Multiple sequence alignment - TraesCS3A01G298800

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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 TraesCS3A01G298800 chr3A 100.000 4821 0 0 1 4821 532938611 532933791 0.000000e+00 8903.0
1 TraesCS3A01G298800 chr3D 92.954 4371 210 46 246 4555 417737673 417742006 0.000000e+00 6276.0
2 TraesCS3A01G298800 chr3D 87.018 285 23 4 4543 4816 417742433 417742714 4.690000e-80 309.0
3 TraesCS3A01G298800 chr3D 86.809 235 26 5 16 248 417737412 417737643 1.720000e-64 257.0
4 TraesCS3A01G298800 chr3B 91.557 4631 264 61 16 4553 544108264 544112860 0.000000e+00 6268.0
5 TraesCS3A01G298800 chr4D 86.747 83 11 0 4403 4485 34077040 34077122 5.140000e-15 93.5


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 TraesCS3A01G298800 chr3A 532933791 532938611 4820 True 8903.000000 8903 100.000 1 4821 1 chr3A.!!$R1 4820
1 TraesCS3A01G298800 chr3D 417737412 417742714 5302 False 2280.666667 6276 88.927 16 4816 3 chr3D.!!$F1 4800
2 TraesCS3A01G298800 chr3B 544108264 544112860 4596 False 6268.000000 6268 91.557 16 4553 1 chr3B.!!$F1 4537

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
237 239 0.032615 AGGGCGAGGAGAGAGAACAT 60.033 55.0 0.0 0.0 0.00 2.71 F
550 608 0.191064 TCCTCCGCCTCCATATTCCT 59.809 55.0 0.0 0.0 0.00 3.36 F
2295 2387 0.250124 AAATCACCCTTGACGACGCA 60.250 50.0 0.0 0.0 33.38 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1542 0.617820 AGAGGTACCCCATGAACGCT 60.618 55.0 8.74 0.00 0.00 5.07 R
2547 2639 0.750911 CTTGGCCCTGCTCCATCTTC 60.751 60.0 0.00 0.00 32.92 2.87 R
4055 4168 0.103026 CGTCGAAGCTGGATGATCCA 59.897 55.0 14.42 14.42 45.98 3.41 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
23 24 4.288626 ACAAACTAGCCCCTAAATCTCACA 59.711 41.667 0.00 0.00 0.00 3.58
40 41 0.179001 ACAAAAAGGACCCCCGACAG 60.179 55.000 0.00 0.00 37.58 3.51
46 47 0.688087 AGGACCCCCGACAGAGAATC 60.688 60.000 0.00 0.00 37.58 2.52
92 93 2.095372 GCTCCGCCAATACAACTTACAC 59.905 50.000 0.00 0.00 0.00 2.90
125 126 8.064814 CCCCAACAAAACATAAAATTACAAACG 58.935 33.333 0.00 0.00 0.00 3.60
126 127 8.818057 CCCAACAAAACATAAAATTACAAACGA 58.182 29.630 0.00 0.00 0.00 3.85
163 164 3.664551 AAAGGGCCCCAAATAGAGTAC 57.335 47.619 21.43 0.00 0.00 2.73
187 188 4.072088 CGCGGTCGTGTCCAAAGC 62.072 66.667 0.00 0.00 0.00 3.51
188 189 3.723348 GCGGTCGTGTCCAAAGCC 61.723 66.667 0.00 0.00 0.00 4.35
215 216 5.700402 CCTAATGGGAAAAGGAGAGAAGA 57.300 43.478 0.00 0.00 37.23 2.87
222 223 3.508012 GGAAAAGGAGAGAAGAAAAGGGC 59.492 47.826 0.00 0.00 0.00 5.19
223 224 2.481289 AAGGAGAGAAGAAAAGGGCG 57.519 50.000 0.00 0.00 0.00 6.13
237 239 0.032615 AGGGCGAGGAGAGAGAACAT 60.033 55.000 0.00 0.00 0.00 2.71
239 241 0.529555 GGCGAGGAGAGAGAACATGC 60.530 60.000 0.00 0.00 0.00 4.06
249 283 3.119029 AGAGAGAACATGCAAGAGAGAGC 60.119 47.826 0.00 0.00 0.00 4.09
297 331 1.207593 GATTGCAGTGACGTGTGGC 59.792 57.895 0.00 0.00 0.00 5.01
323 357 3.052036 ACGCGTACTACGTTTTGTCATT 58.948 40.909 11.67 0.00 44.73 2.57
329 363 5.332732 CGTACTACGTTTTGTCATTGCAAGA 60.333 40.000 4.94 0.00 36.74 3.02
330 364 5.095691 ACTACGTTTTGTCATTGCAAGAG 57.904 39.130 4.94 0.00 0.00 2.85
331 365 4.574828 ACTACGTTTTGTCATTGCAAGAGT 59.425 37.500 4.94 0.00 0.00 3.24
332 366 5.756347 ACTACGTTTTGTCATTGCAAGAGTA 59.244 36.000 4.94 0.57 0.00 2.59
333 367 5.689383 ACGTTTTGTCATTGCAAGAGTAT 57.311 34.783 4.94 0.00 0.00 2.12
