Multiple sequence alignment - TraesCS3A01G475700

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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 TraesCS3A01G475700 chr3A 100.000 2390 0 0 1 2390 707127199 707124810 0.000000e+00 4414.0
1 TraesCS3A01G475700 chr3A 100.000 83 0 0 1 83 574287993 574288075 1.140000e-33 154.0
2 TraesCS3A01G475700 chr3A 97.619 42 0 1 481 521 489193178 489193137 1.190000e-08 71.3
3 TraesCS3A01G475700 chr3A 95.455 44 0 2 484 525 580599743 580599700 4.260000e-08 69.4
4 TraesCS3A01G475700 chr3B 96.738 1870 57 2 521 2390 762309326 762307461 0.000000e+00 3112.0
5 TraesCS3A01G475700 chr3B 85.246 305 33 10 101 398 762309647 762309348 1.070000e-78 303.0
6 TraesCS3A01G475700 chr3B 100.000 43 0 0 450 492 762309364 762309322 1.970000e-11 80.5
7 TraesCS3A01G475700 chr3B 100.000 40 0 0 482 521 435816885 435816924 9.160000e-10 75.0
8 TraesCS3A01G475700 chr3B 97.619 42 0 1 481 521 478078448 478078407 1.190000e-08 71.3
9 TraesCS3A01G475700 chr3D 97.236 1773 37 4 620 2390 573121775 573120013 0.000000e+00 2992.0
10 TraesCS3A01G475700 chr3D 91.837 98 5 2 522 618 573122221 573122126 1.490000e-27 134.0
11 TraesCS3A01G475700 chr3D 100.000 35 0 0 450 484 573122253 573122219 5.510000e-07 65.8
12 TraesCS3A01G475700 chr3D 87.719 57 4 3 466 520 27936547 27936602 1.980000e-06 63.9
13 TraesCS3A01G475700 chr1D 94.147 1777 86 12 620 2390 423056987 423058751 0.000000e+00 2689.0
14 TraesCS3A01G475700 chr1B 93.528 1777 94 14 620 2389 572308822 572310584 0.000000e+00 2625.0
15 TraesCS3A01G475700 chr1A 94.156 1677 76 11 718 2390 518986666 518988324 0.000000e+00 2534.0
16 TraesCS3A01G475700 chr1A 100.000 82 0 0 1 82 373317663 373317582 4.110000e-33 152.0
17 TraesCS3A01G475700 chr1A 96.226 53 1 1 398 449 554284183 554284235 4.230000e-13 86.1
18 TraesCS3A01G475700 chr1A 96.226 53 1 1 398 449 554289510 554289458 4.230000e-13 86.1
19 TraesCS3A01G475700 chr1A 97.297 37 1 0 484 520 131963584 131963620 1.980000e-06 63.9
20 TraesCS3A01G475700 chr7D 93.000 600 34 4 1797 2389 139368876 139369474 0.000000e+00 869.0
21 TraesCS3A01G475700 chr7D 95.604 91 3 1 1 90 581296273 581296363 6.890000e-31 145.0
22 TraesCS3A01G475700 chr7D 98.077 52 0 1 399 449 183786052 183786001 3.270000e-14 89.8
23 TraesCS3A01G475700 chr4A 89.867 602 52 4 1797 2389 220627174 220627775 0.000000e+00 765.0
24 TraesCS3A01G475700 chr6A 93.210 162 10 1 1797 1957 395654132 395653971 1.100000e-58 237.0
25 TraesCS3A01G475700 chr6A 100.000 82 0 0 1 82 287115369 287115450 4.110000e-33 152.0
26 TraesCS3A01G475700 chr2A 91.975 162 12 1 1797 1957 315573836 315573675 2.390000e-55 226.0
27 TraesCS3A01G475700 chr2A 93.333 45 3 0 476 520 23630478 23630434 1.530000e-07 67.6
28 TraesCS3A01G475700 chr2A 93.333 45 3 0 477 521 703708998 703709042 1.530000e-07 67.6
29 TraesCS3A01G475700 chr6B 97.727 88 2 0 1 88 459601643 459601730 4.110000e-33 152.0
30 TraesCS3A01G475700 chr6B 96.296 54 1 1 397 449 585808079 585808026 1.180000e-13 87.9
31 TraesCS3A01G475700 chr6B 94.340 53 1 2 399 450 70569397 70569448 1.970000e-11 80.5
32 TraesCS3A01G475700 chr6B 95.455 44 1 1 477 520 551951965 551951923 4.260000e-08 69.4
33 TraesCS3A01G475700 chr6D 97.674 86 2 0 1 86 91845423 91845508 5.320000e-32 148.0
34 TraesCS3A01G475700 chr7A 96.591 88 3 0 1 88 301100504 301100417 1.910000e-31 147.0
35 TraesCS3A01G475700 chr2B 94.737 95 4 1 1 95 227115837 227115930 1.910000e-31 147.0
36 TraesCS3A01G475700 chr5D 95.455 88 4 0 1 88 37920312 37920399 8.910000e-30 141.0
