Multiple sequence alignment - TraesCS5D01G443700

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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 TraesCS5D01G443700 chr5D 100.000 3263 0 0 1 3263 495032918 495029656 0.000000e+00 6026
1 TraesCS5D01G443700 chr5D 96.571 175 5 1 1 175 327998280 327998107 4.120000e-74 289
2 TraesCS5D01G443700 chr5D 95.882 170 7 0 1 170 504005496 504005665 3.210000e-70 276
3 TraesCS5D01G443700 chr5D 75.758 462 101 10 1738 2195 456751773 456752227 4.240000e-54 222
4 TraesCS5D01G443700 chr5B 92.310 3121 146 55 170 3263 611482083 611479030 0.000000e+00 4348
5 TraesCS5D01G443700 chr5B 75.271 461 105 8 1738 2195 558687039 558687493 9.170000e-51 211
6 TraesCS5D01G443700 chr5A 93.121 2922 99 28 368 3263 619099728 619096883 0.000000e+00 4189
7 TraesCS5D01G443700 chr5A 75.271 461 105 8 1738 2195 574785317 574785771 9.170000e-51 211
8 TraesCS5D01G443700 chr2D 96.571 175 6 0 1 175 37298354 37298180 1.150000e-74 291
9 TraesCS5D01G443700 chr2D 97.633 169 4 0 2 170 587740554 587740722 1.150000e-74 291
10 TraesCS5D01G443700 chr2D 96.532 173 6 0 1 173 15816559 15816387 1.480000e-73 287
11 TraesCS5D01G443700 chr2D 96.471 170 6 0 1 170 4195766 4195935 6.890000e-72 281
12 TraesCS5D01G443700 chr2D 96.471 170 6 0 1 170 57150717 57150886 6.890000e-72 281
13 TraesCS5D01G443700 chr1D 97.093 172 5 0 1 172 475979580 475979751 1.150000e-74 291
14 TraesCS5D01G443700 chr1D 77.353 340 58 16 1137 1467 119010744 119010415 2.000000e-42 183
15 TraesCS5D01G443700 chr3D 96.471 170 6 0 1 170 478139031 478139200 6.890000e-72 281
16 TraesCS5D01G443700 chr1A 77.126 341 57 18 1137 1467 131521532 131521203 9.300000e-41 178
17 TraesCS5D01G443700 chr1B 76.106 339 64 14 1137 1467 181218219 181217890 9.370000e-36 161
18 TraesCS5D01G443700 chr7D 76.678 283 41 20 1214 1482 525774364 525774093 2.040000e-27 134
19 TraesCS5D01G443700 chr7A 76.512 281 45 16 1214 1482 606330896 606330625 2.040000e-27 134
20 TraesCS5D01G443700 chr7B 76.071 280 48 16 1214 1482 562409238 562408967 9.500000e-26 128
21 TraesCS5D01G443700 chr6B 75.180 278 54 12 1214 1482 134000202 133999931 2.060000e-22 117


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 TraesCS5D01G443700 chr5D 495029656 495032918 3262 True 6026 6026 100.000 1 3263 1 chr5D.!!$R2 3262
1 TraesCS5D01G443700 chr5B 611479030 611482083 3053 True 4348 4348 92.310 170 3263 1 chr5B.!!$R1 3093
2 TraesCS5D01G443700 chr5A 619096883 619099728 2845 True 4189 4189 93.121 368 3263 1 chr5A.!!$R1 2895

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
359 361 0.034574 AACACGATGGGCCATAAGCA 60.035 50.0 21.26 0.0 46.5 3.91 F
365 367 0.186873 ATGGGCCATAAGCAAGAGGG 59.813 55.0 19.68 0.0 46.5 4.30 F
568 580 0.397564 TCACTGAGTGCAGGCATCAA 59.602 50.0 7.93 0.0 46.6 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1649 0.180406 AAACCTCTGTGAAGTGCGGT 59.820 50.000 0.0 0.0 0.00 5.68 R
1824 1902 0.820871 GGAGGATCAGCTCGTTGAGT 59.179 55.000 0.0 0.0 36.25 3.41 R
2549 2633 7.357303 ACTAATAACTACACCAAGTTTTTGCG 58.643 34.615 0.0 0.0 40.20 4.85 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
17 18 4.751431 AGCTTGCACCCCTTCATC 57.249 55.556 0.00 0.00 0.00 2.92
18 19 1.769665 AGCTTGCACCCCTTCATCA 59.230 52.632 0.00 0.00 0.00 3.07
19 20 0.333993 AGCTTGCACCCCTTCATCAT 59.666 50.000 0.00 0.00 0.00 2.45
