Multiple sequence alignment - TraesCS5A01G381900

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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 TraesCS5A01G381900 chr5A 100.000 2253 0 0 1 2253 579844500 579842248 0.000000e+00 4161
1 TraesCS5A01G381900 chr5A 92.686 793 48 8 1464 2251 579849488 579848701 0.000000e+00 1134
2 TraesCS5A01G381900 chr5A 87.455 558 57 4 928 1481 579893818 579894366 4.080000e-177 630
3 TraesCS5A01G381900 chr5A 91.972 436 33 2 718 1152 579849932 579849498 5.320000e-171 610
4 TraesCS5A01G381900 chr5A 89.549 421 38 6 1836 2251 579917848 579918267 1.530000e-146 529
5 TraesCS5A01G381900 chr5D 91.691 2058 125 19 207 2253 459758539 459760561 0.000000e+00 2811
6 TraesCS5A01G381900 chr5D 91.545 2058 128 19 207 2253 459763000 459765022 0.000000e+00 2795
7 TraesCS5A01G381900 chr5D 91.593 2034 135 20 207 2227 459750412 459752422 0.000000e+00 2776
8 TraesCS5A01G381900 chr5D 88.555 865 76 6 618 1481 459742120 459742962 0.000000e+00 1027
9 TraesCS5A01G381900 chr5D 82.343 1161 159 28 215 1363 11576707 11575581 0.000000e+00 966
10 TraesCS5A01G381900 chr5B 89.831 1957 149 22 207 2154 564477785 564479700 0.000000e+00 2466
11 TraesCS5A01G381900 chr5B 90.832 1418 101 17 840 2251 564438322 564439716 0.000000e+00 1871
12 TraesCS5A01G381900 chr5B 90.762 1418 104 16 840 2251 564376169 564377565 0.000000e+00 1868
13 TraesCS5A01G381900 chr5B 90.265 1397 103 18 862 2251 564025617 564026987 0.000000e+00 1796
14 TraesCS5A01G381900 chr5B 90.598 1170 90 12 842 2010 564445082 564446232 0.000000e+00 1533
15 TraesCS5A01G381900 chr5B 82.471 1044 152 17 215 1253 11503373 11504390 0.000000e+00 885
16 TraesCS5A01G381900 chr5B 92.063 567 36 6 1690 2251 564316286 564316848 0.000000e+00 789
17 TraesCS5A01G381900 chr5B 84.932 730 104 6 249 974 564509500 564510227 0.000000e+00 734
18 TraesCS5A01G381900 chr5B 84.088 773 84 15 207 974 564457017 564457755 0.000000e+00 710
19 TraesCS5A01G381900 chr5B 88.750 400 36 6 1852 2245 564529655 564530051 4.350000e-132 481
20 TraesCS5A01G381900 chr5B 84.393 173 18 5 207 378 564218439 564218603 6.440000e-36 161
21 TraesCS5A01G381900 chr1A 83.004 1112 153 19 263 1363 99726747 99725661 0.000000e+00 974
22 TraesCS5A01G381900 chr1A 96.651 209 6 1 1 209 48757939 48757732 1.660000e-91 346
23 TraesCS5A01G381900 chr7A 97.129 209 5 1 1 209 578361137 578361344 3.560000e-93 351
24 TraesCS5A01G381900 chr7A 96.682 211 6 1 1 211 713621758 713621967 1.280000e-92 350
25 TraesCS5A01G381900 chr7A 96.682 211 6 1 1 211 713629235 713629444 1.280000e-92 350
26 TraesCS5A01G381900 chr7A 96.682 211 6 1 1 211 713656084 713656293 1.280000e-92 350
27 TraesCS5A01G381900 chr7A 96.651 209 6 1 1 209 572183964 572184171 1.660000e-91 346
28 TraesCS5A01G381900 chr7A 96.651 209 6 1 1 209 641179760 641179967 1.660000e-91 346