37 TraesCS3A01G475700 chr5D 92.063 63 2 2 388 449 225256384 225256324 4.230000e-13 86.1
38 TraesCS3A01G475700 chr4D 96.226 53 1 1 398 449 401088681 401088629 4.230000e-13 86.1
39 TraesCS3A01G475700 chr4D 96.154 52 1 1 399 449 12449216 12449267 1.520000e-12 84.2
40 TraesCS3A01G475700 chr2D 96.154 52 1 1 399 449 512770203 512770254 1.520000e-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 TraesCS3A01G475700 chr3A 707124810 707127199 2389 True 4414.000000 4414 100.000000 1 2390 1 chr3A.!!$R3 2389
1 TraesCS3A01G475700 chr3B 762307461 762309647 2186 True 1165.166667 3112 93.994667 101 2390 3 chr3B.!!$R2 2289
2 TraesCS3A01G475700 chr3D 573120013 573122253 2240 True 1063.933333 2992 96.357667 450 2390 3 chr3D.!!$R1 1940
3 TraesCS3A01G475700 chr1D 423056987 423058751 1764 False 2689.000000 2689 94.147000 620 2390 1 chr1D.!!$F1 1770
4 TraesCS3A01G475700 chr1B 572308822 572310584 1762 False 2625.000000 2625 93.528000 620 2389 1 chr1B.!!$F1 1769
5 TraesCS3A01G475700 chr1A 518986666 518988324 1658 False 2534.000000 2534 94.156000 718 2390 1 chr1A.!!$F2 1672
6 TraesCS3A01G475700 chr7D 139368876 139369474 598 False 869.000000 869 93.000000 1797 2389 1 chr7D.!!$F1 592
7 TraesCS3A01G475700 chr4A 220627174 220627775 601 False 765.000000 765 89.867000 1797 2389 1 chr4A.!!$F1 592

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
429 434 0.039165 GGCACAGTGGTAAAAGCTGC 60.039 55.0 1.84 0.0 33.87 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2686 2.954753 GAGGTCAACAAGTGGCGCG 61.955 63.158 0.0 0.0 29.99 6.86 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
24 25 6.091437 CCCTCCGTAAACTAATATAAGAGCG 58.909 44.000 0.00 0.00 0.00 5.03
25 26 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
26 27 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
27 28 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
28 29 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
29 30 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
30 31 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
77 78 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
79 80 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
85 86 9.939424 ATATTAGTTTACAGAGGGAGTAGAAGT 57.061 33.333 0.00 0.00 0.00 3.01
86 87 8.667592 ATTAGTTTACAGAGGGAGTAGAAGTT 57.332 34.615 0.00 0.00 0.00 2.66
87 88 9.765295 ATTAGTTTACAGAGGGAGTAGAAGTTA 57.235 33.333 0.00 0.00 0.00 2.24
88 89 7.706100 AGTTTACAGAGGGAGTAGAAGTTAG 57.294 40.000 0.00 0.00 0.00 2.34
89 90 7.240167 AGTTTACAGAGGGAGTAGAAGTTAGT 58.760 38.462 0.00 0.00 0.00 2.24
90 91 7.177041 AGTTTACAGAGGGAGTAGAAGTTAGTG 59.823 40.741 0.00 0.00 0.00 2.74
91 92 4.345854 ACAGAGGGAGTAGAAGTTAGTGG 58.654 47.826 0.00 0.00 0.00 4.00
92 93 4.044317 ACAGAGGGAGTAGAAGTTAGTGGA 59.956 45.833 0.00 0.00 0.00 4.02
93 94 5.017490 CAGAGGGAGTAGAAGTTAGTGGAA 58.983 45.833 0.00 0.00 0.00 3.53
94 95 5.126384 CAGAGGGAGTAGAAGTTAGTGGAAG 59.874 48.000 0.00 0.00 0.00 3.46
95 96 3.770388 AGGGAGTAGAAGTTAGTGGAAGC 59.230 47.826 0.00 0.00 0.00 3.86
96 97 3.429135 GGGAGTAGAAGTTAGTGGAAGCG 60.429 52.174 0.00 0.00 0.00 4.68
97 98 3.180613 GAGTAGAAGTTAGTGGAAGCGC 58.819 50.000 0.00 0.00 0.00 5.92
98 99 1.918609 GTAGAAGTTAGTGGAAGCGCG 59.081 52.381 0.00 0.00 0.00 6.86
99 100 0.389948 AGAAGTTAGTGGAAGCGCGG 60.390 55.000 8.83 0.00 0.00 6.46
126 127 2.952310 GTTCATTAGGAATGGGAGGCAC 59.048 50.000 0.00 0.00 39.38 5.01
131 132 1.380380 GGAATGGGAGGCACCTTGG 60.380 63.158 0.00 0.00 38.98 3.61
135 136 1.434513 ATGGGAGGCACCTTGGAACA 61.435 55.000 0.00 0.00 38.98 3.18
