Multiple sequence alignment - TraesCS2D01G217100

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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 TraesCS2D01G217100 chr2D 100.000 4518 0 0 656 5173 180141156 180136639 0.000000e+00 8344
1 TraesCS2D01G217100 chr2D 100.000 281 0 0 1 281 180141811 180141531 2.130000e-143 520
2 TraesCS2D01G217100 chr2D 73.995 746 166 23 1727 2458 180327064 180326333 1.420000e-70 278
3 TraesCS2D01G217100 chr2D 77.251 422 87 6 2617 3032 639396750 639397168 6.690000e-59 239
4 TraesCS2D01G217100 chr2A 94.661 4252 160 35 661 4882 194474850 194470636 0.000000e+00 6532
5 TraesCS2D01G217100 chr2A 95.187 187 7 2 96 281 194475088 194474903 1.410000e-75 294
6 TraesCS2D01G217100 chr2A 77.778 387 85 1 2671 3056 765040628 765041014 2.410000e-58 237
7 TraesCS2D01G217100 chr2A 92.414 145 6 1 5028 5172 194470627 194470488 8.780000e-48 202
8 TraesCS2D01G217100 chr2A 95.062 81 1 2 1 80 194475609 194475531 1.960000e-24 124
9 TraesCS2D01G217100 chr2B 95.481 3430 108 25 1506 4903 236807775 236804361 0.000000e+00 5432
10 TraesCS2D01G217100 chr2B 91.581 879 31 16 656 1507 236808715 236807853 0.000000e+00 1173
11 TraesCS2D01G217100 chr2B 94.662 281 9 4 1 281 236809035 236808761 1.030000e-116 431
12 TraesCS2D01G217100 chr2B 77.378 389 88 0 2671 3059 798614225 798613837 1.120000e-56 231
13 TraesCS2D01G217100 chr7A 77.436 390 86 2 2671 3059 727431451 727431063 1.120000e-56 231
14 TraesCS2D01G217100 chr7D 80.479 292 57 0 2768 3059 638473617 638473908 1.870000e-54 224
15 TraesCS2D01G217100 chrUn 76.864 389 88 2 2671 3058 317233691 317233304 8.720000e-53 219
16 TraesCS2D01G217100 chr7B 76.864 389 88 2 2671 3058 734250249 734249862 8.720000e-53 219


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 TraesCS2D01G217100 chr2D 180136639 180141811 5172 True 4432.000000 8344 100.000 1 5173 2 chr2D.!!$R2 5172
1 TraesCS2D01G217100 chr2D 180326333 180327064 731 True 278.000000 278 73.995 1727 2458 1 chr2D.!!$R1 731
2 TraesCS2D01G217100 chr2A 194470488 194475609 5121 True 1788.000000 6532 94.331 1 5172 4 chr2A.!!$R1 5171
3 TraesCS2D01G217100 chr2B 236804361 236809035 4674 True 2345.333333 5432 93.908 1 4903 3 chr2B.!!$R2 4902

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
94 96 0.458025 GCAGTCACAGGCGGTAGTAC 60.458 60.0 0.00 0.00 0.00 2.73 F
95 97 0.885879 CAGTCACAGGCGGTAGTACA 59.114 55.0 2.06 0.00 0.00 2.90 F
1231 1678 0.094730 GTAAGCGCGTCCACATTCAC 59.905 55.0 8.43 0.00 0.00 3.18 F
1236 1683 0.999406 CGCGTCCACATTCACCTTAG 59.001 55.0 0.00 0.00 0.00 2.18 F
2915 3470 0.599204 TCCCTCAACGCTTCGACAAC 60.599 55.0 0.00 0.00 0.00 3.32 F
2933 3488 0.175760 ACGTTGATCCATCAGACCGG 59.824 55.0 0.00 0.00 38.19 5.28 F
3224 3779 0.663153 GGGTTGTGTCAGCTTCACAC 59.337 55.0 17.63 16.81 43.95 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1162 1609 0.319211 TTGTACGTCCGGAACAGCAG 60.319 55.000 5.23 0.00 0.00 4.24 R
1797 2349 1.068417 CGTCCCCGACAACTGACAA 59.932 57.895 0.00 0.00 35.63 3.18 R
2915 3470 0.175760 ACCGGTCTGATGGATCAACG 59.824 55.000 0.00 0.00 36.18 4.10 R
2933 3488 0.239879 CACGGTTGTGGTTGCCATAC 59.760 55.000 0.00 0.00 42.59 2.39 R
3845 4400 0.301687 GCATGTCATACAAGTCGGCG 59.698 55.000 0.00 0.00 0.00 6.46 R
3989 4544 0.401356 TGAAGAGCAGACCCAATGCA 59.599 50.000 0.00 0.00 46.31 3.96 R
5026 5605 0.114954 AATTGGGCCGGCCATATCAT 59.885 50.000 44.46 25.14 37.98 2.45 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