29 TraesCS5A01G381900 chrUn 96.682 211 6 1 1 211 358639683 358639892 1.280000e-92 350
30 TraesCS5A01G381900 chr1B 96.226 212 7 1 1 212 522754733 522754523 1.660000e-91 346


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 TraesCS5A01G381900 chr5A 579842248 579844500 2252 True 4161 4161 100.000 1 2253 1 chr5A.!!$R1 2252
1 TraesCS5A01G381900 chr5A 579848701 579849932 1231 True 872 1134 92.329 718 2251 2 chr5A.!!$R2 1533
2 TraesCS5A01G381900 chr5A 579893818 579894366 548 False 630 630 87.455 928 1481 1 chr5A.!!$F1 553
3 TraesCS5A01G381900 chr5D 459758539 459765022 6483 False 2803 2811 91.618 207 2253 2 chr5D.!!$F3 2046
4 TraesCS5A01G381900 chr5D 459750412 459752422 2010 False 2776 2776 91.593 207 2227 1 chr5D.!!$F2 2020
5 TraesCS5A01G381900 chr5D 459742120 459742962 842 False 1027 1027 88.555 618 1481 1 chr5D.!!$F1 863
6 TraesCS5A01G381900 chr5D 11575581 11576707 1126 True 966 966 82.343 215 1363 1 chr5D.!!$R1 1148
7 TraesCS5A01G381900 chr5B 564477785 564479700 1915 False 2466 2466 89.831 207 2154 1 chr5B.!!$F9 1947
8 TraesCS5A01G381900 chr5B 564438322 564439716 1394 False 1871 1871 90.832 840 2251 1 chr5B.!!$F6 1411
9 TraesCS5A01G381900 chr5B 564376169 564377565 1396 False 1868 1868 90.762 840 2251 1 chr5B.!!$F5 1411
10 TraesCS5A01G381900 chr5B 564025617 564026987 1370 False 1796 1796 90.265 862 2251 1 chr5B.!!$F2 1389
11 TraesCS5A01G381900 chr5B 564445082 564446232 1150 False 1533 1533 90.598 842 2010 1 chr5B.!!$F7 1168
12 TraesCS5A01G381900 chr5B 11503373 11504390 1017 False 885 885 82.471 215 1253 1 chr5B.!!$F1 1038
13 TraesCS5A01G381900 chr5B 564316286 564316848 562 False 789 789 92.063 1690 2251 1 chr5B.!!$F4 561
14 TraesCS5A01G381900 chr5B 564509500 564510227 727 False 734 734 84.932 249 974 1 chr5B.!!$F10 725
15 TraesCS5A01G381900 chr5B 564457017 564457755 738 False 710 710 84.088 207 974 1 chr5B.!!$F8 767
16 TraesCS5A01G381900 chr1A 99725661 99726747 1086 True 974 974 83.004 263 1363 1 chr1A.!!$R2 1100

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
148 149 0.110867 TGTTTGCACGAATCGCGAAG 60.111 50.0 15.24 10.67 44.57 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1793 0.171231 CAGATCTCTTCGTGCCGACA 59.829 55.0 0.0 0.0 34.89 4.35 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
65 66 8.364142 TCCTAGATTCTAGATAGAAAGCTTTGC 58.636 37.037 18.30 8.41 44.63 3.68
66 67 7.602265 CCTAGATTCTAGATAGAAAGCTTTGCC 59.398 40.741 18.30 2.73 44.63 4.52
67 68 6.893583 AGATTCTAGATAGAAAGCTTTGCCA 58.106 36.000 18.30 1.15 44.63 4.92
68 69 6.765512 AGATTCTAGATAGAAAGCTTTGCCAC 59.234 38.462 18.30 1.49 44.63 5.01
69 70 4.433615 TCTAGATAGAAAGCTTTGCCACG 58.566 43.478 18.30 0.00 0.00 4.94
70 71 1.740025 AGATAGAAAGCTTTGCCACGC 59.260 47.619 18.30 0.25 0.00 5.34
