Multiple sequence alignment - TraesCS3A01G289200

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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 TraesCS3A01G289200 chr3A 100.000 3831 0 0 1 3831 517490256 517494086 0.000000e+00 7075
1 TraesCS3A01G289200 chr3A 92.038 314 25 0 1 314 292508151 292507838 3.510000e-120 442
2 TraesCS3A01G289200 chr3A 91.401 314 27 0 1 314 443785236 443784923 7.600000e-117 431
3 TraesCS3A01G289200 chr3A 90.997 311 28 0 1 311 297762929 297763239 1.650000e-113 420
4 TraesCS3A01G289200 chr3D 94.897 1901 68 13 1249 3121 398300226 398302125 0.000000e+00 2946
5 TraesCS3A01G289200 chr3D 94.744 723 28 6 493 1212 398299130 398299845 0.000000e+00 1116
6 TraesCS3A01G289200 chr3D 93.488 430 21 5 3407 3831 398302126 398302553 1.940000e-177 632
7 TraesCS3A01G289200 chr3D 92.391 184 5 3 311 492 398298908 398299084 1.770000e-63 254
8 TraesCS3A01G289200 chr3B 95.317 1687 30 3 1624 3277 524326292 524327962 0.000000e+00 2632
9 TraesCS3A01G289200 chr3B 91.053 1140 58 11 493 1625 524325032 524326134 0.000000e+00 1500
10 TraesCS3A01G289200 chr3B 91.887 567 33 8 3277 3830 524328014 524328580 0.000000e+00 780
11 TraesCS3A01G289200 chr3B 89.560 182 8 5 311 492 524324817 524324987 1.790000e-53 220
12 TraesCS3A01G289200 chr5A 92.615 325 22 2 1 323 12690105 12689781 2.080000e-127 466
13 TraesCS3A01G289200 chr5A 93.248 311 21 0 1 311 327377047 327377357 3.490000e-125 459
14 TraesCS3A01G289200 chr6D 92.357 314 24 0 1 314 158043938 158043625 7.550000e-122 448
15 TraesCS3A01G289200 chr6D 91.234 308 27 0 7 314 403668571 403668264 1.650000e-113 420
16 TraesCS3A01G289200 chr2D 91.401 314 27 0 1 314 330845169 330845482 7.600000e-117 431
17 TraesCS3A01G289200 chr2D 79.459 185 38 0 1032 1216 94319386 94319202 8.640000e-27 132
18 TraesCS3A01G289200 chr7A 91.318 311 24 3 1 311 362657346 362657653 4.580000e-114 422
19 TraesCS3A01G289200 chr4D 85.165 182 26 1 311 491 5535596 5535415 6.540000e-43 185
20 TraesCS3A01G289200 chr4A 82.199 191 32 2 1026 1215 610490450 610490261 3.060000e-36 163
21 TraesCS3A01G289200 chr5D 81.152 191 34 2 1026 1215 558247759 558247570 6.630000e-33 152
22 TraesCS3A01G289200 chr5B 81.383 188 33 2 1026 1212 704878544 704878730 6.630000e-33 152
23 TraesCS3A01G289200 chr5B 81.646 158 25 4 337 491 570632863 570632707 1.120000e-25 128
24 TraesCS3A01G289200 chr1D 85.816 141 18 2 353 492 413586498 413586359 8.570000e-32 148
25 TraesCS3A01G289200 chr1D 80.412 194 33 5 1021 1212 439022275 439022465 3.990000e-30 143
26 TraesCS3A01G289200 chr1B 80.928 194 32 5 1021 1212 595176887 595177077 8.570000e-32 148
27 TraesCS3A01G289200 chr1B 81.481 162 20 10 337 492 573758708 573758551 1.450000e-24 124
28 TraesCS3A01G289200 chr1A 80.928 194 32 5 1021 1212 535312149 535312339 8.570000e-32 148
29 TraesCS3A01G289200 chr7D 83.125 160 21 5 337 492 577796455 577796298 1.430000e-29 141
30 TraesCS3A01G289200 chr2A 80.337 178 31 3 311 484 723656618 723656795 8.640000e-27 132
31 TraesCS3A01G289200 chr2B 78.882 161 29 5 336 492 134678624 134678465 1.880000e-18 104


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 TraesCS3A01G289200 chr3A 517490256 517494086 3830 False 7075 7075 100.00000 1 3831 1 chr3A.!!$F2 3830
1 TraesCS3A01G289200 chr3D 398298908 398302553 3645 False 1237 2946 93.88000 311 3831 4 chr3D.!!$F1 3520
2 TraesCS3A01G289200 chr3B 524324817 524328580 3763 False 1283 2632 91.95425 311 3830 4 chr3B.!!$F1 3519

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
274 275 0.032615 TTGCTCTCTCCCTCCTCCTC 60.033 60.000 0.00 0.0 0.00 3.71 F
