Multiple sequence alignment - TraesCS4A01G065200

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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 TraesCS4A01G065200 chr4A 100.000 2390 0 0 1 2390 62357227 62359616 0.000000e+00 4414
1 TraesCS4A01G065200 chr4A 81.414 1259 212 20 1138 2390 175750734 175751976 0.000000e+00 1009
2 TraesCS4A01G065200 chr4A 87.786 131 10 6 190 318 602785802 602785676 5.320000e-32 148
3 TraesCS4A01G065200 chr5A 99.336 1507 10 0 884 2390 104221442 104219936 0.000000e+00 2728
4 TraesCS4A01G065200 chr5A 87.218 133 14 2 189 320 624195658 624195788 5.320000e-32 148
5 TraesCS4A01G065200 chr5A 88.710 62 6 1 298 359 29197956 29198016 9.160000e-10 75
6 TraesCS4A01G065200 chr3A 98.938 1507 16 0 884 2390 623044577 623043071 0.000000e+00 2695
7 TraesCS4A01G065200 chr1B 98.477 1510 22 1 881 2390 301042417 301043925 0.000000e+00 2660
8 TraesCS4A01G065200 chr1B 87.135 171 19 2 185 354 514247887 514247719 8.720000e-45 191
9 TraesCS4A01G065200 chr2D 94.747 1504 58 4 887 2390 381512689 381511207 0.000000e+00 2320
10 TraesCS4A01G065200 chrUn 95.031 1449 57 2 942 2390 22791796 22793229 0.000000e+00 2263
11 TraesCS4A01G065200 chr7A 92.659 1512 108 3 881 2390 475197395 475198905 0.000000e+00 2174
12 TraesCS4A01G065200 chr7B 98.755 1205 14 1 1186 2390 581387547 581386344 0.000000e+00 2141
13 TraesCS4A01G065200 chr2B 91.833 1506 119 4 887 2390 359151327 359149824 0.000000e+00 2097
14 TraesCS4A01G065200 chr3B 91.071 1512 127 2 881 2390 366135633 366137138 0.000000e+00 2037
15 TraesCS4A01G065200 chr4D 90.448 513 23 14 396 885 404920494 404921003 0.000000e+00 652
16 TraesCS4A01G065200 chr4B 91.341 358 18 5 537 885 502733292 502733645 5.980000e-131 477
17 TraesCS4A01G065200 chr4B 93.923 181 6 3 1 179 502732991 502733168 3.920000e-68 268
18 TraesCS4A01G065200 chr4B 94.545 110 6 0 396 505 502733187 502733296 1.140000e-38 171
19 TraesCS4A01G065200 chr5D 90.058 171 13 3 190 359 544897224 544897057 4.000000e-53 219
20 TraesCS4A01G065200 chr6A 89.474 171 13 5 190 359 431069371 431069205 6.690000e-51 211
21 TraesCS4A01G065200 chr2A 87.931 174 16 5 190 359 13616100 13615928 1.450000e-47 200
22 TraesCS4A01G065200 chr2A 87.356 174 16 4 190 359 617757241 617757070 6.740000e-46 195
23 TraesCS4A01G065200 chr7D 88.158 152 14 4 186 335 51954324 51954473 6.790000e-41 178
24 TraesCS4A01G065200 chr3D 83.908 174 21 5 188 359 130926318 130926486 2.460000e-35 159
25 TraesCS4A01G065200 chr1A 85.417 144 18 3 213 355 506475393 506475534 1.910000e-31 147


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 TraesCS4A01G065200 chr4A 62357227 62359616 2389 False 4414.000000 4414 100.000000 1 2390 1 chr4A.!!$F1 2389
1 TraesCS4A01G065200 chr4A 175750734 175751976 1242 False 1009.000000 1009 81.414000 1138 2390 1 chr4A.!!$F2 1252
2 TraesCS4A01G065200 chr5A 104219936 104221442 1506 True 2728.000000 2728 99.336000 884 2390 1 chr5A.!!$R1 1506
3 TraesCS4A01G065200 chr3A 623043071 623044577 1506 True 2695.000000 2695 98.938000 884 2390 1 chr3A.!!$R1 1506
4 TraesCS4A01G065200 chr1B 301042417 301043925 1508 False 2660.000000 2660 98.477000 881 2390 1 chr1B.!!$F1 1509
