Multiple sequence alignment - TraesCS3B01G338200

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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 TraesCS3B01G338200 chr3B 100.000 3166 0 0 1 3166 544820617 544817452 0.000000e+00 5847.0
1 TraesCS3B01G338200 chr3B 94.652 187 10 0 183 369 10283369 10283555 1.110000e-74 291.0
2 TraesCS3B01G338200 chr3B 92.857 182 11 2 1838 2018 545008499 545008319 2.420000e-66 263.0
3 TraesCS3B01G338200 chr3B 91.758 182 13 2 1838 2018 544921854 544921674 5.240000e-63 252.0
4 TraesCS3B01G338200 chr3B 94.262 122 3 4 2061 2181 544921673 544921555 1.940000e-42 183.0
5 TraesCS3B01G338200 chr3B 93.600 125 5 3 2061 2184 545008318 545008196 1.940000e-42 183.0
6 TraesCS3B01G338200 chr3B 89.706 136 13 1 1591 1725 544922001 544921866 4.200000e-39 172.0
7 TraesCS3B01G338200 chr3D 91.437 1775 68 26 1436 3166 418410703 418408969 0.000000e+00 2359.0
8 TraesCS3B01G338200 chr3D 91.837 1078 67 7 373 1436 375874523 375873453 0.000000e+00 1483.0
9 TraesCS3B01G338200 chr3D 87.639 1076 117 10 373 1435 183892181 183893253 0.000000e+00 1236.0
10 TraesCS3B01G338200 chr3D 93.460 367 18 4 1838 2198 418482273 418481907 9.990000e-150 540.0
11 TraesCS3B01G338200 chr3D 93.617 282 14 2 1838 2115 418705168 418704887 4.880000e-113 418.0
12 TraesCS3B01G338200 chr3D 91.525 177 12 3 1 175 375874716 375874541 1.130000e-59 241.0
13 TraesCS3B01G338200 chr3D 90.805 174 13 3 1 172 89555727 89555899 2.460000e-56 230.0
14 TraesCS3B01G338200 chr3D 80.000 320 34 4 1436 1725 418705507 418705188 3.200000e-50 209.0
15 TraesCS3B01G338200 chr3D 89.865 148 11 3 1591 1737 418482420 418482276 1.500000e-43 187.0
16 TraesCS3B01G338200 chr3A 90.596 1744 96 26 1436 3166 532644571 532646259 0.000000e+00 2250.0
17 TraesCS3B01G338200 chr3A 94.301 193 7 3 182 372 11754283 11754093 3.090000e-75 292.0
18 TraesCS3B01G338200 chr3A 91.912 136 10 1 1591 1725 532488550 532488685 4.170000e-44 189.0
19 TraesCS3B01G338200 chr2B 92.744 1075 61 5 373 1434 46077461 46076391 0.000000e+00 1537.0
20 TraesCS3B01G338200 chr2B 95.408 196 4 4 183 374 87164746 87164552 1.100000e-79 307.0
21 TraesCS3B01G338200 chr2B 94.304 158 7 2 1 158 46077654 46077499 1.130000e-59 241.0
22 TraesCS3B01G338200 chr2B 91.195 159 11 3 1 159 798327647 798327492 2.470000e-51 213.0
23 TraesCS3B01G338200 chr5D 92.537 1072 65 5 373 1430 466601603 466602673 0.000000e+00 1522.0
24 TraesCS3B01G338200 chr5D 91.379 174 12 3 1 172 466601410 466601582 5.280000e-58 235.0
25 TraesCS3B01G338200 chr5D 100.000 43 0 0 140 182 466601568 466601610 2.620000e-11 80.5
26 TraesCS3B01G338200 chr2D 91.450 1076 76 8 373 1435 53581914 53580842 0.000000e+00 1463.0
27 TraesCS3B01G338200 chr2D 88.941 1067 98 14 382 1434 505641985 505643045 0.000000e+00 1299.0
28 TraesCS3B01G338200 chr2D 91.034 145 13 0 1 145 53582107 53581963 2.490000e-46 196.0
29 TraesCS3B01G338200 chr2D 86.782 174 20 3 1 172 505641792 505641964 1.160000e-44 191.0
30 TraesCS3B01G338200 chr7B 91.188 1044 77 5 403 1433 695985340 695986381 0.000000e+00 1404.0
31 TraesCS3B01G338200 chr4A 92.510 988 60 9 373 1348 649019625 649018640 0.000000e+00 1402.0
32 TraesCS3B01G338200 chr4A 93.443 183 12 0 1263 1445 649061364 649061182 4.020000e-69 272.0
33 TraesCS3B01G338200 chr4A 91.139 158 12 2 1 158 649068418 649068263 2.470000e-51 213.0
34 TraesCS3B01G338200 chr4A 95.000 60 1 2 99 158 649019720 649019663 3.360000e-15 93.5
35 TraesCS3B01G338200 chr4B 90.700 1043 71 7 373 1401 11910499 11909469 0.000000e+00 1365.0
36 TraesCS3B01G338200 chr4B 94.737 190 8 2 184 372 445636922 445636734 8.590000e-76 294.0
37 TraesCS3B01G338200 chr1B 88.693 1079 103 11 373 1434 54991707 54990631 0.000000e+00 1299.0
