Multiple sequence alignment - TraesCS3A01G510400

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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 TraesCS3A01G510400 chr3A 100.000 2573 0 0 1 2573 730381268 730378696 0.000000e+00 4752.0
1 TraesCS3A01G510400 chr3A 98.102 2108 37 3 468 2573 102793536 102795642 0.000000e+00 3668.0
2 TraesCS3A01G510400 chr3A 96.997 2131 29 7 447 2573 696644073 696646172 0.000000e+00 3548.0
3 TraesCS3A01G510400 chr3A 83.444 453 62 11 22 464 730321762 730321313 2.380000e-110 409.0
4 TraesCS3A01G510400 chr3A 79.421 311 41 15 447 738 748243382 748243688 5.620000e-47 198.0
5 TraesCS3A01G510400 chr3D 93.644 236 15 0 1 236 600550217 600550452 1.130000e-93 353.0
6 TraesCS3A01G510400 chr3B 80.597 469 57 20 1 449 807622820 807623274 5.310000e-87 331.0
7 TraesCS3A01G510400 chr3B 93.443 61 3 1 455 515 171295987 171296046 3.530000e-14 89.8
8 TraesCS3A01G510400 chr2B 78.873 284 43 13 467 736 623335614 623335894 2.630000e-40 176.0
9 TraesCS3A01G510400 chr1B 82.222 135 22 1 447 579 511481173 511481307 5.820000e-22 115.0
10 TraesCS3A01G510400 chr6D 88.043 92 9 1 447 536 267807210 267807119 9.740000e-20 108.0
11 TraesCS3A01G510400 chrUn 91.429 70 2 2 447 512 252227196 252227127 2.730000e-15 93.5
12 TraesCS3A01G510400 chr7B 96.078 51 2 0 462 512 340639913 340639863 1.640000e-12 84.2


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 TraesCS3A01G510400 chr3A 730378696 730381268 2572 True 4752 4752 100.000 1 2573 1 chr3A.!!$R2 2572
1 TraesCS3A01G510400 chr3A 102793536 102795642 2106 False 3668 3668 98.102 468 2573 1 chr3A.!!$F1 2105
2 TraesCS3A01G510400 chr3A 696644073 696646172 2099 False 3548 3548 96.997 447 2573 1 chr3A.!!$F2 2126

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
738 741 0.038892 GGTTGCGTGGTTAGACGAGA 60.039 55.0 0.0 0.0 42.1 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2129 5.596845 TGGTCAAAATTTACCTGCACTTTC 58.403 37.5 10.72 0.0 36.67 2.62 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
87 88 9.265901 TCAAAAAGTTTGAAATTTTCAGTGACA 57.734 25.926 11.41 0.00 41.38 3.58
88 89 9.316859 CAAAAAGTTTGAAATTTTCAGTGACAC 57.683 29.630 11.41 0.00 41.38 3.67
89 90 8.831715 AAAAGTTTGAAATTTTCAGTGACACT 57.168 26.923 11.41 1.07 41.38 3.55
90 91 8.831715 AAAGTTTGAAATTTTCAGTGACACTT 57.168 26.923 5.04 11.97 41.38 3.16
91 92 8.831715 AAGTTTGAAATTTTCAGTGACACTTT 57.168 26.923 5.04 0.00 41.38 2.66
92 93 9.921637 AAGTTTGAAATTTTCAGTGACACTTTA 57.078 25.926 5.04 0.00 41.38 1.85
96 97 9.868277 TTGAAATTTTCAGTGACACTTTATTGT 57.132 25.926 5.04 0.00 41.38 2.71
97 98 9.868277 TGAAATTTTCAGTGACACTTTATTGTT 57.132 25.926 5.04 0.00 34.08 2.83
99 100 8.871686 AATTTTCAGTGACACTTTATTGTTCC 57.128 30.769 5.04 0.00 0.00 3.62
100 101 7.397892 TTTTCAGTGACACTTTATTGTTCCA 57.602 32.000 5.04 0.00 0.00 3.53
101 102 7.397892 TTTCAGTGACACTTTATTGTTCCAA 57.602 32.000 5.04 0.00 0.00 3.53
102 103 7.397892 TTCAGTGACACTTTATTGTTCCAAA 57.602 32.000 5.04 0.00 0.00 3.28
103 104 7.397892 TCAGTGACACTTTATTGTTCCAAAA 57.602 32.000 5.04 0.00 0.00 2.44
104 105 7.254852 TCAGTGACACTTTATTGTTCCAAAAC 58.745 34.615 5.04 0.00 35.85 2.43
105 106 7.032580 CAGTGACACTTTATTGTTCCAAAACA 58.967 34.615 5.04 0.00 43.58 2.83
106 107 7.220683 CAGTGACACTTTATTGTTCCAAAACAG 59.779 37.037 5.04 0.00 45.72 3.16