139 140 1.620822 GAGGCACCTTGGAACACATT 58.379 50.000 0.00 0.00 39.29 2.71
148 149 4.141287 CCTTGGAACACATTGACTAACCA 58.859 43.478 0.00 0.00 39.29 3.67
149 150 4.216257 CCTTGGAACACATTGACTAACCAG 59.784 45.833 0.00 0.00 39.29 4.00
151 152 5.042463 TGGAACACATTGACTAACCAGAA 57.958 39.130 0.00 0.00 0.00 3.02
152 153 5.063204 TGGAACACATTGACTAACCAGAAG 58.937 41.667 0.00 0.00 0.00 2.85
153 154 5.063880 GGAACACATTGACTAACCAGAAGT 58.936 41.667 0.00 0.00 0.00 3.01
159 160 6.483307 CACATTGACTAACCAGAAGTTGAAGA 59.517 38.462 0.00 0.00 39.67 2.87
160 161 7.173907 CACATTGACTAACCAGAAGTTGAAGAT 59.826 37.037 0.00 0.00 39.67 2.40
163 164 5.071788 TGACTAACCAGAAGTTGAAGATGGT 59.928 40.000 0.00 0.00 46.05 3.55
167 168 3.152341 CCAGAAGTTGAAGATGGTGCTT 58.848 45.455 0.00 0.00 0.00 3.91
185 186 2.229792 CTTGCAGCAGTACTTTTGGGA 58.770 47.619 0.00 0.00 0.00 4.37
186 187 1.604604 TGCAGCAGTACTTTTGGGAC 58.395 50.000 0.00 0.00 0.00 4.46
188 189 2.370519 TGCAGCAGTACTTTTGGGACTA 59.629 45.455 0.00 0.00 0.00 2.59
197 198 8.613482 GCAGTACTTTTGGGACTAGAAATATTC 58.387 37.037 0.00 0.00 0.00 1.75
207 208 9.535170 TGGGACTAGAAATATTCTATCTGGTAG 57.465 37.037 0.00 0.00 41.17 3.18
211 212 8.516234 ACTAGAAATATTCTATCTGGTAGTGCG 58.484 37.037 0.00 0.00 41.17 5.34
236 237 4.649674 TCAGCAACTATAGGTTAGTCCCTG 59.350 45.833 4.43 0.00 36.23 4.45
238 239 5.128827 CAGCAACTATAGGTTAGTCCCTGAA 59.871 44.000 4.43 0.00 36.23 3.02
239 240 5.128991 AGCAACTATAGGTTAGTCCCTGAAC 59.871 44.000 4.43 0.00 36.23 3.18
240 241 5.684291 GCAACTATAGGTTAGTCCCTGAACC 60.684 48.000 4.43 0.00 44.68 3.62
242 243 5.789535 ACTATAGGTTAGTCCCTGAACCAT 58.210 41.667 4.43 1.61 46.41 3.55
243 244 5.602978 ACTATAGGTTAGTCCCTGAACCATG 59.397 44.000 4.43 0.00 46.41 3.66
244 245 2.915869 AGGTTAGTCCCTGAACCATGA 58.084 47.619 6.57 0.00 46.41 3.07
245 246 3.256704 AGGTTAGTCCCTGAACCATGAA 58.743 45.455 6.57 0.00 46.41 2.57
250 251 3.490348 AGTCCCTGAACCATGAAAAGTG 58.510 45.455 0.00 0.00 0.00 3.16
276 280 2.885266 AGAGCAAGTCGTGTCTGAACTA 59.115 45.455 0.00 0.00 0.00 2.24
278 282 4.700692 AGAGCAAGTCGTGTCTGAACTATA 59.299 41.667 0.00 0.00 0.00 1.31
279 283 4.734917 AGCAAGTCGTGTCTGAACTATAC 58.265 43.478 0.00 0.00 0.00 1.47
292 296 6.908284 GTCTGAACTATACGCTACAGAAAGAG 59.092 42.308 0.00 0.00 36.41 2.85
327 331 2.099921 AGACTGCATACGCTACAGGAAG 59.900 50.000 0.00 0.00 39.64 3.46
329 333 2.695666 ACTGCATACGCTACAGGAAGAT 59.304 45.455 0.00 0.00 39.64 2.40
330 334 3.133003 ACTGCATACGCTACAGGAAGATT 59.867 43.478 0.00 0.00 39.64 2.40
331 335 4.122776 CTGCATACGCTACAGGAAGATTT 58.877 43.478 0.00 0.00 39.64 2.17
332 336 4.513442 TGCATACGCTACAGGAAGATTTT 58.487 39.130 0.00 0.00 39.64 1.82
333 337 4.570772 TGCATACGCTACAGGAAGATTTTC 59.429 41.667 0.00 0.00 39.64 2.29
347 352 7.526142 GGAAGATTTTCCCCACTATTTATCC 57.474 40.000 3.55 0.00 46.03 2.59
404 409 5.635278 TTCATATGCATGAAGAGAAGGGA 57.365 39.130 10.16 0.00 44.44 4.20
405 410 5.224821 TCATATGCATGAAGAGAAGGGAG 57.775 43.478 10.16 0.00 38.25 4.30
406 411 2.345124 ATGCATGAAGAGAAGGGAGC 57.655 50.000 0.00 0.00 0.00 4.70
407 412 0.254178 TGCATGAAGAGAAGGGAGCC 59.746 55.000 0.00 0.00 0.00 4.70
408 413 0.545646 GCATGAAGAGAAGGGAGCCT 59.454 55.000 0.00 0.00 33.87 4.58
409 414 8.878324 CATATGCATGAAGAGAAGGGAGCCTT 62.878 46.154 10.16 0.00 39.47 4.35
410 415 2.641305 CATGAAGAGAAGGGAGCCTTG 58.359 52.381 0.00 0.00 44.82 3.61
411 416 0.987294 TGAAGAGAAGGGAGCCTTGG 59.013 55.000 0.00 0.00 44.82 3.61
412 417 0.393673 GAAGAGAAGGGAGCCTTGGC 60.394 60.000 2.97 2.97 44.82 4.52