5 TraesCS4A01G065200 chr2D 381511207 381512689 1482 True 2320.000000 2320 94.747000 887 2390 1 chr2D.!!$R1 1503
6 TraesCS4A01G065200 chrUn 22791796 22793229 1433 False 2263.000000 2263 95.031000 942 2390 1 chrUn.!!$F1 1448
7 TraesCS4A01G065200 chr7A 475197395 475198905 1510 False 2174.000000 2174 92.659000 881 2390 1 chr7A.!!$F1 1509
8 TraesCS4A01G065200 chr7B 581386344 581387547 1203 True 2141.000000 2141 98.755000 1186 2390 1 chr7B.!!$R1 1204
9 TraesCS4A01G065200 chr2B 359149824 359151327 1503 True 2097.000000 2097 91.833000 887 2390 1 chr2B.!!$R1 1503
10 TraesCS4A01G065200 chr3B 366135633 366137138 1505 False 2037.000000 2037 91.071000 881 2390 1 chr3B.!!$F1 1509
11 TraesCS4A01G065200 chr4D 404920494 404921003 509 False 652.000000 652 90.448000 396 885 1 chr4D.!!$F1 489
12 TraesCS4A01G065200 chr4B 502732991 502733645 654 False 305.333333 477 93.269667 1 885 3 chr4B.!!$F1 884

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
830 864 0.038744 AGGGCATCCAAACTGTCAGG 59.961 55.0 4.53 0.0 34.83 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2176 5.98831 TTCATTGCTCCATGTGAATCTTT 57.012 34.783 0.0 0.0 0.0 2.52 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
50 51 2.435059 GCTGGACCTCACCGCTTC 60.435 66.667 0.00 0.00 0.00 3.86
68 71 7.323656 CACCGCTTCTATGAAAAAGTTTGTAAG 59.676 37.037 0.00 0.00 0.00 2.34
90 93 3.914312 ACATTAATGCTCGAGGGATACG 58.086 45.455 15.58 0.00 37.60 3.06
126 129 3.875134 ACGACGTTTTCCAGACTTTGATT 59.125 39.130 0.00 0.00 0.00 2.57
127 130 4.025145 ACGACGTTTTCCAGACTTTGATTC 60.025 41.667 0.00 0.00 0.00 2.52
129 132 5.503357 CGACGTTTTCCAGACTTTGATTCAA 60.503 40.000 0.00 0.00 0.00 2.69
130 133 5.578776 ACGTTTTCCAGACTTTGATTCAAC 58.421 37.500 0.00 0.00 0.00 3.18
131 134 5.357032 ACGTTTTCCAGACTTTGATTCAACT 59.643 36.000 0.00 0.00 0.00 3.16
132 135 5.682862 CGTTTTCCAGACTTTGATTCAACTG 59.317 40.000 0.00 3.82 0.00 3.16
133 136 6.564328 GTTTTCCAGACTTTGATTCAACTGT 58.436 36.000 12.08 8.59 0.00 3.55
134 137 7.466725 CGTTTTCCAGACTTTGATTCAACTGTA 60.467 37.037 12.08 0.00 0.00 2.74
135 138 6.861065 TTCCAGACTTTGATTCAACTGTAC 57.139 37.500 12.08 0.00 0.00 2.90
161 164 6.690704 ATATATGACAGATGTACGTTTGCG 57.309 37.500 5.55 0.00 44.93 4.85
180 183 4.119334 GCGTTTGCAAAAATGAAAGAGG 57.881 40.909 14.67 0.00 42.15 3.69
181 184 3.555547 GCGTTTGCAAAAATGAAAGAGGT 59.444 39.130 14.67 0.00 42.15 3.85
182 185 4.318050 GCGTTTGCAAAAATGAAAGAGGTC 60.318 41.667 14.67 0.00 42.15 3.85
183 186 5.043248 CGTTTGCAAAAATGAAAGAGGTCT 58.957 37.500 14.67 0.00 0.00 3.85
184 187 6.205784 CGTTTGCAAAAATGAAAGAGGTCTA 58.794 36.000 14.67 0.00 0.00 2.59
185 188 6.863126 CGTTTGCAAAAATGAAAGAGGTCTAT 59.137 34.615 14.67 0.00 0.00 1.98
186 189 7.148918 CGTTTGCAAAAATGAAAGAGGTCTATG 60.149 37.037 14.67 0.00 0.00 2.23
187 190 7.523293 TTGCAAAAATGAAAGAGGTCTATGA 57.477 32.000 0.00 0.00 0.00 2.15
188 191 7.523293 TGCAAAAATGAAAGAGGTCTATGAA 57.477 32.000 0.00 0.00 0.00 2.57
189 192 7.596494 TGCAAAAATGAAAGAGGTCTATGAAG 58.404 34.615 0.00 0.00 0.00 3.02
190 193 7.448161 TGCAAAAATGAAAGAGGTCTATGAAGA 59.552 33.333 0.00 0.00 0.00 2.87
191 194 7.967303 GCAAAAATGAAAGAGGTCTATGAAGAG 59.033 37.037 0.00 0.00 30.45 2.85
192 195 9.007901 CAAAAATGAAAGAGGTCTATGAAGAGT 57.992 33.333 0.00 0.00 30.45 3.24