916 968 0.040425 CAAACCCAACCGAAGAAGCG 60.040 55.000 0.00 0.0 0.00 4.68 F
1212 1264 1.450312 GCGCCAGCTCAACACCTAT 60.450 57.895 0.00 0.0 41.01 2.57 F
2680 3278 0.905809 TTACCGAGCAGCCTGGGTTA 60.906 55.000 5.06 0.0 46.64 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2690 1.404851 GGCAGTCTCCTCTTCTTTCCG 60.405 57.143 0.00 0.00 0.0 4.30 R
2680 3278 0.477204 CCTCCTGATGTGCATGGGAT 59.523 55.000 0.00 0.00 0.0 3.85 R
2692 3290 0.620556 GTTCTGATTGGGCCTCCTGA 59.379 55.000 4.53 0.52 0.0 3.86 R
3669 4343 0.674895 AAGTCTGCCATGCTTCGGAC 60.675 55.000 10.16 10.16 0.0 4.79 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
17 18 2.107141 GTTGGAGGAGATCGCGGG 59.893 66.667 6.13 0.00 0.00 6.13
18 19 3.849951 TTGGAGGAGATCGCGGGC 61.850 66.667 6.13 0.00 0.00 6.13
30 31 3.766691 GCGGGCCGGACTGAAGTA 61.767 66.667 29.48 0.00 0.00 2.24
31 32 2.183555 CGGGCCGGACTGAAGTAC 59.816 66.667 20.56 0.00 0.00 2.73
32 33 2.642254 CGGGCCGGACTGAAGTACA 61.642 63.158 20.56 0.00 0.00 2.90
33 34 1.079336 GGGCCGGACTGAAGTACAC 60.079 63.158 7.57 0.00 0.00 2.90
34 35 1.669440 GGCCGGACTGAAGTACACA 59.331 57.895 5.05 0.00 0.00 3.72
35 36 0.034337 GGCCGGACTGAAGTACACAA 59.966 55.000 5.05 0.00 0.00 3.33
36 37 1.338769 GGCCGGACTGAAGTACACAAT 60.339 52.381 5.05 0.00 0.00 2.71
37 38 2.093869 GGCCGGACTGAAGTACACAATA 60.094 50.000 5.05 0.00 0.00 1.90
38 39 3.431766 GGCCGGACTGAAGTACACAATAT 60.432 47.826 5.05 0.00 0.00 1.28
39 40 4.202182 GGCCGGACTGAAGTACACAATATA 60.202 45.833 5.05 0.00 0.00 0.86
40 41 5.353938 GCCGGACTGAAGTACACAATATAA 58.646 41.667 5.05 0.00 0.00 0.98
41 42 5.989777 GCCGGACTGAAGTACACAATATAAT 59.010 40.000 5.05 0.00 0.00 1.28
42 43 6.073765 GCCGGACTGAAGTACACAATATAATG 60.074 42.308 5.05 0.00 0.00 1.90
43 44 6.984474 CCGGACTGAAGTACACAATATAATGT 59.016 38.462 0.00 0.00 0.00 2.71
69 70 9.680315 TGTTAAAACTACAATCATAAAAACCGG 57.320 29.630 0.00 0.00 0.00 5.28
70 71 9.896263 GTTAAAACTACAATCATAAAAACCGGA 57.104 29.630 9.46 0.00 0.00 5.14
103 104 8.798859 ACAATATCCTTGGATACTTATGATGC 57.201 34.615 11.16 0.00 37.61 3.91
104 105 7.550551 ACAATATCCTTGGATACTTATGATGCG 59.449 37.037 11.16 0.00 37.61 4.73
105 106 4.271696 TCCTTGGATACTTATGATGCGG 57.728 45.455 0.00 0.00 37.61 5.69
106 107 2.744202 CCTTGGATACTTATGATGCGGC 59.256 50.000 0.00 0.00 37.61 6.53
107 108 2.472695 TGGATACTTATGATGCGGCC 57.527 50.000 0.00 0.00 37.61 6.13
108 109 1.696884 TGGATACTTATGATGCGGCCA 59.303 47.619 2.24 0.00 37.61 5.36
109 110 2.289631 TGGATACTTATGATGCGGCCAG 60.290 50.000 2.24 0.00 37.61 4.85
110 111 2.350522 GATACTTATGATGCGGCCAGG 58.649 52.381 2.24 0.00 0.00 4.45
111 112 0.396435 TACTTATGATGCGGCCAGGG 59.604 55.000 2.24 0.00 0.00 4.45
112 113 1.601759 CTTATGATGCGGCCAGGGG 60.602 63.158 2.24 0.00 0.00 4.79
146 147 4.760047 CACTCGGGGGTGGCTTCG 62.760 72.222 0.00 0.00 33.95 3.79
149 150 4.700448 TCGGGGGTGGCTTCGGTA 62.700 66.667 0.00 0.00 0.00 4.02
150 151 3.476419 CGGGGGTGGCTTCGGTAT 61.476 66.667 0.00 0.00 0.00 2.73
151 152 2.509422 GGGGGTGGCTTCGGTATC 59.491 66.667 0.00 0.00 0.00 2.24
152 153 2.108362 GGGGTGGCTTCGGTATCG 59.892 66.667 0.00 0.00 37.82 2.92
153 154 2.108362 GGGTGGCTTCGGTATCGG 59.892 66.667 0.00 0.00 36.95 4.18
154 155 2.428925 GGGTGGCTTCGGTATCGGA 61.429 63.158 0.00 0.00 36.95 4.55
155 156 1.067582 GGTGGCTTCGGTATCGGAG 59.932 63.158 0.00 0.00 44.57 4.63
156 157 1.673808 GGTGGCTTCGGTATCGGAGT 61.674 60.000 5.39 0.00 43.67 3.85
157 158 0.248949 GTGGCTTCGGTATCGGAGTC 60.249 60.000 0.00 0.00 46.25 3.36
158 159 1.363080 GGCTTCGGTATCGGAGTCC 59.637 63.158 5.39 3.48 40.56 3.85
170 171 3.437795 GAGTCCGAGCCGTCCGAA 61.438 66.667 0.00 0.00 0.00 4.30