413 418 1.136329 AAGAGAAGGGAGCCTTGGCA 61.136 55.000 14.54 0.00 44.82 4.92
414 419 1.377856 GAGAAGGGAGCCTTGGCAC 60.378 63.158 14.54 7.49 44.82 5.01
415 420 2.129555 GAGAAGGGAGCCTTGGCACA 62.130 60.000 14.54 0.00 44.82 4.57
416 421 1.676967 GAAGGGAGCCTTGGCACAG 60.677 63.158 14.54 0.00 44.82 3.66
417 422 2.417558 GAAGGGAGCCTTGGCACAGT 62.418 60.000 14.54 0.00 44.82 3.55
418 423 2.674380 GGGAGCCTTGGCACAGTG 60.674 66.667 14.54 0.00 42.39 3.66
419 424 2.674380 GGAGCCTTGGCACAGTGG 60.674 66.667 14.54 0.00 42.39 4.00
420 425 2.113986 GAGCCTTGGCACAGTGGT 59.886 61.111 14.54 0.00 42.39 4.16
421 426 1.374947 GAGCCTTGGCACAGTGGTA 59.625 57.895 14.54 0.00 42.39 3.25
422 427 0.250727 GAGCCTTGGCACAGTGGTAA 60.251 55.000 14.54 0.00 42.39 2.85
423 428 0.184933 AGCCTTGGCACAGTGGTAAA 59.815 50.000 14.54 0.00 42.39 2.01
424 429 1.036707 GCCTTGGCACAGTGGTAAAA 58.963 50.000 6.79 0.00 42.39 1.52
425 430 1.000274 GCCTTGGCACAGTGGTAAAAG 60.000 52.381 6.79 0.00 42.39 2.27
426 431 1.000274 CCTTGGCACAGTGGTAAAAGC 60.000 52.381 1.84 0.00 42.39 3.51
427 432 1.956477 CTTGGCACAGTGGTAAAAGCT 59.044 47.619 1.84 0.00 42.39 3.74
428 433 1.317613 TGGCACAGTGGTAAAAGCTG 58.682 50.000 1.84 0.00 36.41 4.24
429 434 0.039165 GGCACAGTGGTAAAAGCTGC 60.039 55.000 1.84 0.00 33.87 5.25
430 435 0.954452 GCACAGTGGTAAAAGCTGCT 59.046 50.000 1.84 0.00 33.87 4.24
431 436 1.335324 GCACAGTGGTAAAAGCTGCTG 60.335 52.381 1.35 0.00 33.87 4.41
432 437 0.954452 ACAGTGGTAAAAGCTGCTGC 59.046 50.000 1.35 7.62 40.05 5.25
433 438 0.242017 CAGTGGTAAAAGCTGCTGCC 59.758 55.000 12.44 4.43 40.80 4.85
434 439 0.111253 AGTGGTAAAAGCTGCTGCCT 59.889 50.000 12.44 0.00 40.80 4.75
435 440 0.961753 GTGGTAAAAGCTGCTGCCTT 59.038 50.000 12.44 8.67 40.80 4.35
436 441 0.961019 TGGTAAAAGCTGCTGCCTTG 59.039 50.000 12.44 0.00 40.80 3.61
437 442 0.961753 GGTAAAAGCTGCTGCCTTGT 59.038 50.000 12.44 4.13 40.80 3.16
438 443 1.336240 GGTAAAAGCTGCTGCCTTGTG 60.336 52.381 12.44 0.00 40.80 3.33
439 444 1.608590 GTAAAAGCTGCTGCCTTGTGA 59.391 47.619 12.44 0.00 40.80 3.58
440 445 0.386838 AAAAGCTGCTGCCTTGTGAC 59.613 50.000 12.44 0.00 40.80 3.67
441 446 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
442 447 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
443 448 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
444 449 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
445 450 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
446 451 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
447 452 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
493 498 5.752892 GCAAAGGCCTTAATAAGTACTCC 57.247 43.478 20.84 0.00 0.00 3.85
494 499 4.579340 GCAAAGGCCTTAATAAGTACTCCC 59.421 45.833 20.84 0.00 0.00 4.30
495 500 5.631717 GCAAAGGCCTTAATAAGTACTCCCT 60.632 44.000 20.84 0.00 0.00 4.20
496 501 5.890752 AAGGCCTTAATAAGTACTCCCTC 57.109 43.478 18.87 0.00 0.00 4.30
497 502 5.159139 AGGCCTTAATAAGTACTCCCTCT 57.841 43.478 0.00 0.00 0.00 3.69
498 503 4.902448 AGGCCTTAATAAGTACTCCCTCTG 59.098 45.833 0.00 0.00 0.00 3.35
499 504 4.654724 GGCCTTAATAAGTACTCCCTCTGT 59.345 45.833 0.00 0.00 0.00 3.41
500 505 5.837438 GGCCTTAATAAGTACTCCCTCTGTA 59.163 44.000 0.00 0.00 0.00 2.74
501 506 6.325804 GGCCTTAATAAGTACTCCCTCTGTAA 59.674 42.308 0.00 0.00 0.00 2.41
502 507 7.147602 GGCCTTAATAAGTACTCCCTCTGTAAA 60.148 40.741 0.00 0.00 0.00 2.01
503 508 7.927092 GCCTTAATAAGTACTCCCTCTGTAAAG 59.073 40.741 0.00 0.00 0.00 1.85
504 509 9.198475 CCTTAATAAGTACTCCCTCTGTAAAGA 57.802 37.037 0.00 0.00 0.00 2.52
