Multiple sequence alignment - TraesCS1B01G175100

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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 TraesCS1B01G175100 chr1B 100.000 4137 0 0 1 4137 315614369 315618505 0.000000e+00 7640.0
1 TraesCS1B01G175100 chr1B 99.434 3533 14 4 608 4137 315834041 315837570 0.000000e+00 6408.0
2 TraesCS1B01G175100 chr1B 97.872 141 3 0 1 141 315833909 315834049 1.150000e-60 244.0
3 TraesCS1B01G175100 chr1B 92.157 153 11 1 624 776 120492155 120492306 9.010000e-52 215.0
4 TraesCS1B01G175100 chr1B 90.196 153 14 1 624 776 284063347 284063498 9.070000e-47 198.0
5 TraesCS1B01G175100 chr1B 97.959 98 1 1 1 98 659968579 659968675 7.110000e-38 169.0
6 TraesCS1B01G175100 chr1B 85.616 146 9 2 1 134 651903179 651903324 4.310000e-30 143.0
7 TraesCS1B01G175100 chr1B 92.553 94 7 0 683 776 51564254 51564161 7.210000e-28 135.0
8 TraesCS1B01G175100 chr6A 96.170 470 17 1 138 607 105536276 105536744 0.000000e+00 767.0
9 TraesCS1B01G175100 chr6A 95.494 466 20 1 142 607 237919753 237919289 0.000000e+00 743.0
10 TraesCS1B01G175100 chr6A 83.036 112 13 2 2526 2631 480803724 480803613 3.400000e-16 97.1
11 TraesCS1B01G175100 chr3A 96.352 466 16 1 142 607 209408144 209407680 0.000000e+00 765.0
12 TraesCS1B01G175100 chr3A 86.301 146 8 1 1 134 41525548 41525403 9.270000e-32 148.0
13 TraesCS1B01G175100 chr3A 91.463 82 6 1 52 133 58039716 58039636 1.220000e-20 111.0
14 TraesCS1B01G175100 chr3B 95.940 468 17 2 141 608 690854686 690854221 0.000000e+00 758.0
15 TraesCS1B01G175100 chr7A 95.503 467 18 3 141 607 301639636 301639173 0.000000e+00 743.0
16 TraesCS1B01G175100 chr2B 95.494 466 19 2 142 607 679155456 679154993 0.000000e+00 743.0
17 TraesCS1B01G175100 chr2B 88.235 102 10 1 677 776 758565363 758565262 2.020000e-23 121.0
18 TraesCS1B01G175100 chr4B 95.494 466 18 2 142 607 385954111 385954573 0.000000e+00 741.0
19 TraesCS1B01G175100 chr4B 96.939 98 2 1 1 98 238157652 238157556 3.310000e-36 163.0
20 TraesCS1B01G175100 chr4B 88.462 104 8 2 675 776 518655559 518655660 5.620000e-24 122.0
21 TraesCS1B01G175100 chr7B 94.515 474 21 4 136 608 516135398 516134929 0.000000e+00 726.0
22 TraesCS1B01G175100 chr7B 97.581 124 3 0 653 776 700869266 700869143 3.240000e-51 213.0
23 TraesCS1B01G175100 chr7B 86.538 104 12 1 675 776 406682407 406682304 3.380000e-21 113.0
24 TraesCS1B01G175100 chr7B 81.507 146 12 8 1 134 725761474 725761616 5.660000e-19 106.0
25 TraesCS1B01G175100 chr7B 88.710 62 5 2 4034 4095 727611553 727611612 1.600000e-09 75.0
26 TraesCS1B01G175100 chr7D 94.492 472 22 4 141 610 219837017 219836548 0.000000e+00 725.0
27 TraesCS1B01G175100 chr7D 98.148 54 1 0 81 134 511631650 511631703 1.220000e-15 95.3
28 TraesCS1B01G175100 chr7D 93.478 46 2 1 4054 4098 627126661 627126616 2.670000e-07 67.6
29 TraesCS1B01G175100 chr5B 95.652 138 6 0 1 138 455274558 455274421 5.380000e-54 222.0
30 TraesCS1B01G175100 chr5B 81.507 146 12 5 1 134 25288575 25288433 5.660000e-19 106.0
31 TraesCS1B01G175100 chr4A 90.909 154 13 1 624 776 657089277 657089124 5.420000e-49 206.0