107 108 7.033185 GTGACACTTTATTGTTCCAAAACAGT 58.967 34.615 0.00 0.00 45.72 3.55
108 109 7.544217 GTGACACTTTATTGTTCCAAAACAGTT 59.456 33.333 0.00 0.00 45.72 3.16
109 110 7.543868 TGACACTTTATTGTTCCAAAACAGTTG 59.456 33.333 0.00 0.00 45.72 3.16
110 111 6.312672 ACACTTTATTGTTCCAAAACAGTTGC 59.687 34.615 0.00 0.00 45.72 4.17
111 112 6.312426 CACTTTATTGTTCCAAAACAGTTGCA 59.688 34.615 0.00 0.00 45.72 4.08
112 113 6.876257 ACTTTATTGTTCCAAAACAGTTGCAA 59.124 30.769 0.00 0.00 45.72 4.08
113 114 7.389053 ACTTTATTGTTCCAAAACAGTTGCAAA 59.611 29.630 0.00 0.00 45.72 3.68
114 115 7.856145 TTATTGTTCCAAAACAGTTGCAAAT 57.144 28.000 0.00 0.00 45.72 2.32
115 116 5.542616 TTGTTCCAAAACAGTTGCAAATG 57.457 34.783 24.24 24.24 45.72 2.32
116 117 3.373439 TGTTCCAAAACAGTTGCAAATGC 59.627 39.130 25.59 8.20 40.45 3.56
117 118 2.200067 TCCAAAACAGTTGCAAATGCG 58.800 42.857 25.59 12.09 45.83 4.73
118 119 1.261089 CCAAAACAGTTGCAAATGCGG 59.739 47.619 25.59 16.77 45.83 5.69
119 120 1.261089 CAAAACAGTTGCAAATGCGGG 59.739 47.619 25.59 9.98 45.83 6.13
120 121 0.463620 AAACAGTTGCAAATGCGGGT 59.536 45.000 25.59 4.30 45.83 5.28
121 122 0.463620 AACAGTTGCAAATGCGGGTT 59.536 45.000 25.59 10.43 45.83 4.11
122 123 1.323412 ACAGTTGCAAATGCGGGTTA 58.677 45.000 25.59 0.00 45.83 2.85
123 124 1.892474 ACAGTTGCAAATGCGGGTTAT 59.108 42.857 25.59 2.38 45.83 1.89
124 125 3.085533 ACAGTTGCAAATGCGGGTTATA 58.914 40.909 25.59 0.00 45.83 0.98
125 126 3.508012 ACAGTTGCAAATGCGGGTTATAA 59.492 39.130 25.59 0.00 45.83 0.98
126 127 4.159506 ACAGTTGCAAATGCGGGTTATAAT 59.840 37.500 25.59 0.11 45.83 1.28
127 128 5.108517 CAGTTGCAAATGCGGGTTATAATT 58.891 37.500 14.60 0.00 45.83 1.40
128 129 5.231991 CAGTTGCAAATGCGGGTTATAATTC 59.768 40.000 14.60 0.00 45.83 2.17
129 130 4.991153 TGCAAATGCGGGTTATAATTCA 57.009 36.364 0.35 0.00 45.83 2.57
130 131 5.528043 TGCAAATGCGGGTTATAATTCAT 57.472 34.783 0.35 0.00 45.83 2.57
131 132 5.527951 TGCAAATGCGGGTTATAATTCATC 58.472 37.500 0.35 0.00 45.83 2.92
132 133 5.068329 TGCAAATGCGGGTTATAATTCATCA 59.932 36.000 0.35 0.00 45.83 3.07
133 134 5.402270 GCAAATGCGGGTTATAATTCATCAC 59.598 40.000 0.00 0.00 0.00 3.06
134 135 6.502652 CAAATGCGGGTTATAATTCATCACA 58.497 36.000 0.00 0.00 0.00 3.58
135 136 6.707440 AATGCGGGTTATAATTCATCACAA 57.293 33.333 0.00 0.00 0.00 3.33
136 137 5.493133 TGCGGGTTATAATTCATCACAAC 57.507 39.130 0.00 0.00 0.00 3.32
137 138 4.336993 TGCGGGTTATAATTCATCACAACC 59.663 41.667 0.00 0.00 35.71 3.77
138 139 4.336993 GCGGGTTATAATTCATCACAACCA 59.663 41.667 0.00 0.00 37.70 3.67
139 140 5.009610 GCGGGTTATAATTCATCACAACCAT 59.990 40.000 0.00 0.00 37.70 3.55
140 141 6.460953 GCGGGTTATAATTCATCACAACCATT 60.461 38.462 0.00 0.00 37.70 3.16
141 142 7.488322 CGGGTTATAATTCATCACAACCATTT 58.512 34.615 0.00 0.00 37.70 2.32
142 143 8.625651 CGGGTTATAATTCATCACAACCATTTA 58.374 33.333 0.00 0.00 37.70 1.40
182 183 9.798994 ATAATTCAATCAATTTCAGAAGCACTC 57.201 29.630 0.00 0.00 36.09 3.51
183 184 6.889301 TTCAATCAATTTCAGAAGCACTCT 57.111 33.333 0.00 0.00 33.23 3.24
184 185 7.984422 TTCAATCAATTTCAGAAGCACTCTA 57.016 32.000 0.00 0.00 31.12 2.43
185 186 7.369803 TCAATCAATTTCAGAAGCACTCTAC 57.630 36.000 0.00 0.00 31.12 2.59
186 187 6.936335 TCAATCAATTTCAGAAGCACTCTACA 59.064 34.615 0.00 0.00 31.12 2.74
187 188 7.609146 TCAATCAATTTCAGAAGCACTCTACAT 59.391 33.333 0.00 0.00 31.12 2.29