515 520 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
516 521 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
517 522 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
518 523 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
519 524 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
520 525 9.907576 CTCTGTAAAGAAATATAAGAGCGTTTG 57.092 33.333 0.00 0.00 0.00 2.93
521 526 9.431887 TCTGTAAAGAAATATAAGAGCGTTTGT 57.568 29.630 0.00 0.00 0.00 2.83
565 570 9.060347 TCTTCATCTTACCTTTGCATATGATTC 57.940 33.333 6.97 0.00 0.00 2.52
600 605 7.865530 TGACCATAATATTGTAGGCTTCCTA 57.134 36.000 0.00 0.00 34.61 2.94
602 607 9.555411 TGACCATAATATTGTAGGCTTCCTATA 57.445 33.333 0.00 0.00 38.48 1.31
618 972 8.092068 GGCTTCCTATAAACTTCTCCTATTCTC 58.908 40.741 0.00 0.00 0.00 2.87
681 1037 8.787852 AGGAAAATGACTTACAAAACAGAGATC 58.212 33.333 0.00 0.00 0.00 2.75
755 1111 2.307098 AGCCAGCTGGAATAACAGAGTT 59.693 45.455 37.21 0.00 40.97 3.01
763 1119 7.601886 CAGCTGGAATAACAGAGTTATAGGATG 59.398 40.741 5.57 1.08 40.97 3.51
901 1258 6.861065 AATACATGTGATATTCCCGTGTTC 57.139 37.500 9.11 0.00 31.25 3.18
910 1267 1.946984 TTCCCGTGTTCCTATCCTGT 58.053 50.000 0.00 0.00 0.00 4.00
914 1271 2.100197 CCGTGTTCCTATCCTGTCTCA 58.900 52.381 0.00 0.00 0.00 3.27
916 1273 2.755655 CGTGTTCCTATCCTGTCTCACT 59.244 50.000 0.00 0.00 0.00 3.41
1161 1518 2.375174 TGTCCCAGCTGTATTGGAAACT 59.625 45.455 13.81 0.00 37.96 2.66
1179 1536 2.043604 CTCCCATCACTATGCCGGCA 62.044 60.000 34.80 34.80 0.00 5.69
1338 1695 3.990959 ACAACAAACCCAATGGTGTTT 57.009 38.095 11.40 11.40 46.13 2.83
1373 1730 5.902681 TGTCTTGGTAACTGATAAGATCCG 58.097 41.667 0.00 0.00 32.44 4.18
2317 2686 4.932200 AGTGTTGTAGCAGTCTTAATCAGC 59.068 41.667 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1 2 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2 3 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3 4 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
4 5 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
51 52 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
53 54 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
59 60 9.939424 ACTTCTACTCCCTCTGTAAACTAATAT 57.061 33.333 0.00 0.00 0.00 1.28
60 61 9.765295 AACTTCTACTCCCTCTGTAAACTAATA 57.235 33.333 0.00 0.00 0.00 0.98
61 62 8.667592 AACTTCTACTCCCTCTGTAAACTAAT 57.332 34.615 0.00 0.00 0.00 1.73
62 63 9.240734 CTAACTTCTACTCCCTCTGTAAACTAA 57.759 37.037 0.00 0.00 0.00 2.24
63 64 8.389366 ACTAACTTCTACTCCCTCTGTAAACTA 58.611 37.037 0.00 0.00 0.00 2.24
64 65 7.177041 CACTAACTTCTACTCCCTCTGTAAACT 59.823 40.741 0.00 0.00 0.00 2.66
65 66 7.314393 CACTAACTTCTACTCCCTCTGTAAAC 58.686 42.308 0.00 0.00 0.00 2.01
66 67 6.436532 CCACTAACTTCTACTCCCTCTGTAAA 59.563 42.308 0.00 0.00 0.00 2.01
67 68 5.950549 CCACTAACTTCTACTCCCTCTGTAA 59.049 44.000 0.00 0.00 0.00 2.41
68 69 5.252397 TCCACTAACTTCTACTCCCTCTGTA 59.748 44.000 0.00 0.00 0.00 2.74
69 70 4.044317 TCCACTAACTTCTACTCCCTCTGT 59.956 45.833 0.00 0.00 0.00 3.41
70 71 4.601084 TCCACTAACTTCTACTCCCTCTG 58.399 47.826 0.00 0.00 0.00 3.35
71 72 4.949966 TCCACTAACTTCTACTCCCTCT 57.050 45.455 0.00 0.00 0.00 3.69
72 73 4.142116 GCTTCCACTAACTTCTACTCCCTC 60.142 50.000 0.00 0.00 0.00 4.30
73 74 3.770388 GCTTCCACTAACTTCTACTCCCT 59.230 47.826 0.00 0.00 0.00 4.20
74 75 3.429135 CGCTTCCACTAACTTCTACTCCC 60.429 52.174 0.00 0.00 0.00 4.30
75 76 3.771798 CGCTTCCACTAACTTCTACTCC 58.228 50.000 0.00 0.00 0.00 3.85
76 77 3.180613 GCGCTTCCACTAACTTCTACTC 58.819 50.000 0.00 0.00 0.00 2.59