196 199 9.829507 AATGAAAGAGGTCTATGAAGAGTAATG 57.170 33.333 0.00 0.00 30.45 1.90
197 200 7.268586 TGAAAGAGGTCTATGAAGAGTAATGC 58.731 38.462 0.00 0.00 30.45 3.56
198 201 7.124901 TGAAAGAGGTCTATGAAGAGTAATGCT 59.875 37.037 0.00 0.00 30.45 3.79
199 202 8.540507 AAAGAGGTCTATGAAGAGTAATGCTA 57.459 34.615 0.00 0.00 30.45 3.49
200 203 7.519032 AGAGGTCTATGAAGAGTAATGCTAC 57.481 40.000 0.00 0.00 30.45 3.58
201 204 7.063593 AGAGGTCTATGAAGAGTAATGCTACA 58.936 38.462 0.00 0.00 30.45 2.74
202 205 7.013846 AGAGGTCTATGAAGAGTAATGCTACAC 59.986 40.741 0.00 0.00 30.45 2.90
203 206 6.607600 AGGTCTATGAAGAGTAATGCTACACA 59.392 38.462 0.00 0.00 30.45 3.72
204 207 7.288852 AGGTCTATGAAGAGTAATGCTACACAT 59.711 37.037 0.00 0.00 34.24 3.21
205 208 8.577296 GGTCTATGAAGAGTAATGCTACACATA 58.423 37.037 0.00 0.00 32.40 2.29
206 209 9.400638 GTCTATGAAGAGTAATGCTACACATAC 57.599 37.037 0.00 0.00 32.40 2.39
207 210 9.131791 TCTATGAAGAGTAATGCTACACATACA 57.868 33.333 0.00 0.00 38.34 2.29
208 211 9.920133 CTATGAAGAGTAATGCTACACATACAT 57.080 33.333 0.00 0.00 38.34 2.29
237 240 5.467035 ACATGGATTTTACAAACAGGTGG 57.533 39.130 0.00 0.00 0.00 4.61
238 241 4.283212 ACATGGATTTTACAAACAGGTGGG 59.717 41.667 0.00 0.00 0.00 4.61
239 242 3.917300 TGGATTTTACAAACAGGTGGGT 58.083 40.909 0.00 0.00 0.00 4.51
240 243 4.290942 TGGATTTTACAAACAGGTGGGTT 58.709 39.130 0.00 0.00 0.00 4.11
241 244 4.100189 TGGATTTTACAAACAGGTGGGTTG 59.900 41.667 0.00 0.00 0.00 3.77
242 245 4.100344 GGATTTTACAAACAGGTGGGTTGT 59.900 41.667 3.06 3.06 0.00 3.32
243 246 4.457834 TTTTACAAACAGGTGGGTTGTG 57.542 40.909 7.93 0.00 0.00 3.33
244 247 3.367646 TTACAAACAGGTGGGTTGTGA 57.632 42.857 7.93 0.00 0.00 3.58
245 248 2.452600 ACAAACAGGTGGGTTGTGAT 57.547 45.000 0.00 0.00 0.00 3.06
246 249 2.745968 ACAAACAGGTGGGTTGTGATT 58.254 42.857 0.00 0.00 0.00 2.57
247 250 2.430332 ACAAACAGGTGGGTTGTGATTG 59.570 45.455 0.00 0.00 0.00 2.67
248 251 1.703411 AACAGGTGGGTTGTGATTGG 58.297 50.000 0.00 0.00 0.00 3.16
249 252 0.850100 ACAGGTGGGTTGTGATTGGA 59.150 50.000 0.00 0.00 0.00 3.53
250 253 1.202927 ACAGGTGGGTTGTGATTGGAG 60.203 52.381 0.00 0.00 0.00 3.86
251 254 1.073763 CAGGTGGGTTGTGATTGGAGA 59.926 52.381 0.00 0.00 0.00 3.71
252 255 1.995542 AGGTGGGTTGTGATTGGAGAT 59.004 47.619 0.00 0.00 0.00 2.75
253 256 2.379907 AGGTGGGTTGTGATTGGAGATT 59.620 45.455 0.00 0.00 0.00 2.40
254 257 3.591527 AGGTGGGTTGTGATTGGAGATTA 59.408 43.478 0.00 0.00 0.00 1.75
255 258 4.044065 AGGTGGGTTGTGATTGGAGATTAA 59.956 41.667 0.00 0.00 0.00 1.40
256 259 4.399303 GGTGGGTTGTGATTGGAGATTAAG 59.601 45.833 0.00 0.00 0.00 1.85
257 260 5.253330 GTGGGTTGTGATTGGAGATTAAGA 58.747 41.667 0.00 0.00 0.00 2.10
258 261 5.355350 GTGGGTTGTGATTGGAGATTAAGAG 59.645 44.000 0.00 0.00 0.00 2.85
259 262 4.884164 GGGTTGTGATTGGAGATTAAGAGG 59.116 45.833 0.00 0.00 0.00 3.69
260 263 4.884164 GGTTGTGATTGGAGATTAAGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
261 264 5.339200 GGTTGTGATTGGAGATTAAGAGGGA 60.339 44.000 0.00 0.00 0.00 4.20
262 265 5.620738 TGTGATTGGAGATTAAGAGGGAG 57.379 43.478 0.00 0.00 0.00 4.30
263 266 4.410228 TGTGATTGGAGATTAAGAGGGAGG 59.590 45.833 0.00 0.00 0.00 4.30
264 267 4.656112 GTGATTGGAGATTAAGAGGGAGGA 59.344 45.833 0.00 0.00 0.00 3.71