188 189 7.934855 ATCAATTTCAGAAGCACTCTACATT 57.065 32.000 0.00 0.00 31.12 2.71
189 190 7.369803 TCAATTTCAGAAGCACTCTACATTC 57.630 36.000 0.00 0.00 31.12 2.67
190 191 6.936335 TCAATTTCAGAAGCACTCTACATTCA 59.064 34.615 0.00 0.00 31.12 2.57
191 192 7.609146 TCAATTTCAGAAGCACTCTACATTCAT 59.391 33.333 0.00 0.00 31.12 2.57
192 193 7.934855 ATTTCAGAAGCACTCTACATTCATT 57.065 32.000 0.00 0.00 31.12 2.57
193 194 7.750229 TTTCAGAAGCACTCTACATTCATTT 57.250 32.000 0.00 0.00 31.12 2.32
194 195 7.750229 TTCAGAAGCACTCTACATTCATTTT 57.250 32.000 0.00 0.00 31.12 1.82
195 196 7.369803 TCAGAAGCACTCTACATTCATTTTC 57.630 36.000 0.00 0.00 31.12 2.29
196 197 6.936335 TCAGAAGCACTCTACATTCATTTTCA 59.064 34.615 0.00 0.00 31.12 2.69
197 198 7.020010 CAGAAGCACTCTACATTCATTTTCAC 58.980 38.462 0.00 0.00 31.12 3.18
198 199 6.712095 AGAAGCACTCTACATTCATTTTCACA 59.288 34.615 0.00 0.00 30.22 3.58
199 200 6.246420 AGCACTCTACATTCATTTTCACAC 57.754 37.500 0.00 0.00 0.00 3.82
200 201 5.764686 AGCACTCTACATTCATTTTCACACA 59.235 36.000 0.00 0.00 0.00 3.72
201 202 6.262944 AGCACTCTACATTCATTTTCACACAA 59.737 34.615 0.00 0.00 0.00 3.33
202 203 7.040201 AGCACTCTACATTCATTTTCACACAAT 60.040 33.333 0.00 0.00 0.00 2.71
203 204 7.596248 GCACTCTACATTCATTTTCACACAATT 59.404 33.333 0.00 0.00 0.00 2.32
204 205 9.467258 CACTCTACATTCATTTTCACACAATTT 57.533 29.630 0.00 0.00 0.00 1.82
305 306 9.928618 TTTTTCATACATATTACCTCCATTCCA 57.071 29.630 0.00 0.00 0.00 3.53
316 317 5.234466 ACCTCCATTCCATAATACAGAGC 57.766 43.478 0.00 0.00 0.00 4.09
317 318 4.042187 ACCTCCATTCCATAATACAGAGCC 59.958 45.833 0.00 0.00 0.00 4.70
318 319 4.288105 CCTCCATTCCATAATACAGAGCCT 59.712 45.833 0.00 0.00 0.00 4.58
319 320 5.485353 CCTCCATTCCATAATACAGAGCCTA 59.515 44.000 0.00 0.00 0.00 3.93
320 321 6.157645 CCTCCATTCCATAATACAGAGCCTAT 59.842 42.308 0.00 0.00 0.00 2.57
321 322 7.311549 CCTCCATTCCATAATACAGAGCCTATT 60.312 40.741 0.00 0.00 0.00 1.73
322 323 7.624549 TCCATTCCATAATACAGAGCCTATTC 58.375 38.462 0.00 0.00 0.00 1.75
323 324 7.459125 TCCATTCCATAATACAGAGCCTATTCT 59.541 37.037 0.00 0.00 0.00 2.40
324 325 8.105829 CCATTCCATAATACAGAGCCTATTCTT 58.894 37.037 0.00 0.00 0.00 2.52
325 326 9.512588 CATTCCATAATACAGAGCCTATTCTTT 57.487 33.333 0.00 0.00 0.00 2.52
327 328 9.561069 TTCCATAATACAGAGCCTATTCTTTTC 57.439 33.333 0.00 0.00 0.00 2.29
328 329 8.713971 TCCATAATACAGAGCCTATTCTTTTCA 58.286 33.333 0.00 0.00 0.00 2.69
329 330 9.342308 CCATAATACAGAGCCTATTCTTTTCAA 57.658 33.333 0.00 0.00 0.00 2.69
335 336 8.181904 ACAGAGCCTATTCTTTTCAAAATTCA 57.818 30.769 0.00 0.00 0.00 2.57
336 337 8.641541 ACAGAGCCTATTCTTTTCAAAATTCAA 58.358 29.630 0.00 0.00 0.00 2.69
337 338 9.480053 CAGAGCCTATTCTTTTCAAAATTCAAA 57.520 29.630 0.00 0.00 0.00 2.69
338 339 9.481340 AGAGCCTATTCTTTTCAAAATTCAAAC 57.519 29.630 0.00 0.00 0.00 2.93
339 340 9.260002 GAGCCTATTCTTTTCAAAATTCAAACA 57.740 29.630 0.00 0.00 0.00 2.83
340 341 9.783081 AGCCTATTCTTTTCAAAATTCAAACAT 57.217 25.926 0.00 0.00 0.00 2.71
346 347 9.903682 TTCTTTTCAAAATTCAAACATTGCAAA 57.096 22.222 1.71 0.00 0.00 3.68
347 348 9.557338 TCTTTTCAAAATTCAAACATTGCAAAG 57.443 25.926 1.71 0.19 37.36 2.77
348 349 9.344309 CTTTTCAAAATTCAAACATTGCAAAGT 57.656 25.926 1.71 1.06 33.96 2.66
349 350 9.688592 TTTTCAAAATTCAAACATTGCAAAGTT 57.311 22.222 13.99 13.99 0.00 2.66
