Multiple sequence alignment - TraesCS1D01G305100

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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 TraesCS1D01G305100 chr1D 100.000 4352 0 0 1 4352 402821750 402826101 0.000000e+00 8037.0
1 TraesCS1D01G305100 chr1D 90.323 124 11 1 1187 1310 344128544 344128666 1.250000e-35 161.0
2 TraesCS1D01G305100 chr1D 81.633 98 13 3 203 300 402821854 402821946 4.670000e-10 76.8
3 TraesCS1D01G305100 chr1D 81.633 98 13 3 105 197 402821952 402822049 4.670000e-10 76.8
4 TraesCS1D01G305100 chr1B 94.561 3953 136 47 442 4352 540718132 540722047 0.000000e+00 6035.0
5 TraesCS1D01G305100 chr1B 87.302 189 22 1 1 187 540717318 540717506 9.480000e-52 215.0
6 TraesCS1D01G305100 chr1B 92.517 147 8 2 312 455 540717554 540717700 1.590000e-49 207.0
7 TraesCS1D01G305100 chr1A 91.073 3551 169 63 202 3682 498046253 498049725 0.000000e+00 4665.0
8 TraesCS1D01G305100 chr1A 98.734 632 6 2 3722 4352 498049734 498050364 0.000000e+00 1122.0
9 TraesCS1D01G305100 chr1A 88.205 390 25 10 380 758 498042760 498043139 3.090000e-121 446.0
10 TraesCS1D01G305100 chr1A 87.786 393 27 10 377 758 498017269 498017651 1.440000e-119 440.0
11 TraesCS1D01G305100 chr3A 75.890 730 112 43 996 1717 585503035 585502362 9.090000e-82 315.0
12 TraesCS1D01G305100 chr3D 75.791 727 111 43 998 1717 444682356 444681688 1.520000e-79 307.0
13 TraesCS1D01G305100 chr3B 77.024 531 81 27 1194 1717 582477061 582476565 2.580000e-67 267.0
14 TraesCS1D01G305100 chr6B 85.714 119 9 4 1196 1314 677765136 677765026 7.650000e-23 119.0
15 TraesCS1D01G305100 chr6B 86.087 115 8 4 1196 1310 677889011 677888905 2.750000e-22 117.0
16 TraesCS1D01G305100 chr6B 84.348 115 10 4 1196 1310 678065753 678065647 5.950000e-19 106.0
17 TraesCS1D01G305100 chr5D 81.000 100 11 5 950 1049 558186531 558186440 6.040000e-09 73.1


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 TraesCS1D01G305100 chr1D 402821750 402826101 4351 False 8037.000000 8037 100.000000 1 4352 1 chr1D.!!$F2 4351
1 TraesCS1D01G305100 chr1B 540717318 540722047 4729 False 2152.333333 6035 91.460000 1 4352 3 chr1B.!!$F1 4351
2 TraesCS1D01G305100 chr1A 498042760 498050364 7604 False 2077.666667 4665 92.670667 202 4352 3 chr1A.!!$F2 4150
3 TraesCS1D01G305100 chr3A 585502362 585503035 673 True 315.000000 315 75.890000 996 1717 1 chr3A.!!$R1 721
4 TraesCS1D01G305100 chr3D 444681688 444682356 668 True 307.000000 307 75.791000 998 1717 1 chr3D.!!$R1 719

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
19 20 0.108138 TTTTTGGTGGGCCACGTTTG 60.108 50.0 29.18 0.0 46.01 2.93 F
180 181 0.179156 GTCGAGACGATTACGGGCAA 60.179 55.0 0.00 0.0 44.46 4.52 F
1987 5854 0.183492 ACTCTTGCCTTGCCTGTTGA 59.817 50.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 5868 0.824759 GAGGGTAAGTCCATCGCAGT 59.175 55.000 0.00 0.00 37.27 4.40 R
2027 5894 4.998671 ATTCATCCACACAACACAAACA 57.001 36.364 0.00 0.00 0.00 2.83 R
3628 7515 1.444119 TTTGAACGCTGCGCTTCCTT 61.444 50.000 23.51 8.38 0.00 3.36 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 4.035843 TTTTTGGTGGGCCACGTT 57.964 50.000 29.18 0.00 46.01 3.99
19 20 0.108138 TTTTTGGTGGGCCACGTTTG 60.108 50.000 29.18 0.00 46.01 2.93
20 21 2.579684 TTTTGGTGGGCCACGTTTGC 62.580 55.000 29.18 16.01 46.01 3.68
27 28 4.683334 GCCACGTTTGCCAGACGC 62.683 66.667 7.77 0.00 43.92 5.19