32 TraesCS1B01G175100 chr4A 85.876 177 13 7 2147 2311 467259343 467259519 1.180000e-40 178.0
33 TraesCS1B01G175100 chr2A 86.986 146 7 3 1 134 771859068 771859213 1.990000e-33 154.0
34 TraesCS1B01G175100 chr3D 89.189 111 7 3 24 134 604404864 604404969 2.590000e-27 134.0
35 TraesCS1B01G175100 chr2D 96.610 59 2 0 76 134 645272246 645272304 9.460000e-17 99.0
36 TraesCS1B01G175100 chr6B 83.146 89 11 4 4012 4096 14811541 14811629 1.230000e-10 78.7


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 TraesCS1B01G175100 chr1B 315614369 315618505 4136 False 7640 7640 100.000 1 4137 1 chr1B.!!$F3 4136
1 TraesCS1B01G175100 chr1B 315833909 315837570 3661 False 3326 6408 98.653 1 4137 2 chr1B.!!$F6 4136

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
233 234 0.033504 CGCCAGGGCACGATTACTAT 59.966 55.000 11.42 0.0 42.06 2.12 F
349 350 0.250727 GGCCGCATATTTCCAGCCTA 60.251 55.000 0.00 0.0 37.42 3.93 F
362 363 1.001378 CCAGCCTATTATTTGCCGCAC 60.001 52.381 0.00 0.0 0.00 5.34 F
444 445 1.161843 AAAACGTAATCGGGCTGTGG 58.838 50.000 0.00 0.0 41.85 4.17 F
445 446 1.303091 AAACGTAATCGGGCTGTGGC 61.303 55.000 0.00 0.0 41.85 5.01 F
531 532 2.048877 CCGTTTAGACCGTGCCGT 60.049 61.111 0.00 0.0 0.00 5.68 F
613 614 2.190398 TTGGCCAGCTATAGAAGGGA 57.810 50.000 5.11 0.0 0.00 4.20 F
614 615 2.422939 TGGCCAGCTATAGAAGGGAT 57.577 50.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 1980 4.457496 AGCGATCACTGCACCCCG 62.457 66.667 0.00 0.00 33.85 5.73 R
2489 2490 4.580167 ACTGTCAGCTGTAAAGCAATTTCA 59.420 37.500 14.67 0.00 37.25 2.69 R
2521 2522 0.180171 ACCGGATTGCCAATCGATCA 59.820 50.000 9.46 0.00 38.82 2.92 R
2599 2600 0.603707 ACATGCCACTTCTCACACGG 60.604 55.000 0.00 0.00 0.00 4.94 R
2810 2811 1.000060 AGCAAATGTCGCAAGCACAAT 60.000 42.857 0.00 0.00 32.67 2.71 R
2851 2852 5.804639 TGACAATACTTGCCTCACTGTAAT 58.195 37.500 0.00 0.00 0.00 1.89 R
3106 3108 3.790091 CACAGAGACCAGATGTATGTGG 58.210 50.000 6.51 6.51 45.98 4.17 R
3145 3147 5.319453 CCAATAGCCTCATTCACCATGTAT 58.681 41.667 0.00 0.00 34.06 2.29 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
140 141 1.668867 GCTAGCGAGGGAAGGGATC 59.331 63.158 0.00 0.00 0.00 3.36
141 142 1.115930 GCTAGCGAGGGAAGGGATCA 61.116 60.000 0.00 0.00 0.00 2.92
142 143 1.638529 CTAGCGAGGGAAGGGATCAT 58.361 55.000 0.00 0.00 0.00 2.45
143 144 2.808919 CTAGCGAGGGAAGGGATCATA 58.191 52.381 0.00 0.00 0.00 2.15
144 145 1.343069 AGCGAGGGAAGGGATCATAC 58.657 55.000 0.00 0.00 0.00 2.39
145 146 0.321996 GCGAGGGAAGGGATCATACC 59.678 60.000 0.00 0.00 0.00 2.73
146 147 2.016905 CGAGGGAAGGGATCATACCT 57.983 55.000 0.00 0.00 40.96 3.08
147 148 1.620819 CGAGGGAAGGGATCATACCTG 59.379 57.143 0.00 0.00 38.63 4.00
148 149 1.981495 GAGGGAAGGGATCATACCTGG 59.019 57.143 0.00 0.00 38.63 4.45
149 150 0.402121 GGGAAGGGATCATACCTGGC 59.598 60.000 0.00 0.00 38.63 4.85
150 151 0.402121 GGAAGGGATCATACCTGGCC 59.598 60.000 0.00 0.00 38.63 5.36
151 152 1.140312 GAAGGGATCATACCTGGCCA 58.860 55.000 4.71 4.71 38.63 5.36
152 153 1.494721 GAAGGGATCATACCTGGCCAA 59.505 52.381 7.01 0.00 38.63 4.52