20 21 1.565759 AGCTTGCACCCCTTCATCATA 59.434 47.619 0.00 0.00 0.00 2.15
21 22 2.176364 AGCTTGCACCCCTTCATCATAT 59.824 45.455 0.00 0.00 0.00 1.78
22 23 2.295349 GCTTGCACCCCTTCATCATATG 59.705 50.000 0.00 0.00 0.00 1.78
23 24 2.662535 TGCACCCCTTCATCATATGG 57.337 50.000 2.13 0.00 0.00 2.74
24 25 2.134354 TGCACCCCTTCATCATATGGA 58.866 47.619 2.13 0.00 0.00 3.41
25 26 2.718062 TGCACCCCTTCATCATATGGAT 59.282 45.455 2.13 0.00 36.39 3.41
26 27 3.915711 TGCACCCCTTCATCATATGGATA 59.084 43.478 2.13 0.00 33.95 2.59
27 28 4.019051 TGCACCCCTTCATCATATGGATAG 60.019 45.833 2.13 0.00 33.95 2.08
28 29 4.627255 GCACCCCTTCATCATATGGATAGG 60.627 50.000 2.13 5.20 33.95 2.57
29 30 4.784838 CACCCCTTCATCATATGGATAGGA 59.215 45.833 2.13 0.00 33.95 2.94
30 31 5.035556 ACCCCTTCATCATATGGATAGGAG 58.964 45.833 2.13 0.00 33.95 3.69
31 32 5.035556 CCCCTTCATCATATGGATAGGAGT 58.964 45.833 2.13 0.00 33.95 3.85
32 33 6.205298 CCCCTTCATCATATGGATAGGAGTA 58.795 44.000 2.13 0.00 33.95 2.59
33 34 6.326064 CCCCTTCATCATATGGATAGGAGTAG 59.674 46.154 2.13 0.00 33.95 2.57
34 35 6.183360 CCCTTCATCATATGGATAGGAGTAGC 60.183 46.154 2.13 0.00 33.95 3.58
35 36 6.456795 TTCATCATATGGATAGGAGTAGCG 57.543 41.667 2.13 0.00 33.95 4.26
36 37 4.889995 TCATCATATGGATAGGAGTAGCGG 59.110 45.833 2.13 0.00 33.95 5.52
37 38 3.024547 TCATATGGATAGGAGTAGCGGC 58.975 50.000 2.13 0.00 0.00 6.53
38 39 2.597578 TATGGATAGGAGTAGCGGCA 57.402 50.000 1.45 0.00 0.00 5.69
39 40 1.944177 ATGGATAGGAGTAGCGGCAT 58.056 50.000 1.45 0.00 0.00 4.40
40 41 2.597578 TGGATAGGAGTAGCGGCATA 57.402 50.000 1.45 0.00 0.00 3.14
41 42 3.101643 TGGATAGGAGTAGCGGCATAT 57.898 47.619 1.45 0.00 0.00 1.78
42 43 2.760650 TGGATAGGAGTAGCGGCATATG 59.239 50.000 1.45 0.00 0.00 1.78
43 44 2.761208 GGATAGGAGTAGCGGCATATGT 59.239 50.000 1.45 0.00 0.00 2.29
44 45 3.195825 GGATAGGAGTAGCGGCATATGTT 59.804 47.826 1.45 0.00 0.00 2.71
45 46 2.533266 AGGAGTAGCGGCATATGTTG 57.467 50.000 1.45 0.00 0.00 3.33
64 65 2.711711 CCAAGATGGCGGATTCAGG 58.288 57.895 0.00 0.00 0.00 3.86
65 66 1.450531 CCAAGATGGCGGATTCAGGC 61.451 60.000 3.39 3.39 0.00 4.85
72 73 3.719268 TGGCGGATTCAGGCATATTAT 57.281 42.857 8.92 0.00 39.30 1.28
73 74 4.032960 TGGCGGATTCAGGCATATTATT 57.967 40.909 8.92 0.00 39.30 1.40
74 75 3.758023 TGGCGGATTCAGGCATATTATTG 59.242 43.478 8.92 0.00 39.30 1.90
75 76 3.758554 GGCGGATTCAGGCATATTATTGT 59.241 43.478 5.51 0.00 0.00 2.71
76 77 4.941263 GGCGGATTCAGGCATATTATTGTA 59.059 41.667 5.51 0.00 0.00 2.41
77 78 5.163754 GGCGGATTCAGGCATATTATTGTAC 60.164 44.000 5.51 0.00 0.00 2.90
78 79 5.643777 GCGGATTCAGGCATATTATTGTACT 59.356 40.000 0.00 0.00 0.00 2.73
79 80 6.816640 GCGGATTCAGGCATATTATTGTACTA 59.183 38.462 0.00 0.00 0.00 1.82
80 81 7.201530 GCGGATTCAGGCATATTATTGTACTAC 60.202 40.741 0.00 0.00 0.00 2.73
81 82 8.035394 CGGATTCAGGCATATTATTGTACTACT 58.965 37.037 0.00 0.00 0.00 2.57
82 83 9.726438 GGATTCAGGCATATTATTGTACTACTT 57.274 33.333 0.00 0.00 0.00 2.24
85 86 9.899661 TTCAGGCATATTATTGTACTACTTTGT 57.100 29.630 0.00 0.00 0.00 2.83
94 95 8.970691 TTATTGTACTACTTTGTAAGGTCGTC 57.029 34.615 0.00 0.00 0.00 4.20
95 96 5.034554 TGTACTACTTTGTAAGGTCGTCG 57.965 43.478 0.00 0.00 0.00 5.12
96 97 4.754618 TGTACTACTTTGTAAGGTCGTCGA 59.245 41.667 0.00 0.00 0.00 4.20
97 98 4.416505 ACTACTTTGTAAGGTCGTCGAG 57.583 45.455 0.00 0.00 0.00 4.04
98 99 4.067896 ACTACTTTGTAAGGTCGTCGAGA 58.932 43.478 0.00 0.00 0.00 4.04