265 268 4.904251 TGATTGGAGATTAAGAGGGAGGAG 59.096 45.833 0.00 0.00 0.00 3.69
266 269 4.626942 TTGGAGATTAAGAGGGAGGAGA 57.373 45.455 0.00 0.00 0.00 3.71
267 270 4.191804 TGGAGATTAAGAGGGAGGAGAG 57.808 50.000 0.00 0.00 0.00 3.20
268 271 3.116939 TGGAGATTAAGAGGGAGGAGAGG 60.117 52.174 0.00 0.00 0.00 3.69
269 272 2.897326 GAGATTAAGAGGGAGGAGAGGC 59.103 54.545 0.00 0.00 0.00 4.70
270 273 2.248686 AGATTAAGAGGGAGGAGAGGCA 59.751 50.000 0.00 0.00 0.00 4.75
271 274 1.867363 TTAAGAGGGAGGAGAGGCAC 58.133 55.000 0.00 0.00 0.00 5.01
272 275 0.710588 TAAGAGGGAGGAGAGGCACA 59.289 55.000 0.00 0.00 0.00 4.57
273 276 0.907230 AAGAGGGAGGAGAGGCACAC 60.907 60.000 0.00 0.00 0.00 3.82
274 277 2.284995 AGGGAGGAGAGGCACACC 60.285 66.667 0.00 0.00 0.00 4.16
275 278 3.403558 GGGAGGAGAGGCACACCC 61.404 72.222 0.00 0.00 36.11 4.61
276 279 3.403558 GGAGGAGAGGCACACCCC 61.404 72.222 0.00 0.00 36.11 4.95
277 280 2.607750 GAGGAGAGGCACACCCCA 60.608 66.667 0.00 0.00 36.11 4.96
278 281 1.997874 GAGGAGAGGCACACCCCAT 60.998 63.158 0.00 0.00 36.11 4.00
279 282 0.691078 GAGGAGAGGCACACCCCATA 60.691 60.000 0.00 0.00 36.11 2.74
280 283 0.253160 AGGAGAGGCACACCCCATAA 60.253 55.000 0.00 0.00 36.11 1.90
281 284 0.623723 GGAGAGGCACACCCCATAAA 59.376 55.000 0.00 0.00 36.11 1.40
282 285 1.005450 GGAGAGGCACACCCCATAAAA 59.995 52.381 0.00 0.00 36.11 1.52
283 286 2.556559 GGAGAGGCACACCCCATAAAAA 60.557 50.000 0.00 0.00 36.11 1.94
284 287 3.365472 GAGAGGCACACCCCATAAAAAT 58.635 45.455 0.00 0.00 36.11 1.82
285 288 3.365472 AGAGGCACACCCCATAAAAATC 58.635 45.455 0.00 0.00 36.11 2.17
286 289 3.096092 GAGGCACACCCCATAAAAATCA 58.904 45.455 0.00 0.00 36.11 2.57
287 290 3.513515 GAGGCACACCCCATAAAAATCAA 59.486 43.478 0.00 0.00 36.11 2.57
288 291 3.515104 AGGCACACCCCATAAAAATCAAG 59.485 43.478 0.00 0.00 36.11 3.02
289 292 3.369366 GGCACACCCCATAAAAATCAAGG 60.369 47.826 0.00 0.00 0.00 3.61
290 293 3.369366 GCACACCCCATAAAAATCAAGGG 60.369 47.826 0.00 0.00 40.58 3.95
295 298 4.264373 CCCATAAAAATCAAGGGGGAGA 57.736 45.455 0.00 0.00 36.14 3.71
296 299 4.218312 CCCATAAAAATCAAGGGGGAGAG 58.782 47.826 0.00 0.00 36.14 3.20
297 300 4.326132 CCCATAAAAATCAAGGGGGAGAGT 60.326 45.833 0.00 0.00 36.14 3.24
298 301 4.646492 CCATAAAAATCAAGGGGGAGAGTG 59.354 45.833 0.00 0.00 0.00 3.51
299 302 2.907458 AAAATCAAGGGGGAGAGTGG 57.093 50.000 0.00 0.00 0.00 4.00
300 303 1.760405 AAATCAAGGGGGAGAGTGGT 58.240 50.000 0.00 0.00 0.00 4.16
301 304 1.760405 AATCAAGGGGGAGAGTGGTT 58.240 50.000 0.00 0.00 0.00 3.67
302 305 2.661176 ATCAAGGGGGAGAGTGGTTA 57.339 50.000 0.00 0.00 0.00 2.85
303 306 1.952621 TCAAGGGGGAGAGTGGTTAG 58.047 55.000 0.00 0.00 0.00 2.34
304 307 1.151413 TCAAGGGGGAGAGTGGTTAGT 59.849 52.381 0.00 0.00 0.00 2.24
305 308 1.985895 CAAGGGGGAGAGTGGTTAGTT 59.014 52.381 0.00 0.00 0.00 2.24
317 320 8.148999 GGAGAGTGGTTAGTTAGAAAGAAAGAA 58.851 37.037 0.00 0.00 0.00 2.52
318 321 9.198837 GAGAGTGGTTAGTTAGAAAGAAAGAAG 57.801 37.037 0.00 0.00 0.00 2.85
320 323 6.711194 AGTGGTTAGTTAGAAAGAAAGAAGGC 59.289 38.462 0.00 0.00 0.00 4.35
321 324 6.711194 GTGGTTAGTTAGAAAGAAAGAAGGCT 59.289 38.462 0.00 0.00 0.00 4.58
323 326 8.095169 TGGTTAGTTAGAAAGAAAGAAGGCTAG 58.905 37.037 0.00 0.00 0.00 3.42