153 154 1.607225 AGGGATCATACCTGGCCAAA 58.393 50.000 7.01 0.00 36.85 3.28
154 155 1.215423 AGGGATCATACCTGGCCAAAC 59.785 52.381 7.01 0.00 36.85 2.93
155 156 1.308998 GGATCATACCTGGCCAAACG 58.691 55.000 7.01 0.00 0.00 3.60
156 157 1.308998 GATCATACCTGGCCAAACGG 58.691 55.000 7.01 7.56 0.00 4.44
157 158 0.106719 ATCATACCTGGCCAAACGGG 60.107 55.000 7.01 7.12 42.81 5.28
192 193 4.265056 GGCCCGGCCCATCGTAAT 62.265 66.667 18.83 0.00 44.06 1.89
193 194 2.668550 GCCCGGCCCATCGTAATC 60.669 66.667 0.00 0.00 0.00 1.75
194 195 2.357034 CCCGGCCCATCGTAATCG 60.357 66.667 0.00 0.00 38.55 3.34
195 196 2.420043 CCGGCCCATCGTAATCGT 59.580 61.111 0.00 0.00 38.33 3.73
196 197 1.954146 CCGGCCCATCGTAATCGTG 60.954 63.158 0.00 0.00 38.33 4.35
197 198 2.594962 CGGCCCATCGTAATCGTGC 61.595 63.158 0.00 0.00 38.33 5.34
198 199 2.251642 GGCCCATCGTAATCGTGCC 61.252 63.158 0.00 0.00 38.33 5.01
199 200 1.227556 GCCCATCGTAATCGTGCCT 60.228 57.895 0.00 0.00 38.33 4.75
200 201 1.498865 GCCCATCGTAATCGTGCCTG 61.499 60.000 0.00 0.00 38.33 4.85
201 202 0.880278 CCCATCGTAATCGTGCCTGG 60.880 60.000 0.00 0.00 38.33 4.45
202 203 1.498865 CCATCGTAATCGTGCCTGGC 61.499 60.000 12.87 12.87 38.33 4.85
203 204 1.227556 ATCGTAATCGTGCCTGGCC 60.228 57.895 17.53 6.66 38.33 5.36
204 205 2.660258 ATCGTAATCGTGCCTGGCCC 62.660 60.000 17.53 2.94 38.33 5.80
205 206 2.895372 GTAATCGTGCCTGGCCCG 60.895 66.667 17.67 17.67 0.00 6.13
206 207 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
230 231 2.895372 CCGCCAGGGCACGATTAC 60.895 66.667 11.42 0.00 42.06 1.89
231 232 2.186903 CGCCAGGGCACGATTACT 59.813 61.111 11.42 0.00 42.06 2.24
232 233 1.440060 CGCCAGGGCACGATTACTA 59.560 57.895 11.42 0.00 42.06 1.82
233 234 0.033504 CGCCAGGGCACGATTACTAT 59.966 55.000 11.42 0.00 42.06 2.12
234 235 1.271379 CGCCAGGGCACGATTACTATA 59.729 52.381 11.42 0.00 42.06 1.31
235 236 2.685100 GCCAGGGCACGATTACTATAC 58.315 52.381 5.20 0.00 41.49 1.47
236 237 2.925306 GCCAGGGCACGATTACTATACG 60.925 54.545 5.20 0.00 41.49 3.06
237 238 2.352421 CCAGGGCACGATTACTATACGG 60.352 54.545 0.00 0.00 0.00 4.02
238 239 1.891150 AGGGCACGATTACTATACGGG 59.109 52.381 0.00 0.00 0.00 5.28
239 240 1.615392 GGGCACGATTACTATACGGGT 59.385 52.381 0.00 0.00 32.80 5.28
240 241 2.352127 GGGCACGATTACTATACGGGTC 60.352 54.545 0.00 0.00 34.22 4.46
241 242 2.578495 GCACGATTACTATACGGGTCG 58.422 52.381 0.00 0.00 32.80 4.79
242 243 2.031682 GCACGATTACTATACGGGTCGT 60.032 50.000 0.00 0.00 44.35 4.34
243 244 3.885484 ACGATTACTATACGGGTCGTG 57.115 47.619 3.03 0.00 41.39 4.35
244 245 3.466836 ACGATTACTATACGGGTCGTGA 58.533 45.455 3.03 0.00 41.39 4.35
245 246 3.248602 ACGATTACTATACGGGTCGTGAC 59.751 47.826 3.03 0.00 41.39 3.67
246 247 3.662713 CGATTACTATACGGGTCGTGACG 60.663 52.174 0.00 0.00 41.39 4.35
247 248 2.309528 TACTATACGGGTCGTGACGT 57.690 50.000 4.40 0.00 46.17 4.34
248 249 0.729116 ACTATACGGGTCGTGACGTG 59.271 55.000 4.40 0.00 43.93 4.49
249 250 0.590732 CTATACGGGTCGTGACGTGC 60.591 60.000 4.40 0.00 43.93 5.34
250 251 1.992233 TATACGGGTCGTGACGTGCC 61.992 60.000 4.40 8.79 43.93 5.01