334 368 6.072112 ACGTTTTGTCATTGCAAGAGTATT 57.928 33.333 4.94 0.00 0.00 1.89
335 369 7.197071 ACGTTTTGTCATTGCAAGAGTATTA 57.803 32.000 4.94 0.00 0.00 0.98
336 370 7.816640 ACGTTTTGTCATTGCAAGAGTATTAT 58.183 30.769 4.94 0.00 0.00 1.28
337 371 8.941977 ACGTTTTGTCATTGCAAGAGTATTATA 58.058 29.630 4.94 0.00 0.00 0.98
338 372 9.935682 CGTTTTGTCATTGCAAGAGTATTATAT 57.064 29.630 4.94 0.00 0.00 0.86
373 417 0.669625 ACCTCCGCGCTTTTGTACTC 60.670 55.000 5.56 0.00 0.00 2.59
378 422 0.451135 CGCGCTTTTGTACTCTGCAC 60.451 55.000 5.56 0.00 0.00 4.57
399 444 5.273170 CACAAACGCCAATATGGTATTCTG 58.727 41.667 0.00 0.00 40.46 3.02
451 507 2.440253 TCTTCTTCTCCGACCCCAAAAA 59.560 45.455 0.00 0.00 0.00 1.94
482 538 5.245075 AGAAGAGAACCTGATCGAAGAAAGT 59.755 40.000 0.00 0.00 43.58 2.66
488 546 4.815269 ACCTGATCGAAGAAAGTGAAGAG 58.185 43.478 0.00 0.00 43.58 2.85
491 549 5.576384 CCTGATCGAAGAAAGTGAAGAGAAG 59.424 44.000 0.00 0.00 43.58 2.85
492 550 5.473931 TGATCGAAGAAAGTGAAGAGAAGG 58.526 41.667 0.00 0.00 43.58 3.46
548 606 1.902508 TCATCCTCCGCCTCCATATTC 59.097 52.381 0.00 0.00 0.00 1.75
549 607 1.065854 CATCCTCCGCCTCCATATTCC 60.066 57.143 0.00 0.00 0.00 3.01
550 608 0.191064 TCCTCCGCCTCCATATTCCT 59.809 55.000 0.00 0.00 0.00 3.36
581 639 0.981277 TCGTCTTCAATCCCCTCCCC 60.981 60.000 0.00 0.00 0.00 4.81
583 641 2.193248 CTTCAATCCCCTCCCCGC 59.807 66.667 0.00 0.00 0.00 6.13
629 689 4.779733 TGCCCCCGGACTCCTCTC 62.780 72.222 0.73 0.00 0.00 3.20
651 711 1.685820 CAACCCCACTCTCCTTCCC 59.314 63.158 0.00 0.00 0.00 3.97
814 882 2.171725 CGAATTCGCCGTCCCTTCC 61.172 63.158 15.93 0.00 0.00 3.46
835 905 2.359478 CTGCGTTTAGGCGGGGTT 60.359 61.111 0.00 0.00 35.63 4.11
1185 1257 0.393402 TGAATCGCCTCAGCAGCAAT 60.393 50.000 0.00 0.00 39.83 3.56
1230 1302 4.767841 CTCGACTGCAGCGACGCT 62.768 66.667 23.20 18.46 40.77 5.07
1397 1475 2.285368 AGCGGGAGGGGATGTGAA 60.285 61.111 0.00 0.00 0.00 3.18
1599 1677 2.105128 GAGCTCATGTACGCGGCT 59.895 61.111 12.47 7.37 35.86 5.52
1653 1731 1.131638 TCCAGGTGAGGGATGCATAC 58.868 55.000 0.00 0.00 0.00 2.39
1677 1755 5.122396 CGCTCTTATTGGCTTGTTTAGAACT 59.878 40.000 0.00 0.00 0.00 3.01
1685 1764 3.253432 GGCTTGTTTAGAACTCCCAACTG 59.747 47.826 0.00 0.00 0.00 3.16
1687 1766 5.061179 GCTTGTTTAGAACTCCCAACTGTA 58.939 41.667 0.00 0.00 0.00 2.74
1689 1768 6.877322 GCTTGTTTAGAACTCCCAACTGTATA 59.123 38.462 0.00 0.00 0.00 1.47
1690 1769 7.553044 GCTTGTTTAGAACTCCCAACTGTATAT 59.447 37.037 0.00 0.00 0.00 0.86
1691 1770 9.449719 CTTGTTTAGAACTCCCAACTGTATATT 57.550 33.333 0.00 0.00 0.00 1.28
1692 1771 9.802039 TTGTTTAGAACTCCCAACTGTATATTT 57.198 29.630 0.00 0.00 0.00 1.40
1693 1772 9.226606 TGTTTAGAACTCCCAACTGTATATTTG 57.773 33.333 0.00 0.00 0.00 2.32
1694 1773 9.227777 GTTTAGAACTCCCAACTGTATATTTGT 57.772 33.333 0.00 0.00 0.00 2.83
1695 1774 9.802039 TTTAGAACTCCCAACTGTATATTTGTT 57.198 29.630 0.00 0.00 0.00 2.83
1698 1777 9.449719 AGAACTCCCAACTGTATATTTGTTAAG 57.550 33.333 0.00 0.00 0.00 1.85
1744 1836 3.665173 GCTTCAGGCTAGAAATGTTCG 57.335 47.619 0.00 0.00 38.06 3.95
1745 1837 3.262420 GCTTCAGGCTAGAAATGTTCGA 58.738 45.455 0.00 0.00 38.06 3.71
1746 1838 3.062774 GCTTCAGGCTAGAAATGTTCGAC 59.937 47.826 0.00 0.00 38.06 4.20
1747 1839 4.499183 CTTCAGGCTAGAAATGTTCGACT 58.501 43.478 0.00 0.00 34.02 4.18
1748 1840 4.111375 TCAGGCTAGAAATGTTCGACTC 57.889 45.455 0.00 0.00 34.02 3.36