28 29 4.368808 CCACGTTTGCCAGACGCG 62.369 66.667 7.77 3.53 43.92 6.01
29 30 4.368808 CACGTTTGCCAGACGCGG 62.369 66.667 12.47 0.00 43.92 6.46
32 33 2.970324 GTTTGCCAGACGCGGACA 60.970 61.111 12.47 0.00 42.08 4.02
36 37 2.742372 GCCAGACGCGGACATGTT 60.742 61.111 12.47 0.00 0.00 2.71
37 38 3.027170 GCCAGACGCGGACATGTTG 62.027 63.158 12.47 0.00 0.00 3.33
38 39 1.374125 CCAGACGCGGACATGTTGA 60.374 57.895 12.47 0.00 0.00 3.18
39 40 1.626654 CCAGACGCGGACATGTTGAC 61.627 60.000 12.47 0.00 0.00 3.18
40 41 1.733041 AGACGCGGACATGTTGACG 60.733 57.895 12.47 6.99 0.00 4.35
41 42 2.726691 GACGCGGACATGTTGACGG 61.727 63.158 12.47 10.87 0.00 4.79
43 44 2.726691 CGCGGACATGTTGACGGTC 61.727 63.158 16.58 0.00 0.00 4.79
47 48 3.906660 GACATGTTGACGGTCCAGA 57.093 52.632 0.00 0.00 0.00 3.86
49 50 0.319555 ACATGTTGACGGTCCAGACG 60.320 55.000 5.55 0.00 37.36 4.18
50 51 1.374252 ATGTTGACGGTCCAGACGC 60.374 57.895 5.55 0.00 34.00 5.19
51 52 2.737376 GTTGACGGTCCAGACGCC 60.737 66.667 5.55 0.00 34.00 5.68
55 56 2.363276 ACGGTCCAGACGCCCATA 60.363 61.111 0.00 0.00 34.00 2.74
56 57 1.952102 GACGGTCCAGACGCCCATAA 61.952 60.000 0.00 0.00 34.00 1.90
57 58 1.520787 CGGTCCAGACGCCCATAAC 60.521 63.158 0.00 0.00 0.00 1.89
58 59 1.153229 GGTCCAGACGCCCATAACC 60.153 63.158 0.00 0.00 0.00 2.85
59 60 1.153229 GTCCAGACGCCCATAACCC 60.153 63.158 0.00 0.00 0.00 4.11
61 62 2.203015 CAGACGCCCATAACCCCG 60.203 66.667 0.00 0.00 0.00 5.73
63 64 4.171103 GACGCCCATAACCCCGCT 62.171 66.667 0.00 0.00 0.00 5.52
64 65 4.171103 ACGCCCATAACCCCGCTC 62.171 66.667 0.00 0.00 0.00 5.03
65 66 4.929707 CGCCCATAACCCCGCTCC 62.930 72.222 0.00 0.00 0.00 4.70
66 67 4.581093 GCCCATAACCCCGCTCCC 62.581 72.222 0.00 0.00 0.00 4.30
67 68 3.886001 CCCATAACCCCGCTCCCC 61.886 72.222 0.00 0.00 0.00 4.81
68 69 3.093835 CCATAACCCCGCTCCCCA 61.094 66.667 0.00 0.00 0.00 4.96
69 70 2.685534 CCATAACCCCGCTCCCCAA 61.686 63.158 0.00 0.00 0.00 4.12
70 71 1.536676 CATAACCCCGCTCCCCAAT 59.463 57.895 0.00 0.00 0.00 3.16
74 75 1.191489 AACCCCGCTCCCCAATTTTG 61.191 55.000 0.00 0.00 0.00 2.44
75 76 1.609210 CCCCGCTCCCCAATTTTGT 60.609 57.895 0.00 0.00 0.00 2.83
77 78 0.611896 CCCGCTCCCCAATTTTGTCT 60.612 55.000 0.00 0.00 0.00 3.41
79 80 0.811281 CGCTCCCCAATTTTGTCTCC 59.189 55.000 0.00 0.00 0.00 3.71
80 81 0.811281 GCTCCCCAATTTTGTCTCCG 59.189 55.000 0.00 0.00 0.00 4.63
81 82 1.463674 CTCCCCAATTTTGTCTCCGG 58.536 55.000 0.00 0.00 0.00 5.14
82 83 0.774908 TCCCCAATTTTGTCTCCGGT 59.225 50.000 0.00 0.00 0.00 5.28
83 84 1.146152 TCCCCAATTTTGTCTCCGGTT 59.854 47.619 0.00 0.00 0.00 4.44
84 85 1.967779 CCCCAATTTTGTCTCCGGTTT 59.032 47.619 0.00 0.00 0.00 3.27
86 87 2.403259 CCAATTTTGTCTCCGGTTTGC 58.597 47.619 0.00 0.00 0.00 3.68
87 88 2.050691 CAATTTTGTCTCCGGTTTGCG 58.949 47.619 0.00 0.00 0.00 4.85
88 89 0.596082 ATTTTGTCTCCGGTTTGCGG 59.404 50.000 0.00 0.00 0.00 5.69
89 90 1.448922 TTTTGTCTCCGGTTTGCGGG 61.449 55.000 0.00 0.00 36.54 6.13
92 93 1.598685 GTCTCCGGTTTGCGGGAAA 60.599 57.895 0.00 0.00 42.45 3.13
93 94 1.148723 TCTCCGGTTTGCGGGAAAA 59.851 52.632 0.00 0.00 42.45 2.29
95 96 2.049526 CCGGTTTGCGGGAAAAGC 60.050 61.111 0.00 0.00 37.28 3.51
97 98 1.660264 CGGTTTGCGGGAAAAGCAC 60.660 57.895 0.00 0.00 45.10 4.40
103 104 3.419759 CGGGAAAAGCACGTCCGG 61.420 66.667 0.00 0.00 38.99 5.14
104 105 3.733960 GGGAAAAGCACGTCCGGC 61.734 66.667 0.00 0.00 34.47 6.13