38 TraesCS3B01G338200 chr1B 88.415 1079 106 11 373 1434 54950743 54949667 0.000000e+00 1282.0
39 TraesCS3B01G338200 chr4D 87.037 918 91 16 543 1442 152898228 152899135 0.000000e+00 1011.0
40 TraesCS3B01G338200 chr6D 77.754 935 152 39 541 1435 9824626 9823708 1.010000e-144 523.0
41 TraesCS3B01G338200 chr5A 88.194 288 21 3 1164 1438 595103189 595103476 6.550000e-87 331.0
42 TraesCS3B01G338200 chr5A 93.684 190 8 1 180 369 379180500 379180685 6.690000e-72 281.0
43 TraesCS3B01G338200 chr5A 91.667 192 10 3 183 372 451757726 451757539 8.710000e-66 261.0
44 TraesCS3B01G338200 chr5A 83.085 201 15 7 1 182 595088755 595088955 7.030000e-37 165.0
45 TraesCS3B01G338200 chr6B 94.764 191 8 2 180 369 408678602 408678413 2.390000e-76 296.0
46 TraesCS3B01G338200 chr6B 93.717 191 7 2 183 372 264649098 264648912 6.690000e-72 281.0
47 TraesCS3B01G338200 chr6A 93.194 191 8 2 183 372 454642270 454642084 3.110000e-70 276.0


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 TraesCS3B01G338200 chr3B 544817452 544820617 3165 True 5847.00 5847 100.000000 1 3166 1 chr3B.!!$R1 3165
1 TraesCS3B01G338200 chr3D 418408969 418410703 1734 True 2359.00 2359 91.437000 1436 3166 1 chr3D.!!$R1 1730
2 TraesCS3B01G338200 chr3D 183892181 183893253 1072 False 1236.00 1236 87.639000 373 1435 1 chr3D.!!$F2 1062
3 TraesCS3B01G338200 chr3D 375873453 375874716 1263 True 862.00 1483 91.681000 1 1436 2 chr3D.!!$R2 1435
4 TraesCS3B01G338200 chr3D 418481907 418482420 513 True 363.50 540 91.662500 1591 2198 2 chr3D.!!$R3 607
5 TraesCS3B01G338200 chr3D 418704887 418705507 620 True 313.50 418 86.808500 1436 2115 2 chr3D.!!$R4 679
6 TraesCS3B01G338200 chr3A 532644571 532646259 1688 False 2250.00 2250 90.596000 1436 3166 1 chr3A.!!$F2 1730
7 TraesCS3B01G338200 chr2B 46076391 46077654 1263 True 889.00 1537 93.524000 1 1434 2 chr2B.!!$R3 1433
8 TraesCS3B01G338200 chr5D 466601410 466602673 1263 False 612.50 1522 94.638667 1 1430 3 chr5D.!!$F1 1429
9 TraesCS3B01G338200 chr2D 53580842 53582107 1265 True 829.50 1463 91.242000 1 1435 2 chr2D.!!$R1 1434
10 TraesCS3B01G338200 chr2D 505641792 505643045 1253 False 745.00 1299 87.861500 1 1434 2 chr2D.!!$F1 1433
11 TraesCS3B01G338200 chr7B 695985340 695986381 1041 False 1404.00 1404 91.188000 403 1433 1 chr7B.!!$F1 1030
12 TraesCS3B01G338200 chr4A 649018640 649019720 1080 True 747.75 1402 93.755000 99 1348 2 chr4A.!!$R3 1249
13 TraesCS3B01G338200 chr4B 11909469 11910499 1030 True 1365.00 1365 90.700000 373 1401 1 chr4B.!!$R1 1028
14 TraesCS3B01G338200 chr1B 54990631 54991707 1076 True 1299.00 1299 88.693000 373 1434 1 chr1B.!!$R2 1061
15 TraesCS3B01G338200 chr1B 54949667 54950743 1076 True 1282.00 1282 88.415000 373 1434 1 chr1B.!!$R1 1061
16 TraesCS3B01G338200 chr4D 152898228 152899135 907 False 1011.00 1011 87.037000 543 1442 1 chr4D.!!$F1 899
17 TraesCS3B01G338200 chr6D 9823708 9824626 918 True 523.00 523 77.754000 541 1435 1 chr6D.!!$R1 894

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
745 774 0.249699 CCTTGGGGGCGTTGTTTTTC 60.250 55.0 0.0 0.0 0.0 2.29 F
925 965 0.391597 ACGGTGATGTCTCGGTGTTT 59.608 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1750 0.031585 TCGAACCGGCGGATCATAAG 59.968 55.0 35.78 17.28 0.0 1.73 R
2799 2916 0.251077 CTGAAGCCTCCCAAGCAACT 60.251 55.0 0.00 0.00 0.0 3.16 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
39 40 0.321919 GTCTGTGAGGCTTCATGGCA 60.322 55.000 0.30 0.00 44.55 4.92
59 60 0.914417 TCCAGATCCGGCCTTTCCTT 60.914 55.000 0.00 0.00 0.00 3.36
181 201 4.982701 GCTGGTGGCAGCCAAGGT 62.983 66.667 18.28 0.00 42.05 3.50
182 202 2.674380 CTGGTGGCAGCCAAGGTC 60.674 66.667 18.28 2.92 38.18 3.85