1749 1841 3.509967 TCAGGCTAGAAATGTTCGACTCA 59.490 43.478 0.00 0.00 34.02 3.41
1750 1842 4.160439 TCAGGCTAGAAATGTTCGACTCAT 59.840 41.667 0.00 0.00 34.02 2.90
1751 1843 4.269603 CAGGCTAGAAATGTTCGACTCATG 59.730 45.833 0.00 0.00 34.02 3.07
1752 1844 3.557595 GGCTAGAAATGTTCGACTCATGG 59.442 47.826 0.00 0.00 34.02 3.66
1753 1845 4.184629 GCTAGAAATGTTCGACTCATGGT 58.815 43.478 0.00 0.00 34.02 3.55
1754 1846 4.631813 GCTAGAAATGTTCGACTCATGGTT 59.368 41.667 0.00 0.00 34.02 3.67
1755 1847 5.220491 GCTAGAAATGTTCGACTCATGGTTC 60.220 44.000 0.00 5.13 34.02 3.62
1800 1892 1.605710 GACTGTGCACAGACATTTGCT 59.394 47.619 44.82 25.13 46.59 3.91
1830 1922 3.126858 TGGCATGCTAATTCGAAACAGAC 59.873 43.478 18.92 0.12 0.00 3.51
1896 1988 7.652909 TCATGGTTTCATTTCTCAATTTCACAC 59.347 33.333 0.00 0.00 0.00 3.82
1989 2081 1.581934 TTGTTGACAAGACTCTGGCG 58.418 50.000 0.00 0.00 0.00 5.69
2127 2219 2.290577 ACTCCCTCCAGAAATTGCTGAC 60.291 50.000 15.61 0.00 38.14 3.51
2157 2249 3.444703 AAGATCCGTCAGAAATCTCCG 57.555 47.619 0.00 0.00 0.00 4.63
2253 2345 6.149973 TGGATTCTGATGATGTTGAACTTGTC 59.850 38.462 0.00 0.00 0.00 3.18
2286 2378 7.020827 TCTTAATGAGTCTGAAATCACCCTT 57.979 36.000 0.00 0.00 0.00 3.95
2295 2387 0.250124 AAATCACCCTTGACGACGCA 60.250 50.000 0.00 0.00 33.38 5.24
2490 2582 1.527793 GCGTCGCAATTGACAGATGAC 60.528 52.381 13.44 5.62 38.84 3.06
2520 2612 6.258160 CCTTGCAAGTAATATTTGTCGAAGG 58.742 40.000 24.35 0.02 0.00 3.46
2547 2639 9.820229 TTAACAAGACTAAAAGATTACAATGCG 57.180 29.630 0.00 0.00 0.00 4.73
2643 2735 3.300388 TCCTATGACAGCGGAAGATTCT 58.700 45.455 0.00 0.00 0.00 2.40
2700 2792 6.206829 ACATGAAACTAAGCTACCTGGAAAAC 59.793 38.462 0.00 0.00 0.00 2.43
2781 2873 7.369434 TCAATATTAAAATGATGGGGGAGGTT 58.631 34.615 0.00 0.00 0.00 3.50
2798 2891 4.447325 GGAGGTTGAGAAAAAGTACCCCTT 60.447 45.833 0.00 0.00 33.79 3.95
2802 2895 6.102174 AGGTTGAGAAAAAGTACCCCTTTCTA 59.898 38.462 12.11 0.00 42.62 2.10
2861 2957 6.259608 GCATATGCTATAGAAATAGGTGGCTG 59.740 42.308 20.64 0.00 36.37 4.85
2870 2966 5.003804 AGAAATAGGTGGCTGTAACACTTG 58.996 41.667 0.00 0.00 38.83 3.16
2884 2980 0.870393 CACTTGCTGCACATTCGACT 59.130 50.000 0.00 0.00 0.00 4.18
2885 2981 1.136141 CACTTGCTGCACATTCGACTC 60.136 52.381 0.00 0.00 0.00 3.36
2890 2986 1.690283 CTGCACATTCGACTCTGCCG 61.690 60.000 0.79 0.00 0.00 5.69
2945 3041 2.089349 GGTCTCTGCAGTCGCGTTC 61.089 63.158 14.67 0.31 42.97 3.95
3107 3203 2.663826 AAAACAAAAGGCTGCGTTCA 57.336 40.000 8.14 0.00 0.00 3.18
3157 3253 4.106197 GCGAACATGAGTAGTCGATCTTT 58.894 43.478 0.00 0.00 0.00 2.52
3158 3254 4.205385 GCGAACATGAGTAGTCGATCTTTC 59.795 45.833 0.00 0.00 0.00 2.62
3159 3255 4.735822 CGAACATGAGTAGTCGATCTTTCC 59.264 45.833 0.00 0.00 0.00 3.13
3229 3329 5.991328 TGAGAGATCGTTGGATAAATTGC 57.009 39.130 0.00 0.00 31.51 3.56
3233 3333 3.885297 AGATCGTTGGATAAATTGCTGGG 59.115 43.478 0.00 0.00 31.51 4.45
3237 3337 4.638421 TCGTTGGATAAATTGCTGGGTAAG 59.362 41.667 0.00 0.00 0.00 2.34
3261 3361 7.001695 GCTGTTACTAGCTGTTAATACAACC 57.998 40.000 0.00 0.00 40.52 3.77
3276 3376 6.569179 AATACAACCATGTACACAACCTTC 57.431 37.500 0.00 0.00 44.47 3.46
3282 3382 4.253685 CCATGTACACAACCTTCTACCTG 58.746 47.826 0.00 0.00 0.00 4.00
3294 3394 7.601508 ACAACCTTCTACCTGAATAACTTAACG 59.398 37.037 0.00 0.00 33.71 3.18
3295 3395 6.104665 ACCTTCTACCTGAATAACTTAACGC 58.895 40.000 0.00 0.00 33.71 4.84