82 84 2.947890 GCAGTCACAGCGCAGTCAC 61.948 63.158 11.47 3.85 0.00 3.67
86 88 3.720193 CACAGCGCAGTCACAGGC 61.720 66.667 11.47 0.00 0.00 4.85
92 94 2.657237 GCAGTCACAGGCGGTAGT 59.343 61.111 0.00 0.00 0.00 2.73
93 95 1.888018 GCAGTCACAGGCGGTAGTA 59.112 57.895 0.00 0.00 0.00 1.82
94 96 0.458025 GCAGTCACAGGCGGTAGTAC 60.458 60.000 0.00 0.00 0.00 2.73
95 97 0.885879 CAGTCACAGGCGGTAGTACA 59.114 55.000 2.06 0.00 0.00 2.90
96 98 1.135373 CAGTCACAGGCGGTAGTACAG 60.135 57.143 2.06 0.00 0.00 2.74
97 99 0.886563 GTCACAGGCGGTAGTACAGT 59.113 55.000 2.06 0.00 0.00 3.55
99 101 2.097142 GTCACAGGCGGTAGTACAGTAG 59.903 54.545 2.06 0.00 0.00 2.57
100 102 2.089980 CACAGGCGGTAGTACAGTAGT 58.910 52.381 2.06 0.00 0.00 2.73
101 103 3.055167 TCACAGGCGGTAGTACAGTAGTA 60.055 47.826 2.06 0.00 0.00 1.82
168 598 1.142778 GCGACGCAGGCAAAACAAAA 61.143 50.000 16.42 0.00 0.00 2.44
798 1229 2.955660 ACAGATCTCGAGTGGATTCCTC 59.044 50.000 13.13 0.00 0.00 3.71
801 1232 2.534042 TCTCGAGTGGATTCCTCCTT 57.466 50.000 13.13 0.00 42.59 3.36
934 1365 4.962836 GTGCACCACTGGCTGGCT 62.963 66.667 5.22 0.00 45.32 4.75
935 1366 4.960866 TGCACCACTGGCTGGCTG 62.961 66.667 6.56 6.56 45.32 4.85
1221 1668 2.718073 CCCCTACAGGTAAGCGCGT 61.718 63.158 8.43 0.00 0.00 6.01
1223 1670 1.226888 CCTACAGGTAAGCGCGTCC 60.227 63.158 8.43 4.61 0.00 4.79
1225 1672 0.801067 CTACAGGTAAGCGCGTCCAC 60.801 60.000 8.43 2.50 0.00 4.02
1226 1673 1.525718 TACAGGTAAGCGCGTCCACA 61.526 55.000 8.43 3.14 0.00 4.17
1227 1674 1.447838 CAGGTAAGCGCGTCCACAT 60.448 57.895 8.43 0.00 0.00 3.21
1228 1675 1.019278 CAGGTAAGCGCGTCCACATT 61.019 55.000 8.43 1.68 0.00 2.71
1229 1676 0.739813 AGGTAAGCGCGTCCACATTC 60.740 55.000 8.43 0.00 0.00 2.67
1231 1678 0.094730 GTAAGCGCGTCCACATTCAC 59.905 55.000 8.43 0.00 0.00 3.18
1233 1680 2.731691 AAGCGCGTCCACATTCACCT 62.732 55.000 8.43 0.00 0.00 4.00
1234 1681 2.325082 GCGCGTCCACATTCACCTT 61.325 57.895 8.43 0.00 0.00 3.50
1235 1682 1.017177 GCGCGTCCACATTCACCTTA 61.017 55.000 8.43 0.00 0.00 2.69
1236 1683 0.999406 CGCGTCCACATTCACCTTAG 59.001 55.000 0.00 0.00 0.00 2.18
1240 1687 2.993899 CGTCCACATTCACCTTAGACAC 59.006 50.000 0.00 0.00 0.00 3.67
1269 1729 4.220602 TGGTTCTCTTCTGACATTGATCGA 59.779 41.667 0.00 0.00 0.00 3.59
1275 1735 2.207590 TCTGACATTGATCGATGCTGC 58.792 47.619 20.95 12.08 0.00 5.25
1276 1736 1.263484 CTGACATTGATCGATGCTGCC 59.737 52.381 20.95 9.71 0.00 4.85
1280 1740 1.534163 CATTGATCGATGCTGCCGAAT 59.466 47.619 10.05 0.00 39.62 3.34
1320 1781 5.879777 ACTTTGATTTTTGGGGTTTGACTTG 59.120 36.000 0.00 0.00 0.00 3.16
1404 1867 7.939782 TCATGAAACATCATGTAACAGTGTTT 58.060 30.769 14.90 2.39 45.53 2.83
1405 1868 9.061435 TCATGAAACATCATGTAACAGTGTTTA 57.939 29.630 14.90 4.46 45.53 2.01
1406 1869 9.117145 CATGAAACATCATGTAACAGTGTTTAC 57.883 33.333 14.90 10.59 41.50 2.01
1436 1899 3.385193 GCCAAAAGCATGTAAAGGTGT 57.615 42.857 0.00 0.00 42.97 4.16
1438 1901 3.740832 GCCAAAAGCATGTAAAGGTGTTC 59.259 43.478 0.00 0.00 42.97 3.18
1458 1923 7.298854 GTGTTCTCTGACTTATAAGCCAAAAC 58.701 38.462 12.54 11.75 0.00 2.43
1469 1934 8.691797 ACTTATAAGCCAAAACTCAAAAGTCAA 58.308 29.630 12.54 0.00 33.48 3.18
1552 2097 6.119536 CCATAGTGTTTTGCCTGTATCCTAA 58.880 40.000 0.00 0.00 0.00 2.69
1579 2124 6.348868 GGCTTCTTAACTGAATTCTGTTCCAG 60.349 42.308 27.65 23.53 38.62 3.86
1676 2222 8.450578 AATGGCATTAGTTCGATCAAGAAATA 57.549 30.769 11.81 0.00 30.68 1.40