171 172 2.986306 GAGTCCGAGCCGTCCGAAA 61.986 63.158 0.00 0.00 0.00 3.46
172 173 2.506438 GTCCGAGCCGTCCGAAAG 60.506 66.667 0.00 0.00 0.00 2.62
193 194 2.991580 GGATATCTTCCCCCTCTTGGA 58.008 52.381 2.05 0.00 38.75 3.53
194 195 2.640332 GGATATCTTCCCCCTCTTGGAC 59.360 54.545 2.05 0.00 38.75 4.02
195 196 1.789523 TATCTTCCCCCTCTTGGACG 58.210 55.000 0.00 0.00 35.39 4.79
196 197 1.627297 ATCTTCCCCCTCTTGGACGC 61.627 60.000 0.00 0.00 35.39 5.19
197 198 3.327404 TTCCCCCTCTTGGACGCC 61.327 66.667 0.00 0.00 35.39 5.68
214 215 4.208686 CGCCGCCTCTAGGTCCAC 62.209 72.222 0.00 0.00 37.57 4.02
215 216 4.208686 GCCGCCTCTAGGTCCACG 62.209 72.222 0.00 0.00 37.57 4.94
216 217 3.528370 CCGCCTCTAGGTCCACGG 61.528 72.222 0.00 0.00 37.57 4.94
217 218 2.439701 CGCCTCTAGGTCCACGGA 60.440 66.667 0.00 0.00 37.57 4.69
218 219 2.482333 CGCCTCTAGGTCCACGGAG 61.482 68.421 0.00 0.00 37.57 4.63
219 220 2.128507 GCCTCTAGGTCCACGGAGG 61.129 68.421 16.03 16.03 42.64 4.30
220 221 2.128507 CCTCTAGGTCCACGGAGGC 61.129 68.421 10.50 0.00 37.24 4.70
221 222 2.043248 TCTAGGTCCACGGAGGCC 60.043 66.667 0.00 0.00 37.29 5.19
231 232 4.410400 CGGAGGCCGCCCTTTTCT 62.410 66.667 21.07 0.00 43.12 2.52
232 233 2.035783 GGAGGCCGCCCTTTTCTT 59.964 61.111 15.92 0.00 43.12 2.52
233 234 2.046864 GGAGGCCGCCCTTTTCTTC 61.047 63.158 15.92 0.00 43.12 2.87
234 235 1.002011 GAGGCCGCCCTTTTCTTCT 60.002 57.895 5.55 0.00 43.12 2.85
235 236 0.609406 GAGGCCGCCCTTTTCTTCTT 60.609 55.000 5.55 0.00 43.12 2.52
236 237 0.609406 AGGCCGCCCTTTTCTTCTTC 60.609 55.000 5.55 0.00 38.74 2.87
237 238 1.595993 GGCCGCCCTTTTCTTCTTCC 61.596 60.000 0.00 0.00 0.00 3.46
238 239 0.609406 GCCGCCCTTTTCTTCTTCCT 60.609 55.000 0.00 0.00 0.00 3.36
239 240 1.911057 CCGCCCTTTTCTTCTTCCTT 58.089 50.000 0.00 0.00 0.00 3.36
240 241 1.813178 CCGCCCTTTTCTTCTTCCTTC 59.187 52.381 0.00 0.00 0.00 3.46
241 242 1.813178 CGCCCTTTTCTTCTTCCTTCC 59.187 52.381 0.00 0.00 0.00 3.46
242 243 2.171840 GCCCTTTTCTTCTTCCTTCCC 58.828 52.381 0.00 0.00 0.00 3.97
243 244 2.225142 GCCCTTTTCTTCTTCCTTCCCT 60.225 50.000 0.00 0.00 0.00 4.20
244 245 3.755483 GCCCTTTTCTTCTTCCTTCCCTT 60.755 47.826 0.00 0.00 0.00 3.95
245 246 4.508584 GCCCTTTTCTTCTTCCTTCCCTTA 60.509 45.833 0.00 0.00 0.00 2.69
246 247 5.641155 CCCTTTTCTTCTTCCTTCCCTTAA 58.359 41.667 0.00 0.00 0.00 1.85
247 248 5.712446 CCCTTTTCTTCTTCCTTCCCTTAAG 59.288 44.000 0.00 0.00 34.73 1.85
261 262 3.941704 CCTTAAGGGGAGAATTGCTCT 57.058 47.619 14.25 0.00 43.43 4.09
269 270 2.908688 GAGAATTGCTCTCTCCCTCC 57.091 55.000 0.00 0.00 46.32 4.30
270 271 2.397597 GAGAATTGCTCTCTCCCTCCT 58.602 52.381 0.00 0.00 46.32 3.69
271 272 2.365293 GAGAATTGCTCTCTCCCTCCTC 59.635 54.545 0.00 0.00 46.32 3.71
272 273 1.416030 GAATTGCTCTCTCCCTCCTCC 59.584 57.143 0.00 0.00 0.00 4.30
273 274 0.641601 ATTGCTCTCTCCCTCCTCCT 59.358 55.000 0.00 0.00 0.00 3.69
274 275 0.032615 TTGCTCTCTCCCTCCTCCTC 60.033 60.000 0.00 0.00 0.00 3.71
275 276 1.152546 GCTCTCTCCCTCCTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
276 277 1.655114 GCTCTCTCCCTCCTCCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
277 278 0.478507 CTCTCTCCCTCCTCCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
278 279 0.047176 TCTCTCCCTCCTCCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
279 280 0.933700 CTCTCCCTCCTCCTCCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
280 281 0.930726 TCTCCCTCCTCCTCCTCTTC 59.069 60.000 0.00 0.00 0.00 2.87
281 282 0.467290 CTCCCTCCTCCTCCTCTTCG 60.467 65.000 0.00 0.00 0.00 3.79
282 283 1.215679 TCCCTCCTCCTCCTCTTCGT 61.216 60.000 0.00 0.00 0.00 3.85