3296 3396 5.522824 CCTTCTACCTGAATAACTTAACGCC 59.477 44.000 0.00 0.00 33.71 5.68
3336 3436 8.523915 TTGATATTCTGTGCATGAACCTATTT 57.476 30.769 0.00 0.00 0.00 1.40
3423 3523 4.826733 TGTGGCACAAGTTCATTTCTACAT 59.173 37.500 19.74 0.00 44.16 2.29
3501 3612 5.976534 TGTTCAGTGTTGTGTATTTGCATTC 59.023 36.000 0.00 0.00 0.00 2.67
3506 3617 4.618489 GTGTTGTGTATTTGCATTCAGCTC 59.382 41.667 0.00 0.00 45.94 4.09
3520 3631 1.053048 CAGCTCGTTCTGTGTACACG 58.947 55.000 20.61 15.00 35.18 4.49
3529 3640 1.266989 TCTGTGTACACGAGCAGTCTG 59.733 52.381 20.61 0.00 0.00 3.51
3532 3643 1.289066 GTACACGAGCAGTCTGGCA 59.711 57.895 1.14 0.00 35.83 4.92
3571 3682 6.912082 TGAATTAAACATGTCTGTGATGGTG 58.088 36.000 0.00 0.00 35.22 4.17
3661 3772 3.428797 CCTGATGGCCTTGATGCG 58.571 61.111 3.32 0.00 0.00 4.73
3802 3913 0.388649 CCCTGTCGTCAAACTCCTCG 60.389 60.000 0.00 0.00 0.00 4.63
3845 3956 4.451435 GGTACTGTAACAGGCTGTTTTCTC 59.549 45.833 35.13 22.36 41.45 2.87
3857 3968 3.257393 CTGTTTTCTCGAGATGTCAGGG 58.743 50.000 17.44 0.29 0.00 4.45
3912 4023 2.095919 GTGCTCACCATCGTGTAAAACC 60.096 50.000 0.00 0.00 41.09 3.27
4024 4136 4.569228 CCCATCCCAGATTCCCAATATCAG 60.569 50.000 0.00 0.00 0.00 2.90
4041 4154 0.037975 CAGTTTCCCATGCTGGTTGC 60.038 55.000 0.00 0.00 43.25 4.17
4048 4161 1.133253 CATGCTGGTTGCGAAGACG 59.867 57.895 0.00 0.00 46.63 4.18
4054 4167 2.357034 GTTGCGAAGACGGAGCCA 60.357 61.111 0.00 0.00 41.35 4.75
4055 4168 1.741770 GTTGCGAAGACGGAGCCAT 60.742 57.895 0.00 0.00 41.35 4.40
4226 4342 1.002792 GACAGTTGCCCTTTGTCGAAC 60.003 52.381 0.00 0.00 32.81 3.95
4276 4394 7.521509 TTCGTAGCTCAAACTTTATAGAAGC 57.478 36.000 0.00 0.00 0.00 3.86
4316 4434 4.834534 CATTGCCATGGAATCAAAAGGAA 58.165 39.130 18.40 0.00 0.00 3.36
4327 4445 5.923114 GGAATCAAAAGGAAAAGAGCAAGAC 59.077 40.000 0.00 0.00 0.00 3.01
4333 4451 5.966742 AAGGAAAAGAGCAAGACCATAAC 57.033 39.130 0.00 0.00 0.00 1.89
4377 4495 8.920509 TCAATCATCAATTTAGATGCAACAAG 57.079 30.769 0.00 0.00 43.94 3.16
4389 4507 8.887036 TTAGATGCAACAAGATAACGACATAT 57.113 30.769 0.00 0.00 0.00 1.78
4391 4509 7.633621 AGATGCAACAAGATAACGACATATTG 58.366 34.615 0.00 0.00 34.14 1.90
4396 4514 7.250569 CAACAAGATAACGACATATTGCCTTT 58.749 34.615 7.82 0.00 31.71 3.11
4405 4523 5.360714 ACGACATATTGCCTTTGATCCAAAT 59.639 36.000 0.00 0.00 32.70 2.32
4422 4540 5.218885 TCCAAATTAATTGTCGCACACTTG 58.781 37.500 0.39 0.00 37.32 3.16
4428 4546 1.577468 TTGTCGCACACTTGGTACAG 58.423 50.000 0.00 0.00 42.39 2.74
4437 4555 4.151867 GCACACTTGGTACAGCTTTAGTAC 59.848 45.833 4.62 4.62 42.39 2.73
4441 4559 6.824704 ACACTTGGTACAGCTTTAGTACAAAA 59.175 34.615 13.15 7.30 42.73 2.44
4570 5129 9.491675 AAACATAAACAATTCAATGCAAGATCA 57.508 25.926 0.00 0.00 0.00 2.92
4578 5137 3.014623 TCAATGCAAGATCAGAGGCAAG 58.985 45.455 0.00 0.00 40.02 4.01
4579 5138 3.014623 CAATGCAAGATCAGAGGCAAGA 58.985 45.455 0.00 0.00 40.02 3.02
4586 5145 5.608449 CAAGATCAGAGGCAAGACATCATA 58.392 41.667 0.00 0.00 0.00 2.15
4590 5149 8.148437 AGATCAGAGGCAAGACATCATATAAT 57.852 34.615 0.00 0.00 0.00 1.28
4591 5150 9.264653 AGATCAGAGGCAAGACATCATATAATA 57.735 33.333 0.00 0.00 0.00 0.98
4592 5151 9.311916 GATCAGAGGCAAGACATCATATAATAC 57.688 37.037 0.00 0.00 0.00 1.89
4616 5175 7.378181 ACTACTTATTGTGCCCAATTTTTCAG 58.622 34.615 0.00 0.00 41.50 3.02