1677 2223 7.857734 TGGCATTAGTTCGATCAAGAAATAA 57.142 32.000 5.95 5.95 42.34 1.40
1763 2315 2.017138 TCTTCGTATGGCGCATCAAA 57.983 45.000 10.83 0.00 41.07 2.69
1797 2349 6.425735 TCTGATATCATGTGGTTTTGGACAT 58.574 36.000 5.72 0.00 32.90 3.06
1897 2449 2.404559 ACCTGATATGGTCGCCCTTAA 58.595 47.619 0.00 0.00 34.86 1.85
2105 2657 1.376037 CGAGGCCTTGGTTGAGACC 60.376 63.158 12.81 0.00 46.71 3.85
2222 2774 2.777536 TGGAAGTGCACCAGAGGAT 58.222 52.632 14.63 0.00 33.22 3.24
2286 2838 5.918608 AGTTCAAAGAGCACTTAGACTCAA 58.081 37.500 0.00 0.00 35.05 3.02
2464 3016 8.747538 ATTGTTAAGGTATACAAGTTCATCCC 57.252 34.615 5.01 0.00 37.64 3.85
2538 3090 9.268268 CATACTCTCGGTAAGCCAAATTTATTA 57.732 33.333 0.00 0.00 33.74 0.98
2542 3094 5.992729 TCGGTAAGCCAAATTTATTATCGC 58.007 37.500 13.62 1.62 33.03 4.58
2546 3098 5.508200 AAGCCAAATTTATTATCGCGGAA 57.492 34.783 6.13 0.66 0.00 4.30
2553 3105 9.061610 CCAAATTTATTATCGCGGAAATATGTC 57.938 33.333 6.13 0.00 0.00 3.06
2554 3106 9.825972 CAAATTTATTATCGCGGAAATATGTCT 57.174 29.630 6.13 0.00 0.00 3.41
2624 3179 2.364632 CGTGGGCATAATCTTGGTTCA 58.635 47.619 0.00 0.00 0.00 3.18
2627 3182 3.129287 GTGGGCATAATCTTGGTTCACAG 59.871 47.826 0.00 0.00 0.00 3.66
2637 3192 1.827789 GGTTCACAGGCAAGCACCA 60.828 57.895 0.00 0.00 0.00 4.17
2696 3251 5.066634 CCCGATGCTTGTATATATCTCTCGT 59.933 44.000 0.00 0.00 0.00 4.18
2732 3287 3.366374 GCTATGACCACAACAAGAAAGCC 60.366 47.826 0.00 0.00 0.00 4.35
2798 3353 3.173599 CGCGCAATTCATCATCAACTTT 58.826 40.909 8.75 0.00 0.00 2.66
2915 3470 0.599204 TCCCTCAACGCTTCGACAAC 60.599 55.000 0.00 0.00 0.00 3.32
2933 3488 0.175760 ACGTTGATCCATCAGACCGG 59.824 55.000 0.00 0.00 38.19 5.28
3188 3743 4.158394 CCTCCACCCATTAGTGAAACATTG 59.842 45.833 0.00 0.00 41.43 2.82
3224 3779 0.663153 GGGTTGTGTCAGCTTCACAC 59.337 55.000 17.63 16.81 43.95 3.82
3350 3905 4.765273 TGTATTGTACAATGGAGCGTGAT 58.235 39.130 27.62 4.00 35.38 3.06
3470 4025 0.809385 CACTCATAGGTGGTCGTCGT 59.191 55.000 0.00 0.00 33.95 4.34
3477 4032 0.815734 AGGTGGTCGTCGTATCCAAG 59.184 55.000 7.77 0.00 32.82 3.61
3557 4112 1.539388 CTACTCTATGCTCTCAGCCCG 59.461 57.143 0.00 0.00 41.51 6.13
3707 4262 3.713826 TGGTTGGATTACTGGAGGAAC 57.286 47.619 0.00 0.00 0.00 3.62
3731 4286 2.834549 ACAGTTCTTCATGATCGGGTCT 59.165 45.455 0.00 0.00 0.00 3.85
3845 4400 2.030805 GGCAGACACCAATGACAAGTTC 60.031 50.000 0.00 0.00 0.00 3.01
3989 4544 1.971481 TTGCACAGAAGACACATGCT 58.029 45.000 0.00 0.00 37.20 3.79
4109 4664 1.007387 CTTGTTGCCGGTTGCCTTC 60.007 57.895 1.90 0.00 40.16 3.46
4339 4895 6.632834 GCTAATGTCACAACTTACAAGTGTTG 59.367 38.462 0.00 0.00 46.19 3.33
4405 4961 4.219070 TGCAATCTTTGAGCTACAAATGCT 59.781 37.500 22.06 0.00 44.93 3.79
4429 4985 4.970662 AAACAGGATGATCAATCGTTGG 57.029 40.909 0.00 0.00 39.69 3.77
4584 5149 5.991933 TCAGAGTTCAGAGAAGCACTATT 57.008 39.130 0.00 0.00 0.00 1.73
4704 5275 4.222124 AGAATAGCAACCGTCTTGGATT 57.778 40.909 0.00 0.00 42.00 3.01
4717 5288 5.574055 CCGTCTTGGATTTCATTGACATTTG 59.426 40.000 0.00 0.00 42.00 2.32
4727 5298 3.252215 TCATTGACATTTGACCGAACACC 59.748 43.478 0.00 0.00 0.00 4.16
4762 5339 7.593825 CCTCACCGAACAAGAAAAATTATCTT 58.406 34.615 1.57 1.57 37.62 2.40
4806 5385 8.977505 CATATGTTTTCTTTTGAAATTCGGTGT 58.022 29.630 0.00 0.00 46.43 4.16
4813 5392 7.278461 TCTTTTGAAATTCGGTGTAAATGGA 57.722 32.000 0.00 0.00 0.00 3.41
4831 5410 4.996434 AGCTCACGTGTGGCCTGC 62.996 66.667 24.11 15.95 0.00 4.85
4843 5422 4.899239 GCCTGCGGAGATGACGGG 62.899 72.222 5.10 0.00 0.00 5.28