99 100 3.996150 ACTTTGTAAGGTCGTCGAGAA 57.004 42.857 0.00 0.00 0.00 2.87
100 101 4.516365 ACTTTGTAAGGTCGTCGAGAAT 57.484 40.909 0.00 0.00 0.00 2.40
101 102 5.633830 ACTTTGTAAGGTCGTCGAGAATA 57.366 39.130 0.00 0.00 0.00 1.75
102 103 6.017400 ACTTTGTAAGGTCGTCGAGAATAA 57.983 37.500 0.00 0.00 0.00 1.40
103 104 6.628185 ACTTTGTAAGGTCGTCGAGAATAAT 58.372 36.000 0.00 0.00 0.00 1.28
104 105 6.750963 ACTTTGTAAGGTCGTCGAGAATAATC 59.249 38.462 0.00 0.00 0.00 1.75
105 106 5.823209 TGTAAGGTCGTCGAGAATAATCA 57.177 39.130 0.00 0.00 0.00 2.57
106 107 6.198650 TGTAAGGTCGTCGAGAATAATCAA 57.801 37.500 0.00 0.00 0.00 2.57
107 108 6.802608 TGTAAGGTCGTCGAGAATAATCAAT 58.197 36.000 0.00 0.00 0.00 2.57
108 109 7.933396 TGTAAGGTCGTCGAGAATAATCAATA 58.067 34.615 0.00 0.00 0.00 1.90
109 110 8.407832 TGTAAGGTCGTCGAGAATAATCAATAA 58.592 33.333 0.00 0.00 0.00 1.40
110 111 9.241317 GTAAGGTCGTCGAGAATAATCAATAAA 57.759 33.333 0.00 0.00 0.00 1.40
111 112 8.712285 AAGGTCGTCGAGAATAATCAATAAAA 57.288 30.769 0.00 0.00 0.00 1.52
112 113 8.888579 AGGTCGTCGAGAATAATCAATAAAAT 57.111 30.769 0.00 0.00 0.00 1.82
113 114 8.765219 AGGTCGTCGAGAATAATCAATAAAATG 58.235 33.333 0.00 0.00 0.00 2.32
114 115 8.009974 GGTCGTCGAGAATAATCAATAAAATGG 58.990 37.037 0.00 0.00 0.00 3.16
115 116 7.530861 GTCGTCGAGAATAATCAATAAAATGGC 59.469 37.037 0.00 0.00 0.00 4.40
116 117 6.797033 CGTCGAGAATAATCAATAAAATGGCC 59.203 38.462 0.00 0.00 0.00 5.36
117 118 6.797033 GTCGAGAATAATCAATAAAATGGCCG 59.203 38.462 0.00 0.00 0.00 6.13
118 119 5.569059 CGAGAATAATCAATAAAATGGCCGC 59.431 40.000 0.00 0.00 0.00 6.53
119 120 6.403866 AGAATAATCAATAAAATGGCCGCA 57.596 33.333 0.00 0.00 0.00 5.69
120 121 6.996509 AGAATAATCAATAAAATGGCCGCAT 58.003 32.000 0.00 0.00 0.00 4.73
121 122 6.869913 AGAATAATCAATAAAATGGCCGCATG 59.130 34.615 0.00 0.00 0.00 4.06
122 123 2.222007 TCAATAAAATGGCCGCATGC 57.778 45.000 7.91 7.91 40.16 4.06
123 124 1.479730 TCAATAAAATGGCCGCATGCA 59.520 42.857 19.57 0.00 43.89 3.96
124 125 2.102757 TCAATAAAATGGCCGCATGCAT 59.897 40.909 19.57 0.00 43.89 3.96
125 126 2.443887 ATAAAATGGCCGCATGCATC 57.556 45.000 19.57 8.10 43.89 3.91
126 127 1.401761 TAAAATGGCCGCATGCATCT 58.598 45.000 19.57 0.00 43.89 2.90
127 128 0.538118 AAAATGGCCGCATGCATCTT 59.462 45.000 19.57 0.28 43.89 2.40
128 129 0.538118 AAATGGCCGCATGCATCTTT 59.462 45.000 19.57 6.69 43.89 2.52
129 130 0.103572 AATGGCCGCATGCATCTTTC 59.896 50.000 19.57 1.17 43.89 2.62
130 131 1.038681 ATGGCCGCATGCATCTTTCA 61.039 50.000 19.57 7.02 43.89 2.69
131 132 1.065273 GGCCGCATGCATCTTTCAG 59.935 57.895 19.57 0.00 43.89 3.02
132 133 1.378882 GGCCGCATGCATCTTTCAGA 61.379 55.000 19.57 0.00 43.89 3.27
133 134 0.666913 GCCGCATGCATCTTTCAGAT 59.333 50.000 19.57 0.00 40.77 2.90
142 143 1.948145 CATCTTTCAGATGCAGAGGCC 59.052 52.381 0.00 0.00 44.69 5.19
143 144 0.107993 TCTTTCAGATGCAGAGGCCG 60.108 55.000 0.00 0.00 40.13 6.13
144 145 1.078214 TTTCAGATGCAGAGGCCGG 60.078 57.895 0.00 0.00 40.13 6.13
145 146 2.541547 TTTCAGATGCAGAGGCCGGG 62.542 60.000 2.18 0.00 40.13 5.73
146 147 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
152 153 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
242 243 9.073368 CATCATTTGATTCAGCACTAAAAGAAG 57.927 33.333 0.00 0.00 31.21 2.85
251 252 7.545362 TCAGCACTAAAAGAAGATGATTAGC 57.455 36.000 0.00 0.00 0.00 3.09