4627 5186 4.445385 CCCAATTTTTCAGAACTTCTTGCG 59.555 41.667 0.00 0.00 0.00 4.85
4641 5200 4.218417 ACTTCTTGCGCATAGTTTCCAAAT 59.782 37.500 12.75 0.00 0.00 2.32
4645 5204 5.988561 TCTTGCGCATAGTTTCCAAATTTTT 59.011 32.000 12.75 0.00 0.00 1.94
4673 5232 4.624024 CACTCATGTGATGTTTTCCAATGC 59.376 41.667 0.94 0.00 46.55 3.56
4675 5234 4.811908 TCATGTGATGTTTTCCAATGCTG 58.188 39.130 0.00 0.00 0.00 4.41
4781 5351 8.125448 GTCCTTGAGCTATATGTTTTGACATTC 58.875 37.037 0.00 0.00 0.00 2.67
4816 5386 5.952526 ATTAACGGGAAACTTAGGTTGTG 57.047 39.130 0.00 0.00 35.63 3.33
4817 5387 3.286329 AACGGGAAACTTAGGTTGTGT 57.714 42.857 0.00 0.00 35.63 3.72
4818 5388 3.286329 ACGGGAAACTTAGGTTGTGTT 57.714 42.857 0.00 0.00 35.63 3.32
4819 5389 4.420522 ACGGGAAACTTAGGTTGTGTTA 57.579 40.909 0.00 0.00 35.63 2.41
4820 5390 4.976864 ACGGGAAACTTAGGTTGTGTTAT 58.023 39.130 0.00 0.00 35.63 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.288626 TGTGAGATTTAGGGGCTAGTTTGT 59.711 41.667 0.00 0.00 0.00 2.83
1 2 4.843728 TGTGAGATTTAGGGGCTAGTTTG 58.156 43.478 0.00 0.00 0.00 2.93
2 3 5.514500 TTGTGAGATTTAGGGGCTAGTTT 57.486 39.130 0.00 0.00 0.00 2.66
3 4 5.514500 TTTGTGAGATTTAGGGGCTAGTT 57.486 39.130 0.00 0.00 0.00 2.24
4 5 5.514500 TTTTGTGAGATTTAGGGGCTAGT 57.486 39.130 0.00 0.00 0.00 2.57
5 6 5.358160 CCTTTTTGTGAGATTTAGGGGCTAG 59.642 44.000 0.00 0.00 0.00 3.42
6 7 5.014755 TCCTTTTTGTGAGATTTAGGGGCTA 59.985 40.000 0.00 0.00 0.00 3.93
7 8 4.089361 CCTTTTTGTGAGATTTAGGGGCT 58.911 43.478 0.00 0.00 0.00 5.19
8 9 4.082190 GTCCTTTTTGTGAGATTTAGGGGC 60.082 45.833 0.00 0.00 0.00 5.80
9 10 4.462834 GGTCCTTTTTGTGAGATTTAGGGG 59.537 45.833 0.00 0.00 0.00 4.79
10 11 4.462834 GGGTCCTTTTTGTGAGATTTAGGG 59.537 45.833 0.00 0.00 0.00 3.53
11 12 4.462834 GGGGTCCTTTTTGTGAGATTTAGG 59.537 45.833 0.00 0.00 0.00 2.69
12 13 4.462834 GGGGGTCCTTTTTGTGAGATTTAG 59.537 45.833 0.00 0.00 0.00 1.85
13 14 4.412843 GGGGGTCCTTTTTGTGAGATTTA 58.587 43.478 0.00 0.00 0.00 1.40
14 15 3.239449 GGGGGTCCTTTTTGTGAGATTT 58.761 45.455 0.00 0.00 0.00 2.17
20 21 0.466555 TGTCGGGGGTCCTTTTTGTG 60.467 55.000 0.00 0.00 0.00 3.33
23 24 0.400594 CTCTGTCGGGGGTCCTTTTT 59.599 55.000 0.00 0.00 0.00 1.94
40 41 1.518929 CCGATCGCGTTCTTGATTCTC 59.481 52.381 10.32 0.00 35.23 2.87
46 47 1.011968 TGAACCCGATCGCGTTCTTG 61.012 55.000 33.41 11.68 39.30 3.02
92 93 8.614469 ATTTTATGTTTTGTTGGGGTTATGTG 57.386 30.769 0.00 0.00 0.00 3.21
125 126 7.255836 GGGCCCTTTTTGTAAGATTATGGTATC 60.256 40.741 17.04 0.00 0.00 2.24
126 127 6.553476 GGGCCCTTTTTGTAAGATTATGGTAT 59.447 38.462 17.04 0.00 0.00 2.73
127 128 5.894964 GGGCCCTTTTTGTAAGATTATGGTA 59.105 40.000 17.04 0.00 0.00 3.25
207 208 1.550976 TCCTCGCCCTTTTCTTCTCTC 59.449 52.381 0.00 0.00 0.00 3.20
215 216 1.276705 GTTCTCTCTCCTCGCCCTTTT 59.723 52.381 0.00 0.00 0.00 2.27
222 223 2.165234 TCTTGCATGTTCTCTCTCCTCG 59.835 50.000 0.00 0.00 0.00 4.63
223 224 3.446873 TCTCTTGCATGTTCTCTCTCCTC 59.553 47.826 0.00 0.00 0.00 3.71
237 239 1.771783 TTGCCAGGCTCTCTCTTGCA 61.772 55.000 14.15 0.00 0.00 4.08
239 241 0.324285 ACTTGCCAGGCTCTCTCTTG 59.676 55.000 14.15 0.00 0.00 3.02
249 283 0.251297 TTGTGATCCCACTTGCCAGG 60.251 55.000 0.00 0.00 43.55 4.45
335 369 9.095065 GCGGAGGTCATTATTACGAAATTATAT 57.905 33.333 0.00 0.00 0.00 0.86
336 370 7.274033 CGCGGAGGTCATTATTACGAAATTATA 59.726 37.037 0.00 0.00 0.00 0.98
337 371 6.090358 CGCGGAGGTCATTATTACGAAATTAT 59.910 38.462 0.00 0.00 0.00 1.28