4858 5437 2.449777 GGGGCCAAGGAATTGGGT 59.550 61.111 4.39 0.00 42.31 4.51
4860 5439 1.552799 GGGGCCAAGGAATTGGGTTG 61.553 60.000 4.39 0.00 42.31 3.77
4882 5461 2.107546 AACGAGTTTGCCGGACGT 59.892 55.556 5.05 3.40 38.81 4.34
4888 5467 1.370051 GTTTGCCGGACGTGAAAGC 60.370 57.895 5.05 0.00 0.00 3.51
4903 5482 2.185310 AAAGCCGGAATCGCTCCTGT 62.185 55.000 5.05 0.00 42.85 4.00
4904 5483 2.859273 AAGCCGGAATCGCTCCTGTG 62.859 60.000 5.05 0.00 42.85 3.66
4905 5484 2.579201 CCGGAATCGCTCCTGTGT 59.421 61.111 0.00 0.00 42.85 3.72
4906 5485 1.519455 CCGGAATCGCTCCTGTGTC 60.519 63.158 0.00 0.00 42.85 3.67
4907 5486 1.215382 CGGAATCGCTCCTGTGTCA 59.785 57.895 2.40 0.00 42.85 3.58
4908 5487 0.803768 CGGAATCGCTCCTGTGTCAG 60.804 60.000 2.40 0.00 42.85 3.51
4909 5488 0.247736 GGAATCGCTCCTGTGTCAGT 59.752 55.000 0.00 0.00 41.61 3.41
4910 5489 1.476891 GGAATCGCTCCTGTGTCAGTA 59.523 52.381 0.00 0.00 41.61 2.74
4911 5490 2.480416 GGAATCGCTCCTGTGTCAGTAG 60.480 54.545 0.00 0.00 41.61 2.57
4912 5491 0.457851 ATCGCTCCTGTGTCAGTAGC 59.542 55.000 4.62 4.62 39.53 3.58
4913 5492 0.893727 TCGCTCCTGTGTCAGTAGCA 60.894 55.000 13.05 0.69 42.34 3.49
4914 5493 0.038251 CGCTCCTGTGTCAGTAGCAA 60.038 55.000 13.05 0.00 42.34 3.91
4915 5494 1.605457 CGCTCCTGTGTCAGTAGCAAA 60.605 52.381 13.05 0.00 42.34 3.68
4916 5495 2.494059 GCTCCTGTGTCAGTAGCAAAA 58.506 47.619 8.94 0.00 41.92 2.44
4917 5496 2.481952 GCTCCTGTGTCAGTAGCAAAAG 59.518 50.000 8.94 0.00 41.92 2.27
4918 5497 3.733337 CTCCTGTGTCAGTAGCAAAAGT 58.267 45.455 0.00 0.00 0.00 2.66
4919 5498 4.130118 CTCCTGTGTCAGTAGCAAAAGTT 58.870 43.478 0.00 0.00 0.00 2.66
4920 5499 4.523083 TCCTGTGTCAGTAGCAAAAGTTT 58.477 39.130 0.00 0.00 0.00 2.66
4921 5500 4.947388 TCCTGTGTCAGTAGCAAAAGTTTT 59.053 37.500 0.00 0.00 0.00 2.43
4922 5501 5.417580 TCCTGTGTCAGTAGCAAAAGTTTTT 59.582 36.000 0.00 0.00 0.00 1.94
4948 5527 6.995511 TTTAACTGTGTCACTAGCAAAAGT 57.004 33.333 4.27 0.00 0.00 2.66
4949 5528 6.995511 TTAACTGTGTCACTAGCAAAAGTT 57.004 33.333 4.27 6.23 32.95 2.66
4950 5529 8.495361 TTTAACTGTGTCACTAGCAAAAGTTA 57.505 30.769 4.27 5.31 31.64 2.24
4951 5530 8.671384 TTAACTGTGTCACTAGCAAAAGTTAT 57.329 30.769 4.27 0.00 32.37 1.89
4952 5531 6.787085 ACTGTGTCACTAGCAAAAGTTATC 57.213 37.500 4.27 0.00 0.00 1.75
4953 5532 6.288294 ACTGTGTCACTAGCAAAAGTTATCA 58.712 36.000 4.27 0.00 0.00 2.15
4954 5533 6.425114 ACTGTGTCACTAGCAAAAGTTATCAG 59.575 38.462 4.27 0.00 0.00 2.90
4955 5534 6.521162 TGTGTCACTAGCAAAAGTTATCAGA 58.479 36.000 4.27 0.00 0.00 3.27
4956 5535 6.646653 TGTGTCACTAGCAAAAGTTATCAGAG 59.353 38.462 4.27 0.00 0.00 3.35
4957 5536 6.868864 GTGTCACTAGCAAAAGTTATCAGAGA 59.131 38.462 0.00 0.00 0.00 3.10
4958 5537 7.385205 GTGTCACTAGCAAAAGTTATCAGAGAA 59.615 37.037 0.00 0.00 0.00 2.87
4959 5538 7.600375 TGTCACTAGCAAAAGTTATCAGAGAAG 59.400 37.037 0.00 0.00 0.00 2.85
4960 5539 7.815068 GTCACTAGCAAAAGTTATCAGAGAAGA 59.185 37.037 0.00 0.00 0.00 2.87
4961 5540 7.815068 TCACTAGCAAAAGTTATCAGAGAAGAC 59.185 37.037 0.00 0.00 0.00 3.01
4962 5541 7.064016 CACTAGCAAAAGTTATCAGAGAAGACC 59.936 40.741 0.00 0.00 0.00 3.85
4963 5542 4.932200 AGCAAAAGTTATCAGAGAAGACCG 59.068 41.667 0.00 0.00 0.00 4.79
4964 5543 4.093556 GCAAAAGTTATCAGAGAAGACCGG 59.906 45.833 0.00 0.00 0.00 5.28
4965 5544 5.238583 CAAAAGTTATCAGAGAAGACCGGT 58.761 41.667 6.92 6.92 0.00 5.28
4966 5545 4.457834 AAGTTATCAGAGAAGACCGGTG 57.542 45.455 14.63 0.00 0.00 4.94