106 107 2.332654 GGAAAAGCACGTCCGGCAT 61.333 57.895 0.00 0.00 0.00 4.40
107 108 1.134694 GAAAAGCACGTCCGGCATC 59.865 57.895 0.00 0.00 0.00 3.91
108 109 2.253414 GAAAAGCACGTCCGGCATCC 62.253 60.000 0.00 0.00 0.00 3.51
111 112 4.760047 GCACGTCCGGCATCCTGT 62.760 66.667 0.00 0.00 0.00 4.00
113 114 1.226974 CACGTCCGGCATCCTGTAG 60.227 63.158 0.00 0.00 0.00 2.74
114 115 1.379443 ACGTCCGGCATCCTGTAGA 60.379 57.895 0.00 0.00 0.00 2.59
115 116 1.065928 CGTCCGGCATCCTGTAGAC 59.934 63.158 0.00 0.00 0.00 2.59
116 117 1.065928 GTCCGGCATCCTGTAGACG 59.934 63.158 0.00 0.00 0.00 4.18
117 118 1.077285 TCCGGCATCCTGTAGACGA 60.077 57.895 0.00 0.00 0.00 4.20
118 119 0.681887 TCCGGCATCCTGTAGACGAA 60.682 55.000 0.00 0.00 0.00 3.85
119 120 0.389391 CCGGCATCCTGTAGACGAAT 59.611 55.000 0.00 0.00 0.00 3.34
121 122 2.607282 CCGGCATCCTGTAGACGAATAC 60.607 54.545 0.00 0.00 0.00 1.89
142 143 4.655440 CGTATTCGTGTTGGATGACAAA 57.345 40.909 0.00 0.00 41.58 2.83
143 144 5.024768 CGTATTCGTGTTGGATGACAAAA 57.975 39.130 0.00 0.00 41.58 2.44
144 145 4.843984 CGTATTCGTGTTGGATGACAAAAC 59.156 41.667 0.00 0.00 42.74 2.43
145 146 4.909696 ATTCGTGTTGGATGACAAAACA 57.090 36.364 1.84 0.00 45.81 2.83
146 147 3.684103 TCGTGTTGGATGACAAAACAC 57.316 42.857 16.41 16.41 45.81 3.32
148 149 3.414549 GTGTTGGATGACAAAACACGT 57.585 42.857 13.23 0.00 45.02 4.49
150 151 2.356382 TGTTGGATGACAAAACACGTCC 59.644 45.455 0.00 0.00 41.58 4.79
152 153 1.134068 TGGATGACAAAACACGTCCCA 60.134 47.619 0.00 0.00 40.34 4.37
153 154 1.950909 GGATGACAAAACACGTCCCAA 59.049 47.619 0.00 0.00 36.52 4.12
155 156 1.096416 TGACAAAACACGTCCCAACC 58.904 50.000 0.00 0.00 32.15 3.77
158 159 1.407258 ACAAAACACGTCCCAACCATG 59.593 47.619 0.00 0.00 0.00 3.66
159 160 0.387565 AAAACACGTCCCAACCATGC 59.612 50.000 0.00 0.00 0.00 4.06
160 161 1.460273 AAACACGTCCCAACCATGCC 61.460 55.000 0.00 0.00 0.00 4.40
161 162 3.430862 CACGTCCCAACCATGCCG 61.431 66.667 0.00 0.00 0.00 5.69
162 163 3.948719 ACGTCCCAACCATGCCGT 61.949 61.111 0.00 0.00 0.00 5.68
163 164 3.124921 CGTCCCAACCATGCCGTC 61.125 66.667 0.00 0.00 0.00 4.79
164 165 3.124921 GTCCCAACCATGCCGTCG 61.125 66.667 0.00 0.00 0.00 5.12
166 167 2.819595 CCCAACCATGCCGTCGAG 60.820 66.667 0.00 0.00 0.00 4.04
167 168 2.264480 CCAACCATGCCGTCGAGA 59.736 61.111 0.00 0.00 0.00 4.04
168 169 2.100631 CCAACCATGCCGTCGAGAC 61.101 63.158 0.00 0.00 0.00 3.36
178 179 4.298763 GTCGAGACGATTACGGGC 57.701 61.111 0.00 0.00 44.46 6.13
179 180 1.430632 GTCGAGACGATTACGGGCA 59.569 57.895 0.00 0.00 44.46 5.36
180 181 0.179156 GTCGAGACGATTACGGGCAA 60.179 55.000 0.00 0.00 44.46 4.52
181 182 0.742505 TCGAGACGATTACGGGCAAT 59.257 50.000 0.00 0.00 44.46 3.56
183 184 1.931172 CGAGACGATTACGGGCAATTT 59.069 47.619 0.00 0.00 44.46 1.82
184 185 2.285602 CGAGACGATTACGGGCAATTTG 60.286 50.000 0.00 0.00 44.46 2.32
185 186 2.933906 GAGACGATTACGGGCAATTTGA 59.066 45.455 0.00 0.00 44.46 2.69
188 189 2.418628 ACGATTACGGGCAATTTGAGTG 59.581 45.455 0.00 0.00 44.46 3.51
189 190 2.418628 CGATTACGGGCAATTTGAGTGT 59.581 45.455 0.00 0.00 35.72 3.55
190 191 3.485216 CGATTACGGGCAATTTGAGTGTC 60.485 47.826 0.00 0.65 35.72 3.67
191 192 1.434555 TACGGGCAATTTGAGTGTCG 58.565 50.000 0.00 0.00 0.00 4.35
192 193 1.234615 ACGGGCAATTTGAGTGTCGG 61.235 55.000 0.00 0.00 0.00 4.79
195 196 1.574428 GCAATTTGAGTGTCGGCGT 59.426 52.632 6.85 0.00 0.00 5.68