71 72 1.740025 GATAGAAAGCTTTGCCACGCT 59.260 47.619 18.30 8.71 38.30 5.07
72 73 0.874390 TAGAAAGCTTTGCCACGCTG 59.126 50.000 18.30 0.00 36.45 5.18
73 74 2.018324 GAAAGCTTTGCCACGCTGC 61.018 57.895 18.30 0.00 36.45 5.25
74 75 2.682256 GAAAGCTTTGCCACGCTGCA 62.682 55.000 18.30 0.00 40.07 4.41
80 81 3.127451 TGCCACGCTGCAAATGTT 58.873 50.000 0.00 0.00 38.56 2.71
81 82 1.440893 TGCCACGCTGCAAATGTTT 59.559 47.368 0.00 0.00 38.56 2.83
82 83 0.875040 TGCCACGCTGCAAATGTTTG 60.875 50.000 0.00 1.19 38.56 2.93
83 84 0.597118 GCCACGCTGCAAATGTTTGA 60.597 50.000 9.53 0.00 40.55 2.69
84 85 1.850377 CCACGCTGCAAATGTTTGAA 58.150 45.000 9.53 0.00 40.55 2.69
85 86 1.522258 CCACGCTGCAAATGTTTGAAC 59.478 47.619 9.53 0.00 40.55 3.18
86 87 2.462889 CACGCTGCAAATGTTTGAACT 58.537 42.857 9.53 0.00 40.55 3.01
87 88 2.859538 CACGCTGCAAATGTTTGAACTT 59.140 40.909 9.53 0.00 40.55 2.66
88 89 3.061006 CACGCTGCAAATGTTTGAACTTC 60.061 43.478 9.53 0.00 40.55 3.01
89 90 3.114809 CGCTGCAAATGTTTGAACTTCA 58.885 40.909 9.53 0.00 40.55 3.02
90 91 3.551082 CGCTGCAAATGTTTGAACTTCAA 59.449 39.130 9.53 0.00 40.55 2.69
91 92 4.032672 CGCTGCAAATGTTTGAACTTCAAA 59.967 37.500 12.12 12.12 43.37 2.69
92 93 5.445673 CGCTGCAAATGTTTGAACTTCAAAA 60.446 36.000 16.79 9.19 46.53 2.44
93 94 5.734035 GCTGCAAATGTTTGAACTTCAAAAC 59.266 36.000 16.79 12.07 46.53 2.43
94 95 6.620303 GCTGCAAATGTTTGAACTTCAAAACA 60.620 34.615 16.79 16.12 46.53 2.83
95 96 7.375106 TGCAAATGTTTGAACTTCAAAACAT 57.625 28.000 16.79 17.27 46.53 2.71
96 97 7.242079 TGCAAATGTTTGAACTTCAAAACATG 58.758 30.769 16.79 13.98 46.53 3.21
97 98 7.094890 TGCAAATGTTTGAACTTCAAAACATGT 60.095 29.630 16.79 14.07 46.53 3.21
98 99 7.750014 GCAAATGTTTGAACTTCAAAACATGTT 59.250 29.630 16.79 4.92 46.53 2.71
99 100 9.609950 CAAATGTTTGAACTTCAAAACATGTTT 57.390 25.926 18.13 18.13 46.53 2.83
104 105 9.209297 GTTTGAACTTCAAAACATGTTTTATGC 57.791 29.630 30.65 17.77 46.53 3.14
105 106 7.159437 TGAACTTCAAAACATGTTTTATGCG 57.841 32.000 30.65 20.37 40.45 4.73
106 107 6.975197 TGAACTTCAAAACATGTTTTATGCGA 59.025 30.769 30.65 22.02 40.45 5.10
107 108 6.991485 ACTTCAAAACATGTTTTATGCGAG 57.009 33.333 30.65 23.69 40.45 5.03
108 109 6.734137 ACTTCAAAACATGTTTTATGCGAGA 58.266 32.000 30.65 21.10 40.45 4.04
109 110 6.857964 ACTTCAAAACATGTTTTATGCGAGAG 59.142 34.615 30.65 22.44 40.45 3.20
110 111 6.552859 TCAAAACATGTTTTATGCGAGAGA 57.447 33.333 30.65 19.90 40.45 3.10
111 112 6.964908 TCAAAACATGTTTTATGCGAGAGAA 58.035 32.000 30.65 5.47 40.45 2.87
112 113 7.421599 TCAAAACATGTTTTATGCGAGAGAAA 58.578 30.769 30.65 4.84 40.45 2.52
113 114 7.378461 TCAAAACATGTTTTATGCGAGAGAAAC 59.622 33.333 30.65 0.00 40.45 2.78
114 115 5.940192 ACATGTTTTATGCGAGAGAAACA 57.060 34.783 0.00 9.07 43.56 2.83
115 116 6.312399 ACATGTTTTATGCGAGAGAAACAA 57.688 33.333 0.00 0.00 42.93 2.83