291 292 3.953775 CCCAGGCACGACCCAGTT 61.954 66.667 0.00 0.00 40.58 3.16
292 293 2.589157 CCCAGGCACGACCCAGTTA 61.589 63.158 0.00 0.00 40.58 2.24
293 294 1.079127 CCAGGCACGACCCAGTTAG 60.079 63.158 0.00 0.00 40.58 2.34
294 295 1.671742 CAGGCACGACCCAGTTAGT 59.328 57.895 0.00 0.00 40.58 2.24
295 296 0.892755 CAGGCACGACCCAGTTAGTA 59.107 55.000 0.00 0.00 40.58 1.82
296 297 1.274167 CAGGCACGACCCAGTTAGTAA 59.726 52.381 0.00 0.00 40.58 2.24
297 298 1.972795 AGGCACGACCCAGTTAGTAAA 59.027 47.619 0.00 0.00 40.58 2.01
298 299 2.071540 GGCACGACCCAGTTAGTAAAC 58.928 52.381 0.00 0.00 35.72 2.01
299 300 1.723003 GCACGACCCAGTTAGTAAACG 59.277 52.381 0.00 0.00 40.73 3.60
300 301 2.331194 CACGACCCAGTTAGTAAACGG 58.669 52.381 0.00 0.00 40.73 4.44
301 302 1.273327 ACGACCCAGTTAGTAAACGGG 59.727 52.381 13.95 13.95 46.88 5.28
302 303 1.730501 GACCCAGTTAGTAAACGGGC 58.269 55.000 15.04 7.01 46.22 6.13
303 304 0.325933 ACCCAGTTAGTAAACGGGCC 59.674 55.000 15.04 0.00 46.22 5.80
304 305 0.741927 CCCAGTTAGTAAACGGGCCG 60.742 60.000 27.06 27.06 46.22 6.13
305 306 0.741927 CCAGTTAGTAAACGGGCCGG 60.742 60.000 31.78 12.53 42.77 6.13
306 307 1.078918 AGTTAGTAAACGGGCCGGC 60.079 57.895 31.78 21.18 40.73 6.13
307 308 1.375780 GTTAGTAAACGGGCCGGCA 60.376 57.895 31.78 11.85 0.00 5.69
308 309 1.375780 TTAGTAAACGGGCCGGCAC 60.376 57.895 31.78 26.77 0.00 5.01
322 323 2.559330 GCACGTTGGCCCGTTTAG 59.441 61.111 4.13 0.00 39.45 1.85
323 324 2.559330 CACGTTGGCCCGTTTAGC 59.441 61.111 4.13 0.00 39.45 3.09
324 325 2.111460 ACGTTGGCCCGTTTAGCA 59.889 55.556 0.00 0.00 37.96 3.49
325 326 2.255881 ACGTTGGCCCGTTTAGCAC 61.256 57.895 0.00 0.00 37.96 4.40
333 334 3.428282 CGTTTAGCACGGTGGGCC 61.428 66.667 10.60 0.00 45.89 5.80
343 344 3.443588 GGTGGGCCGCATATTTCC 58.556 61.111 20.39 0.00 0.00 3.13
344 345 1.454847 GGTGGGCCGCATATTTCCA 60.455 57.895 20.39 0.00 0.00 3.53
345 346 1.455383 GGTGGGCCGCATATTTCCAG 61.455 60.000 20.39 0.00 0.00 3.86
346 347 1.827789 TGGGCCGCATATTTCCAGC 60.828 57.895 0.00 0.00 0.00 4.85
347 348 2.564721 GGGCCGCATATTTCCAGCC 61.565 63.158 0.00 0.00 39.73 4.85
348 349 1.529244 GGCCGCATATTTCCAGCCT 60.529 57.895 0.00 0.00 37.42 4.58
349 350 0.250727 GGCCGCATATTTCCAGCCTA 60.251 55.000 0.00 0.00 37.42 3.93
350 351 1.614317 GGCCGCATATTTCCAGCCTAT 60.614 52.381 0.00 0.00 37.42 2.57
351 352 2.162681 GCCGCATATTTCCAGCCTATT 58.837 47.619 0.00 0.00 0.00 1.73
352 353 3.343617 GCCGCATATTTCCAGCCTATTA 58.656 45.455 0.00 0.00 0.00 0.98
353 354 3.947834 GCCGCATATTTCCAGCCTATTAT 59.052 43.478 0.00 0.00 0.00 1.28
354 355 4.399303 GCCGCATATTTCCAGCCTATTATT 59.601 41.667 0.00 0.00 0.00 1.40
355 356 5.105756 GCCGCATATTTCCAGCCTATTATTT 60.106 40.000 0.00 0.00 0.00 1.40
356 357 6.324819 CCGCATATTTCCAGCCTATTATTTG 58.675 40.000 0.00 0.00 0.00 2.32
357 358 5.801947 CGCATATTTCCAGCCTATTATTTGC 59.198 40.000 0.00 0.00 0.00 3.68
358 359 6.101997 GCATATTTCCAGCCTATTATTTGCC 58.898 40.000 0.00 0.00 0.00 4.52
359 360 4.853924 ATTTCCAGCCTATTATTTGCCG 57.146 40.909 0.00 0.00 0.00 5.69
360 361 1.604604 TCCAGCCTATTATTTGCCGC 58.395 50.000 0.00 0.00 0.00 6.53