196 197 0.452784 GCAATTTGAGTGTCGGCGTC 60.453 55.000 6.85 0.72 0.00 5.19
198 199 0.953960 AATTTGAGTGTCGGCGTCCC 60.954 55.000 6.85 0.00 0.00 4.46
210 3503 2.961721 CGTCCCGACCATCATGCG 60.962 66.667 0.00 0.00 0.00 4.73
235 3528 6.262273 GGACCAATACATATTCACGTTGGATT 59.738 38.462 8.76 0.00 38.65 3.01
236 3529 7.442969 GGACCAATACATATTCACGTTGGATTA 59.557 37.037 8.76 0.00 38.65 1.75
247 3540 4.094590 TCACGTTGGATTACAAAACACGTT 59.905 37.500 0.00 0.00 41.58 3.99
248 3541 4.794246 CACGTTGGATTACAAAACACGTTT 59.206 37.500 0.00 0.00 41.58 3.60
259 3552 2.052590 CACGTTTCAACCACGCGG 60.053 61.111 12.47 0.00 41.53 6.46
271 3564 4.687215 ACGCGGTGCAGTGCAGAT 62.687 61.111 20.42 0.00 40.08 2.90
283 3576 1.065491 AGTGCAGATGATTACGGGCAA 60.065 47.619 0.00 0.00 32.50 4.52
290 3583 4.336433 CAGATGATTACGGGCAATTTGAGT 59.664 41.667 0.00 0.00 0.00 3.41
299 3592 0.452784 GCAATTTGAGTGTCGGCGTC 60.453 55.000 6.85 0.72 0.00 5.19
405 3727 0.515127 TGCGCTTTGTTGTATGGTCG 59.485 50.000 9.73 0.00 0.00 4.79
460 4228 3.983821 ACACAAAGACCCTTTAACCCAA 58.016 40.909 0.00 0.00 0.00 4.12
506 4274 6.650807 AGAAGAAGAATATGCAACAACGAAGA 59.349 34.615 0.00 0.00 0.00 2.87
626 4402 0.596600 GAACGAGTCCAACAGCGTGA 60.597 55.000 0.00 0.00 37.03 4.35
678 4468 2.742774 CAAGCGGGTGAAAAGGAAAAG 58.257 47.619 0.00 0.00 0.00 2.27
679 4469 2.358322 AGCGGGTGAAAAGGAAAAGA 57.642 45.000 0.00 0.00 0.00 2.52
680 4470 2.876581 AGCGGGTGAAAAGGAAAAGAT 58.123 42.857 0.00 0.00 0.00 2.40
682 4472 4.403734 AGCGGGTGAAAAGGAAAAGATAA 58.596 39.130 0.00 0.00 0.00 1.75
683 4473 5.016831 AGCGGGTGAAAAGGAAAAGATAAT 58.983 37.500 0.00 0.00 0.00 1.28
685 4475 6.318900 AGCGGGTGAAAAGGAAAAGATAATAG 59.681 38.462 0.00 0.00 0.00 1.73
748 4539 3.315191 TCGCAACAGAGGGAAAAAGAAAG 59.685 43.478 0.00 0.00 0.00 2.62
760 4554 5.163301 GGGAAAAAGAAAGGAAAAGAAGGCT 60.163 40.000 0.00 0.00 0.00 4.58
871 4681 2.411290 AAAAACACCACAGGCGCG 59.589 55.556 0.00 0.00 0.00 6.86
980 4805 0.391597 TTCCATTCCCGATACCTCGC 59.608 55.000 0.00 0.00 43.66 5.03
988 4813 2.913060 GATACCTCGCCCTCGCCT 60.913 66.667 0.00 0.00 35.26 5.52
1134 4962 2.669808 CTTCCTCGTCCTCATCGCCG 62.670 65.000 0.00 0.00 0.00 6.46
1721 5564 3.707793 GCCGGATCAAGAAGTAGTAGTG 58.292 50.000 5.05 0.00 0.00 2.74
1727 5570 5.360144 GGATCAAGAAGTAGTAGTGGTAGCA 59.640 44.000 0.00 0.00 0.00 3.49
1728 5571 5.899120 TCAAGAAGTAGTAGTGGTAGCAG 57.101 43.478 0.00 0.00 0.00 4.24
1729 5572 4.158025 TCAAGAAGTAGTAGTGGTAGCAGC 59.842 45.833 0.00 0.00 0.00 5.25
1730 5573 3.970842 AGAAGTAGTAGTGGTAGCAGCT 58.029 45.455 0.00 0.00 0.00 4.24
1741 5588 2.366590 TGGTAGCAGCTATGAGTGGATG 59.633 50.000 5.14 0.00 0.00 3.51
1742 5589 2.630098 GGTAGCAGCTATGAGTGGATGA 59.370 50.000 5.14 0.00 0.00 2.92
1743 5590 2.906691 AGCAGCTATGAGTGGATGAC 57.093 50.000 0.00 0.00 0.00 3.06
1744 5591 2.113807 AGCAGCTATGAGTGGATGACA 58.886 47.619 0.00 0.00 0.00 3.58
1984 5845 0.536006 GTGACTCTTGCCTTGCCTGT 60.536 55.000 0.00 0.00 0.00 4.00
1987 5854 0.183492 ACTCTTGCCTTGCCTGTTGA 59.817 50.000 0.00 0.00 0.00 3.18
1996 5863 4.157656 TGCCTTGCCTGTTGATATACAAAC 59.842 41.667 0.00 0.00 40.36 2.93
2001 5868 7.120579 CCTTGCCTGTTGATATACAAACAAGTA 59.879 37.037 13.79 0.00 40.36 2.24
2015 5882 4.530710 AACAAGTACTGCGATGGACTTA 57.469 40.909 0.00 0.00 31.05 2.24
2016 5883 3.846360 ACAAGTACTGCGATGGACTTAC 58.154 45.455 0.00 0.00 31.05 2.34