350 351 9.688592 TTTCAAAATTCAAACATTGCAAAGTTT 57.311 22.222 23.21 23.21 38.40 2.66
358 359 6.799926 AAACATTGCAAAGTTTGACAAAGT 57.200 29.167 26.80 19.25 36.65 2.66
359 360 6.799926 AACATTGCAAAGTTTGACAAAGTT 57.200 29.167 24.32 24.32 35.70 2.66
360 361 6.799926 ACATTGCAAAGTTTGACAAAGTTT 57.200 29.167 22.45 22.45 42.99 2.66
361 362 7.897575 ACATTGCAAAGTTTGACAAAGTTTA 57.102 28.000 25.83 15.55 40.93 2.01
362 363 7.738345 ACATTGCAAAGTTTGACAAAGTTTAC 58.262 30.769 25.83 22.11 40.93 2.01
363 364 7.386299 ACATTGCAAAGTTTGACAAAGTTTACA 59.614 29.630 25.83 23.89 40.93 2.41
364 365 6.942886 TGCAAAGTTTGACAAAGTTTACAG 57.057 33.333 25.83 17.76 40.93 2.74
365 366 6.682746 TGCAAAGTTTGACAAAGTTTACAGA 58.317 32.000 25.83 12.28 40.93 3.41
366 367 6.806249 TGCAAAGTTTGACAAAGTTTACAGAG 59.194 34.615 25.83 17.22 40.93 3.35
367 368 7.027161 GCAAAGTTTGACAAAGTTTACAGAGA 58.973 34.615 25.83 0.00 40.93 3.10
368 369 7.540745 GCAAAGTTTGACAAAGTTTACAGAGAA 59.459 33.333 25.83 0.00 40.93 2.87
369 370 9.405587 CAAAGTTTGACAAAGTTTACAGAGAAA 57.594 29.630 25.83 0.00 40.93 2.52
393 394 2.871096 TTTTTGCTAGGGTCACCGAT 57.129 45.000 0.00 0.00 43.47 4.18
394 395 2.871096 TTTTGCTAGGGTCACCGATT 57.129 45.000 0.00 0.00 43.47 3.34
395 396 2.107950 TTTGCTAGGGTCACCGATTG 57.892 50.000 0.00 0.00 43.47 2.67
396 397 0.392461 TTGCTAGGGTCACCGATTGC 60.392 55.000 0.00 0.00 43.47 3.56
397 398 1.220749 GCTAGGGTCACCGATTGCA 59.779 57.895 0.00 0.00 43.47 4.08
398 399 0.179045 GCTAGGGTCACCGATTGCAT 60.179 55.000 0.00 0.00 43.47 3.96
399 400 1.070134 GCTAGGGTCACCGATTGCATA 59.930 52.381 0.00 0.00 43.47 3.14
400 401 2.289694 GCTAGGGTCACCGATTGCATAT 60.290 50.000 0.00 0.00 43.47 1.78
401 402 2.550830 AGGGTCACCGATTGCATATC 57.449 50.000 0.00 0.00 43.47 1.63
402 403 1.768275 AGGGTCACCGATTGCATATCA 59.232 47.619 0.00 0.00 43.47 2.15
403 404 2.373169 AGGGTCACCGATTGCATATCAT 59.627 45.455 0.00 0.00 43.47 2.45
404 405 3.149196 GGGTCACCGATTGCATATCATT 58.851 45.455 0.00 0.00 0.00 2.57
405 406 3.058016 GGGTCACCGATTGCATATCATTG 60.058 47.826 0.00 0.00 0.00 2.82
406 407 3.058016 GGTCACCGATTGCATATCATTGG 60.058 47.826 1.39 1.39 0.00 3.16
407 408 3.058016 GTCACCGATTGCATATCATTGGG 60.058 47.826 7.21 4.12 32.38 4.12
408 409 2.886523 CACCGATTGCATATCATTGGGT 59.113 45.455 7.21 4.61 37.55 4.51
409 410 4.071423 CACCGATTGCATATCATTGGGTA 58.929 43.478 7.21 0.00 35.76 3.69
410 411 4.072131 ACCGATTGCATATCATTGGGTAC 58.928 43.478 7.21 0.00 36.04 3.34
411 412 4.071423 CCGATTGCATATCATTGGGTACA 58.929 43.478 0.00 0.00 0.00 2.90
412 413 4.701651 CCGATTGCATATCATTGGGTACAT 59.298 41.667 0.00 0.00 0.00 2.29
413 414 5.163723 CCGATTGCATATCATTGGGTACATC 60.164 44.000 0.00 0.00 0.00 3.06
414 415 5.412286 CGATTGCATATCATTGGGTACATCA 59.588 40.000 0.00 0.00 0.00 3.07
415 416 6.094464 CGATTGCATATCATTGGGTACATCAT 59.906 38.462 0.00 0.00 0.00 2.45
416 417 6.578163 TTGCATATCATTGGGTACATCATG 57.422 37.500 0.00 0.00 0.00 3.07
417 418 5.878627 TGCATATCATTGGGTACATCATGA 58.121 37.500 0.00 0.00 0.00 3.07
418 419 5.941647 TGCATATCATTGGGTACATCATGAG 59.058 40.000 0.09 0.00 0.00 2.90
419 420 6.175471 GCATATCATTGGGTACATCATGAGA 58.825 40.000 0.09 0.00 0.00 3.27
420 421 6.827251 GCATATCATTGGGTACATCATGAGAT 59.173 38.462 0.09 0.00 33.87 2.75
421 422 7.989170 GCATATCATTGGGTACATCATGAGATA 59.011 37.037 0.09 0.00 31.88 1.98
425 426 8.670521 TCATTGGGTACATCATGAGATATACT 57.329 34.615 0.09 0.00 35.09 2.12
