGCGTGGATAAACCTCTTAGATATATA 57.303 33.333 0.00 0.00 39.86 0.86
335 336 9.798885 GCATCTTAAGATAAATAAGTTAGCGTG 57.201 33.333 17.53 2.79 33.14 5.34
336 337 9.542462 TGCATCTTAAGATAAATAAGTTAGCGT 57.458 29.630 17.53 0.00 33.14 5.07
357 358 5.503662 TGATGATGTGGTATGTTTGCATC 57.496 39.130 0.00 0.00 36.58 3.91
370 371 7.662669 TCCCATTCATAACTGTATGATGATGTG 59.337 37.037 0.00 4.61 44.42 3.21
372 373 8.803397 ATCCCATTCATAACTGTATGATGATG 57.197 34.615 0.00 0.85 44.42 3.07
377 378 9.349713 GGTTTTATCCCATTCATAACTGTATGA 57.650 33.333 0.00 0.00 43.57 2.15
378 379 8.576442 GGGTTTTATCCCATTCATAACTGTATG 58.424 37.037 0.00 0.00 46.30 2.39
379 380 8.706322 GGGTTTTATCCCATTCATAACTGTAT 57.294 34.615 0.00 0.00 46.30 2.29
435 436 5.420421 CCATGGATGGTTAATTGTTGTGGTA 59.580 40.000 5.56 0.00 43.05 3.25
454 455 8.931385 ATTTGAACGAAGATATTTTTCCATGG 57.069 30.769 4.97 4.97 0.00 3.66
460 461 9.862585 GTGCAAAATTTGAACGAAGATATTTTT 57.137 25.926 10.26 0.00 27.60 1.94
577 578 2.699954 CTGCGGGAATTAGTTGACAGT 58.300 47.619 0.00 0.00 0.00 3.55
578 579 1.398390 GCTGCGGGAATTAGTTGACAG 59.602 52.381 0.00 0.00 0.00 3.51
600 605 0.249398 AGAGGATACCCGTGTGTTGC 59.751 55.000 0.00 0.00 37.58 4.17
603 608 2.822707 ACTAGAGGATACCCGTGTGT 57.177 50.000 0.00 0.00 37.58 3.72
604 609 5.786264 ATAAACTAGAGGATACCCGTGTG 57.214 43.478 0.00 0.00 37.58 3.82
605 610 6.367983 TGTATAAACTAGAGGATACCCGTGT 58.632 40.000 0.00 0.00 37.58 4.49
635 640 5.059833 CCAGGTGCAGGAAGAATCTAATAC 58.940 45.833 0.00 0.00 0.00 1.89
654 659 3.444034 TCTCGTCTAGACAATGAACCAGG 59.556 47.826 22.37 2.51 0.00 4.45
686 692 0.397535 TCGGTACCTATGGTGGGGAC 60.398 60.000 10.90 0.00 36.19 4.46
690 696 3.055675 TCAAACTTCGGTACCTATGGTGG 60.056 47.826 10.90 0.00 36.19 4.61
691 697 3.930848 GTCAAACTTCGGTACCTATGGTG 59.069 47.826 10.90 4.90 36.19 4.17
692 698 3.836562 AGTCAAACTTCGGTACCTATGGT 59.163 43.478 10.90 0.00 40.16 3.55
718 724 5.228635 GTGATTATCAAACGCATGCAGAAAG 59.771 40.000 19.57 2.94 0.00 2.62
725 731 4.257536 TGTCGTGATTATCAAACGCATG 57.742 40.909 0.00 0.00 37.24 4.06
791 797 2.571212 CACTTTGTACCAAGTGGCTCA 58.429 47.619 25.10 0.00 41.88 4.26
826 1039 6.524734 TGACAAAGAAAGCTCTATCAAGTGA 58.475 36.000 0.00 0.00 0.00 3.41
859 1077 0.320771 GAAGGAAGGAGCTTCGCACA 60.321 55.000 0.00 0.00 40.99 4.57
863 1081 1.276421 TCTTGGAAGGAAGGAGCTTCG 59.724 52.381 0.00 0.00 40.99 3.79
925 1143 2.741211 GTGGTCCGGCCGAACTTC 60.741 66.667 30.73 10.45 41.21 3.01
935 1153 2.686558 CACATTTCAAGTGTGGTCCG 57.313 50.000 5.12 0.00 42.43 4.79
988 1206 1.302431 TGGTCATTGTGGTGCTCCG 60.302 57.895 0.00 0.00 36.30 4.63
1007 1225 1.383523 GAGGATGGAAAAGAAGGCGG 58.616 55.000 0.00 0.00 0.00 6.13
1011 1229 4.719273 AGGACTAGGAGGATGGAAAAGAAG 59.281 45.833 0.00 0.00 0.00 2.85
1263 1490 2.756760 GTTACCGAGGTGAGGTGTGATA 59.243 50.000 4.80 0.00 42.83 2.15
2262 2495 2.505819 AGTTGACATCCCCATGTAGGTC 59.494 50.000 0.00 0.00 43.79 3.85
2341 2574 3.828657 GGGAGACTACCCGTGAAAC 57.171 57.895 0.00 0.00 40.49 2.78
3135 4682 1.013596 CGTGAAGCACCACAAAGACA 58.986 50.000 8.80 0.00 36.89 3.41


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

AutoCloner maintained by Alex Coulton.