338 372 5.403166 CGCGGAGGTCATTATTACGAAATTA 59.597 40.000 0.00 0.00 0.00 1.40
339 373 4.210537 CGCGGAGGTCATTATTACGAAATT 59.789 41.667 0.00 0.00 0.00 1.82
341 375 3.117794 CGCGGAGGTCATTATTACGAAA 58.882 45.455 0.00 0.00 0.00 3.46
342 376 2.734670 CGCGGAGGTCATTATTACGAA 58.265 47.619 0.00 0.00 0.00 3.85
343 377 1.601162 GCGCGGAGGTCATTATTACGA 60.601 52.381 8.83 0.00 0.00 3.43
345 379 2.150397 AGCGCGGAGGTCATTATTAC 57.850 50.000 8.83 0.00 0.00 1.89
346 380 2.902705 AAGCGCGGAGGTCATTATTA 57.097 45.000 8.83 0.00 0.00 0.98
347 381 2.038387 AAAGCGCGGAGGTCATTATT 57.962 45.000 8.83 0.00 0.00 1.40
355 399 0.389948 AGAGTACAAAAGCGCGGAGG 60.390 55.000 8.83 0.00 0.00 4.30
373 417 1.202114 ACCATATTGGCGTTTGTGCAG 59.798 47.619 0.00 0.00 42.67 4.41
378 422 5.273170 CACAGAATACCATATTGGCGTTTG 58.727 41.667 0.00 0.00 42.67 2.93
399 444 4.947147 TTGCACGAGCCACCCCAC 62.947 66.667 1.39 0.00 41.13 4.61
451 507 2.614259 TCAGGTTCTCTTCTCTGGCTT 58.386 47.619 0.00 0.00 0.00 4.35
452 508 2.317371 TCAGGTTCTCTTCTCTGGCT 57.683 50.000 0.00 0.00 0.00 4.75
482 538 3.181399 TCCCTACCTTTCCCTTCTCTTCA 60.181 47.826 0.00 0.00 0.00 3.02
488 546 0.540454 CCGTCCCTACCTTTCCCTTC 59.460 60.000 0.00 0.00 0.00 3.46
491 549 1.306397 TCCCGTCCCTACCTTTCCC 60.306 63.158 0.00 0.00 0.00 3.97
492 550 0.325016 TCTCCCGTCCCTACCTTTCC 60.325 60.000 0.00 0.00 0.00 3.13
549 607 3.507009 GACGACGACGGGGAGGAG 61.507 72.222 12.58 0.00 44.46 3.69
550 608 3.557903 AAGACGACGACGGGGAGGA 62.558 63.158 12.58 0.00 44.46 3.71
629 689 4.410400 GGAGAGTGGGGTTGCGGG 62.410 72.222 0.00 0.00 0.00 6.13
634 694 1.541620 GGGGAAGGAGAGTGGGGTT 60.542 63.158 0.00 0.00 0.00 4.11
735 801 3.712907 CCGGGAGCTTTCGGGGAA 61.713 66.667 17.57 0.00 42.32 3.97
796 864 2.171725 GGAAGGGACGGCGAATTCG 61.172 63.158 23.34 23.34 43.27 3.34
835 905 1.533753 ACGGAAACTCCCCCACGTA 60.534 57.895 0.00 0.00 31.13 3.57
869 939 0.975040 AGGCTTTGTTTGGCACCACA 60.975 50.000 0.00 0.00 0.00 4.17
1158 1230 2.185350 AGGCGATTCAGGCTCACG 59.815 61.111 0.00 0.00 44.09 4.35
1185 1257 4.116585 AGGAGGAGGCGCTCGAGA 62.117 66.667 18.75 0.00 0.00 4.04
1289 1361 2.046892 GGAAGAAGGAGCTGCGCA 60.047 61.111 10.98 10.98 0.00 6.09
1297 1369 1.893801 GAAGAGGTCGTGGAAGAAGGA 59.106 52.381 0.00 0.00 0.00 3.36
1347 1419 2.125753 GAGGCAGAGGCAGTGACG 60.126 66.667 0.00 0.00 43.71 4.35
1449 1527 4.593864 GCTAGGAAGGCCTCGCGG 62.594 72.222 5.23 0.00 45.54 6.46
1464 1542 0.617820 AGAGGTACCCCATGAACGCT 60.618 55.000 8.74 0.00 0.00 5.07
1566 1644 3.908189 TCGACGGCGAACCTGATA 58.092 55.556 13.07 0.00 44.78 2.15
1599 1677 1.271840 CGGGGATCCTGAAGGTCCAA 61.272 60.000 12.58 0.00 37.22 3.53
1653 1731 5.122396 AGTTCTAAACAAGCCAATAAGAGCG 59.878 40.000 0.00 0.00 0.00 5.03
1710 1789 3.204526 CCTGAAGCTGCCAAGATTAGAG 58.795 50.000 0.00 0.00 30.45 2.43
1744 1836 3.133183 GGAGAAGGGTAGAACCATGAGTC 59.867 52.174 0.00 0.00 41.02 3.36
1745 1837 3.108376 GGAGAAGGGTAGAACCATGAGT 58.892 50.000 0.00 0.00 41.02 3.41
1746 1838 3.107601 TGGAGAAGGGTAGAACCATGAG 58.892 50.000 0.00 0.00 41.02 2.90
1747 1839 3.199442 TGGAGAAGGGTAGAACCATGA 57.801 47.619 0.00 0.00 41.02 3.07
1748 1840 4.510167 ATTGGAGAAGGGTAGAACCATG 57.490 45.455 0.00 0.00 41.02 3.66
1749 1841 5.222337 ACAAATTGGAGAAGGGTAGAACCAT 60.222 40.000 0.00 0.00 41.02 3.55
1750 1842 4.105697 ACAAATTGGAGAAGGGTAGAACCA 59.894 41.667 0.00 0.00 41.02 3.67