426 427 9.104713 TCATTGGGTACATCATGAGATATACTT 57.895 33.333 0.09 0.00 35.09 2.24
427 428 9.730705 CATTGGGTACATCATGAGATATACTTT 57.269 33.333 0.09 0.00 35.09 2.66
428 429 9.950496 ATTGGGTACATCATGAGATATACTTTC 57.050 33.333 0.09 0.00 35.09 2.62
429 430 8.491045 TGGGTACATCATGAGATATACTTTCA 57.509 34.615 0.09 0.41 35.09 2.69
430 431 9.104713 TGGGTACATCATGAGATATACTTTCAT 57.895 33.333 0.09 0.00 35.09 2.57
536 539 1.971167 GCATTGGGTCGAACCAGCA 60.971 57.895 24.58 12.39 42.47 4.41
738 741 0.038892 GGTTGCGTGGTTAGACGAGA 60.039 55.000 0.00 0.00 42.10 4.04
880 883 2.890311 ACCGGATTTGTTGCAAGAATGA 59.110 40.909 9.46 0.00 0.00 2.57
943 946 7.730364 ATCTCGTGATTTGTTTACTTTGTCT 57.270 32.000 0.00 0.00 0.00 3.41
944 947 7.173863 TCTCGTGATTTGTTTACTTTGTCTC 57.826 36.000 0.00 0.00 0.00 3.36
945 948 6.759356 TCTCGTGATTTGTTTACTTTGTCTCA 59.241 34.615 0.00 0.00 0.00 3.27
946 949 6.943981 TCGTGATTTGTTTACTTTGTCTCAG 58.056 36.000 0.00 0.00 0.00 3.35
947 950 6.759356 TCGTGATTTGTTTACTTTGTCTCAGA 59.241 34.615 0.00 0.00 0.00 3.27
948 951 7.042725 TCGTGATTTGTTTACTTTGTCTCAGAG 60.043 37.037 0.00 0.00 0.00 3.35
949 952 6.853362 GTGATTTGTTTACTTTGTCTCAGAGC 59.147 38.462 0.00 0.00 0.00 4.09
950 953 5.403897 TTTGTTTACTTTGTCTCAGAGCG 57.596 39.130 0.00 0.00 0.00 5.03
951 954 4.316205 TGTTTACTTTGTCTCAGAGCGA 57.684 40.909 0.00 0.00 0.00 4.93
952 955 4.883083 TGTTTACTTTGTCTCAGAGCGAT 58.117 39.130 0.00 0.00 0.00 4.58
953 956 4.923871 TGTTTACTTTGTCTCAGAGCGATC 59.076 41.667 0.00 0.00 0.00 3.69
954 957 5.164954 GTTTACTTTGTCTCAGAGCGATCT 58.835 41.667 0.00 0.00 0.00 2.75
955 958 3.229276 ACTTTGTCTCAGAGCGATCTG 57.771 47.619 24.40 24.40 39.00 2.90
956 959 1.925847 CTTTGTCTCAGAGCGATCTGC 59.074 52.381 25.45 12.44 46.98 4.26
1133 1157 6.112734 TCAGATGCACGATGGTAAGTTTTAT 58.887 36.000 0.00 0.00 0.00 1.40
1428 1452 2.065512 CTGGTTTTTGGCCATTTACGC 58.934 47.619 6.09 0.23 35.19 4.42
1830 1856 4.999939 CGGCCGCACCACAAAAGC 63.000 66.667 14.67 0.00 39.03 3.51
2103 2129 3.436700 AAAAGTCTGACCCGCAAAAAG 57.563 42.857 3.76 0.00 0.00 2.27
2552 2580 1.985159 TCAGGCTTTACTGGTGGTCAT 59.015 47.619 0.00 0.00 38.98 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 9.265901 TGTCACTGAAAATTTCAAACTTTTTGA 57.734 25.926 9.85 0.00 39.58 2.69
62 63 9.316859 GTGTCACTGAAAATTTCAAACTTTTTG 57.683 29.630 9.85 0.00 39.58 2.44
63 64 9.271828 AGTGTCACTGAAAATTTCAAACTTTTT 57.728 25.926 9.85 0.00 39.58 1.94
64 65 8.831715 AGTGTCACTGAAAATTTCAAACTTTT 57.168 26.923 9.85 0.00 39.58 2.27
65 66 8.831715 AAGTGTCACTGAAAATTTCAAACTTT 57.168 26.923 6.18 5.44 39.58 2.66
66 67 8.831715 AAAGTGTCACTGAAAATTTCAAACTT 57.168 26.923 6.18 10.76 39.58 2.66
70 71 9.868277 ACAATAAAGTGTCACTGAAAATTTCAA 57.132 25.926 6.18 0.00 39.58 2.69
71 72 9.868277 AACAATAAAGTGTCACTGAAAATTTCA 57.132 25.926 6.18 8.25 38.17 2.69
73 74 9.313118 GGAACAATAAAGTGTCACTGAAAATTT 57.687 29.630 6.18 0.57 0.00 1.82
74 75 8.474025 TGGAACAATAAAGTGTCACTGAAAATT 58.526 29.630 6.18 0.00 31.92 1.82
75 76 8.006298 TGGAACAATAAAGTGTCACTGAAAAT 57.994 30.769 6.18 0.00 31.92 1.82
76 77 7.397892 TGGAACAATAAAGTGTCACTGAAAA 57.602 32.000 6.18 0.00 31.92 2.29
90 91 7.678218 GCATTTGCAACTGTTTTGGAACAATAA 60.678 33.333 17.00 0.00 41.96 1.40
91 92 6.238320 GCATTTGCAACTGTTTTGGAACAATA 60.238 34.615 17.00 0.00 41.96 1.90