324 327 8.095792 GGTTAGTTAGAAAGAAAGAAGGCTAGT 58.904 37.037 0.00 0.00 0.00 2.57
325 328 9.142515 GTTAGTTAGAAAGAAAGAAGGCTAGTC 57.857 37.037 0.00 0.00 0.00 2.59
326 329 7.304497 AGTTAGAAAGAAAGAAGGCTAGTCA 57.696 36.000 0.00 0.00 0.00 3.41
327 330 7.382898 AGTTAGAAAGAAAGAAGGCTAGTCAG 58.617 38.462 0.00 0.00 0.00 3.51
338 341 2.721129 GCTAGTCAGCGTGTAATTGC 57.279 50.000 0.00 0.00 38.22 3.56
339 342 1.005975 GCTAGTCAGCGTGTAATTGCG 60.006 52.381 0.00 0.00 38.22 4.85
340 343 2.259618 CTAGTCAGCGTGTAATTGCGT 58.740 47.619 0.00 0.00 35.87 5.24
341 344 0.790207 AGTCAGCGTGTAATTGCGTG 59.210 50.000 0.00 0.00 35.87 5.34
342 345 0.511221 GTCAGCGTGTAATTGCGTGT 59.489 50.000 0.00 0.00 35.87 4.49
343 346 1.722464 GTCAGCGTGTAATTGCGTGTA 59.278 47.619 0.00 0.00 35.87 2.90
344 347 2.156117 GTCAGCGTGTAATTGCGTGTAA 59.844 45.455 0.00 0.00 35.87 2.41
345 348 2.156117 TCAGCGTGTAATTGCGTGTAAC 59.844 45.455 0.00 0.00 35.87 2.50
346 349 2.156891 CAGCGTGTAATTGCGTGTAACT 59.843 45.455 0.00 0.00 35.87 2.24
347 350 2.803956 AGCGTGTAATTGCGTGTAACTT 59.196 40.909 0.00 0.00 35.87 2.66
348 351 3.249080 AGCGTGTAATTGCGTGTAACTTT 59.751 39.130 0.00 0.00 35.87 2.66
349 352 3.969981 GCGTGTAATTGCGTGTAACTTTT 59.030 39.130 0.00 0.00 31.75 2.27
350 353 4.438471 GCGTGTAATTGCGTGTAACTTTTT 59.562 37.500 0.00 0.00 31.75 1.94
351 354 5.606515 GCGTGTAATTGCGTGTAACTTTTTG 60.607 40.000 0.00 0.00 31.75 2.44
352 355 5.452944 CGTGTAATTGCGTGTAACTTTTTGT 59.547 36.000 0.00 0.00 31.75 2.83
353 356 6.628065 CGTGTAATTGCGTGTAACTTTTTGTA 59.372 34.615 0.00 0.00 31.75 2.41
354 357 7.321746 CGTGTAATTGCGTGTAACTTTTTGTAT 59.678 33.333 0.00 0.00 31.75 2.29
355 358 9.596677 GTGTAATTGCGTGTAACTTTTTGTATA 57.403 29.630 0.00 0.00 31.75 1.47
433 436 5.883328 TCGAGTTAGTATATTTTGCTGCG 57.117 39.130 0.00 0.00 0.00 5.18
485 488 1.896465 GTGGGGCACTAGGCTAGATAG 59.104 57.143 27.59 16.62 44.01 2.08
502 505 2.969821 TAGCCAAACACCAACCTCAT 57.030 45.000 0.00 0.00 0.00 2.90
513 516 9.703892 CAAACACCAACCTCATATAAATTTGAA 57.296 29.630 0.00 0.00 0.00 2.69
581 584 5.470777 TGTTACTTTCTACATTTCCCCAACG 59.529 40.000 0.00 0.00 0.00 4.10
597 600 2.475864 CCAACGACCATGCACAATTTTG 59.524 45.455 0.00 0.00 0.00 2.44
683 692 7.118680 CCCGCAAACTTTTCTTAACTCATACTA 59.881 37.037 0.00 0.00 0.00 1.82
684 693 7.955864 CCGCAAACTTTTCTTAACTCATACTAC 59.044 37.037 0.00 0.00 0.00 2.73
685 694 8.709646 CGCAAACTTTTCTTAACTCATACTACT 58.290 33.333 0.00 0.00 0.00 2.57
729 741 2.193536 GTGGCAGTTGGCGGTTCTT 61.194 57.895 1.08 0.00 46.16 2.52
756 768 4.699257 GCTAATGGGATTGATAGGCTTCAG 59.301 45.833 0.00 0.00 0.00 3.02
793 827 4.844998 AGTCGAGGTGATGTATCTGATG 57.155 45.455 0.00 0.00 0.00 3.07
830 864 0.038744 AGGGCATCCAAACTGTCAGG 59.961 55.000 4.53 0.00 34.83 3.86
2128 2167 1.000731 CGAGCTCAAGGAGATCCATCC 59.999 57.143 15.40 0.00 41.41 3.51
2137 2176 3.662078 AGGAGATCCATCCACAGAATCA 58.338 45.455 0.92 0.00 42.26 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 71 3.921021 CGTATCCCTCGAGCATTAATGTC 59.079 47.826 16.61 11.41 0.00 3.06
90 93 2.268298 ACGTCGTTTGTCATATGGAGC 58.732 47.619 2.13 0.00 0.00 4.70
134 137 9.140286 GCAAACGTACATCTGTCATATATATGT 57.860 33.333 19.78 6.46 35.26 2.29
135 138 8.313931 CGCAAACGTACATCTGTCATATATATG 58.686 37.037 15.47 15.47 32.94 1.78