183 203 3.496309 CTGGTGGCAGCCAAGGTCA 62.496 63.158 18.28 11.44 38.18 4.02
184 204 2.674380 GGTGGCAGCCAAGGTCAG 60.674 66.667 18.28 0.00 34.18 3.51
185 205 2.113986 GTGGCAGCCAAGGTCAGT 59.886 61.111 18.28 0.00 34.18 3.41
186 206 2.113774 TGGCAGCCAAGGTCAGTG 59.886 61.111 13.33 0.00 0.00 3.66
187 207 2.674380 GGCAGCCAAGGTCAGTGG 60.674 66.667 6.55 0.00 39.33 4.00
192 212 2.046892 CCAAGGTCAGTGGCGGAG 60.047 66.667 0.00 0.00 0.00 4.63
218 238 1.839424 AAAAAGAATGAGGAGGGCCG 58.161 50.000 0.00 0.00 39.96 6.13
219 239 0.991920 AAAAGAATGAGGAGGGCCGA 59.008 50.000 0.00 0.00 39.96 5.54
220 240 0.543749 AAAGAATGAGGAGGGCCGAG 59.456 55.000 0.00 0.00 39.96 4.63
221 241 0.618968 AAGAATGAGGAGGGCCGAGT 60.619 55.000 0.00 0.00 39.96 4.18
222 242 1.144936 GAATGAGGAGGGCCGAGTG 59.855 63.158 0.00 0.00 39.96 3.51
223 243 1.613630 AATGAGGAGGGCCGAGTGT 60.614 57.895 0.00 0.00 39.96 3.55
224 244 1.201429 AATGAGGAGGGCCGAGTGTT 61.201 55.000 0.00 0.00 39.96 3.32
225 245 1.903877 ATGAGGAGGGCCGAGTGTTG 61.904 60.000 0.00 0.00 39.96 3.33
226 246 3.959991 GAGGAGGGCCGAGTGTTGC 62.960 68.421 0.00 0.00 39.96 4.17
233 253 4.379243 CCGAGTGTTGCCGAGCCT 62.379 66.667 0.00 0.00 0.00 4.58
234 254 2.357517 CGAGTGTTGCCGAGCCTT 60.358 61.111 0.00 0.00 0.00 4.35
235 255 2.671177 CGAGTGTTGCCGAGCCTTG 61.671 63.158 0.00 0.00 0.00 3.61
236 256 1.598130 GAGTGTTGCCGAGCCTTGT 60.598 57.895 0.00 0.00 0.00 3.16
237 257 1.569479 GAGTGTTGCCGAGCCTTGTC 61.569 60.000 0.00 0.00 0.00 3.18
238 258 1.891919 GTGTTGCCGAGCCTTGTCA 60.892 57.895 0.00 0.00 0.00 3.58
239 259 1.597854 TGTTGCCGAGCCTTGTCAG 60.598 57.895 0.00 0.00 0.00 3.51
240 260 2.032528 TTGCCGAGCCTTGTCAGG 59.967 61.111 0.00 0.00 44.28 3.86
241 261 3.551496 TTGCCGAGCCTTGTCAGGG 62.551 63.158 0.00 0.00 41.21 4.45
242 262 3.706373 GCCGAGCCTTGTCAGGGA 61.706 66.667 4.91 0.00 41.21 4.20
243 263 2.581354 CCGAGCCTTGTCAGGGAG 59.419 66.667 4.91 0.00 41.21 4.30
244 264 2.581354 CGAGCCTTGTCAGGGAGG 59.419 66.667 4.91 0.00 41.21 4.30
245 265 2.993853 GAGCCTTGTCAGGGAGGG 59.006 66.667 4.91 0.00 41.21 4.30
246 266 3.334054 AGCCTTGTCAGGGAGGGC 61.334 66.667 4.91 0.00 41.21 5.19
247 267 4.432741 GCCTTGTCAGGGAGGGCC 62.433 72.222 4.91 0.00 41.21 5.80
248 268 2.935481 CCTTGTCAGGGAGGGCCA 60.935 66.667 6.18 0.00 36.36 5.36
249 269 2.538141 CCTTGTCAGGGAGGGCCAA 61.538 63.158 6.18 0.00 36.36 4.52
250 270 1.303643 CTTGTCAGGGAGGGCCAAC 60.304 63.158 6.18 0.00 35.15 3.77
251 271 2.771328 CTTGTCAGGGAGGGCCAACC 62.771 65.000 6.18 7.46 40.67 3.77
263 283 2.445682 GGCCAACCCACCATAATACA 57.554 50.000 0.00 0.00 0.00 2.29
264 284 2.028876 GGCCAACCCACCATAATACAC 58.971 52.381 0.00 0.00 0.00 2.90
265 285 2.028876 GCCAACCCACCATAATACACC 58.971 52.381 0.00 0.00 0.00 4.16
266 286 2.621929 GCCAACCCACCATAATACACCA 60.622 50.000 0.00 0.00 0.00 4.17
267 287 3.909732 CCAACCCACCATAATACACCAT 58.090 45.455 0.00 0.00 0.00 3.55
268 288 4.285863 CCAACCCACCATAATACACCATT 58.714 43.478 0.00 0.00 0.00 3.16
269 289 4.714308 CCAACCCACCATAATACACCATTT 59.286 41.667 0.00 0.00 0.00 2.32
270 290 5.188751 CCAACCCACCATAATACACCATTTT 59.811 40.000 0.00 0.00 0.00 1.82
271 291 6.337356 CAACCCACCATAATACACCATTTTC 58.663 40.000 0.00 0.00 0.00 2.29
272 292 5.584913 ACCCACCATAATACACCATTTTCA 58.415 37.500 0.00 0.00 0.00 2.69
273 293 6.201591 ACCCACCATAATACACCATTTTCAT 58.798 36.000 0.00 0.00 0.00 2.57
274 294 7.358263 ACCCACCATAATACACCATTTTCATA 58.642 34.615 0.00 0.00 0.00 2.15
275 295 7.505585 ACCCACCATAATACACCATTTTCATAG 59.494 37.037 0.00 0.00 0.00 2.23
276 296 7.370383 CCACCATAATACACCATTTTCATAGC 58.630 38.462 0.00 0.00 0.00 2.97
277 297 7.014134 CCACCATAATACACCATTTTCATAGCA 59.986 37.037 0.00 0.00 0.00 3.49