281 282 2.552743 TCAACACCGGCGAGATAGATAG 59.447 50.000 9.30 0.00 0.00 2.08
282 283 2.552743 CAACACCGGCGAGATAGATAGA 59.447 50.000 9.30 0.00 0.00 1.98
283 284 3.074675 ACACCGGCGAGATAGATAGAT 57.925 47.619 9.30 0.00 0.00 1.98
284 285 4.217836 ACACCGGCGAGATAGATAGATA 57.782 45.455 9.30 0.00 0.00 1.98
285 286 4.193090 ACACCGGCGAGATAGATAGATAG 58.807 47.826 9.30 0.00 0.00 2.08
300 301 9.747293 ATAGATAGATAGATCAACATCATTGCG 57.253 33.333 0.00 0.00 0.00 4.85
359 361 0.034574 AACACGATGGGCCATAAGCA 60.035 50.000 21.26 0.00 46.50 3.91
365 367 0.186873 ATGGGCCATAAGCAAGAGGG 59.813 55.000 19.68 0.00 46.50 4.30
378 380 6.956202 AAGCAAGAGGGATTAATGAATGAG 57.044 37.500 0.00 0.00 0.00 2.90
478 486 4.202161 ACGTGCATTCCACCAATAACAAAA 60.202 37.500 0.00 0.00 41.53 2.44
479 487 4.928615 CGTGCATTCCACCAATAACAAAAT 59.071 37.500 0.00 0.00 41.53 1.82
480 488 5.163972 CGTGCATTCCACCAATAACAAAATG 60.164 40.000 0.00 0.00 41.53 2.32
481 489 4.694509 TGCATTCCACCAATAACAAAATGC 59.305 37.500 9.55 9.55 44.69 3.56
485 493 7.646314 CATTCCACCAATAACAAAATGCAAAA 58.354 30.769 0.00 0.00 0.00 2.44
486 494 7.630242 TTCCACCAATAACAAAATGCAAAAA 57.370 28.000 0.00 0.00 0.00 1.94
487 495 7.020914 TCCACCAATAACAAAATGCAAAAAC 57.979 32.000 0.00 0.00 0.00 2.43
488 496 5.906285 CCACCAATAACAAAATGCAAAAACG 59.094 36.000 0.00 0.00 0.00 3.60
489 497 6.238211 CCACCAATAACAAAATGCAAAAACGA 60.238 34.615 0.00 0.00 0.00 3.85
543 555 1.235724 GAAGAAAACGGTCAGTGGGG 58.764 55.000 0.00 0.00 0.00 4.96
568 580 0.397564 TCACTGAGTGCAGGCATCAA 59.602 50.000 7.93 0.00 46.60 2.57
569 581 1.003928 TCACTGAGTGCAGGCATCAAT 59.996 47.619 7.93 0.00 46.60 2.57
570 582 1.400846 CACTGAGTGCAGGCATCAATC 59.599 52.381 0.00 0.00 46.60 2.67
571 583 1.003928 ACTGAGTGCAGGCATCAATCA 59.996 47.619 0.00 8.42 46.60 2.57
572 584 1.671328 CTGAGTGCAGGCATCAATCAG 59.329 52.381 17.34 17.34 45.80 2.90
573 585 1.003928 TGAGTGCAGGCATCAATCAGT 59.996 47.619 0.00 0.00 34.21 3.41
574 586 1.669779 GAGTGCAGGCATCAATCAGTC 59.330 52.381 0.00 0.00 0.00 3.51
575 587 1.281287 AGTGCAGGCATCAATCAGTCT 59.719 47.619 0.00 0.00 0.00 3.24
589 605 0.861837 CAGTCTGTCTTTGACCGTGC 59.138 55.000 0.00 0.00 35.21 5.34
594 610 2.027625 GTCTTTGACCGTGCCCTCG 61.028 63.158 0.00 0.00 0.00 4.63
642 659 3.880490 ACACGACAGCCAAAGTCAATTTA 59.120 39.130 0.00 0.00 35.77 1.40
648 665 5.631119 ACAGCCAAAGTCAATTTACTAGGT 58.369 37.500 10.96 0.35 31.03 3.08
751 771 3.865700 GGTCAACCGAAGCTTTTGG 57.134 52.632 15.09 15.09 40.28 3.28
761 781 6.597262 ACCGAAGCTTTTGGTTTTATTTTG 57.403 33.333 16.26 0.00 45.33 2.44
762 782 5.007234 ACCGAAGCTTTTGGTTTTATTTTGC 59.993 36.000 16.26 0.00 45.33 3.68
763 783 5.007136 CCGAAGCTTTTGGTTTTATTTTGCA 59.993 36.000 0.00 0.00 40.61 4.08
819 839 8.610896 GGACATCATCATTAAACAAAGAGAGAG 58.389 37.037 0.00 0.00 0.00 3.20
827 847 9.083422 TCATTAAACAAAGAGAGAGAGAGAGAA 57.917 33.333 0.00 0.00 0.00 2.87
837 857 7.886338 AGAGAGAGAGAGAGAAAGAAAGAAAC 58.114 38.462 0.00 0.00 0.00 2.78
838 858 7.505585 AGAGAGAGAGAGAGAAAGAAAGAAACA 59.494 37.037 0.00 0.00 0.00 2.83
839 859 8.193953 AGAGAGAGAGAGAAAGAAAGAAACAT 57.806 34.615 0.00 0.00 0.00 2.71
840 860 9.308000 AGAGAGAGAGAGAAAGAAAGAAACATA 57.692 33.333 0.00 0.00 0.00 2.29
841 861 9.573133 GAGAGAGAGAGAAAGAAAGAAACATAG 57.427 37.037 0.00 0.00 0.00 2.23
842 862 9.308000 AGAGAGAGAGAAAGAAAGAAACATAGA 57.692 33.333 0.00 0.00 0.00 1.98