161 164 7.867403 TCATAGACCTCTTTCATTTTTGCAAAC 59.133 33.333 12.39 0.00 0.00 2.93
172 175 7.124901 AGCATTACTCTTCATAGACCTCTTTCA 59.875 37.037 0.00 0.00 0.00 2.69
173 176 7.496747 AGCATTACTCTTCATAGACCTCTTTC 58.503 38.462 0.00 0.00 0.00 2.62
174 177 7.430760 AGCATTACTCTTCATAGACCTCTTT 57.569 36.000 0.00 0.00 0.00 2.52
175 178 7.561722 TGTAGCATTACTCTTCATAGACCTCTT 59.438 37.037 0.00 0.00 0.00 2.85
176 179 7.013846 GTGTAGCATTACTCTTCATAGACCTCT 59.986 40.741 0.00 0.00 0.00 3.69
177 180 7.142680 GTGTAGCATTACTCTTCATAGACCTC 58.857 42.308 0.00 0.00 0.00 3.85
178 181 6.607600 TGTGTAGCATTACTCTTCATAGACCT 59.392 38.462 0.00 0.00 0.00 3.85
179 182 6.806751 TGTGTAGCATTACTCTTCATAGACC 58.193 40.000 0.00 0.00 0.00 3.85
180 183 9.400638 GTATGTGTAGCATTACTCTTCATAGAC 57.599 37.037 0.00 0.00 38.94 2.59
181 184 9.131791 TGTATGTGTAGCATTACTCTTCATAGA 57.868 33.333 0.00 0.00 38.94 1.98
182 185 9.920133 ATGTATGTGTAGCATTACTCTTCATAG 57.080 33.333 0.00 0.00 38.94 2.23
211 214 8.093927 CCACCTGTTTGTAAAATCCATGTAAAT 58.906 33.333 0.00 0.00 0.00 1.40
212 215 7.437748 CCACCTGTTTGTAAAATCCATGTAAA 58.562 34.615 0.00 0.00 0.00 2.01
213 216 6.015010 CCCACCTGTTTGTAAAATCCATGTAA 60.015 38.462 0.00 0.00 0.00 2.41
214 217 5.478679 CCCACCTGTTTGTAAAATCCATGTA 59.521 40.000 0.00 0.00 0.00 2.29
215 218 4.283212 CCCACCTGTTTGTAAAATCCATGT 59.717 41.667 0.00 0.00 0.00 3.21
216 219 4.283212 ACCCACCTGTTTGTAAAATCCATG 59.717 41.667 0.00 0.00 0.00 3.66
217 220 4.488770 ACCCACCTGTTTGTAAAATCCAT 58.511 39.130 0.00 0.00 0.00 3.41
218 221 3.917300 ACCCACCTGTTTGTAAAATCCA 58.083 40.909 0.00 0.00 0.00 3.41
219 222 4.100344 ACAACCCACCTGTTTGTAAAATCC 59.900 41.667 0.00 0.00 0.00 3.01
220 223 5.047188 CACAACCCACCTGTTTGTAAAATC 58.953 41.667 0.00 0.00 0.00 2.17
221 224 4.712337 TCACAACCCACCTGTTTGTAAAAT 59.288 37.500 0.00 0.00 0.00 1.82
222 225 4.087182 TCACAACCCACCTGTTTGTAAAA 58.913 39.130 0.00 0.00 0.00 1.52
223 226 3.698289 TCACAACCCACCTGTTTGTAAA 58.302 40.909 0.00 0.00 0.00 2.01
224 227 3.367646 TCACAACCCACCTGTTTGTAA 57.632 42.857 0.00 0.00 0.00 2.41
225 228 3.586470 ATCACAACCCACCTGTTTGTA 57.414 42.857 0.00 0.00 0.00 2.41
226 229 2.430332 CAATCACAACCCACCTGTTTGT 59.570 45.455 0.00 0.00 0.00 2.83
227 230 2.224018 CCAATCACAACCCACCTGTTTG 60.224 50.000 0.00 0.00 0.00 2.93
228 231 2.038659 CCAATCACAACCCACCTGTTT 58.961 47.619 0.00 0.00 0.00 2.83
229 232 1.216678 TCCAATCACAACCCACCTGTT 59.783 47.619 0.00 0.00 0.00 3.16
230 233 0.850100 TCCAATCACAACCCACCTGT 59.150 50.000 0.00 0.00 0.00 4.00
231 234 1.073763 TCTCCAATCACAACCCACCTG 59.926 52.381 0.00 0.00 0.00 4.00
232 235 1.444933 TCTCCAATCACAACCCACCT 58.555 50.000 0.00 0.00 0.00 4.00
233 236 2.514458 ATCTCCAATCACAACCCACC 57.486 50.000 0.00 0.00 0.00 4.61
234 237 5.253330 TCTTAATCTCCAATCACAACCCAC 58.747 41.667 0.00 0.00 0.00 4.61
235 238 5.500234 CTCTTAATCTCCAATCACAACCCA 58.500 41.667 0.00 0.00 0.00 4.51
236 239 4.884164 CCTCTTAATCTCCAATCACAACCC 59.116 45.833 0.00 0.00 0.00 4.11
237 240 4.884164 CCCTCTTAATCTCCAATCACAACC 59.116 45.833 0.00 0.00 0.00 3.77
238 241 5.745227 TCCCTCTTAATCTCCAATCACAAC 58.255 41.667 0.00 0.00 0.00 3.32
239 242 5.104360 CCTCCCTCTTAATCTCCAATCACAA 60.104 44.000 0.00 0.00 0.00 3.33