92 93 5.448904 GCATTTGCAACTGTTTTGGAACAAT 60.449 36.000 17.00 0.00 41.96 2.71
93 94 4.142730 GCATTTGCAACTGTTTTGGAACAA 60.143 37.500 17.00 0.00 41.96 2.83
94 95 3.373439 GCATTTGCAACTGTTTTGGAACA 59.627 39.130 17.00 0.00 41.11 3.18
95 96 3.543852 CGCATTTGCAACTGTTTTGGAAC 60.544 43.478 17.00 0.00 42.21 3.62
96 97 2.606725 CGCATTTGCAACTGTTTTGGAA 59.393 40.909 17.00 0.00 42.21 3.53
97 98 2.200067 CGCATTTGCAACTGTTTTGGA 58.800 42.857 17.00 0.00 42.21 3.53
98 99 1.261089 CCGCATTTGCAACTGTTTTGG 59.739 47.619 17.00 10.64 42.21 3.28
99 100 1.261089 CCCGCATTTGCAACTGTTTTG 59.739 47.619 17.00 6.19 42.21 2.44
100 101 1.134551 ACCCGCATTTGCAACTGTTTT 60.135 42.857 17.00 0.00 42.21 2.43
101 102 0.463620 ACCCGCATTTGCAACTGTTT 59.536 45.000 17.00 0.00 42.21 2.83
102 103 0.463620 AACCCGCATTTGCAACTGTT 59.536 45.000 17.00 2.17 42.21 3.16
103 104 1.323412 TAACCCGCATTTGCAACTGT 58.677 45.000 17.00 1.03 42.21 3.55
104 105 2.652941 ATAACCCGCATTTGCAACTG 57.347 45.000 12.16 12.16 42.21 3.16
105 106 5.105554 TGAATTATAACCCGCATTTGCAACT 60.106 36.000 0.00 0.00 42.21 3.16
106 107 5.105752 TGAATTATAACCCGCATTTGCAAC 58.894 37.500 0.00 0.00 42.21 4.17
107 108 5.330455 TGAATTATAACCCGCATTTGCAA 57.670 34.783 0.00 0.00 42.21 4.08
108 109 4.991153 TGAATTATAACCCGCATTTGCA 57.009 36.364 3.13 0.00 42.21 4.08
109 110 5.402270 GTGATGAATTATAACCCGCATTTGC 59.598 40.000 0.00 0.00 37.78 3.68
110 111 6.502652 TGTGATGAATTATAACCCGCATTTG 58.497 36.000 0.00 0.00 0.00 2.32
111 112 6.707440 TGTGATGAATTATAACCCGCATTT 57.293 33.333 0.00 0.00 0.00 2.32
112 113 6.460953 GGTTGTGATGAATTATAACCCGCATT 60.461 38.462 3.26 0.00 33.40 3.56
113 114 5.009610 GGTTGTGATGAATTATAACCCGCAT 59.990 40.000 3.26 0.00 33.40 4.73
114 115 4.336993 GGTTGTGATGAATTATAACCCGCA 59.663 41.667 3.26 0.00 33.40 5.69
115 116 4.336993 TGGTTGTGATGAATTATAACCCGC 59.663 41.667 10.05 0.00 36.94 6.13
116 117 6.633500 ATGGTTGTGATGAATTATAACCCG 57.367 37.500 10.05 0.00 36.94 5.28
156 157 9.798994 GAGTGCTTCTGAAATTGATTGAATTAT 57.201 29.630 0.00 0.00 32.76 1.28
157 158 9.017509 AGAGTGCTTCTGAAATTGATTGAATTA 57.982 29.630 0.00 0.00 31.75 1.40
158 159 7.893658 AGAGTGCTTCTGAAATTGATTGAATT 58.106 30.769 0.00 0.00 33.29 2.17
159 160 7.463961 AGAGTGCTTCTGAAATTGATTGAAT 57.536 32.000 0.00 0.00 33.93 2.57
160 161 6.889301 AGAGTGCTTCTGAAATTGATTGAA 57.111 33.333 0.00 0.00 33.93 2.69
161 162 6.936335 TGTAGAGTGCTTCTGAAATTGATTGA 59.064 34.615 2.11 0.00 36.61 2.57
162 163 7.137490 TGTAGAGTGCTTCTGAAATTGATTG 57.863 36.000 2.11 0.00 36.61 2.67
163 164 7.934855 ATGTAGAGTGCTTCTGAAATTGATT 57.065 32.000 2.11 0.00 36.61 2.57
164 165 7.609146 TGAATGTAGAGTGCTTCTGAAATTGAT 59.391 33.333 2.11 0.00 36.61 2.57
165 166 6.936335 TGAATGTAGAGTGCTTCTGAAATTGA 59.064 34.615 2.11 0.00 36.61 2.57
166 167 7.137490 TGAATGTAGAGTGCTTCTGAAATTG 57.863 36.000 2.11 0.00 36.61 2.32
167 168 7.934855 ATGAATGTAGAGTGCTTCTGAAATT 57.065 32.000 2.11 0.47 36.61 1.82
168 169 7.934855 AATGAATGTAGAGTGCTTCTGAAAT 57.065 32.000 2.11 0.00 36.61 2.17
169 170 7.750229 AAATGAATGTAGAGTGCTTCTGAAA 57.250 32.000 2.11 0.00 36.61 2.69
170 171 7.445096 TGAAAATGAATGTAGAGTGCTTCTGAA 59.555 33.333 2.11 0.00 36.61 3.02
171 172 6.936335 TGAAAATGAATGTAGAGTGCTTCTGA 59.064 34.615 2.11 0.00 36.61 3.27
172 173 7.020010 GTGAAAATGAATGTAGAGTGCTTCTG 58.980 38.462 2.11 0.00 36.61 3.02