283 284 0.753848 CCCTCCTCCTCCTCTTCGTC 60.754 65.000 0.00 0.00 0.00 4.20
284 285 0.257616 CCTCCTCCTCCTCTTCGTCT 59.742 60.000 0.00 0.00 0.00 4.18
285 286 1.341581 CCTCCTCCTCCTCTTCGTCTT 60.342 57.143 0.00 0.00 0.00 3.01
286 287 2.021457 CTCCTCCTCCTCTTCGTCTTC 58.979 57.143 0.00 0.00 0.00 2.87
287 288 1.354705 TCCTCCTCCTCTTCGTCTTCA 59.645 52.381 0.00 0.00 0.00 3.02
288 289 2.024846 TCCTCCTCCTCTTCGTCTTCAT 60.025 50.000 0.00 0.00 0.00 2.57
289 290 2.360801 CCTCCTCCTCTTCGTCTTCATC 59.639 54.545 0.00 0.00 0.00 2.92
290 291 3.287222 CTCCTCCTCTTCGTCTTCATCT 58.713 50.000 0.00 0.00 0.00 2.90
291 292 3.283751 TCCTCCTCTTCGTCTTCATCTC 58.716 50.000 0.00 0.00 0.00 2.75
292 293 2.360801 CCTCCTCTTCGTCTTCATCTCC 59.639 54.545 0.00 0.00 0.00 3.71
293 294 2.360801 CTCCTCTTCGTCTTCATCTCCC 59.639 54.545 0.00 0.00 0.00 4.30
294 295 2.024846 TCCTCTTCGTCTTCATCTCCCT 60.025 50.000 0.00 0.00 0.00 4.20
295 296 2.360801 CCTCTTCGTCTTCATCTCCCTC 59.639 54.545 0.00 0.00 0.00 4.30
296 297 2.017782 TCTTCGTCTTCATCTCCCTCG 58.982 52.381 0.00 0.00 0.00 4.63
297 298 1.746220 CTTCGTCTTCATCTCCCTCGT 59.254 52.381 0.00 0.00 0.00 4.18
298 299 1.095600 TCGTCTTCATCTCCCTCGTG 58.904 55.000 0.00 0.00 0.00 4.35
299 300 0.101399 CGTCTTCATCTCCCTCGTGG 59.899 60.000 0.00 0.00 0.00 4.94
381 383 2.043115 GGGGGAAGAGAGTGGGAAAAAT 59.957 50.000 0.00 0.00 0.00 1.82
392 395 4.757692 AGTGGGAAAAATGGTGGGAATTA 58.242 39.130 0.00 0.00 0.00 1.40
397 400 4.775253 GGAAAAATGGTGGGAATTAGGTGA 59.225 41.667 0.00 0.00 0.00 4.02
437 440 1.978580 AGAGAGTGGGGATTTTGTCGT 59.021 47.619 0.00 0.00 0.00 4.34
445 448 2.560981 GGGGATTTTGTCGTGGAAACAT 59.439 45.455 0.00 0.00 46.14 2.71
518 566 4.998672 CCTACATTTGGTTCCTGTTTACGA 59.001 41.667 0.00 0.00 0.00 3.43
550 598 2.730733 GGATCGCTCGGCAGATCA 59.269 61.111 20.27 0.00 38.91 2.92
558 606 2.759191 GCTCGGCAGATCAATACATGA 58.241 47.619 0.00 0.00 43.67 3.07
560 608 3.801638 GCTCGGCAGATCAATACATGACT 60.802 47.826 0.00 0.00 41.93 3.41
618 666 4.216324 CAAAACATATGCGAGCGTTTTG 57.784 40.909 17.61 17.61 46.63 2.44
627 675 1.301479 GAGCGTTTTGAGGGTCGGT 60.301 57.895 0.00 0.00 36.76 4.69
639 687 0.177373 GGGTCGGTGTTGGAGATACC 59.823 60.000 0.00 0.00 36.26 2.73
722 771 0.652592 AGCGCGTATTCATTGAGCAC 59.347 50.000 8.43 0.00 0.00 4.40
723 772 0.316196 GCGCGTATTCATTGAGCACC 60.316 55.000 8.43 0.00 0.00 5.01
859 911 4.307443 GGAAAATTCCGCTAATCCAAGG 57.693 45.455 0.00 0.00 37.65 3.61
916 968 0.040425 CAAACCCAACCGAAGAAGCG 60.040 55.000 0.00 0.00 0.00 4.68
1212 1264 1.450312 GCGCCAGCTCAACACCTAT 60.450 57.895 0.00 0.00 41.01 2.57
1277 1673 2.509336 AATCTCTGTTCCGCCGCG 60.509 61.111 5.59 5.59 0.00 6.46
1476 1872 3.802329 GCTGCTTAGTGTGCCGGATTATA 60.802 47.826 5.05 0.00 0.00 0.98
1536 1932 5.774498 AAGGTCAACTCTTGATTTGTTCC 57.226 39.130 1.68 5.58 42.47 3.62
1547 1943 8.299570 ACTCTTGATTTGTTCCATATGTGAAAC 58.700 33.333 1.24 4.25 37.35 2.78
1553 1949 6.951062 TTGTTCCATATGTGAAACTCAACA 57.049 33.333 1.24 0.00 38.04 3.33
1570 1966 3.802139 TCAACAAGCTTCGTTCAGTACTG 59.198 43.478 17.17 17.17 0.00 2.74
1575 1971 2.885266 AGCTTCGTTCAGTACTGTCTCA 59.115 45.455 21.99 0.00 0.00 3.27
1596 2008 1.754226 TCTTGGGGCTGTTTGACAAAC 59.246 47.619 21.68 21.68 41.73 2.93
1691 2262 6.003326 TGGTAATGGTAATGCATGATACCTG 58.997 40.000 22.39 0.00 41.76 4.00
2031 2602 5.360591 AGACAAACTATTTGCTATCGAGGG 58.639 41.667 1.23 0.00 44.39 4.30
2087 2658 5.999205 AATTGTGAATGCACCTGGATTTA 57.001 34.783 0.00 0.00 44.51 1.40
2096 2667 4.207165 TGCACCTGGATTTATTTCTAGCC 58.793 43.478 0.00 0.00 0.00 3.93
2099 2670 5.684704 CACCTGGATTTATTTCTAGCCTCA 58.315 41.667 0.00 0.00 0.00 3.86