116 117 6.734137 ACATGTTTTATGCGAGAGAAACAAA 58.266 32.000 0.00 0.00 42.93 2.83
117 118 7.199766 ACATGTTTTATGCGAGAGAAACAAAA 58.800 30.769 0.00 0.00 42.93 2.44
118 119 7.704472 ACATGTTTTATGCGAGAGAAACAAAAA 59.296 29.630 0.00 0.00 42.93 1.94
146 147 1.203065 GTGTTTGCACGAATCGCGA 59.797 52.632 13.09 13.09 44.57 5.87
147 148 0.383737 GTGTTTGCACGAATCGCGAA 60.384 50.000 15.24 0.00 44.57 4.70
148 149 0.110867 TGTTTGCACGAATCGCGAAG 60.111 50.000 15.24 10.67 44.57 3.79
162 163 1.645455 CGAAGCGCAGAATGGATGG 59.355 57.895 11.47 0.00 35.86 3.51
163 164 0.811219 CGAAGCGCAGAATGGATGGA 60.811 55.000 11.47 0.00 35.86 3.41
164 165 1.602311 GAAGCGCAGAATGGATGGAT 58.398 50.000 11.47 0.00 35.86 3.41
165 166 2.771089 GAAGCGCAGAATGGATGGATA 58.229 47.619 11.47 0.00 35.86 2.59
166 167 2.469274 AGCGCAGAATGGATGGATAG 57.531 50.000 11.47 0.00 35.86 2.08
167 168 1.973515 AGCGCAGAATGGATGGATAGA 59.026 47.619 11.47 0.00 35.86 1.98
168 169 2.570752 AGCGCAGAATGGATGGATAGAT 59.429 45.455 11.47 0.00 35.86 1.98
169 170 3.771479 AGCGCAGAATGGATGGATAGATA 59.229 43.478 11.47 0.00 35.86 1.98
170 171 4.118410 GCGCAGAATGGATGGATAGATAG 58.882 47.826 0.30 0.00 35.86 2.08
171 172 4.691175 CGCAGAATGGATGGATAGATAGG 58.309 47.826 0.00 0.00 35.86 2.57
172 173 4.403752 CGCAGAATGGATGGATAGATAGGA 59.596 45.833 0.00 0.00 35.86 2.94
173 174 5.105187 CGCAGAATGGATGGATAGATAGGAA 60.105 44.000 0.00 0.00 35.86 3.36
174 175 6.347696 GCAGAATGGATGGATAGATAGGAAG 58.652 44.000 0.00 0.00 35.86 3.46
175 176 6.632219 GCAGAATGGATGGATAGATAGGAAGG 60.632 46.154 0.00 0.00 35.86 3.46
176 177 5.969402 AGAATGGATGGATAGATAGGAAGGG 59.031 44.000 0.00 0.00 0.00 3.95
177 178 3.454858 TGGATGGATAGATAGGAAGGGC 58.545 50.000 0.00 0.00 0.00 5.19
178 179 2.774809 GGATGGATAGATAGGAAGGGCC 59.225 54.545 0.00 0.00 0.00 5.80
187 188 4.748144 GGAAGGGCCTGGGTGCAG 62.748 72.222 6.92 0.00 0.00 4.41
188 189 4.748144 GAAGGGCCTGGGTGCAGG 62.748 72.222 6.92 0.00 44.98 4.85
192 193 4.603535 GGCCTGGGTGCAGGTGTT 62.604 66.667 0.00 0.00 44.07 3.32
193 194 2.985847 GCCTGGGTGCAGGTGTTC 60.986 66.667 0.00 0.00 44.07 3.18
194 195 2.839098 CCTGGGTGCAGGTGTTCT 59.161 61.111 0.00 0.00 37.57 3.01
195 196 2.066340 CCTGGGTGCAGGTGTTCTA 58.934 57.895 0.00 0.00 37.57 2.10
196 197 0.620556 CCTGGGTGCAGGTGTTCTAT 59.379 55.000 0.00 0.00 37.57 1.98
197 198 1.004745 CCTGGGTGCAGGTGTTCTATT 59.995 52.381 0.00 0.00 37.57 1.73
198 199 2.238646 CCTGGGTGCAGGTGTTCTATTA 59.761 50.000 0.00 0.00 37.57 0.98
199 200 3.117888 CCTGGGTGCAGGTGTTCTATTAT 60.118 47.826 0.00 0.00 37.57 1.28
200 201 4.102524 CCTGGGTGCAGGTGTTCTATTATA 59.897 45.833 0.00 0.00 37.57 0.98
201 202 5.221925 CCTGGGTGCAGGTGTTCTATTATAT 60.222 44.000 0.00 0.00 37.57 0.86
202 203 6.013725 CCTGGGTGCAGGTGTTCTATTATATA 60.014 42.308 0.00 0.00 37.57 0.86