843 863 9.573133 GAGAGAGAGAAAGAAAGAAACATAGAG 57.427 37.037 0.00 0.00 0.00 2.43
844 864 8.531146 AGAGAGAGAAAGAAAGAAACATAGAGG 58.469 37.037 0.00 0.00 0.00 3.69
845 865 7.102993 AGAGAGAAAGAAAGAAACATAGAGGC 58.897 38.462 0.00 0.00 0.00 4.70
896 920 3.365969 CGAACACCCAAGGAATAACAAGC 60.366 47.826 0.00 0.00 0.00 4.01
965 1002 6.992715 GGCAGGACATATACTAGAACACAAAT 59.007 38.462 0.00 0.00 0.00 2.32
966 1003 7.499232 GGCAGGACATATACTAGAACACAAATT 59.501 37.037 0.00 0.00 0.00 1.82
1485 1550 2.529389 ACCGGCAACTTCCCCTCT 60.529 61.111 0.00 0.00 0.00 3.69
1560 1634 6.723282 CATCATCATCATCATCATCATCTGC 58.277 40.000 0.00 0.00 0.00 4.26
1602 1676 5.504173 GCACTTCACAGAGGTTTAACAACTC 60.504 44.000 0.00 0.00 32.90 3.01
1603 1677 5.584649 CACTTCACAGAGGTTTAACAACTCA 59.415 40.000 0.00 0.00 32.90 3.41
1625 1703 0.459237 GTCTGTCCATGGCGTCTCTG 60.459 60.000 6.96 0.00 0.00 3.35
2139 2217 2.125552 CAGAACTGCATCGCCGGA 60.126 61.111 5.05 0.00 0.00 5.14
2238 2316 4.501714 TCGCCACCGCCGATGTAC 62.502 66.667 0.00 0.00 0.00 2.90
2549 2633 1.815817 AATTTGGCGGTGTGGCTTCC 61.816 55.000 0.00 0.00 45.14 3.46
2642 2726 8.233190 GTCAGAATTCAGTTCAGAATTAGTTGG 58.767 37.037 8.44 0.00 45.51 3.77
2643 2727 7.025963 CAGAATTCAGTTCAGAATTAGTTGGC 58.974 38.462 8.44 0.00 45.51 4.52
2908 2993 2.166459 CAGAGGACGGAGCAAGTAATGA 59.834 50.000 0.00 0.00 0.00 2.57
3026 3111 7.888021 TGGTCAGAGAGGAATTAATAAAAAGCA 59.112 33.333 0.00 0.00 0.00 3.91
3093 3179 4.196193 TCGTTGGTTGATCAACTCAAAGT 58.804 39.130 31.81 0.00 45.27 2.66
3109 3195 3.316308 TCAAAGTGCAAGAAGCTTCTTCC 59.684 43.478 33.73 27.56 45.23 3.46
3161 3247 1.654023 GGGTTCCTTTCCGCAATCCG 61.654 60.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.333993 ATGATGAAGGGGTGCAAGCT 59.666 50.000 0.00 0.00 0.00 3.74
1 2 2.057137 TATGATGAAGGGGTGCAAGC 57.943 50.000 0.00 0.00 0.00 4.01
2 3 2.889045 CCATATGATGAAGGGGTGCAAG 59.111 50.000 3.65 0.00 0.00 4.01
3 4 2.513317 TCCATATGATGAAGGGGTGCAA 59.487 45.455 3.65 0.00 0.00 4.08
4 5 2.134354 TCCATATGATGAAGGGGTGCA 58.866 47.619 3.65 0.00 0.00 4.57
5 6 2.957402 TCCATATGATGAAGGGGTGC 57.043 50.000 3.65 0.00 0.00 5.01
6 7 4.784838 TCCTATCCATATGATGAAGGGGTG 59.215 45.833 3.65 0.00 34.76 4.61
7 8 5.035556 CTCCTATCCATATGATGAAGGGGT 58.964 45.833 3.65 0.00 34.76 4.95
8 9 5.035556 ACTCCTATCCATATGATGAAGGGG 58.964 45.833 3.65 7.84 34.76 4.79
9 10 6.183360 GCTACTCCTATCCATATGATGAAGGG 60.183 46.154 3.65 1.54 34.76 3.95
10 11 6.460814 CGCTACTCCTATCCATATGATGAAGG 60.461 46.154 3.65 5.74 34.76 3.46
11 12 6.460814 CCGCTACTCCTATCCATATGATGAAG 60.461 46.154 3.65 0.00 34.76 3.02
12 13 5.360999 CCGCTACTCCTATCCATATGATGAA 59.639 44.000 3.65 0.00 34.76 2.57
13 14 4.889995 CCGCTACTCCTATCCATATGATGA 59.110 45.833 3.65 0.00 34.76 2.92
14 15 4.500545 GCCGCTACTCCTATCCATATGATG 60.501 50.000 3.65 0.00 34.76 3.07
15 16 3.639094 GCCGCTACTCCTATCCATATGAT 59.361 47.826 3.65 0.00 37.49 2.45
16 17 3.024547 GCCGCTACTCCTATCCATATGA 58.975 50.000 3.65 0.00 0.00 2.15
17 18 2.760650 TGCCGCTACTCCTATCCATATG 59.239 50.000 0.00 0.00 0.00 1.78
18 19 3.101643 TGCCGCTACTCCTATCCATAT 57.898 47.619 0.00 0.00 0.00 1.78
19 20 2.597578 TGCCGCTACTCCTATCCATA 57.402 50.000 0.00 0.00 0.00 2.74
20 21 1.944177 ATGCCGCTACTCCTATCCAT 58.056 50.000 0.00 0.00 0.00 3.41
21 22 2.597578 TATGCCGCTACTCCTATCCA 57.402 50.000 0.00 0.00 0.00 3.41
22 23 2.761208 ACATATGCCGCTACTCCTATCC 59.239 50.000 1.58 0.00 0.00 2.59