2119 2690 6.147492 GCCTCATAGAACAATCTGATCATCAC 59.853 42.308 0.00 0.00 37.10 3.06
2201 2772 4.398988 GGAACCAGATTATGCATTGTGACA 59.601 41.667 3.54 0.00 0.00 3.58
2498 3096 1.676384 GCCAGCTGTCCAGAGAGTT 59.324 57.895 13.81 0.00 0.00 3.01
2680 3278 0.905809 TTACCGAGCAGCCTGGGTTA 60.906 55.000 5.06 0.00 46.64 2.85
2834 3435 4.241681 CTCAGCTGAGAAAACCTGAGTAC 58.758 47.826 35.69 0.00 43.81 2.73
2894 3495 3.310774 CAGAAACATTAGGACGATGGCAG 59.689 47.826 0.00 0.00 0.00 4.85
3049 3653 4.171005 TGTCAACGACTCGTGATATTTCC 58.829 43.478 4.50 0.00 39.99 3.13
3122 3726 4.039852 TGCCTGTTGGAGGGTTTTTATTTC 59.960 41.667 0.00 0.00 43.07 2.17
3128 3732 9.423061 CTGTTGGAGGGTTTTTATTTCTATTTG 57.577 33.333 0.00 0.00 0.00 2.32
3163 3767 4.403432 CCAGCTATTTGAACCATGGTCAAT 59.597 41.667 20.07 18.04 0.00 2.57
3227 3831 3.379240 CGTAGTGGCTTCAGATGATCAG 58.621 50.000 0.09 0.00 0.00 2.90
3234 3838 5.638657 GTGGCTTCAGATGATCAGTGATATC 59.361 44.000 5.38 9.47 0.00 1.63
3247 3857 6.947644 TCAGTGATATCATGGTTCATTTGG 57.052 37.500 9.02 0.00 0.00 3.28
3321 3983 0.886563 CTTGGCTGCTTTTCCCTGAG 59.113 55.000 0.00 0.00 0.00 3.35
3360 4022 3.090219 GCCTCGCCCTGGATTACGT 62.090 63.158 0.00 0.00 0.00 3.57
3363 4025 1.315690 CTCGCCCTGGATTACGTAGA 58.684 55.000 0.00 0.00 0.00 2.59
3400 4062 2.673326 GCAAAAGGATCCTTTGCTGCTC 60.673 50.000 35.85 20.57 44.50 4.26
3545 4216 1.211743 GCACTGGAAGCTTGCAAAAC 58.788 50.000 21.68 9.73 36.12 2.43
3593 4267 0.740737 GTTGCATGCATGGTCCTACC 59.259 55.000 27.34 9.80 39.22 3.18
3611 4285 1.614413 ACCAAGAACTCTGGTCTCGAC 59.386 52.381 0.00 0.00 0.00 4.20
3669 4343 1.201921 CGGACATTTCTTTCGCTTCGG 60.202 52.381 0.00 0.00 0.00 4.30
3673 4347 1.076332 ATTTCTTTCGCTTCGGTCCG 58.924 50.000 4.39 4.39 0.00 4.79
3736 4410 3.064682 TGCAAATTGTGAATCGTATCCGG 59.935 43.478 0.00 0.00 33.95 5.14
3817 4498 0.251916 CCGGAGCCAGTTATCCAACA 59.748 55.000 0.00 0.00 37.10 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.107141 CCCGCGATCTCCTCCAAC 59.893 66.667 8.23 0.00 0.00 3.77
1 2 3.849951 GCCCGCGATCTCCTCCAA 61.850 66.667 8.23 0.00 0.00 3.53
13 14 3.766691 TACTTCAGTCCGGCCCGC 61.767 66.667 0.00 0.00 0.00 6.13
14 15 2.183555 GTACTTCAGTCCGGCCCG 59.816 66.667 0.00 0.00 0.00 6.13
15 16 1.079336 GTGTACTTCAGTCCGGCCC 60.079 63.158 0.00 0.00 0.00 5.80
16 17 0.034337 TTGTGTACTTCAGTCCGGCC 59.966 55.000 0.00 0.00 0.00 6.13
17 18 2.094762 ATTGTGTACTTCAGTCCGGC 57.905 50.000 0.00 0.00 0.00 6.13
18 19 6.984474 ACATTATATTGTGTACTTCAGTCCGG 59.016 38.462 0.00 0.00 0.00 5.14
19 20 7.841486 CACATTATATTGTGTACTTCAGTCCG 58.159 38.462 16.27 0.00 41.65 4.79
43 44 9.680315 CCGGTTTTTATGATTGTAGTTTTAACA 57.320 29.630 0.00 0.00 0.00 2.41
44 45 9.896263 TCCGGTTTTTATGATTGTAGTTTTAAC 57.104 29.630 0.00 0.00 0.00 2.01
77 78 9.890629 GCATCATAAGTATCCAAGGATATTGTA 57.109 33.333 11.72 5.71 39.04 2.41
78 79 7.550551 CGCATCATAAGTATCCAAGGATATTGT 59.449 37.037 11.72 3.89 39.04 2.71
79 80 7.011763 CCGCATCATAAGTATCCAAGGATATTG 59.988 40.741 11.72 8.04 39.04 1.90
80 81 7.050377 CCGCATCATAAGTATCCAAGGATATT 58.950 38.462 11.72 5.29 39.04 1.28
81 82 6.586344 CCGCATCATAAGTATCCAAGGATAT 58.414 40.000 11.72 0.41 39.04 1.63
82 83 5.626809 GCCGCATCATAAGTATCCAAGGATA 60.627 44.000 4.71 4.71 36.17 2.59
83 84 4.836825 CCGCATCATAAGTATCCAAGGAT 58.163 43.478 6.84 6.84 38.54 3.24
84 85 3.557054 GCCGCATCATAAGTATCCAAGGA 60.557 47.826 0.00 0.00 0.00 3.36
85 86 2.744202 GCCGCATCATAAGTATCCAAGG 59.256 50.000 0.00 0.00 0.00 3.61
86 87 2.744202 GGCCGCATCATAAGTATCCAAG 59.256 50.000 0.00 0.00 0.00 3.61
87 88 2.105649 TGGCCGCATCATAAGTATCCAA 59.894 45.455 0.00 0.00 0.00 3.53
88 89 1.696884 TGGCCGCATCATAAGTATCCA 59.303 47.619 0.00 0.00 0.00 3.41