361 362 1.133945 TCCAGCCTATTATTTGCCGCA 60.134 47.619 0.00 0.00 0.00 5.69
362 363 1.001378 CCAGCCTATTATTTGCCGCAC 60.001 52.381 0.00 0.00 0.00 5.34
363 364 1.949525 CAGCCTATTATTTGCCGCACT 59.050 47.619 0.00 0.00 0.00 4.40
364 365 1.949525 AGCCTATTATTTGCCGCACTG 59.050 47.619 0.00 0.00 0.00 3.66
365 366 1.946768 GCCTATTATTTGCCGCACTGA 59.053 47.619 0.00 0.00 0.00 3.41
366 367 2.031682 GCCTATTATTTGCCGCACTGAG 60.032 50.000 0.00 0.00 0.00 3.35
367 368 2.031682 CCTATTATTTGCCGCACTGAGC 60.032 50.000 0.00 0.00 40.87 4.26
398 399 9.830186 TTTAGCCTATTTTTATATATTGGGCCA 57.170 29.630 0.00 0.00 37.98 5.36
443 444 2.981400 AAAAACGTAATCGGGCTGTG 57.019 45.000 0.00 0.00 41.85 3.66
444 445 1.161843 AAAACGTAATCGGGCTGTGG 58.838 50.000 0.00 0.00 41.85 4.17
445 446 1.303091 AAACGTAATCGGGCTGTGGC 61.303 55.000 0.00 0.00 41.85 5.01
446 447 3.261951 CGTAATCGGGCTGTGGCG 61.262 66.667 0.00 0.00 39.81 5.69
447 448 2.125269 GTAATCGGGCTGTGGCGT 60.125 61.111 0.00 0.00 39.81 5.68
448 449 2.125310 TAATCGGGCTGTGGCGTG 60.125 61.111 0.00 0.00 39.81 5.34
525 526 4.825252 CCCGGCCCGTTTAGACCG 62.825 72.222 0.85 0.00 45.21 4.79
526 527 4.073200 CCGGCCCGTTTAGACCGT 62.073 66.667 0.85 0.00 44.14 4.83
527 528 2.812178 CGGCCCGTTTAGACCGTG 60.812 66.667 0.00 0.00 40.77 4.94
528 529 3.122971 GGCCCGTTTAGACCGTGC 61.123 66.667 0.00 0.00 0.00 5.34
529 530 3.122971 GCCCGTTTAGACCGTGCC 61.123 66.667 0.00 0.00 0.00 5.01
530 531 2.812178 CCCGTTTAGACCGTGCCG 60.812 66.667 0.00 0.00 0.00 5.69
531 532 2.048877 CCGTTTAGACCGTGCCGT 60.049 61.111 0.00 0.00 0.00 5.68
532 533 2.377310 CCGTTTAGACCGTGCCGTG 61.377 63.158 0.00 0.00 0.00 4.94
533 534 2.858158 GTTTAGACCGTGCCGTGC 59.142 61.111 0.00 0.00 0.00 5.34
534 535 2.357760 TTTAGACCGTGCCGTGCC 60.358 61.111 0.00 0.00 0.00 5.01
535 536 2.874664 TTTAGACCGTGCCGTGCCT 61.875 57.895 0.00 0.00 0.00 4.75
536 537 3.583276 TTAGACCGTGCCGTGCCTG 62.583 63.158 0.00 0.00 0.00 4.85
608 609 2.957402 CCCATTTGGCCAGCTATAGA 57.043 50.000 5.11 0.00 0.00 1.98
609 610 3.228188 CCCATTTGGCCAGCTATAGAA 57.772 47.619 5.11 0.00 0.00 2.10
610 611 3.152341 CCCATTTGGCCAGCTATAGAAG 58.848 50.000 5.11 0.00 0.00 2.85
611 612 3.152341 CCATTTGGCCAGCTATAGAAGG 58.848 50.000 5.11 5.24 0.00 3.46
612 613 3.152341 CATTTGGCCAGCTATAGAAGGG 58.848 50.000 5.11 2.20 0.00 3.95
613 614 2.190398 TTGGCCAGCTATAGAAGGGA 57.810 50.000 5.11 0.00 0.00 4.20
614 615 2.422939 TGGCCAGCTATAGAAGGGAT 57.577 50.000 0.00 0.00 0.00 3.85
1762 1763 3.981071 TGCTATTGCAGTACAAGAGGT 57.019 42.857 0.00 0.00 45.78 3.85
1763 1764 3.599343 TGCTATTGCAGTACAAGAGGTG 58.401 45.455 0.00 0.00 45.78 4.00
1764 1765 2.939103 GCTATTGCAGTACAAGAGGTGG 59.061 50.000 0.11 0.00 45.78 4.61
2489 2490 4.012374 CTGTTCCTGGTCAATTATGTGCT 58.988 43.478 0.00 0.00 0.00 4.40
2521 2522 2.991250 ACAGCTGACAGTTTTGTGTCT 58.009 42.857 23.35 0.00 46.06 3.41
2599 2600 8.477709 GTTAGATATGTAGTGTCGTGCAAATAC 58.522 37.037 0.00 0.00 0.00 1.89
2661 2662 6.331845 TGTGCAGTCAATTTATTTGCATAGG 58.668 36.000 0.53 0.00 45.31 2.57
2810 2811 6.122277 GGACCCTCATCATGAGTTTTTGATA 58.878 40.000 13.82 0.00 42.80 2.15