23 24 4.177026 CAACATATGCCGCTACTCCTATC 58.823 47.826 1.58 0.00 0.00 2.08
24 25 4.193826 CAACATATGCCGCTACTCCTAT 57.806 45.455 1.58 0.00 0.00 2.57
25 26 3.660501 CAACATATGCCGCTACTCCTA 57.339 47.619 1.58 0.00 0.00 2.94
26 27 2.533266 CAACATATGCCGCTACTCCT 57.467 50.000 1.58 0.00 0.00 3.69
46 47 1.450531 GCCTGAATCCGCCATCTTGG 61.451 60.000 0.00 0.00 41.55 3.61
47 48 0.749091 TGCCTGAATCCGCCATCTTG 60.749 55.000 0.00 0.00 0.00 3.02
48 49 0.184451 ATGCCTGAATCCGCCATCTT 59.816 50.000 0.00 0.00 0.00 2.40
49 50 1.059098 TATGCCTGAATCCGCCATCT 58.941 50.000 0.00 0.00 0.00 2.90
50 51 2.119801 ATATGCCTGAATCCGCCATC 57.880 50.000 0.00 0.00 0.00 3.51
51 52 2.592102 AATATGCCTGAATCCGCCAT 57.408 45.000 0.00 0.00 0.00 4.40
52 53 3.719268 ATAATATGCCTGAATCCGCCA 57.281 42.857 0.00 0.00 0.00 5.69
53 54 3.758554 ACAATAATATGCCTGAATCCGCC 59.241 43.478 0.00 0.00 0.00 6.13
54 55 5.643777 AGTACAATAATATGCCTGAATCCGC 59.356 40.000 0.00 0.00 0.00 5.54
55 56 8.035394 AGTAGTACAATAATATGCCTGAATCCG 58.965 37.037 2.52 0.00 0.00 4.18
56 57 9.726438 AAGTAGTACAATAATATGCCTGAATCC 57.274 33.333 2.52 0.00 0.00 3.01
59 60 9.899661 ACAAAGTAGTACAATAATATGCCTGAA 57.100 29.630 2.52 0.00 0.00 3.02
68 69 9.578439 GACGACCTTACAAAGTAGTACAATAAT 57.422 33.333 2.52 0.00 0.00 1.28
69 70 7.750458 CGACGACCTTACAAAGTAGTACAATAA 59.250 37.037 2.52 0.00 0.00 1.40
70 71 7.119116 TCGACGACCTTACAAAGTAGTACAATA 59.881 37.037 2.52 0.00 0.00 1.90
71 72 6.072508 TCGACGACCTTACAAAGTAGTACAAT 60.073 38.462 2.52 0.00 0.00 2.71
72 73 5.238432 TCGACGACCTTACAAAGTAGTACAA 59.762 40.000 2.52 0.00 0.00 2.41
73 74 4.754618 TCGACGACCTTACAAAGTAGTACA 59.245 41.667 2.52 0.00 0.00 2.90
74 75 5.120830 TCTCGACGACCTTACAAAGTAGTAC 59.879 44.000 0.00 0.00 0.00 2.73
75 76 5.237815 TCTCGACGACCTTACAAAGTAGTA 58.762 41.667 0.00 0.00 0.00 1.82
76 77 4.067896 TCTCGACGACCTTACAAAGTAGT 58.932 43.478 0.00 0.00 0.00 2.73
77 78 4.675190 TCTCGACGACCTTACAAAGTAG 57.325 45.455 0.00 0.00 0.00 2.57
78 79 5.633830 ATTCTCGACGACCTTACAAAGTA 57.366 39.130 0.00 0.00 0.00 2.24
79 80 3.996150 TTCTCGACGACCTTACAAAGT 57.004 42.857 0.00 0.00 0.00 2.66
80 81 6.750501 TGATTATTCTCGACGACCTTACAAAG 59.249 38.462 0.00 0.00 0.00 2.77
81 82 6.623486 TGATTATTCTCGACGACCTTACAAA 58.377 36.000 0.00 0.00 0.00 2.83
82 83 6.198650 TGATTATTCTCGACGACCTTACAA 57.801 37.500 0.00 0.00 0.00 2.41
83 84 5.823209 TGATTATTCTCGACGACCTTACA 57.177 39.130 0.00 0.00 0.00 2.41
84 85 8.792831 TTATTGATTATTCTCGACGACCTTAC 57.207 34.615 0.00 0.00 0.00 2.34
85 86 9.806203 TTTTATTGATTATTCTCGACGACCTTA 57.194 29.630 0.00 0.00 0.00 2.69
86 87 8.712285 TTTTATTGATTATTCTCGACGACCTT 57.288 30.769 0.00 0.00 0.00 3.50
87 88 8.765219 CATTTTATTGATTATTCTCGACGACCT 58.235 33.333 0.00 0.00 0.00 3.85
88 89 8.009974 CCATTTTATTGATTATTCTCGACGACC 58.990 37.037 0.00 0.00 0.00 4.79
89 90 7.530861 GCCATTTTATTGATTATTCTCGACGAC 59.469 37.037 0.00 0.00 0.00 4.34
90 91 7.307751 GGCCATTTTATTGATTATTCTCGACGA 60.308 37.037 0.00 0.00 0.00 4.20
91 92 6.797033 GGCCATTTTATTGATTATTCTCGACG 59.203 38.462 0.00 0.00 0.00 5.12
92 93 6.797033 CGGCCATTTTATTGATTATTCTCGAC 59.203 38.462 2.24 0.00 0.00 4.20
93 94 6.567701 GCGGCCATTTTATTGATTATTCTCGA 60.568 38.462 2.24 0.00 0.00 4.04
94 95 5.569059 GCGGCCATTTTATTGATTATTCTCG 59.431 40.000 2.24 0.00 0.00 4.04
95 96 6.446318 TGCGGCCATTTTATTGATTATTCTC 58.554 36.000 2.24 0.00 0.00 2.87