89 90 2.350522 CTGGCCGCATCATAAGTATCC 58.649 52.381 0.00 0.00 0.00 2.59
90 91 2.350522 CCTGGCCGCATCATAAGTATC 58.649 52.381 0.00 0.00 0.00 2.24
91 92 1.003580 CCCTGGCCGCATCATAAGTAT 59.996 52.381 0.00 0.00 0.00 2.12
92 93 0.396435 CCCTGGCCGCATCATAAGTA 59.604 55.000 0.00 0.00 0.00 2.24
93 94 1.149174 CCCTGGCCGCATCATAAGT 59.851 57.895 0.00 0.00 0.00 2.24
94 95 1.601759 CCCCTGGCCGCATCATAAG 60.602 63.158 0.00 0.00 0.00 1.73
95 96 2.515398 CCCCTGGCCGCATCATAA 59.485 61.111 0.00 0.00 0.00 1.90
96 97 4.269523 GCCCCTGGCCGCATCATA 62.270 66.667 0.00 0.00 44.06 2.15
107 108 4.101448 CCCAGGTCGAAGCCCCTG 62.101 72.222 11.85 11.85 43.10 4.45
129 130 4.760047 CGAAGCCACCCCCGAGTG 62.760 72.222 0.00 0.00 37.51 3.51
132 133 3.988050 ATACCGAAGCCACCCCCGA 62.988 63.158 0.00 0.00 0.00 5.14
133 134 3.456105 GATACCGAAGCCACCCCCG 62.456 68.421 0.00 0.00 0.00 5.73
134 135 2.509422 GATACCGAAGCCACCCCC 59.491 66.667 0.00 0.00 0.00 5.40
135 136 2.108362 CGATACCGAAGCCACCCC 59.892 66.667 0.00 0.00 38.22 4.95
136 137 2.108362 CCGATACCGAAGCCACCC 59.892 66.667 0.00 0.00 38.22 4.61
137 138 1.067582 CTCCGATACCGAAGCCACC 59.932 63.158 0.00 0.00 38.22 4.61
138 139 0.248949 GACTCCGATACCGAAGCCAC 60.249 60.000 0.00 0.00 38.22 5.01
139 140 1.389609 GGACTCCGATACCGAAGCCA 61.390 60.000 0.00 0.00 38.22 4.75
140 141 1.363080 GGACTCCGATACCGAAGCC 59.637 63.158 0.00 0.00 38.22 4.35
153 154 2.868999 CTTTCGGACGGCTCGGACTC 62.869 65.000 0.00 0.00 0.00 3.36
154 155 2.987547 TTTCGGACGGCTCGGACT 60.988 61.111 0.00 0.00 0.00 3.85
155 156 2.506438 CTTTCGGACGGCTCGGAC 60.506 66.667 0.00 0.00 0.00 4.79
156 157 3.755628 CCTTTCGGACGGCTCGGA 61.756 66.667 0.00 0.00 0.00 4.55
157 158 4.814294 CCCTTTCGGACGGCTCGG 62.814 72.222 0.00 0.00 0.00 4.63
158 159 1.731433 TATCCCTTTCGGACGGCTCG 61.731 60.000 0.00 0.00 46.09 5.03
159 160 0.680061 ATATCCCTTTCGGACGGCTC 59.320 55.000 0.00 0.00 46.09 4.70
160 161 0.680061 GATATCCCTTTCGGACGGCT 59.320 55.000 0.00 0.00 46.09 5.52
161 162 0.680061 AGATATCCCTTTCGGACGGC 59.320 55.000 0.00 0.00 46.09 5.68
162 163 2.288886 GGAAGATATCCCTTTCGGACGG 60.289 54.545 0.00 0.00 46.09 4.79
163 164 3.027974 GGAAGATATCCCTTTCGGACG 57.972 52.381 0.00 0.00 46.09 4.79
174 175 2.300437 CGTCCAAGAGGGGGAAGATATC 59.700 54.545 0.00 0.00 36.19 1.63
175 176 2.330216 CGTCCAAGAGGGGGAAGATAT 58.670 52.381 0.00 0.00 36.19 1.63
176 177 1.789523 CGTCCAAGAGGGGGAAGATA 58.210 55.000 0.00 0.00 36.19 1.98
177 178 1.627297 GCGTCCAAGAGGGGGAAGAT 61.627 60.000 0.00 0.00 36.19 2.40
178 179 2.291043 GCGTCCAAGAGGGGGAAGA 61.291 63.158 0.00 0.00 36.19 2.87
179 180 2.269241 GCGTCCAAGAGGGGGAAG 59.731 66.667 0.00 0.00 35.88 3.46
180 181 3.327404 GGCGTCCAAGAGGGGGAA 61.327 66.667 0.00 0.00 35.88 3.97
197 198 4.208686 GTGGACCTAGAGGCGGCG 62.209 72.222 0.51 0.51 39.32 6.46
198 199 4.208686 CGTGGACCTAGAGGCGGC 62.209 72.222 0.00 0.00 39.32 6.53
199 200 3.528370 CCGTGGACCTAGAGGCGG 61.528 72.222 0.00 0.00 39.32 6.13
200 201 2.439701 TCCGTGGACCTAGAGGCG 60.440 66.667 0.00 0.00 39.32 5.52
201 202 2.128507 CCTCCGTGGACCTAGAGGC 61.129 68.421 10.81 0.00 39.54 4.70
202 203 4.261701 CCTCCGTGGACCTAGAGG 57.738 66.667 9.69 9.69 40.00 3.69
203 204 2.128507 GGCCTCCGTGGACCTAGAG 61.129 68.421 0.00 0.00 38.13 2.43
204 205 2.043248 GGCCTCCGTGGACCTAGA 60.043 66.667 0.00 0.00 38.13 2.43
205 206 3.528370 CGGCCTCCGTGGACCTAG 61.528 72.222 0.00 0.00 42.31 3.02
215 216 2.035783 AAGAAAAGGGCGGCCTCC 59.964 61.111 32.90 22.12 0.00 4.30
216 217 0.609406 AAGAAGAAAAGGGCGGCCTC 60.609 55.000 32.90 19.44 0.00 4.70
217 218 0.609406 GAAGAAGAAAAGGGCGGCCT 60.609 55.000 27.45 27.45 0.00 5.19