278 298 8.412456 CACCATAATACACCATTTTCATAGCAA 58.588 33.333 0.00 0.00 0.00 3.91
279 299 8.976353 ACCATAATACACCATTTTCATAGCAAA 58.024 29.630 0.00 0.00 0.00 3.68
280 300 9.985730 CCATAATACACCATTTTCATAGCAAAT 57.014 29.630 0.00 0.00 0.00 2.32
286 306 8.931385 ACACCATTTTCATAGCAAATAATCAC 57.069 30.769 0.00 0.00 0.00 3.06
287 307 8.752187 ACACCATTTTCATAGCAAATAATCACT 58.248 29.630 0.00 0.00 0.00 3.41
288 308 9.590451 CACCATTTTCATAGCAAATAATCACTT 57.410 29.630 0.00 0.00 0.00 3.16
289 309 9.590451 ACCATTTTCATAGCAAATAATCACTTG 57.410 29.630 0.00 0.00 0.00 3.16
290 310 9.590451 CCATTTTCATAGCAAATAATCACTTGT 57.410 29.630 0.00 0.00 0.00 3.16
294 314 9.844790 TTTCATAGCAAATAATCACTTGTTCAG 57.155 29.630 0.00 0.00 0.00 3.02
295 315 8.791327 TCATAGCAAATAATCACTTGTTCAGA 57.209 30.769 0.00 0.00 0.00 3.27
296 316 9.399797 TCATAGCAAATAATCACTTGTTCAGAT 57.600 29.630 0.00 0.00 0.00 2.90
297 317 9.447040 CATAGCAAATAATCACTTGTTCAGATG 57.553 33.333 0.00 0.00 0.00 2.90
298 318 7.458409 AGCAAATAATCACTTGTTCAGATGT 57.542 32.000 0.00 0.00 0.00 3.06
299 319 8.565896 AGCAAATAATCACTTGTTCAGATGTA 57.434 30.769 0.00 0.00 0.00 2.29
300 320 9.182214 AGCAAATAATCACTTGTTCAGATGTAT 57.818 29.630 0.00 0.00 0.00 2.29
307 327 8.839310 ATCACTTGTTCAGATGTATATTAGGC 57.161 34.615 0.00 0.00 0.00 3.93
308 328 8.023021 TCACTTGTTCAGATGTATATTAGGCT 57.977 34.615 0.00 0.00 0.00 4.58
309 329 8.486210 TCACTTGTTCAGATGTATATTAGGCTT 58.514 33.333 0.00 0.00 0.00 4.35
310 330 9.764363 CACTTGTTCAGATGTATATTAGGCTTA 57.236 33.333 0.00 0.00 0.00 3.09
327 347 8.974060 TTAGGCTTAAATCAGTTGTATTAGGG 57.026 34.615 0.00 0.00 0.00 3.53
328 348 6.365520 AGGCTTAAATCAGTTGTATTAGGGG 58.634 40.000 0.00 0.00 0.00 4.79
329 349 5.535030 GGCTTAAATCAGTTGTATTAGGGGG 59.465 44.000 0.00 0.00 0.00 5.40
371 391 4.856801 CCCCCGTCTCCGCCATTG 62.857 72.222 0.00 0.00 0.00 2.82
431 451 0.319040 GTGAGCAGCTGTGTCTTCGA 60.319 55.000 16.64 0.00 0.00 3.71
451 471 1.073897 GCTTCTTGCTGGACCTGGT 59.926 57.895 0.00 0.00 38.95 4.00
455 475 2.449518 TTGCTGGACCTGGTGGGA 60.450 61.111 2.82 0.00 38.76 4.37
485 505 1.073897 GACTAGCATGGGGATGGGC 59.926 63.158 0.00 0.00 0.00 5.36
486 506 2.033141 CTAGCATGGGGATGGGCG 59.967 66.667 0.00 0.00 0.00 6.13
487 507 2.447572 TAGCATGGGGATGGGCGA 60.448 61.111 0.00 0.00 0.00 5.54
574 597 2.193536 GCCTTGTGCCGACCTTGTT 61.194 57.895 0.00 0.00 0.00 2.83
650 677 4.281527 AGCTGCTGCCACCTGCTT 62.282 61.111 12.44 0.00 42.00 3.91
664 692 1.406069 CCTGCTTATTCGTGTGCTCCT 60.406 52.381 0.00 0.00 0.00 3.69
725 754 2.419297 GGCATCTTGATGTCGTTCTCCT 60.419 50.000 11.61 0.00 0.00 3.69
745 774 0.249699 CCTTGGGGGCGTTGTTTTTC 60.250 55.000 0.00 0.00 0.00 2.29
925 965 0.391597 ACGGTGATGTCTCGGTGTTT 59.608 50.000 0.00 0.00 0.00 2.83
936 976 1.826054 CGGTGTTTGGTGCCCTTCA 60.826 57.895 0.00 0.00 0.00 3.02
949 989 2.733218 CTTCAACGGCGCGTGAGA 60.733 61.111 6.90 2.72 39.99 3.27
1035 1075 3.325753 GGTGCAGGGGCTGTCTCT 61.326 66.667 0.00 0.00 41.91 3.10
1083 1123 2.691771 GGCTCTCTCTGTCGCGACA 61.692 63.158 36.96 36.96 39.32 4.35
1155 1197 0.969149 AAGGTGTGAGTGATCGCAGA 59.031 50.000 9.33 0.00 45.75 4.26
1243 1288 1.036707 GCTCCTGCTCTCTCGGTTAT 58.963 55.000 0.00 0.00 36.03 1.89
1250 1295 3.478509 TGCTCTCTCGGTTATCCTAGTC 58.521 50.000 0.00 0.00 0.00 2.59
1275 1331 1.301677 GGGTGCTGTCAGCTACTTGC 61.302 60.000 24.76 9.19 42.97 4.01
1365 1427 2.224549 GTGCAGCCGTTGTGTTTGTATA 59.775 45.455 0.00 0.00 0.00 1.47
1461 1523 3.007920 CTGAGGAGGTGCAGGCCT 61.008 66.667 0.00 0.00 42.53 5.19
1499 1561 4.221422 GATGGCGTCGGGCTGCTA 62.221 66.667 0.00 0.00 42.94 3.49
1670 1770 0.677288 TTATGATCCGCCGGTTCGAT 59.323 50.000 1.63 0.97 0.00 3.59
1739 1839 6.156256 TGATGATGATGATGGCATGAGATCTA 59.844 38.462 3.81 0.00 34.11 1.98