96 97 6.403866 TGCGGCCATTTTATTGATTATTCT 57.596 33.333 2.24 0.00 0.00 2.40
97 98 6.401367 GCATGCGGCCATTTTATTGATTATTC 60.401 38.462 0.00 0.00 36.11 1.75
98 99 5.409214 GCATGCGGCCATTTTATTGATTATT 59.591 36.000 0.00 0.00 36.11 1.40
99 100 4.931002 GCATGCGGCCATTTTATTGATTAT 59.069 37.500 0.00 0.00 36.11 1.28
100 101 4.202192 TGCATGCGGCCATTTTATTGATTA 60.202 37.500 14.09 0.00 43.89 1.75
101 102 3.132925 GCATGCGGCCATTTTATTGATT 58.867 40.909 0.00 0.00 36.11 2.57
102 103 2.102757 TGCATGCGGCCATTTTATTGAT 59.897 40.909 14.09 0.00 43.89 2.57
103 104 1.479730 TGCATGCGGCCATTTTATTGA 59.520 42.857 14.09 0.00 43.89 2.57
104 105 1.937278 TGCATGCGGCCATTTTATTG 58.063 45.000 14.09 0.00 43.89 1.90
105 106 2.366266 AGATGCATGCGGCCATTTTATT 59.634 40.909 14.09 0.00 43.89 1.40
106 107 1.965643 AGATGCATGCGGCCATTTTAT 59.034 42.857 14.09 0.00 43.89 1.40
107 108 1.401761 AGATGCATGCGGCCATTTTA 58.598 45.000 14.09 0.00 43.89 1.52
108 109 0.538118 AAGATGCATGCGGCCATTTT 59.462 45.000 14.09 0.00 43.89 1.82
109 110 0.538118 AAAGATGCATGCGGCCATTT 59.462 45.000 14.09 6.76 43.89 2.32
110 111 0.103572 GAAAGATGCATGCGGCCATT 59.896 50.000 14.09 4.23 43.89 3.16
111 112 1.038681 TGAAAGATGCATGCGGCCAT 61.039 50.000 14.09 0.00 43.89 4.40
112 113 1.659622 CTGAAAGATGCATGCGGCCA 61.660 55.000 14.09 4.22 37.87 5.36
113 114 1.065273 CTGAAAGATGCATGCGGCC 59.935 57.895 14.09 4.40 37.87 6.13
114 115 2.100846 TCTGAAAGATGCATGCGGC 58.899 52.632 14.09 7.38 38.67 6.53
125 126 1.094073 CCGGCCTCTGCATCTGAAAG 61.094 60.000 0.00 0.00 40.13 2.62
126 127 1.078214 CCGGCCTCTGCATCTGAAA 60.078 57.895 0.00 0.00 40.13 2.69
127 128 2.586245 CCGGCCTCTGCATCTGAA 59.414 61.111 0.00 0.00 40.13 3.02
128 129 3.473647 CCCGGCCTCTGCATCTGA 61.474 66.667 0.00 0.00 40.13 3.27
129 130 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
135 136 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
188 189 4.158579 GCCCAGGAAAAGGAAAAGTATCAG 59.841 45.833 0.00 0.00 0.00 2.90
189 190 4.086457 GCCCAGGAAAAGGAAAAGTATCA 58.914 43.478 0.00 0.00 0.00 2.15
202 203 7.819675 ATCAAATGATGACCTGCCCAGGAAA 62.820 44.000 20.59 8.49 45.02 3.13
203 204 6.417598 ATCAAATGATGACCTGCCCAGGAA 62.418 45.833 20.59 8.82 45.02 3.36
204 205 4.980086 ATCAAATGATGACCTGCCCAGGA 61.980 47.826 20.59 0.00 45.02 3.86
242 243 8.171196 CGGTGTTGATTATATGTGCTAATCATC 58.829 37.037 6.27 6.51 42.28 2.92
251 252 3.127589 TCGCCGGTGTTGATTATATGTG 58.872 45.455 16.01 0.00 0.00 3.21
264 265 4.443621 TCTATCTATCTATCTCGCCGGTG 58.556 47.826 9.28 9.28 0.00 4.94
281 282 5.233225 TCCTCGCAATGATGTTGATCTATC 58.767 41.667 0.00 0.00 0.00 2.08
282 283 5.219343 TCCTCGCAATGATGTTGATCTAT 57.781 39.130 0.00 0.00 0.00 1.98
283 284 4.670896 TCCTCGCAATGATGTTGATCTA 57.329 40.909 0.00 0.00 0.00 1.98
284 285 3.548745 TCCTCGCAATGATGTTGATCT 57.451 42.857 0.00 0.00 0.00 2.75
285 286 4.621068 TTTCCTCGCAATGATGTTGATC 57.379 40.909 0.00 0.00 0.00 2.92
300 301 4.023193 ACCAATTCACAACGTCATTTCCTC 60.023 41.667 0.00 0.00 0.00 3.71
359 361 5.659849 AGCCTCATTCATTAATCCCTCTT 57.340 39.130 0.00 0.00 0.00 2.85
365 367 7.967303 GCTATTGCTTAGCCTCATTCATTAATC 59.033 37.037 0.29 0.00 46.47 1.75
478 486 7.861630 AGCGTATAGATAAATCGTTTTTGCAT 58.138 30.769 0.00 0.00 0.00 3.96
479 487 7.223971 AGAGCGTATAGATAAATCGTTTTTGCA 59.776 33.333 0.00 0.00 0.00 4.08
480 488 7.527516 CAGAGCGTATAGATAAATCGTTTTTGC 59.472 37.037 0.00 0.00 0.00 3.68