218 219 1.595993 GGAAGAAGAAAAGGGCGGCC 61.596 60.000 22.67 22.67 0.00 6.13
219 220 0.609406 AGGAAGAAGAAAAGGGCGGC 60.609 55.000 0.00 0.00 0.00 6.53
220 221 1.813178 GAAGGAAGAAGAAAAGGGCGG 59.187 52.381 0.00 0.00 0.00 6.13
221 222 1.813178 GGAAGGAAGAAGAAAAGGGCG 59.187 52.381 0.00 0.00 0.00 6.13
222 223 2.171840 GGGAAGGAAGAAGAAAAGGGC 58.828 52.381 0.00 0.00 0.00 5.19
223 224 3.816398 AGGGAAGGAAGAAGAAAAGGG 57.184 47.619 0.00 0.00 0.00 3.95
224 225 6.825944 CTTAAGGGAAGGAAGAAGAAAAGG 57.174 41.667 0.00 0.00 0.00 3.11
241 242 3.814625 GAGAGCAATTCTCCCCTTAAGG 58.185 50.000 15.14 15.14 45.53 2.69
251 252 2.397597 GAGGAGGGAGAGAGCAATTCT 58.602 52.381 0.00 0.00 39.43 2.40
252 253 1.416030 GGAGGAGGGAGAGAGCAATTC 59.584 57.143 0.00 0.00 0.00 2.17
253 254 1.009429 AGGAGGAGGGAGAGAGCAATT 59.991 52.381 0.00 0.00 0.00 2.32
254 255 0.641601 AGGAGGAGGGAGAGAGCAAT 59.358 55.000 0.00 0.00 0.00 3.56
255 256 0.032615 GAGGAGGAGGGAGAGAGCAA 60.033 60.000 0.00 0.00 0.00 3.91
256 257 1.618030 GAGGAGGAGGGAGAGAGCA 59.382 63.158 0.00 0.00 0.00 4.26
257 258 1.152546 GGAGGAGGAGGGAGAGAGC 60.153 68.421 0.00 0.00 0.00 4.09
258 259 0.478507 GAGGAGGAGGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
259 260 0.047176 AGAGGAGGAGGAGGGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10
260 261 0.933700 AAGAGGAGGAGGAGGGAGAG 59.066 60.000 0.00 0.00 0.00 3.20
261 262 0.930726 GAAGAGGAGGAGGAGGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
262 263 0.467290 CGAAGAGGAGGAGGAGGGAG 60.467 65.000 0.00 0.00 0.00 4.30
263 264 1.215679 ACGAAGAGGAGGAGGAGGGA 61.216 60.000 0.00 0.00 0.00 4.20
264 265 0.753848 GACGAAGAGGAGGAGGAGGG 60.754 65.000 0.00 0.00 0.00 4.30
265 266 0.257616 AGACGAAGAGGAGGAGGAGG 59.742 60.000 0.00 0.00 0.00 4.30
266 267 2.021457 GAAGACGAAGAGGAGGAGGAG 58.979 57.143 0.00 0.00 0.00 3.69
267 268 1.354705 TGAAGACGAAGAGGAGGAGGA 59.645 52.381 0.00 0.00 0.00 3.71
268 269 1.840737 TGAAGACGAAGAGGAGGAGG 58.159 55.000 0.00 0.00 0.00 4.30
269 270 3.287222 AGATGAAGACGAAGAGGAGGAG 58.713 50.000 0.00 0.00 0.00 3.69
270 271 3.283751 GAGATGAAGACGAAGAGGAGGA 58.716 50.000 0.00 0.00 0.00 3.71
271 272 2.360801 GGAGATGAAGACGAAGAGGAGG 59.639 54.545 0.00 0.00 0.00 4.30
272 273 2.360801 GGGAGATGAAGACGAAGAGGAG 59.639 54.545 0.00 0.00 0.00 3.69
273 274 2.024846 AGGGAGATGAAGACGAAGAGGA 60.025 50.000 0.00 0.00 0.00 3.71
274 275 2.360801 GAGGGAGATGAAGACGAAGAGG 59.639 54.545 0.00 0.00 0.00 3.69
275 276 2.032799 CGAGGGAGATGAAGACGAAGAG 59.967 54.545 0.00 0.00 0.00 2.85
276 277 2.017782 CGAGGGAGATGAAGACGAAGA 58.982 52.381 0.00 0.00 0.00 2.87
277 278 1.746220 ACGAGGGAGATGAAGACGAAG 59.254 52.381 0.00 0.00 0.00 3.79
278 279 1.472878 CACGAGGGAGATGAAGACGAA 59.527 52.381 0.00 0.00 0.00 3.85
279 280 1.095600 CACGAGGGAGATGAAGACGA 58.904 55.000 0.00 0.00 0.00 4.20
280 281 0.101399 CCACGAGGGAGATGAAGACG 59.899 60.000 0.00 0.00 40.01 4.18
293 294 3.151022 GCTCCCTCCTCCCACGAG 61.151 72.222 0.00 0.00 35.72 4.18
294 295 4.779733 GGCTCCCTCCTCCCACGA 62.780 72.222 0.00 0.00 0.00 4.35
295 296 4.787280 AGGCTCCCTCCTCCCACG 62.787 72.222 0.00 0.00 0.00 4.94
296 297 2.766229 GAGGCTCCCTCCTCCCAC 60.766 72.222 2.15 0.00 44.36 4.61
306 307 4.475135 GCCGGAGTTGGAGGCTCC 62.475 72.222 26.95 26.95 46.83 4.70
381 383 2.026262 GCTCTTCACCTAATTCCCACCA 60.026 50.000 0.00 0.00 0.00 4.17
392 395 1.613630 ATCCCACCGCTCTTCACCT 60.614 57.895 0.00 0.00 0.00 4.00
397 400 2.370445 CCTCCATCCCACCGCTCTT 61.370 63.158 0.00 0.00 0.00 2.85
437 440 2.676121 CTGCCCGCCATGTTTCCA 60.676 61.111 0.00 0.00 0.00 3.53