240 243 4.410228 CCTCCCTCTTAATCTCCAATCACA 59.590 45.833 0.00 0.00 0.00 3.58
241 244 4.656112 TCCTCCCTCTTAATCTCCAATCAC 59.344 45.833 0.00 0.00 0.00 3.06
242 245 4.895836 TCCTCCCTCTTAATCTCCAATCA 58.104 43.478 0.00 0.00 0.00 2.57
243 246 5.151454 TCTCCTCCCTCTTAATCTCCAATC 58.849 45.833 0.00 0.00 0.00 2.67
244 247 5.154418 CTCTCCTCCCTCTTAATCTCCAAT 58.846 45.833 0.00 0.00 0.00 3.16
245 248 4.551671 CTCTCCTCCCTCTTAATCTCCAA 58.448 47.826 0.00 0.00 0.00 3.53
246 249 3.116939 CCTCTCCTCCCTCTTAATCTCCA 60.117 52.174 0.00 0.00 0.00 3.86
247 250 3.506398 CCTCTCCTCCCTCTTAATCTCC 58.494 54.545 0.00 0.00 0.00 3.71
248 251 2.897326 GCCTCTCCTCCCTCTTAATCTC 59.103 54.545 0.00 0.00 0.00 2.75
249 252 2.248686 TGCCTCTCCTCCCTCTTAATCT 59.751 50.000 0.00 0.00 0.00 2.40
250 253 2.367241 GTGCCTCTCCTCCCTCTTAATC 59.633 54.545 0.00 0.00 0.00 1.75
251 254 2.293184 TGTGCCTCTCCTCCCTCTTAAT 60.293 50.000 0.00 0.00 0.00 1.40
252 255 1.078823 TGTGCCTCTCCTCCCTCTTAA 59.921 52.381 0.00 0.00 0.00 1.85
253 256 0.710588 TGTGCCTCTCCTCCCTCTTA 59.289 55.000 0.00 0.00 0.00 2.10
254 257 0.907230 GTGTGCCTCTCCTCCCTCTT 60.907 60.000 0.00 0.00 0.00 2.85
255 258 1.305718 GTGTGCCTCTCCTCCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
256 259 2.363172 GGTGTGCCTCTCCTCCCTC 61.363 68.421 0.00 0.00 0.00 4.30
257 260 2.284995 GGTGTGCCTCTCCTCCCT 60.285 66.667 0.00 0.00 0.00 4.20
258 261 3.403558 GGGTGTGCCTCTCCTCCC 61.404 72.222 0.00 0.00 34.45 4.30
259 262 3.403558 GGGGTGTGCCTCTCCTCC 61.404 72.222 0.00 0.00 34.45 4.30
260 263 0.691078 TATGGGGTGTGCCTCTCCTC 60.691 60.000 0.00 0.00 35.83 3.71
261 264 0.253160 TTATGGGGTGTGCCTCTCCT 60.253 55.000 0.00 0.00 35.83 3.69
262 265 0.623723 TTTATGGGGTGTGCCTCTCC 59.376 55.000 0.00 0.00 35.83 3.71
263 266 2.507407 TTTTATGGGGTGTGCCTCTC 57.493 50.000 0.00 0.00 35.83 3.20
264 267 2.990740 TTTTTATGGGGTGTGCCTCT 57.009 45.000 0.00 0.00 35.83 3.69
265 268 3.096092 TGATTTTTATGGGGTGTGCCTC 58.904 45.455 0.00 0.00 35.21 4.70
266 269 3.182887 TGATTTTTATGGGGTGTGCCT 57.817 42.857 0.00 0.00 34.45 4.75
267 270 3.369366 CCTTGATTTTTATGGGGTGTGCC 60.369 47.826 0.00 0.00 0.00 5.01
268 271 3.369366 CCCTTGATTTTTATGGGGTGTGC 60.369 47.826 0.00 0.00 34.46 4.57
269 272 4.470334 CCCTTGATTTTTATGGGGTGTG 57.530 45.455 0.00 0.00 34.46 3.82
274 277 4.218312 CTCTCCCCCTTGATTTTTATGGG 58.782 47.826 0.00 0.00 37.68 4.00
275 278 4.646492 CACTCTCCCCCTTGATTTTTATGG 59.354 45.833 0.00 0.00 0.00 2.74
276 279 4.646492 CCACTCTCCCCCTTGATTTTTATG 59.354 45.833 0.00 0.00 0.00 1.90
277 280 4.294970 ACCACTCTCCCCCTTGATTTTTAT 59.705 41.667 0.00 0.00 0.00 1.40
278 281 3.660669 ACCACTCTCCCCCTTGATTTTTA 59.339 43.478 0.00 0.00 0.00 1.52
279 282 2.450886 ACCACTCTCCCCCTTGATTTTT 59.549 45.455 0.00 0.00 0.00 1.94
280 283 2.073776 ACCACTCTCCCCCTTGATTTT 58.926 47.619 0.00 0.00 0.00 1.82
281 284 1.760405 ACCACTCTCCCCCTTGATTT 58.240 50.000 0.00 0.00 0.00 2.17
282 285 1.760405 AACCACTCTCCCCCTTGATT 58.240 50.000 0.00 0.00 0.00 2.57
283 286 2.225908 ACTAACCACTCTCCCCCTTGAT 60.226 50.000 0.00 0.00 0.00 2.57
284 287 1.151413 ACTAACCACTCTCCCCCTTGA 59.849 52.381 0.00 0.00 0.00 3.02
285 288 1.657804 ACTAACCACTCTCCCCCTTG 58.342 55.000 0.00 0.00 0.00 3.61