481 489 8.540492 ACAGAGCGTATAGATAAATCGTTTTTG 58.460 33.333 0.00 0.00 0.00 2.44
485 493 6.641314 CCAACAGAGCGTATAGATAAATCGTT 59.359 38.462 0.00 0.00 0.00 3.85
486 494 6.150318 CCAACAGAGCGTATAGATAAATCGT 58.850 40.000 0.00 0.00 0.00 3.73
487 495 5.061064 GCCAACAGAGCGTATAGATAAATCG 59.939 44.000 0.00 0.00 0.00 3.34
488 496 6.396459 GCCAACAGAGCGTATAGATAAATC 57.604 41.667 0.00 0.00 0.00 2.17
543 555 1.268743 GCCTGCACTCAGTGACAAAAC 60.269 52.381 9.70 0.00 38.66 2.43
568 580 2.868044 GCACGGTCAAAGACAGACTGAT 60.868 50.000 10.08 0.00 43.46 2.90
569 581 1.538204 GCACGGTCAAAGACAGACTGA 60.538 52.381 10.08 0.00 43.46 3.41
570 582 0.861837 GCACGGTCAAAGACAGACTG 59.138 55.000 0.00 0.00 45.63 3.51
571 583 0.249911 GGCACGGTCAAAGACAGACT 60.250 55.000 4.38 0.00 36.29 3.24
572 584 1.228657 GGGCACGGTCAAAGACAGAC 61.229 60.000 4.38 0.00 33.68 3.51
573 585 1.070786 GGGCACGGTCAAAGACAGA 59.929 57.895 4.38 0.00 33.68 3.41
574 586 0.951040 GAGGGCACGGTCAAAGACAG 60.951 60.000 0.00 0.00 33.68 3.51
575 587 1.070786 GAGGGCACGGTCAAAGACA 59.929 57.895 0.00 0.00 33.68 3.41
611 627 0.882927 GGCTGTCGTGTGCCTTTGTA 60.883 55.000 7.77 0.00 45.26 2.41
642 659 3.305608 CGTCCGTGTTTTTCCTACCTAGT 60.306 47.826 0.00 0.00 0.00 2.57
648 665 3.319755 GTGATCGTCCGTGTTTTTCCTA 58.680 45.455 0.00 0.00 0.00 2.94
819 839 7.277760 GCCTCTATGTTTCTTTCTTTCTCTCTC 59.722 40.741 0.00 0.00 0.00 3.20
827 847 5.819991 TCATGGCCTCTATGTTTCTTTCTT 58.180 37.500 3.32 0.00 0.00 2.52
837 857 3.270027 TCGTTTGTTCATGGCCTCTATG 58.730 45.455 3.32 0.00 0.00 2.23
838 858 3.627395 TCGTTTGTTCATGGCCTCTAT 57.373 42.857 3.32 0.00 0.00 1.98
839 859 3.270027 CATCGTTTGTTCATGGCCTCTA 58.730 45.455 3.32 0.00 0.00 2.43
840 860 2.086869 CATCGTTTGTTCATGGCCTCT 58.913 47.619 3.32 0.00 0.00 3.69
841 861 1.468054 GCATCGTTTGTTCATGGCCTC 60.468 52.381 3.32 0.00 0.00 4.70
842 862 0.527565 GCATCGTTTGTTCATGGCCT 59.472 50.000 3.32 0.00 0.00 5.19
843 863 0.243365 TGCATCGTTTGTTCATGGCC 59.757 50.000 0.00 0.00 0.00 5.36
844 864 1.068333 AGTGCATCGTTTGTTCATGGC 60.068 47.619 0.00 0.00 0.00 4.40
845 865 2.725759 CGAGTGCATCGTTTGTTCATGG 60.726 50.000 9.48 0.00 46.62 3.66
965 1002 3.316308 GTCTGCTGCTTCTTTTCTTGGAA 59.684 43.478 0.00 0.00 0.00 3.53
966 1003 2.880890 GTCTGCTGCTTCTTTTCTTGGA 59.119 45.455 0.00 0.00 0.00 3.53
1575 1649 0.180406 AAACCTCTGTGAAGTGCGGT 59.820 50.000 0.00 0.00 0.00 5.68
1602 1676 1.004560 ACGCCATGGACAGACAGTG 60.005 57.895 18.40 0.00 0.00 3.66
1603 1677 1.188219 AGACGCCATGGACAGACAGT 61.188 55.000 18.40 2.60 0.00 3.55
1625 1703 3.852205 GCCGCAGAAGTTGTTAAACCTTC 60.852 47.826 0.00 0.00 36.94 3.46
1824 1902 0.820871 GGAGGATCAGCTCGTTGAGT 59.179 55.000 0.00 0.00 36.25 3.41
2549 2633 7.357303 ACTAATAACTACACCAAGTTTTTGCG 58.643 34.615 0.00 0.00 40.20 4.85
2642 2726 0.391793 GCAGTGGTCCTAAGTCCTGC 60.392 60.000 0.00 0.00 38.58 4.85
2643 2727 1.270907 AGCAGTGGTCCTAAGTCCTG 58.729 55.000 0.00 0.00 0.00 3.86
2812 2896 4.397417 GCTCTTTGGCAGTGTTTGATATCT 59.603 41.667 3.98 0.00 0.00 1.98
3026 3111 1.700739 TGGAACCCATGAACGGTACTT 59.299 47.619 0.00 0.00 31.69 2.24
3109 3195 0.529378 GCCAGCAAAGATGAAGGGTG 59.471 55.000 0.00 0.00 0.00 4.61
3161 3247 0.944311 TGAAGCCGTCTTGTTCGAGC 60.944 55.000 0.00 0.00 31.48 5.03


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

AutoCloner maintained by Alex Coulton.