77 78 2.415625 CGCGCTTCCACTAACTTCTACT 60.416 50.000 5.56 0.00 0.00 2.57
78 79 1.918609 CGCGCTTCCACTAACTTCTAC 59.081 52.381 5.56 0.00 0.00 2.59
79 80 1.135199 CCGCGCTTCCACTAACTTCTA 60.135 52.381 5.56 0.00 0.00 2.10
80 81 0.389948 CCGCGCTTCCACTAACTTCT 60.390 55.000 5.56 0.00 0.00 2.85
81 82 1.967597 GCCGCGCTTCCACTAACTTC 61.968 60.000 5.56 0.00 0.00 3.01
82 83 2.033194 GCCGCGCTTCCACTAACTT 61.033 57.895 5.56 0.00 0.00 2.66
83 84 2.434359 GCCGCGCTTCCACTAACT 60.434 61.111 5.56 0.00 0.00 2.24
84 85 2.434359 AGCCGCGCTTCCACTAAC 60.434 61.111 5.56 0.00 33.89 2.34
85 86 1.879737 TACAGCCGCGCTTCCACTAA 61.880 55.000 5.56 0.00 36.40 2.24
86 87 2.279502 CTACAGCCGCGCTTCCACTA 62.280 60.000 5.56 0.00 36.40 2.74
87 88 3.649277 CTACAGCCGCGCTTCCACT 62.649 63.158 5.56 0.00 36.40 4.00
88 89 3.188786 CTACAGCCGCGCTTCCAC 61.189 66.667 5.56 0.00 36.40 4.02
89 90 3.234630 AACTACAGCCGCGCTTCCA 62.235 57.895 5.56 0.00 36.40 3.53
90 91 2.434359 AACTACAGCCGCGCTTCC 60.434 61.111 5.56 0.00 36.40 3.46
91 92 1.084370 ATGAACTACAGCCGCGCTTC 61.084 55.000 5.56 0.00 36.40 3.86
92 93 0.673644 AATGAACTACAGCCGCGCTT 60.674 50.000 5.56 0.00 36.40 4.68
93 94 0.174845 TAATGAACTACAGCCGCGCT 59.825 50.000 5.56 0.00 40.77 5.92
94 95 0.577269 CTAATGAACTACAGCCGCGC 59.423 55.000 0.00 0.00 0.00 6.86
95 96 1.202371 TCCTAATGAACTACAGCCGCG 60.202 52.381 0.00 0.00 0.00 6.46
96 97 2.596904 TCCTAATGAACTACAGCCGC 57.403 50.000 0.00 0.00 0.00 6.53
97 98 3.809832 CCATTCCTAATGAACTACAGCCG 59.190 47.826 1.23 0.00 41.46 5.52
98 99 4.137543 CCCATTCCTAATGAACTACAGCC 58.862 47.826 1.23 0.00 41.46 4.85
99 100 5.036117 TCCCATTCCTAATGAACTACAGC 57.964 43.478 1.23 0.00 41.46 4.40
126 127 4.141287 TGGTTAGTCAATGTGTTCCAAGG 58.859 43.478 0.00 0.00 0.00 3.61
131 132 6.260050 TCAACTTCTGGTTAGTCAATGTGTTC 59.740 38.462 0.00 0.00 36.23 3.18
135 136 6.591935 TCTTCAACTTCTGGTTAGTCAATGT 58.408 36.000 0.00 0.00 36.23 2.71
139 140 5.071788 ACCATCTTCAACTTCTGGTTAGTCA 59.928 40.000 0.00 0.00 36.86 3.41
148 149 2.555757 GCAAGCACCATCTTCAACTTCT 59.444 45.455 0.00 0.00 0.00 2.85
149 150 2.294233 TGCAAGCACCATCTTCAACTTC 59.706 45.455 0.00 0.00 0.00 3.01
151 152 1.884579 CTGCAAGCACCATCTTCAACT 59.115 47.619 0.00 0.00 0.00 3.16
152 153 2.342910 CTGCAAGCACCATCTTCAAC 57.657 50.000 0.00 0.00 0.00 3.18
167 168 1.142870 AGTCCCAAAAGTACTGCTGCA 59.857 47.619 0.88 0.88 0.00 4.41
185 186 8.516234 CGCACTACCAGATAGAATATTTCTAGT 58.484 37.037 3.63 0.00 44.80 2.57
186 187 8.731605 TCGCACTACCAGATAGAATATTTCTAG 58.268 37.037 3.63 0.00 44.80 2.43
188 189 7.526142 TCGCACTACCAGATAGAATATTTCT 57.474 36.000 0.00 0.00 43.72 2.52
197 198 2.294512 TGCTGATCGCACTACCAGATAG 59.705 50.000 7.93 0.00 45.47 2.08
200 201 2.578683 TGCTGATCGCACTACCAGA 58.421 52.632 7.93 0.00 45.47 3.86
211 212 5.540719 AGGGACTAACCTATAGTTGCTGATC 59.459 44.000 0.00 0.00 39.65 2.92
223 224 4.069312 TCATGGTTCAGGGACTAACCTA 57.931 45.455 5.88 0.00 40.35 3.08
224 225 2.915869 TCATGGTTCAGGGACTAACCT 58.084 47.619 5.88 0.00 40.35 3.50
232 233 5.070001 TCTTACACTTTTCATGGTTCAGGG 58.930 41.667 0.00 0.00 0.00 4.45
236 237 5.470098 TGCTCTCTTACACTTTTCATGGTTC 59.530 40.000 0.00 0.00 0.00 3.62
238 239 4.973168 TGCTCTCTTACACTTTTCATGGT 58.027 39.130 0.00 0.00 0.00 3.55
239 240 5.471456 ACTTGCTCTCTTACACTTTTCATGG 59.529 40.000 0.00 0.00 0.00 3.66
240 241 6.551385 ACTTGCTCTCTTACACTTTTCATG 57.449 37.500 0.00 0.00 0.00 3.07
242 243 4.745125 CGACTTGCTCTCTTACACTTTTCA 59.255 41.667 0.00 0.00 0.00 2.69
243 244 4.745620 ACGACTTGCTCTCTTACACTTTTC 59.254 41.667 0.00 0.00 0.00 2.29