2851 2852 4.380128 GCTCAAGACATTGCATCACATTGA 60.380 41.667 0.00 0.00 36.30 2.57
3106 3108 5.412594 TGTGGTTCAGCAGAAATCTAATCAC 59.587 40.000 0.00 0.00 35.08 3.06
3145 3147 4.588951 TCTGTGCAGGAGTAGAAGAGAAAA 59.411 41.667 0.00 0.00 0.00 2.29
4061 4065 1.384222 GGGCTGATAAGCGGGTTTGG 61.384 60.000 0.00 0.00 35.24 3.28
4095 4099 0.939577 CGAACAGACCCCGCATATCG 60.940 60.000 0.00 0.00 38.08 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 2.408241 CCTCGTCTCCCGTCTCCAC 61.408 68.421 0.00 0.00 37.94 4.02
140 141 3.918544 CCCGTTTGGCCAGGTATG 58.081 61.111 5.11 0.95 0.00 2.39
176 177 2.668550 GATTACGATGGGCCGGGC 60.669 66.667 22.00 22.00 0.00 6.13
177 178 2.357034 CGATTACGATGGGCCGGG 60.357 66.667 2.18 0.00 42.66 5.73
178 179 1.954146 CACGATTACGATGGGCCGG 60.954 63.158 0.00 0.00 42.66 6.13
179 180 2.594962 GCACGATTACGATGGGCCG 61.595 63.158 0.00 0.00 42.66 6.13
180 181 2.251642 GGCACGATTACGATGGGCC 61.252 63.158 0.00 0.00 42.66 5.80
181 182 1.227556 AGGCACGATTACGATGGGC 60.228 57.895 0.00 0.00 42.66 5.36
182 183 0.880278 CCAGGCACGATTACGATGGG 60.880 60.000 0.00 0.00 42.66 4.00
183 184 1.498865 GCCAGGCACGATTACGATGG 61.499 60.000 6.55 0.00 42.66 3.51
184 185 1.498865 GGCCAGGCACGATTACGATG 61.499 60.000 15.19 0.00 42.66 3.84
185 186 1.227556 GGCCAGGCACGATTACGAT 60.228 57.895 15.19 0.00 42.66 3.73
186 187 2.185867 GGCCAGGCACGATTACGA 59.814 61.111 15.19 0.00 42.66 3.43
187 188 2.895372 GGGCCAGGCACGATTACG 60.895 66.667 15.19 0.00 45.75 3.18
213 214 2.023414 TAGTAATCGTGCCCTGGCGG 62.023 60.000 3.32 0.00 45.51 6.13
214 215 0.033504 ATAGTAATCGTGCCCTGGCG 59.966 55.000 3.32 0.00 45.51 5.69
215 216 2.685100 GTATAGTAATCGTGCCCTGGC 58.315 52.381 0.00 0.00 42.35 4.85
216 217 2.352421 CCGTATAGTAATCGTGCCCTGG 60.352 54.545 0.00 0.00 0.00 4.45
217 218 2.352421 CCCGTATAGTAATCGTGCCCTG 60.352 54.545 0.00 0.00 0.00 4.45
218 219 1.891150 CCCGTATAGTAATCGTGCCCT 59.109 52.381 0.00 0.00 0.00 5.19
219 220 1.615392 ACCCGTATAGTAATCGTGCCC 59.385 52.381 0.00 0.00 0.00 5.36
220 221 2.666619 CGACCCGTATAGTAATCGTGCC 60.667 54.545 0.00 0.00 0.00 5.01
221 222 2.031682 ACGACCCGTATAGTAATCGTGC 60.032 50.000 0.00 0.00 40.95 5.34
222 223 3.885484 ACGACCCGTATAGTAATCGTG 57.115 47.619 0.00 0.00 40.95 4.35
223 224 3.248602 GTCACGACCCGTATAGTAATCGT 59.751 47.826 0.00 0.00 43.08 3.73
224 225 3.662713 CGTCACGACCCGTATAGTAATCG 60.663 52.174 0.00 0.00 38.32 3.34
225 226 3.248602 ACGTCACGACCCGTATAGTAATC 59.751 47.826 2.91 0.00 38.32 1.75
226 227 3.002656 CACGTCACGACCCGTATAGTAAT 59.997 47.826 2.91 0.00 38.32 1.89
227 228 2.351418 CACGTCACGACCCGTATAGTAA 59.649 50.000 2.91 0.00 38.32 2.24
228 229 1.933181 CACGTCACGACCCGTATAGTA 59.067 52.381 2.91 0.00 38.32 1.82
229 230 0.729116 CACGTCACGACCCGTATAGT 59.271 55.000 2.91 0.00 38.32 2.12
230 231 0.590732 GCACGTCACGACCCGTATAG 60.591 60.000 2.91 0.00 38.32 1.31
231 232 1.429021 GCACGTCACGACCCGTATA 59.571 57.895 2.91 0.00 38.32 1.47
232 233 2.180017 GCACGTCACGACCCGTAT 59.820 61.111 2.91 0.00 38.32 3.06
233 234 4.041917 GGCACGTCACGACCCGTA 62.042 66.667 2.91 0.00 38.32 4.02
274 275 2.521958 CTAACTGGGTCGTGCCTGGG 62.522 65.000 0.00 0.00 37.43 4.45