2027 5894 4.157840 GCGATGGACTTACCCTCAAAAATT 59.842 41.667 0.00 0.00 38.00 1.82
2055 5922 6.112734 TGTGTTGTGTGGATGAATAGATACC 58.887 40.000 0.00 0.00 0.00 2.73
2139 6018 8.816894 TCTTTATTCTCTGAGATGGTAGTTGTT 58.183 33.333 8.42 0.00 0.00 2.83
2143 6022 6.419484 TCTCTGAGATGGTAGTTGTTTTCA 57.581 37.500 2.58 0.00 0.00 2.69
2188 6074 6.147985 TGAACTGTTTGGTTTTGTTTTAAGCC 59.852 34.615 0.00 0.00 0.00 4.35
2209 6095 2.147150 GTGTTGAGCTGAAAGTCTCCC 58.853 52.381 0.00 0.00 36.63 4.30
2372 6258 6.094881 CCATGGTTTACCTGTATTAAGTGTGG 59.905 42.308 2.57 0.00 36.82 4.17
2383 6269 0.883153 TAAGTGTGGCGCTTACTCGA 59.117 50.000 7.64 0.00 35.69 4.04
2642 6529 9.956640 AAATGCCAGGAAAAATTATTTGTATGA 57.043 25.926 0.00 0.00 0.00 2.15
2737 6624 3.617531 GCCTATACCCTTGATCACCATCG 60.618 52.174 0.00 0.00 0.00 3.84
3608 7495 8.613482 GGTTCTTTAATTGCTAGACTGTATTCC 58.387 37.037 0.00 0.00 0.00 3.01
3793 7681 8.947115 GTCTTGGTTAAGAGCTTATTACACAAT 58.053 33.333 0.00 0.00 43.29 2.71
3891 7779 3.719268 TTGCATAGTTCTGTCACCCAT 57.281 42.857 0.00 0.00 0.00 4.00
4072 7960 4.128643 CAAAATTTCATGGCCTGTGTGTT 58.871 39.130 3.32 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.595538 TCCGCGTCTGGCAAACGT 62.596 61.111 15.50 0.00 43.84 3.99
14 15 4.072088 GTCCGCGTCTGGCAAACG 62.072 66.667 9.38 9.38 43.84 3.60
15 16 2.325082 ATGTCCGCGTCTGGCAAAC 61.325 57.895 4.92 0.00 43.84 2.93
17 18 2.741985 CATGTCCGCGTCTGGCAA 60.742 61.111 4.92 0.00 43.84 4.52
19 20 2.742372 AACATGTCCGCGTCTGGC 60.742 61.111 4.92 0.00 38.69 4.85
20 21 1.374125 TCAACATGTCCGCGTCTGG 60.374 57.895 4.92 0.00 0.00 3.86
21 22 1.781555 GTCAACATGTCCGCGTCTG 59.218 57.895 4.92 0.00 0.00 3.51
22 23 1.733041 CGTCAACATGTCCGCGTCT 60.733 57.895 4.92 0.00 0.00 4.18
23 24 2.726691 CCGTCAACATGTCCGCGTC 61.727 63.158 4.92 0.00 0.00 5.19
24 25 2.736995 CCGTCAACATGTCCGCGT 60.737 61.111 4.92 0.00 0.00 6.01
25 26 2.726691 GACCGTCAACATGTCCGCG 61.727 63.158 0.00 0.00 0.00 6.46
26 27 2.388232 GGACCGTCAACATGTCCGC 61.388 63.158 0.00 0.00 39.22 5.54
27 28 3.870606 GGACCGTCAACATGTCCG 58.129 61.111 0.00 1.97 39.22 4.79
29 30 1.429463 GTCTGGACCGTCAACATGTC 58.571 55.000 0.00 0.00 0.00 3.06
32 33 1.374252 GCGTCTGGACCGTCAACAT 60.374 57.895 0.00 0.00 0.00 2.71
41 42 1.153229 GGGTTATGGGCGTCTGGAC 60.153 63.158 0.00 0.00 0.00 4.02
43 44 2.192175 GGGGTTATGGGCGTCTGG 59.808 66.667 0.00 0.00 0.00 3.86
45 46 4.171103 GCGGGGTTATGGGCGTCT 62.171 66.667 0.00 0.00 0.00 4.18
46 47 4.171103 AGCGGGGTTATGGGCGTC 62.171 66.667 0.00 0.00 0.00 5.19
47 48 4.171103 GAGCGGGGTTATGGGCGT 62.171 66.667 0.00 0.00 0.00 5.68
49 50 4.581093 GGGAGCGGGGTTATGGGC 62.581 72.222 0.00 0.00 0.00 5.36
50 51 3.886001 GGGGAGCGGGGTTATGGG 61.886 72.222 0.00 0.00 0.00 4.00
51 52 2.006805 ATTGGGGAGCGGGGTTATGG 62.007 60.000 0.00 0.00 0.00 2.74
53 54 0.634465 AAATTGGGGAGCGGGGTTAT 59.366 50.000 0.00 0.00 0.00 1.89
55 56 1.157513 AAAATTGGGGAGCGGGGTT 59.842 52.632 0.00 0.00 0.00 4.11
56 57 1.609210 CAAAATTGGGGAGCGGGGT 60.609 57.895 0.00 0.00 0.00 4.95
57 58 1.604147 GACAAAATTGGGGAGCGGGG 61.604 60.000 0.00 0.00 0.00 5.73
58 59 0.611896 AGACAAAATTGGGGAGCGGG 60.612 55.000 0.00 0.00 0.00 6.13
59 60 0.811281 GAGACAAAATTGGGGAGCGG 59.189 55.000 0.00 0.00 0.00 5.52
61 62 0.811281 CGGAGACAAAATTGGGGAGC 59.189 55.000 0.00 0.00 0.00 4.70
63 64 0.774908 ACCGGAGACAAAATTGGGGA 59.225 50.000 9.46 0.00 0.00 4.81