4967 5546 2.761208 AGTTATCAGAGAAGACCGGTGG 59.239 50.000 14.63 0.00 0.00 4.61
4968 5547 2.496470 GTTATCAGAGAAGACCGGTGGT 59.504 50.000 14.63 0.00 39.44 4.16
4969 5548 1.645710 ATCAGAGAAGACCGGTGGTT 58.354 50.000 14.63 4.81 35.25 3.67
4970 5549 1.420430 TCAGAGAAGACCGGTGGTTT 58.580 50.000 14.63 2.98 35.25 3.27
4971 5550 2.600790 TCAGAGAAGACCGGTGGTTTA 58.399 47.619 14.63 0.00 35.25 2.01
4972 5551 2.298163 TCAGAGAAGACCGGTGGTTTAC 59.702 50.000 14.63 0.00 35.25 2.01
4973 5552 1.622312 AGAGAAGACCGGTGGTTTACC 59.378 52.381 14.63 0.00 46.56 2.85
5067 5646 3.071874 TGTTTCATGAAGCTCCGGATT 57.928 42.857 21.00 0.00 0.00 3.01
5087 5666 5.351740 GGATTTATAGCGGGCTGAGTATTTC 59.648 44.000 2.86 0.00 0.00 2.17
5092 5671 0.249489 CGGGCTGAGTATTTCGAGGG 60.249 60.000 0.00 0.00 0.00 4.30
5097 5676 1.757118 CTGAGTATTTCGAGGGCCAGA 59.243 52.381 6.18 1.01 0.00 3.86
5101 5680 1.134907 GTATTTCGAGGGCCAGACGAA 60.135 52.381 22.09 22.09 42.70 3.85
5123 5702 3.506108 CTGGCGAAGGATGCAAGG 58.494 61.111 0.00 0.00 29.33 3.61
5127 5706 0.965363 GGCGAAGGATGCAAGGGAAA 60.965 55.000 0.00 0.00 0.00 3.13
5128 5707 0.171231 GCGAAGGATGCAAGGGAAAC 59.829 55.000 0.00 0.00 0.00 2.78
5129 5708 0.447801 CGAAGGATGCAAGGGAAACG 59.552 55.000 0.00 0.00 0.00 3.60
5130 5709 1.821216 GAAGGATGCAAGGGAAACGA 58.179 50.000 0.00 0.00 0.00 3.85
5131 5710 2.159382 GAAGGATGCAAGGGAAACGAA 58.841 47.619 0.00 0.00 0.00 3.85
5162 5741 5.732633 TGTTGGGCATGGATTTATTTTCAG 58.267 37.500 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 5.545588 TCTATACTACTGTACTACCGCCTG 58.454 45.833 0.00 0.00 0.00 4.85
86 88 6.625362 TCCGATCTATACTACTGTACTACCG 58.375 44.000 0.00 0.00 0.00 4.02
87 89 7.434897 CGATCCGATCTATACTACTGTACTACC 59.565 44.444 6.81 0.00 0.00 3.18
88 90 7.973388 ACGATCCGATCTATACTACTGTACTAC 59.027 40.741 6.81 0.00 0.00 2.73
89 91 8.060931 ACGATCCGATCTATACTACTGTACTA 57.939 38.462 6.81 0.00 0.00 1.82
92 94 6.091849 GCAACGATCCGATCTATACTACTGTA 59.908 42.308 6.81 0.00 0.00 2.74
93 95 5.106634 GCAACGATCCGATCTATACTACTGT 60.107 44.000 6.81 0.00 0.00 3.55
94 96 5.106673 TGCAACGATCCGATCTATACTACTG 60.107 44.000 6.81 0.00 0.00 2.74
95 97 5.001874 TGCAACGATCCGATCTATACTACT 58.998 41.667 6.81 0.00 0.00 2.57
96 98 5.087397 GTGCAACGATCCGATCTATACTAC 58.913 45.833 6.81 0.00 0.00 2.73
97 99 4.155462 GGTGCAACGATCCGATCTATACTA 59.845 45.833 6.81 0.00 38.12 1.82
99 101 3.243336 GGTGCAACGATCCGATCTATAC 58.757 50.000 6.81 0.00 38.12 1.47
100 102 2.888414 TGGTGCAACGATCCGATCTATA 59.112 45.455 6.81 0.00 38.12 1.31
101 103 1.686587 TGGTGCAACGATCCGATCTAT 59.313 47.619 6.81 0.00 38.12 1.98
168 598 2.436646 CGCGGAAGGTCAGGCATT 60.437 61.111 0.00 0.00 0.00 3.56
200 630 4.274950 GGTCAAGCAAGCACAGTTAGTTTA 59.725 41.667 0.00 0.00 0.00 2.01
933 1364 2.329678 CTACGACTCGAGCCAGCCAG 62.330 65.000 13.61 0.00 0.00 4.85
934 1365 2.360726 TACGACTCGAGCCAGCCA 60.361 61.111 13.61 0.00 0.00 4.75
935 1366 2.409651 CTACGACTCGAGCCAGCC 59.590 66.667 13.61 0.00 0.00 4.85
936 1367 2.272918 AAGCTACGACTCGAGCCAGC 62.273 60.000 13.61 15.23 39.65 4.85
1162 1609 0.319211 TTGTACGTCCGGAACAGCAG 60.319 55.000 5.23 0.00 0.00 4.24
1221 1668 4.698201 TTGTGTCTAAGGTGAATGTGGA 57.302 40.909 0.00 0.00 0.00 4.02
1223 1670 6.144854 CACATTTGTGTCTAAGGTGAATGTG 58.855 40.000 10.64 10.64 43.29 3.21
1225 1672 5.241506 ACCACATTTGTGTCTAAGGTGAATG 59.758 40.000 9.66 0.00 44.21 2.67
1226 1673 5.385198 ACCACATTTGTGTCTAAGGTGAAT 58.615 37.500 9.66 0.00 44.21 2.57