445 448 1.971167 CTTTTGTAGCTGCCCGCCA 60.971 57.895 0.00 0.00 40.39 5.69
545 593 7.201794 CCATTCAAAGCAGTCATGTATTGATCT 60.202 37.037 0.00 0.00 36.54 2.75
550 598 4.708421 AGCCATTCAAAGCAGTCATGTATT 59.292 37.500 0.00 0.00 0.00 1.89
558 606 1.270550 CCGAAAGCCATTCAAAGCAGT 59.729 47.619 1.34 0.00 37.96 4.40
560 608 1.000385 CACCGAAAGCCATTCAAAGCA 60.000 47.619 1.34 0.00 37.96 3.91
562 610 2.351738 GGACACCGAAAGCCATTCAAAG 60.352 50.000 1.34 0.00 37.96 2.77
592 640 1.742831 GCTCGCATATGTTTTGGACCA 59.257 47.619 4.29 0.00 0.00 4.02
603 651 1.299541 CCCTCAAAACGCTCGCATAT 58.700 50.000 0.00 0.00 0.00 1.78
618 666 1.136500 GTATCTCCAACACCGACCCTC 59.864 57.143 0.00 0.00 0.00 4.30
916 968 4.097361 GGAGTGGGGTTCGGCTCC 62.097 72.222 0.00 0.00 40.39 4.70
979 1031 1.997874 CCTCCACCCCCTTCTCCTG 60.998 68.421 0.00 0.00 0.00 3.86
1212 1264 4.448210 GGTGTGAAGTTGTTCTCCTTACA 58.552 43.478 0.00 0.00 33.38 2.41
1347 1743 2.465860 TTCCACGATAACCCACACAG 57.534 50.000 0.00 0.00 0.00 3.66
1536 1932 5.791974 CGAAGCTTGTTGAGTTTCACATATG 59.208 40.000 2.10 0.00 43.48 1.78
1547 1943 4.051922 AGTACTGAACGAAGCTTGTTGAG 58.948 43.478 18.93 18.93 36.74 3.02
1553 1949 3.318275 TGAGACAGTACTGAACGAAGCTT 59.682 43.478 29.30 0.00 0.00 3.74
1570 1966 1.815003 CAAACAGCCCCAAGATGAGAC 59.185 52.381 0.00 0.00 0.00 3.36
1575 1971 2.365293 GTTTGTCAAACAGCCCCAAGAT 59.635 45.455 21.08 0.00 41.04 2.40
1596 2008 3.506067 GGAAGTGGGTGTGGTAGATTTTG 59.494 47.826 0.00 0.00 0.00 2.44
1691 2262 2.004583 TAGCCTCACATACGCACAAC 57.995 50.000 0.00 0.00 0.00 3.32
2087 2658 8.027524 TCAGATTGTTCTATGAGGCTAGAAAT 57.972 34.615 0.00 0.00 38.96 2.17
2096 2667 6.365518 CCGTGATGATCAGATTGTTCTATGAG 59.634 42.308 0.09 0.00 0.00 2.90
2099 2670 6.410942 TCCGTGATGATCAGATTGTTCTAT 57.589 37.500 0.09 0.00 0.00 1.98
2119 2690 1.404851 GGCAGTCTCCTCTTCTTTCCG 60.405 57.143 0.00 0.00 0.00 4.30
2201 2772 3.072915 TCATGAGTTGGTGAGTTGACCAT 59.927 43.478 0.00 0.00 45.64 3.55
2537 3135 5.071923 TGACATCTATCTCGGAGACCTTAGA 59.928 44.000 10.41 13.60 0.00 2.10
2680 3278 0.477204 CCTCCTGATGTGCATGGGAT 59.523 55.000 0.00 0.00 0.00 3.85
2692 3290 0.620556 GTTCTGATTGGGCCTCCTGA 59.379 55.000 4.53 0.52 0.00 3.86
2834 3435 7.525688 TCAGCTACAAGAAATGAGAAATACG 57.474 36.000 0.00 0.00 0.00 3.06
2894 3495 1.055040 AGGCATATCTCACTGGGAGC 58.945 55.000 0.94 0.00 43.70 4.70
3049 3653 5.043248 GTCACAAAAGAACCACAAATCTGG 58.957 41.667 0.00 0.00 37.33 3.86
3227 3831 7.775120 AGAAACCAAATGAACCATGATATCAC 58.225 34.615 7.78 0.00 0.00 3.06
3234 3838 3.429543 CGCAAGAAACCAAATGAACCATG 59.570 43.478 0.00 0.00 43.02 3.66
3247 3857 2.298300 CGATGACACAACGCAAGAAAC 58.702 47.619 0.00 0.00 43.62 2.78
3321 3983 1.138247 CTGCGGATTTGCTGAAGCC 59.862 57.895 0.00 0.00 40.49 4.35
3400 4062 0.879400 CATAGCAAGAGGAGCAGGCG 60.879 60.000 0.00 0.00 0.00 5.52
3411 4073 1.466856 TTGAGCCAAGCCATAGCAAG 58.533 50.000 0.00 0.00 43.56 4.01
3466 4128 4.060900 GTCCTCACACTATATGCATGTGG 58.939 47.826 17.16 12.08 43.21 4.17
3467 4129 4.748600 CAGTCCTCACACTATATGCATGTG 59.251 45.833 10.16 11.70 44.14 3.21
3545 4216 5.515626 GGAGTACTACAACGCATCTGTAAAG 59.484 44.000 0.00 0.00 0.00 1.85
3593 4267 2.094957 GGAGTCGAGACCAGAGTTCTTG 60.095 54.545 0.00 0.00 0.00 3.02
3669 4343 0.674895 AAGTCTGCCATGCTTCGGAC 60.675 55.000 10.16 10.16 0.00 4.79
3673 4347 4.418392 CACAAATAAGTCTGCCATGCTTC 58.582 43.478 0.00 0.00 0.00 3.86
3697 4371 3.039588 AAGTACCACGCGGCGTTG 61.040 61.111 27.24 24.79 38.32 4.10
3736 4410 3.579151 CCCTAAGGAGGCATAGGTAAGAC 59.421 52.174 0.00 0.00 42.21 3.01
3809 4490 4.359434 TGTTTGCAGGTAGTGTTGGATA 57.641 40.909 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.