1766 1866 3.724508 TGCCCACACATACAAAAACTG 57.275 42.857 0.00 0.00 0.00 3.16
1786 1886 6.492007 ACTGAACTTCTATGCAAGACATTG 57.508 37.500 0.00 0.00 40.38 2.82
1832 1933 0.250901 GGTGGCCTCTCTTTTGCTCA 60.251 55.000 3.32 0.00 0.00 4.26
1941 2046 6.852420 TTGTTCTATAGCCAACTAGACTGT 57.148 37.500 0.00 0.00 0.00 3.55
1963 2068 5.222151 TGTCTTAATATCCCAACACCCACAA 60.222 40.000 0.00 0.00 0.00 3.33
2133 2241 5.866633 CAGCAGTAGCCTATAAATAGCACTC 59.133 44.000 0.00 0.00 43.56 3.51
2237 2350 4.574828 TGCTCCAGTAAAAAGAACAGACAC 59.425 41.667 0.00 0.00 0.00 3.67
2241 2354 5.522460 TCCAGTAAAAAGAACAGACACGAAG 59.478 40.000 0.00 0.00 0.00 3.79
2244 2357 1.594331 AAAGAACAGACACGAAGGCC 58.406 50.000 0.00 0.00 0.00 5.19
2246 2359 1.671379 GAACAGACACGAAGGCCCC 60.671 63.158 0.00 0.00 0.00 5.80
2277 2390 3.494332 ACCTGTACACTACGGTCTTCTT 58.506 45.455 0.00 0.00 32.75 2.52
2279 2392 3.425892 CCTGTACACTACGGTCTTCTTCG 60.426 52.174 0.00 0.00 33.14 3.79
2283 2396 0.963962 ACTACGGTCTTCTTCGCCAA 59.036 50.000 0.00 0.00 0.00 4.52
2323 2436 2.701163 CTAGATTGCCCCGACGAGCC 62.701 65.000 0.00 0.00 0.00 4.70
2363 2476 3.997021 ACTGCACAGAGTTACAGCAATAC 59.003 43.478 4.31 0.00 34.45 1.89
2488 2601 9.965902 ATGAGATTAATCTGAAACCTACACTTT 57.034 29.630 22.61 0.00 37.25 2.66
2536 2650 1.839994 CCTGAGCCCATGGAACTTCTA 59.160 52.381 15.22 0.86 0.00 2.10
2538 2652 2.237143 CTGAGCCCATGGAACTTCTACA 59.763 50.000 15.22 3.74 0.00 2.74
2545 2659 3.686726 CCATGGAACTTCTACAAGCTCAC 59.313 47.826 5.56 0.00 32.09 3.51
2547 2661 3.728845 TGGAACTTCTACAAGCTCACAC 58.271 45.455 0.00 0.00 32.09 3.82
2549 2663 3.244249 GGAACTTCTACAAGCTCACACCT 60.244 47.826 0.00 0.00 32.09 4.00
2550 2664 4.381411 GAACTTCTACAAGCTCACACCTT 58.619 43.478 0.00 0.00 32.09 3.50
2551 2665 4.423625 ACTTCTACAAGCTCACACCTTT 57.576 40.909 0.00 0.00 32.09 3.11
2552 2666 5.546621 ACTTCTACAAGCTCACACCTTTA 57.453 39.130 0.00 0.00 32.09 1.85
2564 2678 4.585879 TCACACCTTTACTTATCAAGGGC 58.414 43.478 3.10 0.00 43.59 5.19
2573 2687 3.290710 ACTTATCAAGGGCGCAATCATT 58.709 40.909 10.83 0.00 0.00 2.57
2583 2697 2.097954 GGCGCAATCATTCATGTCTTCA 59.902 45.455 10.83 0.00 0.00 3.02
2590 2704 8.715088 CGCAATCATTCATGTCTTCAGATATAA 58.285 33.333 0.00 0.00 0.00 0.98
2598 2712 9.770097 TTCATGTCTTCAGATATAAGAATCACC 57.230 33.333 0.00 0.00 34.86 4.02
2599 2713 8.927411 TCATGTCTTCAGATATAAGAATCACCA 58.073 33.333 0.00 0.00 34.86 4.17
2603 2720 8.370940 GTCTTCAGATATAAGAATCACCATCCA 58.629 37.037 0.00 0.00 34.86 3.41
2608 2725 9.736414 CAGATATAAGAATCACCATCCAAAGAT 57.264 33.333 0.00 0.00 0.00 2.40
2616 2733 4.269183 TCACCATCCAAAGATAATTGCGT 58.731 39.130 0.00 0.00 0.00 5.24
2617 2734 4.335315 TCACCATCCAAAGATAATTGCGTC 59.665 41.667 0.00 0.00 0.00 5.19
2618 2735 3.632145 ACCATCCAAAGATAATTGCGTCC 59.368 43.478 0.00 0.00 0.00 4.79
2632 2749 1.153549 CGTCCAGGCCTTGAGCTAC 60.154 63.158 6.82 0.00 43.05 3.58
2635 2752 0.833287 TCCAGGCCTTGAGCTACATC 59.167 55.000 0.00 0.00 43.05 3.06
2657 2774 1.978580 ACCAGGAACCGATTCAGAAGT 59.021 47.619 0.00 0.00 36.46 3.01
2700 2817 1.076727 GGGGGTAAAACTGCTGGCT 59.923 57.895 0.00 0.00 0.00 4.75
2724 2841 1.656095 GTGGTTCTCTGAGCGAAATCG 59.344 52.381 0.00 0.00 43.27 3.34
2760 2877 0.880278 GCTGCTCGTTTGTGTGAGGA 60.880 55.000 0.00 0.00 32.78 3.71
2799 2916 0.543277 CAACTGGCATCTCCCTGCTA 59.457 55.000 0.00 0.00 41.95 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.131638 TGAAGCCTCACAGACCAAGT 58.868 50.000 0.00 0.00 0.00 3.16
39 40 0.695803 AGGAAAGGCCGGATCTGGAT 60.696 55.000 25.54 8.89 43.43 3.41
175 195 2.046892 CTCCGCCACTGACCTTGG 60.047 66.667 0.00 0.00 37.17 3.61
176 196 2.743928 GCTCCGCCACTGACCTTG 60.744 66.667 0.00 0.00 0.00 3.61