286 289 2.435203 AACTAACCACTCTCCCCCTT 57.565 50.000 0.00 0.00 0.00 3.95
287 290 2.658489 TCTAACTAACCACTCTCCCCCT 59.342 50.000 0.00 0.00 0.00 4.79
288 291 3.111741 TCTAACTAACCACTCTCCCCC 57.888 52.381 0.00 0.00 0.00 5.40
289 292 4.776308 TCTTTCTAACTAACCACTCTCCCC 59.224 45.833 0.00 0.00 0.00 4.81
290 293 5.997384 TCTTTCTAACTAACCACTCTCCC 57.003 43.478 0.00 0.00 0.00 4.30
291 294 7.668492 TCTTTCTTTCTAACTAACCACTCTCC 58.332 38.462 0.00 0.00 0.00 3.71
292 295 9.198837 CTTCTTTCTTTCTAACTAACCACTCTC 57.801 37.037 0.00 0.00 0.00 3.20
293 296 8.151596 CCTTCTTTCTTTCTAACTAACCACTCT 58.848 37.037 0.00 0.00 0.00 3.24
294 297 7.095144 GCCTTCTTTCTTTCTAACTAACCACTC 60.095 40.741 0.00 0.00 0.00 3.51
295 298 6.711194 GCCTTCTTTCTTTCTAACTAACCACT 59.289 38.462 0.00 0.00 0.00 4.00
296 299 6.711194 AGCCTTCTTTCTTTCTAACTAACCAC 59.289 38.462 0.00 0.00 0.00 4.16
297 300 6.838382 AGCCTTCTTTCTTTCTAACTAACCA 58.162 36.000 0.00 0.00 0.00 3.67
298 301 8.095792 ACTAGCCTTCTTTCTTTCTAACTAACC 58.904 37.037 0.00 0.00 0.00 2.85
299 302 9.142515 GACTAGCCTTCTTTCTTTCTAACTAAC 57.857 37.037 0.00 0.00 0.00 2.34
300 303 8.867097 TGACTAGCCTTCTTTCTTTCTAACTAA 58.133 33.333 0.00 0.00 0.00 2.24
301 304 8.418597 TGACTAGCCTTCTTTCTTTCTAACTA 57.581 34.615 0.00 0.00 0.00 2.24
302 305 7.304497 TGACTAGCCTTCTTTCTTTCTAACT 57.696 36.000 0.00 0.00 0.00 2.24
303 306 6.091577 GCTGACTAGCCTTCTTTCTTTCTAAC 59.908 42.308 0.00 0.00 44.33 2.34
304 307 6.166982 GCTGACTAGCCTTCTTTCTTTCTAA 58.833 40.000 0.00 0.00 44.33 2.10
305 308 5.725362 GCTGACTAGCCTTCTTTCTTTCTA 58.275 41.667 0.00 0.00 44.33 2.10
320 323 2.028045 CACGCAATTACACGCTGACTAG 59.972 50.000 0.00 0.00 0.00 2.57
321 324 1.989864 CACGCAATTACACGCTGACTA 59.010 47.619 0.00 0.00 0.00 2.59
323 326 0.511221 ACACGCAATTACACGCTGAC 59.489 50.000 0.00 0.00 0.00 3.51
324 327 2.067414 TACACGCAATTACACGCTGA 57.933 45.000 0.00 0.00 0.00 4.26
325 328 2.156891 AGTTACACGCAATTACACGCTG 59.843 45.455 0.00 0.00 0.00 5.18
326 329 2.409975 AGTTACACGCAATTACACGCT 58.590 42.857 0.00 0.00 0.00 5.07
327 330 2.867456 AGTTACACGCAATTACACGC 57.133 45.000 0.00 0.00 0.00 5.34
328 331 5.452944 ACAAAAAGTTACACGCAATTACACG 59.547 36.000 0.00 0.00 0.00 4.49
329 332 6.799786 ACAAAAAGTTACACGCAATTACAC 57.200 33.333 0.00 0.00 0.00 2.90
433 436 3.858503 GCAAACCAGACTTGATTTGGCTC 60.859 47.826 0.00 0.00 35.35 4.70
485 488 5.652994 TTTATATGAGGTTGGTGTTTGGC 57.347 39.130 0.00 0.00 0.00 4.52
502 505 8.275015 TGAAGCGTGGAAGATTCAAATTTATA 57.725 30.769 0.00 0.00 42.58 0.98
513 516 0.984230 TCCCTTGAAGCGTGGAAGAT 59.016 50.000 0.00 0.00 0.00 2.40
517 520 0.536460 GGTTTCCCTTGAAGCGTGGA 60.536 55.000 0.00 0.00 32.94 4.02
549 552 7.335924 GGAAATGTAGAAAGTAACATGCACCTA 59.664 37.037 0.00 0.00 36.47 3.08
729 741 3.557054 GCCTATCAATCCCATTAGCGTGA 60.557 47.826 0.00 0.00 0.00 4.35
756 768 6.858993 CACCTCGACTAATTACTATCTGAAGC 59.141 42.308 0.00 0.00 0.00 3.86
793 827 3.119955 GCCCTAATTCCACAAACTTCGTC 60.120 47.826 0.00 0.00 0.00 4.20
830 864 1.133730 TGGTTGTTGGGGTAAGGTGAC 60.134 52.381 0.00 0.00 0.00 3.67
2128 2167 6.505044 TCCATGTGAATCTTTGATTCTGTG 57.495 37.500 17.60 13.46 0.00 3.66
2137 2176 5.988310 TTCATTGCTCCATGTGAATCTTT 57.012 34.783 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.