173 174 6.712095 TGTGAAAATGAATGTAGAGTGCTTCT 59.288 34.615 0.00 0.00 40.06 2.85
174 175 6.798959 GTGTGAAAATGAATGTAGAGTGCTTC 59.201 38.462 0.00 0.00 0.00 3.86
175 176 6.262944 TGTGTGAAAATGAATGTAGAGTGCTT 59.737 34.615 0.00 0.00 0.00 3.91
176 177 5.764686 TGTGTGAAAATGAATGTAGAGTGCT 59.235 36.000 0.00 0.00 0.00 4.40
177 178 6.000891 TGTGTGAAAATGAATGTAGAGTGC 57.999 37.500 0.00 0.00 0.00 4.40
178 179 9.467258 AAATTGTGTGAAAATGAATGTAGAGTG 57.533 29.630 0.00 0.00 0.00 3.51
279 280 9.928618 TGGAATGGAGGTAATATGTATGAAAAA 57.071 29.630 0.00 0.00 0.00 1.94
290 291 8.540388 GCTCTGTATTATGGAATGGAGGTAATA 58.460 37.037 0.00 0.00 0.00 0.98
291 292 7.398024 GCTCTGTATTATGGAATGGAGGTAAT 58.602 38.462 0.00 0.00 0.00 1.89
292 293 6.239887 GGCTCTGTATTATGGAATGGAGGTAA 60.240 42.308 0.00 0.00 0.00 2.85
293 294 5.248477 GGCTCTGTATTATGGAATGGAGGTA 59.752 44.000 0.00 0.00 0.00 3.08
294 295 4.042187 GGCTCTGTATTATGGAATGGAGGT 59.958 45.833 0.00 0.00 0.00 3.85
295 296 4.288105 AGGCTCTGTATTATGGAATGGAGG 59.712 45.833 0.00 0.00 0.00 4.30
296 297 5.495926 AGGCTCTGTATTATGGAATGGAG 57.504 43.478 0.00 0.00 0.00 3.86
297 298 7.459125 AGAATAGGCTCTGTATTATGGAATGGA 59.541 37.037 0.00 0.00 0.00 3.41
298 299 7.628234 AGAATAGGCTCTGTATTATGGAATGG 58.372 38.462 0.00 0.00 0.00 3.16
299 300 9.512588 AAAGAATAGGCTCTGTATTATGGAATG 57.487 33.333 0.00 0.00 0.00 2.67
301 302 9.561069 GAAAAGAATAGGCTCTGTATTATGGAA 57.439 33.333 0.00 0.00 0.00 3.53
302 303 8.713971 TGAAAAGAATAGGCTCTGTATTATGGA 58.286 33.333 0.00 0.00 0.00 3.41
303 304 8.908786 TGAAAAGAATAGGCTCTGTATTATGG 57.091 34.615 0.00 0.00 0.00 2.74
309 310 9.295825 TGAATTTTGAAAAGAATAGGCTCTGTA 57.704 29.630 0.00 0.00 0.00 2.74
310 311 8.181904 TGAATTTTGAAAAGAATAGGCTCTGT 57.818 30.769 0.00 0.00 0.00 3.41
311 312 9.480053 TTTGAATTTTGAAAAGAATAGGCTCTG 57.520 29.630 0.00 0.00 0.00 3.35
312 313 9.481340 GTTTGAATTTTGAAAAGAATAGGCTCT 57.519 29.630 0.00 0.00 0.00 4.09
313 314 9.260002 TGTTTGAATTTTGAAAAGAATAGGCTC 57.740 29.630 0.00 0.00 0.00 4.70
314 315 9.783081 ATGTTTGAATTTTGAAAAGAATAGGCT 57.217 25.926 0.00 0.00 0.00 4.58
320 321 9.903682 TTTGCAATGTTTGAATTTTGAAAAGAA 57.096 22.222 0.00 0.00 0.00 2.52
321 322 9.557338 CTTTGCAATGTTTGAATTTTGAAAAGA 57.443 25.926 11.14 0.00 43.10 2.52
322 323 9.344309 ACTTTGCAATGTTTGAATTTTGAAAAG 57.656 25.926 11.92 13.66 44.72 2.27
323 324 9.688592 AACTTTGCAATGTTTGAATTTTGAAAA 57.311 22.222 21.39 0.00 0.00 2.29
324 325 9.688592 AAACTTTGCAATGTTTGAATTTTGAAA 57.311 22.222 31.27 0.00 35.67 2.69
334 335 6.601264 ACTTTGTCAAACTTTGCAATGTTTG 58.399 32.000 39.20 39.20 46.71 2.93
335 336 6.799926 ACTTTGTCAAACTTTGCAATGTTT 57.200 29.167 28.29 28.29 36.91 2.83
336 337 6.799926 AACTTTGTCAAACTTTGCAATGTT 57.200 29.167 21.39 21.39 38.52 2.71
337 338 6.799926 AAACTTTGTCAAACTTTGCAATGT 57.200 29.167 11.92 11.92 37.03 2.71
338 339 7.737395 TGTAAACTTTGTCAAACTTTGCAATG 58.263 30.769 14.30 10.58 33.02 2.82
339 340 7.816995 TCTGTAAACTTTGTCAAACTTTGCAAT 59.183 29.630 16.12 0.00 30.75 3.56
340 341 7.148641 TCTGTAAACTTTGTCAAACTTTGCAA 58.851 30.769 16.12 0.00 0.00 4.08
341 342 6.682746 TCTGTAAACTTTGTCAAACTTTGCA 58.317 32.000 15.20 15.20 0.00 4.08
342 343 7.027161 TCTCTGTAAACTTTGTCAAACTTTGC 58.973 34.615 11.16 10.47 0.00 3.68
343 344 8.964420 TTCTCTGTAAACTTTGTCAAACTTTG 57.036 30.769 11.16 0.00 0.00 2.77
374 375 2.817258 CAATCGGTGACCCTAGCAAAAA 59.183 45.455 0.00 0.00 0.00 1.94