199 219 1.354368 TCGGCCCTCCTCATTCTTTTT 59.646 47.619 0.00 0.00 0.00 1.94
200 220 0.991920 TCGGCCCTCCTCATTCTTTT 59.008 50.000 0.00 0.00 0.00 2.27
201 221 0.543749 CTCGGCCCTCCTCATTCTTT 59.456 55.000 0.00 0.00 0.00 2.52
202 222 0.618968 ACTCGGCCCTCCTCATTCTT 60.619 55.000 0.00 0.00 0.00 2.52
203 223 1.002274 ACTCGGCCCTCCTCATTCT 59.998 57.895 0.00 0.00 0.00 2.40
204 224 1.144936 CACTCGGCCCTCCTCATTC 59.855 63.158 0.00 0.00 0.00 2.67
205 225 1.201429 AACACTCGGCCCTCCTCATT 61.201 55.000 0.00 0.00 0.00 2.57
206 226 1.613630 AACACTCGGCCCTCCTCAT 60.614 57.895 0.00 0.00 0.00 2.90
207 227 2.203788 AACACTCGGCCCTCCTCA 60.204 61.111 0.00 0.00 0.00 3.86
208 228 2.266055 CAACACTCGGCCCTCCTC 59.734 66.667 0.00 0.00 0.00 3.71
209 229 4.021925 GCAACACTCGGCCCTCCT 62.022 66.667 0.00 0.00 0.00 3.69
216 236 3.883744 AAGGCTCGGCAACACTCGG 62.884 63.158 0.00 0.00 0.00 4.63
217 237 2.357517 AAGGCTCGGCAACACTCG 60.358 61.111 0.00 0.00 0.00 4.18
218 238 1.569479 GACAAGGCTCGGCAACACTC 61.569 60.000 0.00 0.00 0.00 3.51
219 239 1.598130 GACAAGGCTCGGCAACACT 60.598 57.895 0.00 0.00 0.00 3.55
220 240 1.845809 CTGACAAGGCTCGGCAACAC 61.846 60.000 0.00 0.00 0.00 3.32
221 241 1.597854 CTGACAAGGCTCGGCAACA 60.598 57.895 0.00 0.00 0.00 3.33
222 242 2.328099 CCTGACAAGGCTCGGCAAC 61.328 63.158 0.00 0.00 36.56 4.17
223 243 2.032528 CCTGACAAGGCTCGGCAA 59.967 61.111 0.00 0.00 36.56 4.52
224 244 4.020617 CCCTGACAAGGCTCGGCA 62.021 66.667 0.00 0.00 42.96 5.69
225 245 3.672295 CTCCCTGACAAGGCTCGGC 62.672 68.421 0.00 0.00 42.96 5.54
226 246 2.581354 CTCCCTGACAAGGCTCGG 59.419 66.667 0.00 0.00 42.96 4.63
227 247 2.581354 CCTCCCTGACAAGGCTCG 59.419 66.667 0.00 0.00 42.96 5.03
228 248 2.993853 CCCTCCCTGACAAGGCTC 59.006 66.667 0.00 0.00 42.96 4.70
229 249 3.334054 GCCCTCCCTGACAAGGCT 61.334 66.667 0.00 0.00 42.96 4.58
230 250 4.432741 GGCCCTCCCTGACAAGGC 62.433 72.222 0.00 0.00 42.96 4.35
231 251 2.538141 TTGGCCCTCCCTGACAAGG 61.538 63.158 0.00 0.00 44.06 3.61
232 252 1.303643 GTTGGCCCTCCCTGACAAG 60.304 63.158 0.00 0.00 0.00 3.16
233 253 2.840753 GGTTGGCCCTCCCTGACAA 61.841 63.158 0.00 0.00 0.00 3.18
234 254 3.256960 GGTTGGCCCTCCCTGACA 61.257 66.667 0.00 0.00 0.00 3.58
244 264 2.028876 GTGTATTATGGTGGGTTGGCC 58.971 52.381 0.00 0.00 0.00 5.36
245 265 2.028876 GGTGTATTATGGTGGGTTGGC 58.971 52.381 0.00 0.00 0.00 4.52
246 266 3.374042 TGGTGTATTATGGTGGGTTGG 57.626 47.619 0.00 0.00 0.00 3.77
247 267 5.930837 AAATGGTGTATTATGGTGGGTTG 57.069 39.130 0.00 0.00 0.00 3.77
248 268 6.019748 TGAAAATGGTGTATTATGGTGGGTT 58.980 36.000 0.00 0.00 0.00 4.11
249 269 5.584913 TGAAAATGGTGTATTATGGTGGGT 58.415 37.500 0.00 0.00 0.00 4.51
250 270 6.729690 ATGAAAATGGTGTATTATGGTGGG 57.270 37.500 0.00 0.00 0.00 4.61
251 271 7.014134 TGCTATGAAAATGGTGTATTATGGTGG 59.986 37.037 0.00 0.00 0.00 4.61
252 272 7.939782 TGCTATGAAAATGGTGTATTATGGTG 58.060 34.615 0.00 0.00 0.00 4.17
253 273 8.532186 TTGCTATGAAAATGGTGTATTATGGT 57.468 30.769 0.00 0.00 0.00 3.55
254 274 9.985730 ATTTGCTATGAAAATGGTGTATTATGG 57.014 29.630 0.00 0.00 0.00 2.74
261 281 8.752187 AGTGATTATTTGCTATGAAAATGGTGT 58.248 29.630 0.00 0.00 0.00 4.16
262 282 9.590451 AAGTGATTATTTGCTATGAAAATGGTG 57.410 29.630 0.00 0.00 0.00 4.17
263 283 9.590451 CAAGTGATTATTTGCTATGAAAATGGT 57.410 29.630 0.00 0.00 0.00 3.55
264 284 9.590451 ACAAGTGATTATTTGCTATGAAAATGG 57.410 29.630 0.00 0.00 0.00 3.16
268 288 9.844790 CTGAACAAGTGATTATTTGCTATGAAA 57.155 29.630 0.00 0.00 0.00 2.69
269 289 9.230122 TCTGAACAAGTGATTATTTGCTATGAA 57.770 29.630 0.00 0.00 0.00 2.57
270 290 8.791327 TCTGAACAAGTGATTATTTGCTATGA 57.209 30.769 0.00 0.00 0.00 2.15
271 291 9.447040 CATCTGAACAAGTGATTATTTGCTATG 57.553 33.333 0.00 0.00 0.00 2.23