275 276 1.079127 CTAACTGGGTCGTGCCTGG 60.079 63.158 0.00 0.00 37.43 4.45
276 277 0.892755 TACTAACTGGGTCGTGCCTG 59.107 55.000 0.00 0.00 37.43 4.85
277 278 1.636148 TTACTAACTGGGTCGTGCCT 58.364 50.000 0.00 0.00 37.43 4.75
278 279 2.071540 GTTTACTAACTGGGTCGTGCC 58.928 52.381 0.00 0.00 0.00 5.01
279 280 1.723003 CGTTTACTAACTGGGTCGTGC 59.277 52.381 0.00 0.00 31.89 5.34
280 281 2.331194 CCGTTTACTAACTGGGTCGTG 58.669 52.381 0.00 0.00 31.89 4.35
281 282 1.273327 CCCGTTTACTAACTGGGTCGT 59.727 52.381 0.00 0.00 40.32 4.34
282 283 2.000429 CCCGTTTACTAACTGGGTCG 58.000 55.000 0.00 0.00 40.32 4.79
283 284 1.676916 GGCCCGTTTACTAACTGGGTC 60.677 57.143 14.69 10.98 43.73 4.46
284 285 0.325933 GGCCCGTTTACTAACTGGGT 59.674 55.000 14.69 0.00 43.73 4.51
285 286 0.741927 CGGCCCGTTTACTAACTGGG 60.742 60.000 0.00 11.19 44.21 4.45
286 287 0.741927 CCGGCCCGTTTACTAACTGG 60.742 60.000 0.85 0.00 40.48 4.00
287 288 1.363885 GCCGGCCCGTTTACTAACTG 61.364 60.000 18.11 0.00 31.89 3.16
288 289 1.078918 GCCGGCCCGTTTACTAACT 60.079 57.895 18.11 0.00 31.89 2.24
289 290 1.375780 TGCCGGCCCGTTTACTAAC 60.376 57.895 26.77 0.00 0.00 2.34
290 291 1.375780 GTGCCGGCCCGTTTACTAA 60.376 57.895 26.77 0.00 0.00 2.24
291 292 2.265424 GTGCCGGCCCGTTTACTA 59.735 61.111 26.77 0.00 0.00 1.82
294 295 4.622650 AACGTGCCGGCCCGTTTA 62.623 61.111 38.23 11.19 44.16 2.01
308 309 2.559330 GTGCTAAACGGGCCAACG 59.441 61.111 4.39 1.48 40.31 4.10
326 327 1.454847 TGGAAATATGCGGCCCACC 60.455 57.895 0.00 0.00 0.00 4.61
327 328 2.032981 CTGGAAATATGCGGCCCAC 58.967 57.895 0.00 0.00 0.00 4.61
328 329 1.827789 GCTGGAAATATGCGGCCCA 60.828 57.895 0.00 0.00 42.97 5.36
329 330 3.042560 GCTGGAAATATGCGGCCC 58.957 61.111 0.00 0.00 42.97 5.80
332 333 6.324819 CAAATAATAGGCTGGAAATATGCGG 58.675 40.000 0.00 0.00 0.00 5.69
333 334 5.801947 GCAAATAATAGGCTGGAAATATGCG 59.198 40.000 0.00 0.00 0.00 4.73
334 335 6.101997 GGCAAATAATAGGCTGGAAATATGC 58.898 40.000 0.00 0.00 0.00 3.14
335 336 6.324819 CGGCAAATAATAGGCTGGAAATATG 58.675 40.000 0.00 0.00 0.00 1.78
336 337 5.105756 GCGGCAAATAATAGGCTGGAAATAT 60.106 40.000 0.00 0.00 34.52 1.28
337 338 4.217550 GCGGCAAATAATAGGCTGGAAATA 59.782 41.667 0.00 0.00 34.52 1.40
338 339 3.005791 GCGGCAAATAATAGGCTGGAAAT 59.994 43.478 0.00 0.00 34.52 2.17
339 340 2.360801 GCGGCAAATAATAGGCTGGAAA 59.639 45.455 0.00 0.00 34.52 3.13
340 341 1.953686 GCGGCAAATAATAGGCTGGAA 59.046 47.619 0.00 0.00 34.52 3.53
341 342 1.133945 TGCGGCAAATAATAGGCTGGA 60.134 47.619 0.00 0.00 34.52 3.86
342 343 1.001378 GTGCGGCAAATAATAGGCTGG 60.001 52.381 3.23 0.00 34.52 4.85
343 344 1.949525 AGTGCGGCAAATAATAGGCTG 59.050 47.619 3.23 0.00 36.99 4.85
344 345 1.949525 CAGTGCGGCAAATAATAGGCT 59.050 47.619 3.23 0.00 0.00 4.58
345 346 1.946768 TCAGTGCGGCAAATAATAGGC 59.053 47.619 3.23 0.00 0.00 3.93
346 347 2.031682 GCTCAGTGCGGCAAATAATAGG 60.032 50.000 3.23 0.00 0.00 2.57
347 348 3.259207 GCTCAGTGCGGCAAATAATAG 57.741 47.619 3.23 0.00 0.00 1.73
372 373 9.830186 TGGCCCAATATATAAAAATAGGCTAAA 57.170 29.630 0.00 0.00 37.98 1.85
424 425 1.538075 CCACAGCCCGATTACGTTTTT 59.462 47.619 0.00 0.00 37.88 1.94