64 65 1.627864 AACCGGAGACAAAATTGGGG 58.372 50.000 9.46 0.00 0.00 4.96
65 66 2.866065 GCAAACCGGAGACAAAATTGGG 60.866 50.000 9.46 0.00 0.00 4.12
66 67 2.403259 GCAAACCGGAGACAAAATTGG 58.597 47.619 9.46 0.00 0.00 3.16
67 68 2.050691 CGCAAACCGGAGACAAAATTG 58.949 47.619 9.46 1.26 0.00 2.32
68 69 2.415697 CGCAAACCGGAGACAAAATT 57.584 45.000 9.46 0.00 0.00 1.82
79 80 1.660264 GTGCTTTTCCCGCAAACCG 60.660 57.895 0.00 0.00 39.39 4.44
80 81 1.660264 CGTGCTTTTCCCGCAAACC 60.660 57.895 0.00 0.00 39.39 3.27
81 82 0.933047 GACGTGCTTTTCCCGCAAAC 60.933 55.000 0.00 0.00 39.39 2.93
82 83 1.357334 GACGTGCTTTTCCCGCAAA 59.643 52.632 0.00 0.00 39.39 3.68
83 84 2.548295 GGACGTGCTTTTCCCGCAA 61.548 57.895 0.00 0.00 39.39 4.85
84 85 2.975799 GGACGTGCTTTTCCCGCA 60.976 61.111 0.00 0.00 34.52 5.69
86 87 3.419759 CCGGACGTGCTTTTCCCG 61.420 66.667 5.27 3.90 39.85 5.14
87 88 3.733960 GCCGGACGTGCTTTTCCC 61.734 66.667 5.05 0.00 0.00 3.97
88 89 2.253414 GATGCCGGACGTGCTTTTCC 62.253 60.000 5.05 0.00 0.00 3.13
89 90 1.134694 GATGCCGGACGTGCTTTTC 59.865 57.895 5.05 0.00 0.00 2.29
92 93 3.706373 AGGATGCCGGACGTGCTT 61.706 61.111 5.05 0.00 30.60 3.91
93 94 4.457496 CAGGATGCCGGACGTGCT 62.457 66.667 5.05 5.90 36.17 4.40
95 96 1.226974 CTACAGGATGCCGGACGTG 60.227 63.158 5.05 10.16 42.53 4.49
97 98 1.065928 GTCTACAGGATGCCGGACG 59.934 63.158 5.05 0.00 42.53 4.79
98 99 1.065928 CGTCTACAGGATGCCGGAC 59.934 63.158 5.05 0.00 42.53 4.79
99 100 0.681887 TTCGTCTACAGGATGCCGGA 60.682 55.000 5.05 0.00 42.53 5.14
100 101 0.389391 ATTCGTCTACAGGATGCCGG 59.611 55.000 0.00 0.00 42.53 6.13
101 102 2.662700 GTATTCGTCTACAGGATGCCG 58.337 52.381 0.00 0.00 42.53 5.69
102 103 2.662700 CGTATTCGTCTACAGGATGCC 58.337 52.381 0.00 0.00 42.53 4.40
121 122 4.655440 TTTGTCATCCAACACGAATACG 57.345 40.909 0.00 0.00 37.96 3.06
124 125 4.606961 GTGTTTTGTCATCCAACACGAAT 58.393 39.130 0.00 0.00 40.56 3.34
125 126 4.022464 GTGTTTTGTCATCCAACACGAA 57.978 40.909 0.00 0.00 40.56 3.85
126 127 3.684103 GTGTTTTGTCATCCAACACGA 57.316 42.857 0.00 0.00 40.56 4.35
128 129 3.359654 GACGTGTTTTGTCATCCAACAC 58.640 45.455 0.00 10.90 44.54 3.32
130 131 2.287368 GGGACGTGTTTTGTCATCCAAC 60.287 50.000 0.00 0.00 38.10 3.77
132 133 1.134068 TGGGACGTGTTTTGTCATCCA 60.134 47.619 0.00 0.00 38.10 3.41
133 134 1.600023 TGGGACGTGTTTTGTCATCC 58.400 50.000 0.00 0.00 38.10 3.51
134 135 2.287368 GGTTGGGACGTGTTTTGTCATC 60.287 50.000 0.00 0.00 38.10 2.92
137 138 1.096416 TGGTTGGGACGTGTTTTGTC 58.904 50.000 0.00 0.00 35.60 3.18
139 140 1.867698 GCATGGTTGGGACGTGTTTTG 60.868 52.381 0.00 0.00 0.00 2.44
141 142 1.460273 GGCATGGTTGGGACGTGTTT 61.460 55.000 0.00 0.00 0.00 2.83
142 143 1.901464 GGCATGGTTGGGACGTGTT 60.901 57.895 0.00 0.00 0.00 3.32
143 144 2.282180 GGCATGGTTGGGACGTGT 60.282 61.111 0.00 0.00 0.00 4.49
144 145 3.430862 CGGCATGGTTGGGACGTG 61.431 66.667 0.00 0.00 0.00 4.49
145 146 3.894547 GACGGCATGGTTGGGACGT 62.895 63.158 0.00 0.00 37.26 4.34
146 147 3.124921 GACGGCATGGTTGGGACG 61.125 66.667 0.00 0.00 0.00 4.79
147 148 3.124921 CGACGGCATGGTTGGGAC 61.125 66.667 0.00 0.00 0.00 4.46
148 149 3.309436 CTCGACGGCATGGTTGGGA 62.309 63.158 0.00 0.00 0.00 4.37
150 151 2.100631 GTCTCGACGGCATGGTTGG 61.101 63.158 0.00 0.00 0.00 3.77
161 162 0.179156 TTGCCCGTAATCGTCTCGAC 60.179 55.000 0.00 0.00 39.18 4.20