272 292 9.182214 ACATCTGAACAAGTGATTATTTGCTAT 57.818 29.630 0.00 0.00 0.00 2.97
273 293 8.565896 ACATCTGAACAAGTGATTATTTGCTA 57.434 30.769 0.00 0.00 0.00 3.49
274 294 7.458409 ACATCTGAACAAGTGATTATTTGCT 57.542 32.000 0.00 0.00 0.00 3.91
281 301 9.277783 GCCTAATATACATCTGAACAAGTGATT 57.722 33.333 0.00 0.00 0.00 2.57
282 302 8.654997 AGCCTAATATACATCTGAACAAGTGAT 58.345 33.333 0.00 0.00 0.00 3.06
283 303 8.023021 AGCCTAATATACATCTGAACAAGTGA 57.977 34.615 0.00 0.00 0.00 3.41
284 304 8.668510 AAGCCTAATATACATCTGAACAAGTG 57.331 34.615 0.00 0.00 0.00 3.16
301 321 9.574516 CCCTAATACAACTGATTTAAGCCTAAT 57.425 33.333 0.00 0.00 0.00 1.73
302 322 7.996644 CCCCTAATACAACTGATTTAAGCCTAA 59.003 37.037 0.00 0.00 0.00 2.69
303 323 7.420913 CCCCCTAATACAACTGATTTAAGCCTA 60.421 40.741 0.00 0.00 0.00 3.93
304 324 6.365520 CCCCTAATACAACTGATTTAAGCCT 58.634 40.000 0.00 0.00 0.00 4.58
305 325 5.535030 CCCCCTAATACAACTGATTTAAGCC 59.465 44.000 0.00 0.00 0.00 4.35
306 326 6.635030 CCCCCTAATACAACTGATTTAAGC 57.365 41.667 0.00 0.00 0.00 3.09
366 386 0.901580 AGAGCAACCTTGGCCAATGG 60.902 55.000 20.85 23.02 0.00 3.16
367 387 1.838112 TAGAGCAACCTTGGCCAATG 58.162 50.000 20.85 19.34 0.00 2.82
368 388 2.171003 GTTAGAGCAACCTTGGCCAAT 58.829 47.619 20.85 1.79 0.00 3.16
369 389 1.144913 AGTTAGAGCAACCTTGGCCAA 59.855 47.619 19.25 19.25 37.93 4.52
370 390 0.771127 AGTTAGAGCAACCTTGGCCA 59.229 50.000 0.00 0.00 37.93 5.36
371 391 1.454201 GAGTTAGAGCAACCTTGGCC 58.546 55.000 0.00 0.00 37.93 5.36
418 438 1.342819 AGAAGCTTCGAAGACACAGCT 59.657 47.619 28.95 15.23 44.71 4.24
455 475 2.178521 CTAGTCACGGCGAGCGTT 59.821 61.111 16.62 0.00 0.00 4.84
485 505 2.743664 TGATTCCAGCAACACAAGATCG 59.256 45.455 0.00 0.00 0.00 3.69
486 506 4.730657 CTTGATTCCAGCAACACAAGATC 58.269 43.478 0.00 0.00 35.45 2.75
487 507 3.057033 GCTTGATTCCAGCAACACAAGAT 60.057 43.478 0.00 0.00 35.45 2.40
574 597 2.281139 TCGCCGTCATTGTTGCCA 60.281 55.556 0.00 0.00 0.00 4.92
650 677 1.153647 CGCCAGGAGCACACGAATA 60.154 57.895 0.00 0.00 44.04 1.75
664 692 2.561478 AGGTTCTAAAGCTTTCGCCA 57.439 45.000 16.57 0.00 35.27 5.69
725 754 0.688087 AAAAACAACGCCCCCAAGGA 60.688 50.000 0.00 0.00 38.24 3.36
745 774 2.095263 ACAATGAATTTTCGTGGCTCCG 60.095 45.455 0.00 0.00 0.00 4.63
758 788 2.093306 TCGAGCAACCGACAATGAAT 57.907 45.000 0.00 0.00 33.14 2.57
936 976 1.206578 CAAAATCTCACGCGCCGTT 59.793 52.632 5.73 0.00 38.32 4.44
949 989 4.996062 GCACTATGCAAAGCAACAAAAT 57.004 36.364 0.00 0.00 43.62 1.82
1035 1075 2.751436 GAAGGGCAATGCTCCGCA 60.751 61.111 0.00 0.00 44.86 5.69
1083 1123 0.541296 GCATCCCATTGCCTAGCCAT 60.541 55.000 0.00 0.00 36.60 4.40
1155 1197 1.004440 GAAGAAGTCACCCGCTGCT 60.004 57.895 0.00 0.00 0.00 4.24
1243 1288 0.324368 AGCACCCATCACGACTAGGA 60.324 55.000 0.00 0.00 0.00 2.94
1250 1295 2.393768 GCTGACAGCACCCATCACG 61.394 63.158 22.62 0.00 41.89 4.35
1275 1331 0.036306 AACCAGGAAACCAGCTACGG 59.964 55.000 0.00 0.00 0.00 4.02
1283 1339 3.493767 ACAGAGAAGAACCAGGAAACC 57.506 47.619 0.00 0.00 0.00 3.27
1445 1507 2.530151 AAGGCCTGCACCTCCTCA 60.530 61.111 5.69 0.00 39.93 3.86
1461 1523 0.468226 GTATCCGTGGAGGCCATCAA 59.532 55.000 5.01 0.00 40.77 2.57
1489 1551 2.829003 CCTCGTCTAGCAGCCCGA 60.829 66.667 0.00 0.00 0.00 5.14
1543 1607 2.037381 ACCTGTTTTCCTCTTCCTCGTC 59.963 50.000 0.00 0.00 0.00 4.20
1585 1649 2.884685 CTTGAGGCTGAGCTCGCG 60.885 66.667 19.37 0.00 0.00 5.87
1586 1650 3.194308 GCTTGAGGCTGAGCTCGC 61.194 66.667 18.35 18.35 38.06 5.03
1637 1728 3.865745 GGATCATAAGTTGACACTGTCGG 59.134 47.826 4.71 0.00 37.11 4.79
1649 1749 0.249322 CGAACCGGCGGATCATAAGT 60.249 55.000 35.78 3.72 0.00 2.24
1650 1750 0.031585 TCGAACCGGCGGATCATAAG 59.968 55.000 35.78 17.28 0.00 1.73