1751 1843 4.663334 ACAAATTGGAGAAGGGTAGAACC 58.337 43.478 0.00 0.00 37.60 3.62
1752 1844 6.650427 AAACAAATTGGAGAAGGGTAGAAC 57.350 37.500 0.00 0.00 0.00 3.01
1753 1845 8.950007 AATAAACAAATTGGAGAAGGGTAGAA 57.050 30.769 0.00 0.00 0.00 2.10
1754 1846 8.802267 CAAATAAACAAATTGGAGAAGGGTAGA 58.198 33.333 0.00 0.00 0.00 2.59
1755 1847 8.802267 TCAAATAAACAAATTGGAGAAGGGTAG 58.198 33.333 0.00 0.00 0.00 3.18
1800 1892 7.503521 TTCGAATTAGCATGCCAAATATACA 57.496 32.000 15.66 0.00 0.00 2.29
1830 1922 8.789881 TCATGTACCAAATTTACTGTTTTTCG 57.210 30.769 0.00 0.00 0.00 3.46
1887 1979 4.887655 AGAAAGAAAGGGTCGTGTGAAATT 59.112 37.500 0.00 0.00 0.00 1.82
1896 1988 2.037251 TCACCAGAGAAAGAAAGGGTCG 59.963 50.000 0.00 0.00 0.00 4.79
1989 2081 3.869832 GCAAAATAGGTAGGACGTCTTCC 59.130 47.826 16.46 14.58 46.33 3.46
2139 2231 1.492720 GCGGAGATTTCTGACGGATC 58.507 55.000 0.00 0.00 0.00 3.36
2145 2237 3.348647 TCAATTGGCGGAGATTTCTGA 57.651 42.857 5.42 0.00 0.00 3.27
2253 2345 6.791887 TCAGACTCATTAAGAAGCAACTTG 57.208 37.500 5.82 0.00 0.00 3.16
2490 2582 1.092921 TATTACTTGCAAGGCGGCCG 61.093 55.000 29.18 24.05 0.00 6.13
2547 2639 0.750911 CTTGGCCCTGCTCCATCTTC 60.751 60.000 0.00 0.00 32.92 2.87
2643 2735 2.375174 AGCCAATAAAGGTGAGGTGACA 59.625 45.455 0.00 0.00 0.00 3.58
2771 2863 1.856920 ACTTTTTCTCAACCTCCCCCA 59.143 47.619 0.00 0.00 0.00 4.96
2772 2864 2.677542 ACTTTTTCTCAACCTCCCCC 57.322 50.000 0.00 0.00 0.00 5.40
2823 2919 1.843376 ATATGCACCGGAGAGGGGG 60.843 63.158 9.46 0.00 46.01 5.40
2833 2929 6.540189 CCACCTATTTCTATAGCATATGCACC 59.460 42.308 28.62 0.29 45.16 5.01
2861 2957 2.223144 TCGAATGTGCAGCAAGTGTTAC 59.777 45.455 0.00 0.00 0.00 2.50
2870 2966 1.423056 GCAGAGTCGAATGTGCAGC 59.577 57.895 27.24 2.54 39.19 5.25
2890 2986 6.699575 ACATCTTATGAAAAGGGTGCATAC 57.300 37.500 0.00 0.00 0.00 2.39
2921 3017 0.529833 CGACTGCAGAGACCACAGAT 59.470 55.000 23.35 0.00 35.38 2.90
2952 3048 1.163554 GCTTCAGCAGGGAAGAACAG 58.836 55.000 14.59 0.00 45.66 3.16
2954 3050 0.320771 TCGCTTCAGCAGGGAAGAAC 60.321 55.000 14.59 0.57 45.66 3.01
2993 3089 0.530650 CTGGTGTGACGTCTGCTTGT 60.531 55.000 17.92 0.00 0.00 3.16
3101 3197 1.971167 TGCATCCACCCTTGAACGC 60.971 57.895 0.00 0.00 0.00 4.84
3107 3203 1.221840 CGCTAGTGCATCCACCCTT 59.778 57.895 0.00 0.00 43.09 3.95
3157 3253 5.595133 ACCGGACAAAGTAAAATTGAAAGGA 59.405 36.000 9.46 0.00 0.00 3.36
3158 3254 5.689961 CACCGGACAAAGTAAAATTGAAAGG 59.310 40.000 9.46 0.00 0.00 3.11
3159 3255 5.174943 GCACCGGACAAAGTAAAATTGAAAG 59.825 40.000 9.46 0.00 0.00 2.62
3237 3337 6.592607 TGGTTGTATTAACAGCTAGTAACAGC 59.407 38.462 0.00 0.00 42.12 4.40
3261 3361 5.147330 TCAGGTAGAAGGTTGTGTACATG 57.853 43.478 0.00 0.00 0.00 3.21
3276 3376 4.427312 ACGGCGTTAAGTTATTCAGGTAG 58.573 43.478 6.77 0.00 0.00 3.18
3282 3382 5.967088 CCCAATAAACGGCGTTAAGTTATTC 59.033 40.000 27.05 0.00 0.00 1.75
3294 3394 3.859411 TCAATGAACCCAATAAACGGC 57.141 42.857 0.00 0.00 0.00 5.68
3295 3395 7.862372 CAGAATATCAATGAACCCAATAAACGG 59.138 37.037 0.00 0.00 0.00 4.44
3296 3396 8.405531 ACAGAATATCAATGAACCCAATAAACG 58.594 33.333 0.00 0.00 0.00 3.60
3423 3523 8.717821 GTTGCAAAGACACATACTAGAAACATA 58.282 33.333 0.00 0.00 0.00 2.29
3501 3612 1.053048 CGTGTACACAGAACGAGCTG 58.947 55.000 24.98 7.54 39.64 4.24
3506 3617 1.053048 CTGCTCGTGTACACAGAACG 58.947 55.000 24.98 11.34 38.64 3.95