1227 1674 4.787551 ACCACATTTGTGTCTAAGGTGAA 58.212 39.130 9.66 0.00 44.21 3.18
1228 1675 4.431416 ACCACATTTGTGTCTAAGGTGA 57.569 40.909 9.66 0.00 44.21 4.02
1229 1676 4.821805 AGAACCACATTTGTGTCTAAGGTG 59.178 41.667 9.66 0.00 44.21 4.00
1231 1678 5.308825 AGAGAACCACATTTGTGTCTAAGG 58.691 41.667 9.66 0.00 44.21 2.69
1233 1680 6.483307 CAGAAGAGAACCACATTTGTGTCTAA 59.517 38.462 9.66 0.00 44.21 2.10
1234 1681 5.991606 CAGAAGAGAACCACATTTGTGTCTA 59.008 40.000 9.66 0.00 44.21 2.59
1235 1682 4.818546 CAGAAGAGAACCACATTTGTGTCT 59.181 41.667 9.66 6.72 44.21 3.41
1236 1683 4.816385 TCAGAAGAGAACCACATTTGTGTC 59.184 41.667 9.66 2.18 44.21 3.67
1240 1687 5.954296 ATGTCAGAAGAGAACCACATTTG 57.046 39.130 0.00 0.00 0.00 2.32
1248 1708 5.276773 GCATCGATCAATGTCAGAAGAGAAC 60.277 44.000 0.00 0.00 0.00 3.01
1251 1711 4.209495 CAGCATCGATCAATGTCAGAAGAG 59.791 45.833 0.00 0.00 0.00 2.85
1269 1729 3.501396 CCGTCAATTCGGCAGCAT 58.499 55.556 0.00 0.00 43.96 3.79
1276 1736 5.464965 AGTTAAGCATAACCGTCAATTCG 57.535 39.130 8.17 0.00 41.98 3.34
1280 1740 6.811253 ATCAAAGTTAAGCATAACCGTCAA 57.189 33.333 8.17 0.00 41.98 3.18
1348 1811 3.320673 AAAACAAACCCAAAAGCACGA 57.679 38.095 0.00 0.00 0.00 4.35
1399 1862 7.223777 TGCTTTTGGCTTTGAATTAGTAAACAC 59.776 33.333 0.00 0.00 42.39 3.32
1404 1867 6.991938 ACATGCTTTTGGCTTTGAATTAGTA 58.008 32.000 0.00 0.00 42.39 1.82
1405 1868 5.857268 ACATGCTTTTGGCTTTGAATTAGT 58.143 33.333 0.00 0.00 42.39 2.24
1406 1869 7.887996 TTACATGCTTTTGGCTTTGAATTAG 57.112 32.000 0.00 0.00 42.39 1.73
1436 1899 7.450074 TGAGTTTTGGCTTATAAGTCAGAGAA 58.550 34.615 18.60 12.52 42.31 2.87
1438 1901 7.672983 TTGAGTTTTGGCTTATAAGTCAGAG 57.327 36.000 18.60 0.00 42.31 3.35
1458 1923 9.297586 GGTTAGGTTTAACTTTTGACTTTTGAG 57.702 33.333 0.00 0.00 39.30 3.02
1552 2097 6.207614 GGAACAGAATTCAGTTAAGAAGCCTT 59.792 38.462 15.33 0.00 36.43 4.35
1684 2230 5.759273 GCCCTGCATGCATGAAAATATTTAA 59.241 36.000 30.64 0.00 0.00 1.52
1763 2315 8.985315 ACCACATGATATCAGATTTGTTATGT 57.015 30.769 11.78 4.42 0.00 2.29
1797 2349 1.068417 CGTCCCCGACAACTGACAA 59.932 57.895 0.00 0.00 35.63 3.18
1897 2449 3.234353 TCTGGGAGATCATATTGTCGCT 58.766 45.455 0.00 0.00 0.00 4.93
2222 2774 7.823799 TGTACACTGCTATGATCATTCTTGAAA 59.176 33.333 14.65 0.00 34.96 2.69
2286 2838 6.102897 ACGCTTGGAAATAGCACTAGATAT 57.897 37.500 0.00 0.00 38.55 1.63
2521 3073 5.049267 TCCGCGATAATAAATTTGGCTTACC 60.049 40.000 8.23 0.00 0.00 2.85
2538 3090 9.817809 ACATATTATAAGACATATTTCCGCGAT 57.182 29.630 8.23 0.00 0.00 4.58
2593 3148 3.279875 GCCCACGGATCGAATGGC 61.280 66.667 0.00 1.83 33.51 4.40
2624 3179 1.675720 GGTTGTTGGTGCTTGCCTGT 61.676 55.000 0.00 0.00 0.00 4.00
2627 3182 1.363807 GAGGTTGTTGGTGCTTGCC 59.636 57.895 0.00 0.00 0.00 4.52
2637 3192 1.308998 CTGGCGAAGTTGAGGTTGTT 58.691 50.000 0.00 0.00 0.00 2.83
2696 3251 3.561313 GGTCATAGCTTGGGTTCTTTCCA 60.561 47.826 0.00 0.00 0.00 3.53
2732 3287 2.546645 ATTGCGCATTCAAGGCACCG 62.547 55.000 12.75 0.00 36.23 4.94
2798 3353 1.253100 TGATGTAGTGGTCGCAGTCA 58.747 50.000 0.00 0.00 0.00 3.41
2915 3470 0.175760 ACCGGTCTGATGGATCAACG 59.824 55.000 0.00 0.00 36.18 4.10
2933 3488 0.239879 CACGGTTGTGGTTGCCATAC 59.760 55.000 0.00 0.00 42.59 2.39
2987 3542 2.482494 AGGTAAGATGGACCTTGGAGG 58.518 52.381 0.00 0.00 45.40 4.30
3188 3743 0.394899 CCCTTTCCATCTCAGCCACC 60.395 60.000 0.00 0.00 0.00 4.61
3470 4025 0.107703 CACGCTGAAGGGCTTGGATA 60.108 55.000 0.00 0.00 0.00 2.59