375 376 2.432444 CAATCGGTGACCCTAGCAAAA 58.568 47.619 0.00 0.00 0.00 2.44
376 377 1.948611 GCAATCGGTGACCCTAGCAAA 60.949 52.381 0.00 0.00 0.00 3.68
377 378 0.392461 GCAATCGGTGACCCTAGCAA 60.392 55.000 0.00 0.00 0.00 3.91
378 379 1.220749 GCAATCGGTGACCCTAGCA 59.779 57.895 0.00 0.00 0.00 3.49
379 380 0.179045 ATGCAATCGGTGACCCTAGC 60.179 55.000 0.00 0.00 0.00 3.42
380 381 3.006859 TGATATGCAATCGGTGACCCTAG 59.993 47.826 0.00 0.00 0.00 3.02
381 382 2.969262 TGATATGCAATCGGTGACCCTA 59.031 45.455 0.00 0.00 0.00 3.53
382 383 1.768275 TGATATGCAATCGGTGACCCT 59.232 47.619 0.00 0.00 0.00 4.34
383 384 2.254546 TGATATGCAATCGGTGACCC 57.745 50.000 0.00 0.00 0.00 4.46
384 385 3.058016 CCAATGATATGCAATCGGTGACC 60.058 47.826 0.00 0.00 0.00 4.02
385 386 3.058016 CCCAATGATATGCAATCGGTGAC 60.058 47.826 0.00 0.00 0.00 3.67
386 387 3.148412 CCCAATGATATGCAATCGGTGA 58.852 45.455 0.00 0.00 0.00 4.02
387 388 2.886523 ACCCAATGATATGCAATCGGTG 59.113 45.455 0.00 0.00 0.00 4.94
388 389 3.228188 ACCCAATGATATGCAATCGGT 57.772 42.857 0.00 0.00 0.00 4.69
389 390 4.071423 TGTACCCAATGATATGCAATCGG 58.929 43.478 0.00 0.00 0.00 4.18
390 391 5.412286 TGATGTACCCAATGATATGCAATCG 59.588 40.000 0.00 0.00 0.00 3.34
391 392 6.822667 TGATGTACCCAATGATATGCAATC 57.177 37.500 0.00 0.00 0.00 2.67
392 393 6.949463 TCATGATGTACCCAATGATATGCAAT 59.051 34.615 0.00 0.00 0.00 3.56
393 394 6.305411 TCATGATGTACCCAATGATATGCAA 58.695 36.000 0.00 0.00 0.00 4.08
394 395 5.878627 TCATGATGTACCCAATGATATGCA 58.121 37.500 0.00 0.00 0.00 3.96
395 396 6.175471 TCTCATGATGTACCCAATGATATGC 58.825 40.000 0.00 0.00 0.00 3.14
399 400 9.276791 AGTATATCTCATGATGTACCCAATGAT 57.723 33.333 0.00 0.00 43.72 2.45
400 401 8.670521 AGTATATCTCATGATGTACCCAATGA 57.329 34.615 0.00 0.00 43.72 2.57
401 402 9.730705 AAAGTATATCTCATGATGTACCCAATG 57.269 33.333 0.00 0.00 43.72 2.82
402 403 9.950496 GAAAGTATATCTCATGATGTACCCAAT 57.050 33.333 0.00 0.00 43.72 3.16
403 404 8.933653 TGAAAGTATATCTCATGATGTACCCAA 58.066 33.333 0.00 0.00 43.72 4.12
404 405 8.491045 TGAAAGTATATCTCATGATGTACCCA 57.509 34.615 0.00 0.00 43.72 4.51
420 421 9.407380 ACCAAAGATGTGCAATATGAAAGTATA 57.593 29.630 0.00 0.00 0.00 1.47
421 422 8.297470 ACCAAAGATGTGCAATATGAAAGTAT 57.703 30.769 0.00 0.00 0.00 2.12
422 423 7.701539 ACCAAAGATGTGCAATATGAAAGTA 57.298 32.000 0.00 0.00 0.00 2.24
423 424 6.594788 ACCAAAGATGTGCAATATGAAAGT 57.405 33.333 0.00 0.00 0.00 2.66
460 461 3.386726 CCCTGGGTGACGAATAGACAATA 59.613 47.826 3.97 0.00 0.00 1.90
536 539 0.386476 TATTCTTACGCCGCGTGGAT 59.614 50.000 28.10 14.70 41.39 3.41
738 741 4.349365 TCCCGATTTTTGCTCCCTTTTAT 58.651 39.130 0.00 0.00 0.00 1.40
880 883 1.328279 CCAAAACGAAGGAGGCCTTT 58.672 50.000 6.77 0.00 44.82 3.11
947 950 9.933723 TGCAATATTATATATATGCAGATCGCT 57.066 29.630 12.59 0.00 43.06 4.93
1090 1114 4.765339 TCTGAATTGTCTCGGTACTCTGAA 59.235 41.667 0.00 0.00 0.00 3.02
1133 1157 3.758023 TCGGTGTAAAATCAGAGTCGGTA 59.242 43.478 0.00 0.00 0.00 4.02
1428 1452 0.386100 CGATATCGCCTGACAGTCGG 60.386 60.000 12.95 1.86 0.00 4.79
1988 2014 6.438741 AGAGATAGGGCATCGAATCATCTTTA 59.561 38.462 0.00 0.00 38.81 1.85
2103 2129 5.596845 TGGTCAAAATTTACCTGCACTTTC 58.403 37.500 10.72 0.00 36.67 2.62


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

AutoCloner maintained by Alex Coulton.