244 245 4.508124 CACGACTTGCTCTCTTACACTTTT 59.492 41.667 0.00 0.00 0.00 2.27
245 246 4.051922 CACGACTTGCTCTCTTACACTTT 58.948 43.478 0.00 0.00 0.00 2.66
250 251 3.058155 TCAGACACGACTTGCTCTCTTAC 60.058 47.826 0.00 0.00 0.00 2.34
276 280 6.701145 TCTGAATCTCTTTCTGTAGCGTAT 57.299 37.500 0.00 0.00 35.44 3.06
278 282 5.392767 TTCTGAATCTCTTTCTGTAGCGT 57.607 39.130 0.00 0.00 35.44 5.07
279 283 6.183360 CCTTTTCTGAATCTCTTTCTGTAGCG 60.183 42.308 0.00 0.00 35.44 4.26
292 296 5.893897 ATGCAGTCTTCCTTTTCTGAATC 57.106 39.130 0.00 0.00 0.00 2.52
327 331 8.923270 TCAAATGGATAAATAGTGGGGAAAATC 58.077 33.333 0.00 0.00 0.00 2.17
329 333 8.852671 ATCAAATGGATAAATAGTGGGGAAAA 57.147 30.769 0.00 0.00 33.37 2.29
330 334 8.852671 AATCAAATGGATAAATAGTGGGGAAA 57.147 30.769 0.00 0.00 34.28 3.13
331 335 8.064389 TGAATCAAATGGATAAATAGTGGGGAA 58.936 33.333 0.00 0.00 34.28 3.97
332 336 7.590907 TGAATCAAATGGATAAATAGTGGGGA 58.409 34.615 0.00 0.00 34.28 4.81
333 337 7.838079 TGAATCAAATGGATAAATAGTGGGG 57.162 36.000 0.00 0.00 34.28 4.96
383 388 4.504514 GCTCCCTTCTCTTCATGCATATGA 60.505 45.833 6.97 0.00 41.44 2.15
384 389 3.752222 GCTCCCTTCTCTTCATGCATATG 59.248 47.826 0.00 0.00 35.57 1.78
385 390 3.244840 GGCTCCCTTCTCTTCATGCATAT 60.245 47.826 0.00 0.00 0.00 1.78
386 391 2.105477 GGCTCCCTTCTCTTCATGCATA 59.895 50.000 0.00 0.00 0.00 3.14
387 392 1.133853 GGCTCCCTTCTCTTCATGCAT 60.134 52.381 0.00 0.00 0.00 3.96
388 393 0.254178 GGCTCCCTTCTCTTCATGCA 59.746 55.000 0.00 0.00 0.00 3.96
389 394 0.545646 AGGCTCCCTTCTCTTCATGC 59.454 55.000 0.00 0.00 0.00 4.06
390 395 2.641305 CAAGGCTCCCTTCTCTTCATG 58.359 52.381 0.00 0.00 42.67 3.07
391 396 1.563410 CCAAGGCTCCCTTCTCTTCAT 59.437 52.381 0.00 0.00 42.67 2.57
392 397 0.987294 CCAAGGCTCCCTTCTCTTCA 59.013 55.000 0.00 0.00 42.67 3.02
393 398 0.393673 GCCAAGGCTCCCTTCTCTTC 60.394 60.000 3.29 0.00 42.67 2.87
394 399 1.136329 TGCCAAGGCTCCCTTCTCTT 61.136 55.000 12.96 0.00 42.67 2.85
395 400 1.539869 TGCCAAGGCTCCCTTCTCT 60.540 57.895 12.96 0.00 42.67 3.10
396 401 1.377856 GTGCCAAGGCTCCCTTCTC 60.378 63.158 12.96 0.00 42.67 2.87
397 402 2.134630 CTGTGCCAAGGCTCCCTTCT 62.135 60.000 12.96 0.00 42.67 2.85
398 403 1.676967 CTGTGCCAAGGCTCCCTTC 60.677 63.158 12.96 0.00 42.67 3.46
399 404 2.437897 CTGTGCCAAGGCTCCCTT 59.562 61.111 12.96 0.00 45.88 3.95
400 405 2.856000 ACTGTGCCAAGGCTCCCT 60.856 61.111 12.96 0.00 42.51 4.20
401 406 2.674380 CACTGTGCCAAGGCTCCC 60.674 66.667 12.96 1.13 42.51 4.30
402 407 2.124507 TACCACTGTGCCAAGGCTCC 62.125 60.000 12.96 3.64 42.51 4.70
403 408 0.250727 TTACCACTGTGCCAAGGCTC 60.251 55.000 12.96 9.45 42.51 4.70
404 409 0.184933 TTTACCACTGTGCCAAGGCT 59.815 50.000 12.96 0.00 42.51 4.58
405 410 1.000274 CTTTTACCACTGTGCCAAGGC 60.000 52.381 3.61 3.61 42.35 4.35
406 411 1.000274 GCTTTTACCACTGTGCCAAGG 60.000 52.381 1.29 0.00 0.00 3.61
407 412 1.956477 AGCTTTTACCACTGTGCCAAG 59.044 47.619 1.29 2.71 0.00 3.61
408 413 1.680735 CAGCTTTTACCACTGTGCCAA 59.319 47.619 1.29 0.00 0.00 4.52
409 414 1.317613 CAGCTTTTACCACTGTGCCA 58.682 50.000 1.29 0.00 0.00 4.92
410 415 0.039165 GCAGCTTTTACCACTGTGCC 60.039 55.000 1.29 0.00 33.87 5.01
411 416 0.954452 AGCAGCTTTTACCACTGTGC 59.046 50.000 1.29 0.00 33.87 4.57
412 417 1.335324 GCAGCAGCTTTTACCACTGTG 60.335 52.381 0.00 0.00 37.91 3.66
413 418 0.954452 GCAGCAGCTTTTACCACTGT 59.046 50.000 0.00 0.00 37.91 3.55
414 419 0.242017 GGCAGCAGCTTTTACCACTG 59.758 55.000 0.00 0.00 41.70 3.66
415 420 0.111253 AGGCAGCAGCTTTTACCACT 59.889 50.000 0.00 0.00 41.70 4.00