3477 4032 1.605058 TAGGAGACACGCTGAAGGGC 61.605 60.000 0.00 0.00 0.00 5.19
3557 4112 1.490490 TCAGGGATAAGCCACATCACC 59.510 52.381 0.00 0.00 38.95 4.02
3707 4262 2.604914 CCCGATCATGAAGAACTGTTCG 59.395 50.000 14.35 1.45 35.44 3.95
3731 4286 0.459899 CTGCTGGGTATGCACTCGTA 59.540 55.000 0.00 0.00 36.37 3.43
3845 4400 0.301687 GCATGTCATACAAGTCGGCG 59.698 55.000 0.00 0.00 0.00 6.46
3950 4505 2.418368 TTGTCCATGCTCCCATGTAC 57.582 50.000 3.34 0.00 45.90 2.90
3989 4544 0.401356 TGAAGAGCAGACCCAATGCA 59.599 50.000 0.00 0.00 46.31 3.96
4109 4664 7.220683 GCAACATATACAAGGCAAACTATTGTG 59.779 37.037 0.30 0.00 37.69 3.33
4322 4878 5.811399 TTCCTCAACACTTGTAAGTTGTG 57.189 39.130 0.00 0.00 44.08 3.33
4405 4961 5.106197 CCAACGATTGATCATCCTGTTTTCA 60.106 40.000 0.00 0.00 0.00 2.69
4429 4985 1.484038 TTTTGGCATCCATAGTGGGC 58.516 50.000 0.00 0.00 38.32 5.36
4584 5149 9.847224 ATCCTTTGTCTGTACTCTTTCTTTTTA 57.153 29.630 0.00 0.00 0.00 1.52
4692 5263 3.750371 TGTCAATGAAATCCAAGACGGT 58.250 40.909 0.00 0.00 36.96 4.83
4696 5267 6.570186 CGGTCAAATGTCAATGAAATCCAAGA 60.570 38.462 0.00 0.00 0.00 3.02
4698 5269 5.242615 TCGGTCAAATGTCAATGAAATCCAA 59.757 36.000 0.00 0.00 0.00 3.53
4704 5275 4.261405 GGTGTTCGGTCAAATGTCAATGAA 60.261 41.667 0.00 0.00 0.00 2.57
4717 5288 0.528470 CTCTCCTCAGGTGTTCGGTC 59.472 60.000 0.00 0.00 0.00 4.79
4762 5339 5.533528 ACATATGATTAATGCTCTGCTTGCA 59.466 36.000 10.38 0.00 44.95 4.08
4806 5385 2.422597 CCACACGTGAGCTTCCATTTA 58.577 47.619 25.01 0.00 0.00 1.40
4813 5392 2.281070 CAGGCCACACGTGAGCTT 60.281 61.111 25.01 17.69 36.20 3.74
4831 5410 3.740128 CTTGGCCCCGTCATCTCCG 62.740 68.421 0.00 0.00 0.00 4.63
4882 5461 1.449601 GGAGCGATTCCGGCTTTCA 60.450 57.895 0.00 0.00 41.72 2.69
4923 5502 7.822658 ACTTTTGCTAGTGACACAGTTAAAAA 58.177 30.769 8.59 7.09 0.00 1.94
4924 5503 7.385778 ACTTTTGCTAGTGACACAGTTAAAA 57.614 32.000 8.59 8.94 0.00 1.52
4925 5504 6.995511 ACTTTTGCTAGTGACACAGTTAAA 57.004 33.333 8.59 1.63 0.00 1.52
4926 5505 6.995511 AACTTTTGCTAGTGACACAGTTAA 57.004 33.333 8.59 0.00 0.00 2.01
4927 5506 7.929245 TGATAACTTTTGCTAGTGACACAGTTA 59.071 33.333 8.59 10.88 32.01 2.24
4928 5507 6.765989 TGATAACTTTTGCTAGTGACACAGTT 59.234 34.615 8.59 9.07 0.00 3.16
4929 5508 6.288294 TGATAACTTTTGCTAGTGACACAGT 58.712 36.000 8.59 0.00 0.00 3.55
4930 5509 6.646653 TCTGATAACTTTTGCTAGTGACACAG 59.353 38.462 8.59 4.66 0.00 3.66
4931 5510 6.521162 TCTGATAACTTTTGCTAGTGACACA 58.479 36.000 8.59 0.00 0.00 3.72
4932 5511 6.868864 TCTCTGATAACTTTTGCTAGTGACAC 59.131 38.462 0.00 0.00 0.00 3.67
4933 5512 6.993079 TCTCTGATAACTTTTGCTAGTGACA 58.007 36.000 0.00 0.00 0.00 3.58
4934 5513 7.815068 TCTTCTCTGATAACTTTTGCTAGTGAC 59.185 37.037 0.00 0.00 0.00 3.67
4935 5514 7.815068 GTCTTCTCTGATAACTTTTGCTAGTGA 59.185 37.037 0.00 0.00 0.00 3.41
4936 5515 7.064016 GGTCTTCTCTGATAACTTTTGCTAGTG 59.936 40.741 0.00 0.00 0.00 2.74
4937 5516 7.100409 GGTCTTCTCTGATAACTTTTGCTAGT 58.900 38.462 0.00 0.00 0.00 2.57
4938 5517 6.254589 CGGTCTTCTCTGATAACTTTTGCTAG 59.745 42.308 0.00 0.00 0.00 3.42
4939 5518 6.100004 CGGTCTTCTCTGATAACTTTTGCTA 58.900 40.000 0.00 0.00 0.00 3.49
4940 5519 4.932200 CGGTCTTCTCTGATAACTTTTGCT 59.068 41.667 0.00 0.00 0.00 3.91
4941 5520 4.093556 CCGGTCTTCTCTGATAACTTTTGC 59.906 45.833 0.00 0.00 0.00 3.68
4942 5521 5.120830 CACCGGTCTTCTCTGATAACTTTTG 59.879 44.000 2.59 0.00 0.00 2.44
4943 5522 5.238583 CACCGGTCTTCTCTGATAACTTTT 58.761 41.667 2.59 0.00 0.00 2.27