3520 3631 6.814506 ATAAATATGATTGCCAGACTGCTC 57.185 37.500 0.00 0.00 0.00 4.26
3661 3772 2.256461 CCGCTTTGCTGCTGGAAC 59.744 61.111 0.00 0.00 0.00 3.62
3718 3829 1.816863 GCACGTCCTCCTTCACCTCA 61.817 60.000 0.00 0.00 0.00 3.86
3781 3892 1.671379 GGAGTTTGACGACAGGGCC 60.671 63.158 0.00 0.00 0.00 5.80
3802 3913 0.108804 TTCACTTCATCGCCGAGGAC 60.109 55.000 0.00 0.00 0.00 3.85
3845 3956 2.223923 CCTCTTTAGCCCTGACATCTCG 60.224 54.545 0.00 0.00 0.00 4.04
3857 3968 0.466124 ACCAGCGATCCCTCTTTAGC 59.534 55.000 0.00 0.00 0.00 3.09
3912 4023 4.023707 GGCCTCCTTTCATGTTCATATTCG 60.024 45.833 0.00 0.00 0.00 3.34
3961 4072 3.096092 ACAAACTCCAAGTCCAGCAAAA 58.904 40.909 0.00 0.00 0.00 2.44
4041 4154 0.598680 GATCCATGGCTCCGTCTTCG 60.599 60.000 6.96 0.00 0.00 3.79
4055 4168 0.103026 CGTCGAAGCTGGATGATCCA 59.897 55.000 14.42 14.42 45.98 3.41
4143 4256 3.386402 AGCCTCAATTGCCTACTACTCTC 59.614 47.826 0.00 0.00 0.00 3.20
4144 4257 3.133721 CAGCCTCAATTGCCTACTACTCT 59.866 47.826 0.00 0.00 0.00 3.24
4155 4271 1.667724 CTTCCGCTACAGCCTCAATTG 59.332 52.381 0.00 0.00 37.91 2.32
4156 4272 1.279271 ACTTCCGCTACAGCCTCAATT 59.721 47.619 0.00 0.00 37.91 2.32
4217 4333 8.144155 TGTATTGATAACAACAGTTCGACAAA 57.856 30.769 0.00 0.00 38.90 2.83
4276 4394 0.673985 TGCACTGGCGCTATACTAGG 59.326 55.000 7.64 0.00 45.35 3.02
4316 4434 4.273148 ACTCGTTATGGTCTTGCTCTTT 57.727 40.909 0.00 0.00 0.00 2.52
4327 4445 4.858692 CCAAAGCAAATGAACTCGTTATGG 59.141 41.667 0.00 0.00 0.00 2.74
4333 4451 4.424061 TGATCCAAAGCAAATGAACTCG 57.576 40.909 0.00 0.00 0.00 4.18
4377 4495 6.204688 TGGATCAAAGGCAATATGTCGTTATC 59.795 38.462 0.00 0.00 0.00 1.75
4389 4507 6.589523 CGACAATTAATTTGGATCAAAGGCAA 59.410 34.615 0.00 0.00 39.80 4.52
4391 4509 5.005682 GCGACAATTAATTTGGATCAAAGGC 59.994 40.000 0.00 0.00 39.80 4.35
4396 4514 5.182950 AGTGTGCGACAATTAATTTGGATCA 59.817 36.000 0.00 0.00 39.80 2.92
4405 4523 4.127907 TGTACCAAGTGTGCGACAATTAA 58.872 39.130 2.53 0.00 33.79 1.40
4470 4588 5.684030 GCGAGAAATGTTACTCCCTTGGATA 60.684 44.000 0.00 0.00 0.00 2.59
4474 4592 3.600388 AGCGAGAAATGTTACTCCCTTG 58.400 45.455 0.00 0.00 0.00 3.61
4475 4593 3.983044 AGCGAGAAATGTTACTCCCTT 57.017 42.857 0.00 0.00 0.00 3.95
4555 5114 3.628008 TGCCTCTGATCTTGCATTGAAT 58.372 40.909 0.00 0.00 0.00 2.57
4562 5121 2.105006 TGTCTTGCCTCTGATCTTGC 57.895 50.000 0.00 0.00 0.00 4.01
4570 5129 9.540538 AGTAGTATTATATGATGTCTTGCCTCT 57.459 33.333 0.00 0.00 0.00 3.69
4590 5149 8.410673 TGAAAAATTGGGCACAATAAGTAGTA 57.589 30.769 16.06 0.00 46.25 1.82
4591 5150 7.232534 TCTGAAAAATTGGGCACAATAAGTAGT 59.767 33.333 16.06 0.00 46.25 2.73
4592 5151 7.601856 TCTGAAAAATTGGGCACAATAAGTAG 58.398 34.615 16.06 10.11 46.25 2.57
4616 5175 3.188460 TGGAAACTATGCGCAAGAAGTTC 59.812 43.478 26.36 19.82 35.99 3.01
4627 5186 8.611757 AGTGTTTCAAAAATTTGGAAACTATGC 58.388 29.630 28.52 19.24 37.40 3.14
4641 5200 8.545229 AAAACATCACATGAGTGTTTCAAAAA 57.455 26.923 19.85 0.00 43.14 1.94
4645 5204 5.359292 TGGAAAACATCACATGAGTGTTTCA 59.641 36.000 19.85 14.66 43.14 2.69
4673 5232 6.254281 AGTTTTCCATTCATAAACGTCCAG 57.746 37.500 0.00 0.00 36.98 3.86
4675 5234 8.241367 ACATAAGTTTTCCATTCATAAACGTCC 58.759 33.333 0.00 0.00 36.98 4.79
4798 5368 3.286329 AACACAACCTAAGTTTCCCGT 57.714 42.857 0.00 0.00 32.45 5.28


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

AutoCloner maintained by Alex Coulton.