162 163 0.742505 ATTGCCCGTAATCGTCTCGA 59.257 50.000 0.00 0.00 41.13 4.04
163 164 1.567504 AATTGCCCGTAATCGTCTCG 58.432 50.000 0.00 0.00 35.01 4.04
164 165 2.933906 TCAAATTGCCCGTAATCGTCTC 59.066 45.455 0.00 0.00 35.01 3.36
166 167 2.676342 ACTCAAATTGCCCGTAATCGTC 59.324 45.455 0.00 0.00 35.01 4.20
167 168 2.418628 CACTCAAATTGCCCGTAATCGT 59.581 45.455 0.00 0.00 35.01 3.73
168 169 2.418628 ACACTCAAATTGCCCGTAATCG 59.581 45.455 0.00 0.00 0.00 3.34
169 170 3.485216 CGACACTCAAATTGCCCGTAATC 60.485 47.826 0.00 0.00 0.00 1.75
170 171 2.418628 CGACACTCAAATTGCCCGTAAT 59.581 45.455 0.00 0.00 0.00 1.89
172 173 1.434555 CGACACTCAAATTGCCCGTA 58.565 50.000 0.00 0.00 0.00 4.02
175 176 1.212751 GCCGACACTCAAATTGCCC 59.787 57.895 0.00 0.00 0.00 5.36
176 177 1.154225 CGCCGACACTCAAATTGCC 60.154 57.895 0.00 0.00 0.00 4.52
177 178 0.452784 GACGCCGACACTCAAATTGC 60.453 55.000 0.00 0.00 0.00 3.56
178 179 0.165944 GGACGCCGACACTCAAATTG 59.834 55.000 0.00 0.00 0.00 2.32
179 180 0.953960 GGGACGCCGACACTCAAATT 60.954 55.000 0.00 0.00 0.00 1.82
180 181 1.375523 GGGACGCCGACACTCAAAT 60.376 57.895 0.00 0.00 0.00 2.32
181 182 2.029964 GGGACGCCGACACTCAAA 59.970 61.111 0.00 0.00 0.00 2.69
195 196 2.762043 TCCGCATGATGGTCGGGA 60.762 61.111 10.78 0.00 43.10 5.14
196 197 2.588877 GTCCGCATGATGGTCGGG 60.589 66.667 10.78 0.00 43.10 5.14
198 199 0.815213 ATTGGTCCGCATGATGGTCG 60.815 55.000 0.00 0.00 0.00 4.79
200 201 1.211703 TGTATTGGTCCGCATGATGGT 59.788 47.619 0.00 0.00 0.00 3.55
201 202 1.965935 TGTATTGGTCCGCATGATGG 58.034 50.000 0.00 0.00 0.00 3.51
202 203 5.412286 TGAATATGTATTGGTCCGCATGATG 59.588 40.000 0.00 0.00 0.00 3.07
204 205 4.754618 GTGAATATGTATTGGTCCGCATGA 59.245 41.667 0.00 0.00 0.00 3.07
205 206 4.377328 CGTGAATATGTATTGGTCCGCATG 60.377 45.833 0.00 0.00 0.00 4.06
210 3503 5.120399 TCCAACGTGAATATGTATTGGTCC 58.880 41.667 0.00 0.00 29.55 4.46
235 3528 3.744987 CGTGGTTGAAACGTGTTTTGTA 58.255 40.909 0.00 0.00 36.31 2.41
236 3529 2.586900 CGTGGTTGAAACGTGTTTTGT 58.413 42.857 0.00 0.00 36.31 2.83
259 3552 1.328680 CCGTAATCATCTGCACTGCAC 59.671 52.381 0.00 0.00 33.79 4.57
260 3553 1.655484 CCGTAATCATCTGCACTGCA 58.345 50.000 3.11 3.11 36.92 4.41
261 3554 0.940126 CCCGTAATCATCTGCACTGC 59.060 55.000 0.00 0.00 0.00 4.40
262 3555 0.940126 GCCCGTAATCATCTGCACTG 59.060 55.000 0.00 0.00 0.00 3.66
263 3556 0.541392 TGCCCGTAATCATCTGCACT 59.459 50.000 0.00 0.00 0.00 4.40
264 3557 1.378531 TTGCCCGTAATCATCTGCAC 58.621 50.000 0.00 0.00 0.00 4.57
266 3559 3.066621 TCAAATTGCCCGTAATCATCTGC 59.933 43.478 0.00 0.00 0.00 4.26
271 3564 3.417101 ACACTCAAATTGCCCGTAATCA 58.583 40.909 0.00 0.00 0.00 2.57
283 3576 1.736645 CCGACGCCGACACTCAAAT 60.737 57.895 0.00 0.00 38.22 2.32
290 3583 4.492160 GCATCTCCGACGCCGACA 62.492 66.667 0.00 0.00 38.22 4.35
299 3592 3.119101 ACCTTGTAGTTAGTGCATCTCCG 60.119 47.826 0.00 0.00 0.00 4.63
405 3727 1.846648 CGAGAGTCACACGTTGCAC 59.153 57.895 0.00 0.00 0.00 4.57
460 4228 3.564053 TCTTTACGGTTGGACCTTTGT 57.436 42.857 0.00 0.00 35.66 2.83
506 4274 9.429359 CTTGCCAATATTCTAAGATAACTCGAT 57.571 33.333 0.00 0.00 0.00 3.59
626 4402 0.957395 CGTTTCAGGTGCAGGCTCAT 60.957 55.000 0.00 0.00 0.00 2.90
678 4468 4.569564 ACACGGCGTTCTTTTCCTATTATC 59.430 41.667 11.19 0.00 0.00 1.75
679 4469 4.331717 CACACGGCGTTCTTTTCCTATTAT 59.668 41.667 11.19 0.00 0.00 1.28
680 4470 3.680937 CACACGGCGTTCTTTTCCTATTA 59.319 43.478 11.19 0.00 0.00 0.98