4944 5523 4.322801 CCACCGGTCTTCTCTGATAACTTT 60.323 45.833 2.59 0.00 0.00 2.66
4945 5524 3.195825 CCACCGGTCTTCTCTGATAACTT 59.804 47.826 2.59 0.00 0.00 2.66
4946 5525 2.761208 CCACCGGTCTTCTCTGATAACT 59.239 50.000 2.59 0.00 0.00 2.24
4947 5526 2.496470 ACCACCGGTCTTCTCTGATAAC 59.504 50.000 2.59 0.00 0.00 1.89
4948 5527 2.816411 ACCACCGGTCTTCTCTGATAA 58.184 47.619 2.59 0.00 0.00 1.75
4949 5528 2.526888 ACCACCGGTCTTCTCTGATA 57.473 50.000 2.59 0.00 0.00 2.15
4950 5529 1.645710 AACCACCGGTCTTCTCTGAT 58.354 50.000 2.59 0.00 33.12 2.90
4951 5530 1.420430 AAACCACCGGTCTTCTCTGA 58.580 50.000 2.59 0.00 33.12 3.27
4952 5531 2.612221 GGTAAACCACCGGTCTTCTCTG 60.612 54.545 2.59 0.00 37.63 3.35
4953 5532 1.622312 GGTAAACCACCGGTCTTCTCT 59.378 52.381 2.59 0.00 37.63 3.10
4954 5533 2.090400 GGTAAACCACCGGTCTTCTC 57.910 55.000 2.59 0.00 37.63 2.87
5004 5583 7.345691 TCATCAGCTATATGTTCCCTCAAAAA 58.654 34.615 7.82 0.00 0.00 1.94
5005 5584 6.899089 TCATCAGCTATATGTTCCCTCAAAA 58.101 36.000 7.82 0.00 0.00 2.44
5006 5585 6.499106 TCATCAGCTATATGTTCCCTCAAA 57.501 37.500 7.82 0.00 0.00 2.69
5007 5586 6.692849 ATCATCAGCTATATGTTCCCTCAA 57.307 37.500 7.82 0.00 0.00 3.02
5008 5587 7.147602 CCATATCATCAGCTATATGTTCCCTCA 60.148 40.741 11.50 0.00 35.28 3.86
5009 5588 7.215789 CCATATCATCAGCTATATGTTCCCTC 58.784 42.308 11.50 0.00 35.28 4.30
5010 5589 6.409005 GCCATATCATCAGCTATATGTTCCCT 60.409 42.308 11.50 0.00 35.28 4.20
5011 5590 5.762218 GCCATATCATCAGCTATATGTTCCC 59.238 44.000 11.50 0.00 35.28 3.97
5012 5591 5.762218 GGCCATATCATCAGCTATATGTTCC 59.238 44.000 0.00 8.99 35.28 3.62
5013 5592 5.464722 CGGCCATATCATCAGCTATATGTTC 59.535 44.000 2.24 5.06 35.28 3.18
5014 5593 5.363101 CGGCCATATCATCAGCTATATGTT 58.637 41.667 2.24 5.61 35.28 2.71
5015 5594 4.202295 CCGGCCATATCATCAGCTATATGT 60.202 45.833 2.24 2.70 35.28 2.29
5016 5595 4.313282 CCGGCCATATCATCAGCTATATG 58.687 47.826 2.24 7.09 36.33 1.78
5017 5596 3.244353 GCCGGCCATATCATCAGCTATAT 60.244 47.826 18.11 0.00 0.00 0.86
5018 5597 2.103094 GCCGGCCATATCATCAGCTATA 59.897 50.000 18.11 0.00 0.00 1.31
5019 5598 1.134280 GCCGGCCATATCATCAGCTAT 60.134 52.381 18.11 0.00 0.00 2.97
5020 5599 0.250234 GCCGGCCATATCATCAGCTA 59.750 55.000 18.11 0.00 0.00 3.32
5021 5600 1.002868 GCCGGCCATATCATCAGCT 60.003 57.895 18.11 0.00 0.00 4.24
5022 5601 2.042831 GGCCGGCCATATCATCAGC 61.043 63.158 40.73 8.02 35.81 4.26
5023 5602 1.377725 GGGCCGGCCATATCATCAG 60.378 63.158 44.46 0.00 37.98 2.90
5024 5603 1.714011 TTGGGCCGGCCATATCATCA 61.714 55.000 44.46 28.89 37.98 3.07
5025 5604 0.323725 ATTGGGCCGGCCATATCATC 60.324 55.000 44.46 26.57 37.98 2.92
5026 5605 0.114954 AATTGGGCCGGCCATATCAT 59.885 50.000 44.46 25.14 37.98 2.45
5067 5646 3.570975 TCGAAATACTCAGCCCGCTATAA 59.429 43.478 0.00 0.00 0.00 0.98
5087 5666 4.796231 CCGTTCGTCTGGCCCTCG 62.796 72.222 0.00 2.18 0.00 4.63
5101 5680 4.473520 CATCCTTCGCCAGGCCGT 62.474 66.667 5.63 0.00 43.55 5.68
5123 5702 4.446385 GCCCAACAGTTTAATTTCGTTTCC 59.554 41.667 0.00 0.00 0.00 3.13
5127 5706 4.555262 CATGCCCAACAGTTTAATTTCGT 58.445 39.130 0.00 0.00 0.00 3.85
5128 5707 3.925913 CCATGCCCAACAGTTTAATTTCG 59.074 43.478 0.00 0.00 0.00 3.46
5129 5708 5.146010 TCCATGCCCAACAGTTTAATTTC 57.854 39.130 0.00 0.00 0.00 2.17
5130 5709 5.760484 ATCCATGCCCAACAGTTTAATTT 57.240 34.783 0.00 0.00 0.00 1.82
5131 5710 5.760484 AATCCATGCCCAACAGTTTAATT 57.240 34.783 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.