416 421 0.961753 AAGGCAGCAGCTTTTACCAC 59.038 50.000 0.00 0.00 36.57 4.16
417 422 0.961019 CAAGGCAGCAGCTTTTACCA 59.039 50.000 0.00 0.00 38.07 3.25
418 423 0.961753 ACAAGGCAGCAGCTTTTACC 59.038 50.000 0.00 0.00 38.07 2.85
419 424 1.608590 TCACAAGGCAGCAGCTTTTAC 59.391 47.619 0.00 0.00 38.07 2.01
420 425 1.608590 GTCACAAGGCAGCAGCTTTTA 59.391 47.619 0.00 0.00 38.07 1.52
421 426 0.386838 GTCACAAGGCAGCAGCTTTT 59.613 50.000 0.00 0.00 38.07 2.27
422 427 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
423 428 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
424 429 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
425 430 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
426 431 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
427 432 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
428 433 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
429 434 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
430 435 1.357137 TACCTCATGGTCACAAGGCA 58.643 50.000 0.00 0.00 44.78 4.75
431 436 2.717639 ATACCTCATGGTCACAAGGC 57.282 50.000 0.00 0.00 44.78 4.35
432 437 4.220693 TGAATACCTCATGGTCACAAGG 57.779 45.455 0.00 0.00 44.78 3.61
433 438 6.072838 GCATATGAATACCTCATGGTCACAAG 60.073 42.308 6.97 0.00 44.78 3.16
434 439 5.764686 GCATATGAATACCTCATGGTCACAA 59.235 40.000 6.97 0.00 44.78 3.33
435 440 5.163216 TGCATATGAATACCTCATGGTCACA 60.163 40.000 6.97 0.00 44.78 3.58
436 441 5.308014 TGCATATGAATACCTCATGGTCAC 58.692 41.667 6.97 0.00 44.78 3.67
437 442 5.565455 TGCATATGAATACCTCATGGTCA 57.435 39.130 6.97 0.00 44.78 4.02
438 443 6.175471 TCATGCATATGAATACCTCATGGTC 58.825 40.000 6.97 0.00 44.84 4.02
439 444 6.130692 TCATGCATATGAATACCTCATGGT 57.869 37.500 6.97 0.00 44.84 3.55
492 497 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
493 498 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
494 499 9.907576 CAAACGCTCTTATATTTCTTTACAGAG 57.092 33.333 0.00 0.00 0.00 3.35
495 500 9.431887 ACAAACGCTCTTATATTTCTTTACAGA 57.568 29.630 0.00 0.00 0.00 3.41
502 507 9.542462 TGCTATTACAAACGCTCTTATATTTCT 57.458 29.630 0.00 0.00 0.00 2.52
589 594 6.734502 AGGAGAAGTTTATAGGAAGCCTAC 57.265 41.667 0.00 0.00 39.10 3.18
600 605 8.528044 AGAAGTCGAGAATAGGAGAAGTTTAT 57.472 34.615 0.00 0.00 0.00 1.40
602 607 6.844097 AGAAGTCGAGAATAGGAGAAGTTT 57.156 37.500 0.00 0.00 0.00 2.66
603 608 6.626302 CAAGAAGTCGAGAATAGGAGAAGTT 58.374 40.000 0.00 0.00 0.00 2.66
618 972 2.031769 TGAATTGTGCAGCAAGAAGTCG 60.032 45.455 0.00 0.00 40.86 4.18
681 1037 4.142204 TGTGTAATTTGCTGGGCATACATG 60.142 41.667 7.42 0.00 38.76 3.21
716 1072 3.782889 GCTGGTTGGCCTATTTACAAG 57.217 47.619 3.32 0.00 35.27 3.16
824 1180 2.620115 GGACTGCATCCCACACATATTG 59.380 50.000 4.36 0.00 42.46 1.90
845 1201 3.500558 TCTGTCAGATTTCAGAGCTCG 57.499 47.619 8.37 3.55 36.04 5.03
889 1246 3.640029 GACAGGATAGGAACACGGGAATA 59.360 47.826 0.00 0.00 0.00 1.75
901 1258 0.755686 GGGCAGTGAGACAGGATAGG 59.244 60.000 0.00 0.00 0.00 2.57
910 1267 1.621317 TGTCATTTACGGGCAGTGAGA 59.379 47.619 0.00 0.00 0.00 3.27
914 1271 2.851263 TCTTGTCATTTACGGGCAGT 57.149 45.000 0.00 0.00 0.00 4.40
916 1273 4.138290 TCTTTTCTTGTCATTTACGGGCA 58.862 39.130 0.00 0.00 0.00 5.36
1161 1518 1.631071 TTGCCGGCATAGTGATGGGA 61.631 55.000 33.25 8.24 33.26 4.37
1373 1730 6.363357 GGTTGCTGATCACTTGATTACAAAAC 59.637 38.462 0.00 0.00 35.49 2.43
2317 2686 2.954753 GAGGTCAACAAGTGGCGCG 61.955 63.158 0.00 0.00 29.99 6.86


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

AutoCloner maintained by Alex Coulton.