682 4472 2.073816 CACACGGCGTTCTTTTCCTAT 58.926 47.619 11.19 0.00 0.00 2.57
683 4473 1.068895 TCACACGGCGTTCTTTTCCTA 59.931 47.619 11.19 0.00 0.00 2.94
685 4475 0.658897 TTCACACGGCGTTCTTTTCC 59.341 50.000 11.19 0.00 0.00 3.13
738 4529 5.687730 CGAGCCTTCTTTTCCTTTCTTTTTC 59.312 40.000 0.00 0.00 0.00 2.29
748 4539 1.027255 GGAGCCGAGCCTTCTTTTCC 61.027 60.000 0.00 0.00 0.00 3.13
871 4681 4.688966 GATCTGATCGGCCCCGGC 62.689 72.222 6.90 0.00 40.25 6.13
874 4684 4.008933 CGGGATCTGATCGGCCCC 62.009 72.222 17.32 17.32 37.27 5.80
875 4685 4.688966 GCGGGATCTGATCGGCCC 62.689 72.222 16.80 10.74 37.21 5.80
1116 4944 2.771639 CGGCGATGAGGACGAGGAA 61.772 63.158 0.00 0.00 42.31 3.36
1122 4950 2.278013 GACGACGGCGATGAGGAC 60.278 66.667 22.49 0.00 41.64 3.85
1134 4962 2.624437 ATAGCTTTCCCCGCGACGAC 62.624 60.000 8.23 0.00 0.00 4.34
1721 5564 2.630098 TCATCCACTCATAGCTGCTACC 59.370 50.000 12.26 0.00 0.00 3.18
1727 5570 3.131933 GTGTCTGTCATCCACTCATAGCT 59.868 47.826 0.00 0.00 0.00 3.32
1728 5571 3.452474 GTGTCTGTCATCCACTCATAGC 58.548 50.000 0.00 0.00 0.00 2.97
1729 5572 3.448660 TGGTGTCTGTCATCCACTCATAG 59.551 47.826 0.00 0.00 0.00 2.23
1730 5573 3.440127 TGGTGTCTGTCATCCACTCATA 58.560 45.455 0.00 0.00 0.00 2.15
1741 5588 2.024319 GTGAGCGCTGGTGTCTGTC 61.024 63.158 18.48 0.00 0.00 3.51
1742 5589 2.029666 GTGAGCGCTGGTGTCTGT 59.970 61.111 18.48 0.00 0.00 3.41
1743 5590 2.025969 CAGTGAGCGCTGGTGTCTG 61.026 63.158 18.48 11.80 33.11 3.51
1744 5591 2.341543 CAGTGAGCGCTGGTGTCT 59.658 61.111 18.48 2.30 33.11 3.41
1793 5645 7.062839 GCAAGAGCACTGTATTATAGAGTATGC 59.937 40.741 1.63 3.29 41.58 3.14
1984 5845 7.011016 CCATCGCAGTACTTGTTTGTATATCAA 59.989 37.037 0.00 0.00 0.00 2.57
1987 5854 6.479001 GTCCATCGCAGTACTTGTTTGTATAT 59.521 38.462 0.00 0.00 0.00 0.86
1996 5863 3.187700 GGTAAGTCCATCGCAGTACTTG 58.812 50.000 0.00 0.00 34.23 3.16
2001 5868 0.824759 GAGGGTAAGTCCATCGCAGT 59.175 55.000 0.00 0.00 37.27 4.40
2015 5882 5.411053 CACAACACAAACAATTTTTGAGGGT 59.589 36.000 15.45 9.88 33.83 4.34
2016 5883 5.411053 ACACAACACAAACAATTTTTGAGGG 59.589 36.000 15.45 9.47 33.83 4.30
2027 5894 4.998671 ATTCATCCACACAACACAAACA 57.001 36.364 0.00 0.00 0.00 2.83
2055 5922 5.580691 TCGTTCAACCAGCATATAAACTGAG 59.419 40.000 6.88 1.43 35.90 3.35
2131 6010 6.060028 TGCAGACTTCATGAAAACAACTAC 57.940 37.500 9.88 1.09 0.00 2.73
2139 6018 6.578163 TCAATTGATGCAGACTTCATGAAA 57.422 33.333 9.88 0.00 30.75 2.69
2188 6074 1.795286 GGAGACTTTCAGCTCAACACG 59.205 52.381 0.00 0.00 32.83 4.49
2209 6095 3.009916 AGAAGCTATCCCTGCCATTATGG 59.990 47.826 6.92 6.92 41.55 2.74
2372 6258 0.739813 ACCACCAATCGAGTAAGCGC 60.740 55.000 0.00 0.00 0.00 5.92
2383 6269 6.352516 CAAAGATAGCTAGAGAACCACCAAT 58.647 40.000 0.00 0.00 0.00 3.16
2580 6467 3.331150 TGGTGATTAAACTGCGTAGGTG 58.669 45.455 5.26 0.00 0.00 4.00
2737 6624 5.294306 TGATCTGAACACTCAAAACACTGAC 59.706 40.000 0.00 0.00 0.00 3.51
3556 7443 2.738314 GAGCGAAAAAGCAATTTGGCAT 59.262 40.909 18.41 7.85 43.73 4.40
3628 7515 1.444119 TTTGAACGCTGCGCTTCCTT 61.444 50.000 23.51 8.38 0.00 3.36
3694 7581 1.606601 AGCTACCACTCTCGTGCCA 60.607 57.895 0.00 0.00 39.86 4.92
3793 7681 4.401022 TCGAGGTGAGGTACTGAAACTAA 58.599 43.478 0.00 0.00 41.55 2.24


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

AutoCloner maintained by Alex Coulton.