1696 1796 1.067846 TCATGGTCTTGAACTCGTCGG 60.068 52.381 0.00 0.00 0.00 4.79
1739 1839 6.849085 TTTTGTATGTGTGGGCATAATCTT 57.151 33.333 0.00 0.00 33.67 2.40
1766 1866 4.702131 ACCCAATGTCTTGCATAGAAGTTC 59.298 41.667 0.00 0.00 36.67 3.01
1806 1906 3.403558 GAGAGGCCACCCTGTCCC 61.404 72.222 5.01 0.00 43.86 4.46
1841 1942 6.272558 ACCAGAGAAAGTATACAAAGTTCCCT 59.727 38.462 5.50 0.00 0.00 4.20
1941 2046 5.258051 GTTGTGGGTGTTGGGATATTAAGA 58.742 41.667 0.00 0.00 0.00 2.10
1963 2068 3.118775 GGCACTTTGTTTTTCTCAAGGGT 60.119 43.478 0.00 0.00 0.00 4.34
2133 2241 6.016024 CAGGTATGTTGGAATAATGATGGGTG 60.016 42.308 0.00 0.00 0.00 4.61
2244 2357 0.389948 GTACAGGTTCGACTGCTGGG 60.390 60.000 3.10 0.00 42.21 4.45
2246 2359 1.000163 AGTGTACAGGTTCGACTGCTG 60.000 52.381 0.00 0.00 42.21 4.41
2279 2392 2.102161 CGTTTATGCGCCCTTGGC 59.898 61.111 4.18 0.00 46.75 4.52
2283 2396 3.253921 AGTTTTTAACGTTTATGCGCCCT 59.746 39.130 5.91 0.00 36.23 5.19
2323 2436 1.021390 GTGGATGAACCGGTCAGCTG 61.021 60.000 8.04 7.63 42.56 4.24
2363 2476 2.993899 GACCGTGGAGAACATGTACTTG 59.006 50.000 0.00 7.18 34.14 3.16
2488 2601 6.663953 AGTAGCCTTATTCAGTCTGTGACTTA 59.336 38.462 0.00 0.00 41.37 2.24
2536 2650 5.865085 TGATAAGTAAAGGTGTGAGCTTGT 58.135 37.500 0.00 0.00 35.89 3.16
2538 2652 5.940470 CCTTGATAAGTAAAGGTGTGAGCTT 59.060 40.000 0.00 0.00 38.53 3.74
2545 2659 2.354821 GCGCCCTTGATAAGTAAAGGTG 59.645 50.000 0.00 0.00 41.25 4.00
2547 2661 2.639065 TGCGCCCTTGATAAGTAAAGG 58.361 47.619 4.18 0.00 42.29 3.11
2549 2663 4.265893 TGATTGCGCCCTTGATAAGTAAA 58.734 39.130 4.18 0.00 0.00 2.01
2550 2664 3.879998 TGATTGCGCCCTTGATAAGTAA 58.120 40.909 4.18 0.00 0.00 2.24
2551 2665 3.552132 TGATTGCGCCCTTGATAAGTA 57.448 42.857 4.18 0.00 0.00 2.24
2552 2666 2.418368 TGATTGCGCCCTTGATAAGT 57.582 45.000 4.18 0.00 0.00 2.24
2564 2678 4.870221 TCTGAAGACATGAATGATTGCG 57.130 40.909 0.00 0.00 0.00 4.85
2573 2687 8.927411 TGGTGATTCTTATATCTGAAGACATGA 58.073 33.333 0.00 0.00 32.68 3.07
2590 2704 6.238842 CGCAATTATCTTTGGATGGTGATTCT 60.239 38.462 0.00 0.00 33.71 2.40
2591 2705 5.916883 CGCAATTATCTTTGGATGGTGATTC 59.083 40.000 0.00 0.00 33.71 2.52
2593 2707 4.889409 ACGCAATTATCTTTGGATGGTGAT 59.111 37.500 0.00 0.00 33.71 3.06
2594 2708 4.269183 ACGCAATTATCTTTGGATGGTGA 58.731 39.130 0.00 0.00 33.71 4.02
2595 2709 4.498009 GGACGCAATTATCTTTGGATGGTG 60.498 45.833 0.00 0.00 33.71 4.17
2596 2710 3.632145 GGACGCAATTATCTTTGGATGGT 59.368 43.478 0.00 0.00 33.71 3.55
2598 2712 4.261322 CCTGGACGCAATTATCTTTGGATG 60.261 45.833 0.00 0.00 33.71 3.51
2599 2713 3.885297 CCTGGACGCAATTATCTTTGGAT 59.115 43.478 0.00 0.00 36.07 3.41
2603 2720 2.024414 GGCCTGGACGCAATTATCTTT 58.976 47.619 0.00 0.00 0.00 2.52
2608 2725 0.326595 TCAAGGCCTGGACGCAATTA 59.673 50.000 5.69 0.00 0.00 1.40
2616 2733 0.833287 GATGTAGCTCAAGGCCTGGA 59.167 55.000 10.21 10.21 43.05 3.86
2617 2734 0.543277 TGATGTAGCTCAAGGCCTGG 59.457 55.000 5.69 1.80 43.05 4.45
2618 2735 2.012673 GTTGATGTAGCTCAAGGCCTG 58.987 52.381 5.69 0.00 43.05 4.85
2632 2749 2.679837 CTGAATCGGTTCCTGGTTGATG 59.320 50.000 5.84 0.00 33.26 3.07
2635 2752 2.472695 TCTGAATCGGTTCCTGGTTG 57.527 50.000 5.84 0.00 33.26 3.77
2657 2774 1.218047 GCTAGCGGTGGACACATCA 59.782 57.895 0.71 0.00 0.00 3.07
2685 2802 1.586541 GCCAGCCAGCAGTTTTACC 59.413 57.895 0.00 0.00 0.00 2.85
2686 2803 1.210155 CGCCAGCCAGCAGTTTTAC 59.790 57.895 0.00 0.00 0.00 2.01
2700 2817 2.343758 GCTCAGAGAACCACGCCA 59.656 61.111 0.00 0.00 0.00 5.69
2781 2898 1.903500 ACTAGCAGGGAGATGCCAGTT 60.904 52.381 0.00 0.00 44.19 3.16
2799 2916 0.251077 CTGAAGCCTCCCAAGCAACT 60.251 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.