425 426 1.161843 CCACAGCCCGATTACGTTTT 58.838 50.000 0.00 0.00 37.88 2.43
426 427 1.303091 GCCACAGCCCGATTACGTTT 61.303 55.000 0.00 0.00 37.88 3.60
427 428 1.743995 GCCACAGCCCGATTACGTT 60.744 57.895 0.00 0.00 37.88 3.99
428 429 2.125269 GCCACAGCCCGATTACGT 60.125 61.111 0.00 0.00 37.88 3.57
429 430 3.261951 CGCCACAGCCCGATTACG 61.262 66.667 0.00 0.00 39.43 3.18
430 431 2.125269 ACGCCACAGCCCGATTAC 60.125 61.111 0.00 0.00 34.57 1.89
431 432 2.125310 CACGCCACAGCCCGATTA 60.125 61.111 0.00 0.00 34.57 1.75
508 509 4.825252 CGGTCTAAACGGGCCGGG 62.825 72.222 31.78 16.63 40.45 5.73
589 590 2.957402 TCTATAGCTGGCCAAATGGG 57.043 50.000 7.01 0.00 40.85 4.00
590 591 3.152341 CCTTCTATAGCTGGCCAAATGG 58.848 50.000 7.01 3.05 38.53 3.16
591 592 3.152341 CCCTTCTATAGCTGGCCAAATG 58.848 50.000 7.01 0.00 0.00 2.32
592 593 3.056080 TCCCTTCTATAGCTGGCCAAAT 58.944 45.455 7.01 3.30 0.00 2.32
593 594 2.487775 TCCCTTCTATAGCTGGCCAAA 58.512 47.619 7.01 0.00 0.00 3.28
594 595 2.190398 TCCCTTCTATAGCTGGCCAA 57.810 50.000 7.01 0.00 0.00 4.52
595 596 2.260822 GATCCCTTCTATAGCTGGCCA 58.739 52.381 4.71 4.71 0.00 5.36
596 597 1.205893 CGATCCCTTCTATAGCTGGCC 59.794 57.143 0.00 0.00 0.00 5.36
597 598 2.171840 TCGATCCCTTCTATAGCTGGC 58.828 52.381 0.00 0.00 0.00 4.85
598 599 3.131933 CCATCGATCCCTTCTATAGCTGG 59.868 52.174 0.00 0.00 0.00 4.85
599 600 3.766591 ACCATCGATCCCTTCTATAGCTG 59.233 47.826 0.00 0.00 0.00 4.24
600 601 4.054359 ACCATCGATCCCTTCTATAGCT 57.946 45.455 0.00 0.00 0.00 3.32
601 602 4.339814 CCTACCATCGATCCCTTCTATAGC 59.660 50.000 0.00 0.00 0.00 2.97
602 603 4.890581 CCCTACCATCGATCCCTTCTATAG 59.109 50.000 0.00 0.00 0.00 1.31
603 604 4.294168 ACCCTACCATCGATCCCTTCTATA 59.706 45.833 0.00 0.00 0.00 1.31
604 605 3.077695 ACCCTACCATCGATCCCTTCTAT 59.922 47.826 0.00 0.00 0.00 1.98
605 606 2.449730 ACCCTACCATCGATCCCTTCTA 59.550 50.000 0.00 0.00 0.00 2.10
606 607 1.220750 ACCCTACCATCGATCCCTTCT 59.779 52.381 0.00 0.00 0.00 2.85
607 608 1.718280 ACCCTACCATCGATCCCTTC 58.282 55.000 0.00 0.00 0.00 3.46
608 609 2.191981 AACCCTACCATCGATCCCTT 57.808 50.000 0.00 0.00 0.00 3.95
609 610 2.191981 AAACCCTACCATCGATCCCT 57.808 50.000 0.00 0.00 0.00 4.20
610 611 3.292492 AAAAACCCTACCATCGATCCC 57.708 47.619 0.00 0.00 0.00 3.85
1979 1980 4.457496 AGCGATCACTGCACCCCG 62.457 66.667 0.00 0.00 33.85 5.73
2489 2490 4.580167 ACTGTCAGCTGTAAAGCAATTTCA 59.420 37.500 14.67 0.00 37.25 2.69
2521 2522 0.180171 ACCGGATTGCCAATCGATCA 59.820 50.000 9.46 0.00 38.82 2.92
2599 2600 0.603707 ACATGCCACTTCTCACACGG 60.604 55.000 0.00 0.00 0.00 4.94
2810 2811 1.000060 AGCAAATGTCGCAAGCACAAT 60.000 42.857 0.00 0.00 32.67 2.71
2851 2852 5.804639 TGACAATACTTGCCTCACTGTAAT 58.195 37.500 0.00 0.00 0.00 1.89
3106 3108 3.790091 CACAGAGACCAGATGTATGTGG 58.210 50.000 6.51 6.51 45.98 4.17
3145 3147 5.319453 CCAATAGCCTCATTCACCATGTAT 58.681 41.667 0.00 0.00 34.06 2.29
4061 4065 0.948623 GTTCGGGCCACAAAAATGCC 60.949 55.000 4.39 0.00 44.59 4.40


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

AutoCloner maintained by Alex Coulton.