203 204 7.311297 CCTGGGTGCAGGTGTTCTATTATATAT 60.311 40.741 0.00 0.00 37.57 0.86
204 205 7.984475 TGGGTGCAGGTGTTCTATTATATATT 58.016 34.615 0.00 0.00 0.00 1.28
205 206 8.444783 TGGGTGCAGGTGTTCTATTATATATTT 58.555 33.333 0.00 0.00 0.00 1.40
206 207 9.297037 GGGTGCAGGTGTTCTATTATATATTTT 57.703 33.333 0.00 0.00 0.00 1.82
209 210 9.214957 TGCAGGTGTTCTATTATATATTTTCGG 57.785 33.333 0.00 0.00 0.00 4.30
210 211 9.216117 GCAGGTGTTCTATTATATATTTTCGGT 57.784 33.333 0.00 0.00 0.00 4.69
232 233 4.166011 GCGTCCGCCATCTGCAAC 62.166 66.667 0.00 0.00 41.33 4.17
241 242 1.968017 CATCTGCAACCACTGGCGT 60.968 57.895 0.00 0.00 0.00 5.68
242 243 1.672356 ATCTGCAACCACTGGCGTC 60.672 57.895 0.00 0.00 0.00 5.19
243 244 3.716006 CTGCAACCACTGGCGTCG 61.716 66.667 0.00 0.00 0.00 5.12
308 309 3.970410 CAAGCCCTCCACTGCCCA 61.970 66.667 0.00 0.00 0.00 5.36
317 318 1.195442 TCCACTGCCCATACCGACAA 61.195 55.000 0.00 0.00 0.00 3.18
429 432 1.270839 GGGTCGTGGTATCATCCCATG 60.271 57.143 8.40 0.00 39.83 3.66
430 433 1.416401 GGTCGTGGTATCATCCCATGT 59.584 52.381 0.00 0.00 39.53 3.21
528 532 2.573869 CGACGACATCAGGTGCCT 59.426 61.111 0.00 0.00 0.00 4.75
546 550 2.426024 GCCTCATGATGATTTGTGCAGT 59.574 45.455 1.72 0.00 0.00 4.40
648 652 0.401738 CCGGGCATGGAGTATTGGAT 59.598 55.000 0.00 0.00 0.00 3.41
707 711 2.097110 AGACCTGACTTACCACCACA 57.903 50.000 0.00 0.00 0.00 4.17
724 729 3.327404 AGATGGTTCCGGGCCGTT 61.327 61.111 26.32 1.60 0.00 4.44
844 853 1.153429 GCACACTGGGGGATCGTAC 60.153 63.158 0.00 0.00 0.00 3.67
952 962 0.901124 CCAGCTCTTCAGGCTACAGT 59.099 55.000 0.00 0.00 38.03 3.55
991 1007 3.019003 GCTTCCTAGTCCTGGCGCA 62.019 63.158 10.83 0.00 0.00 6.09
1213 1229 4.512914 GCCTGCCATGGTCTCCCC 62.513 72.222 14.67 0.00 0.00 4.81
1260 1280 4.098155 TGGTACCACCACTAATTGAGCTA 58.902 43.478 11.60 0.00 44.79 3.32
1261 1281 4.719773 TGGTACCACCACTAATTGAGCTAT 59.280 41.667 11.60 0.00 44.79 2.97
1262 1282 5.900699 TGGTACCACCACTAATTGAGCTATA 59.099 40.000 11.60 0.00 44.79 1.31
1263 1283 6.183360 TGGTACCACCACTAATTGAGCTATAC 60.183 42.308 11.60 0.00 44.79 1.47
1264 1284 5.291905 ACCACCACTAATTGAGCTATACC 57.708 43.478 0.00 0.00 0.00 2.73
1265 1285 4.102681 ACCACCACTAATTGAGCTATACCC 59.897 45.833 0.00 0.00 0.00 3.69
1266 1286 4.102524 CCACCACTAATTGAGCTATACCCA 59.897 45.833 0.00 0.00 0.00 4.51
1267 1287 5.397447 CCACCACTAATTGAGCTATACCCAA 60.397 44.000 0.00 0.00 0.00 4.12
1275 1295 3.726790 TGAGCTATACCCAAGTACCCAA 58.273 45.455 0.00 0.00 0.00 4.12
1307 1332 6.932960 CAGTTTGAGGCATCATACAGATATCA 59.067 38.462 21.10 0.00 39.17 2.15
1364 1392 4.272504 TGCTCCTCGTTAGTGTTTCTTTTG 59.727 41.667 0.00 0.00 0.00 2.44
1441 1469 1.608109 CCAGTTTGCTGTATGTGTGCA 59.392 47.619 0.00 0.00 41.02 4.57
1459 1487 6.090628 TGTGTGCAAAATTTGAAGTCTGTTTC 59.909 34.615 10.26 0.00 0.00 2.78
1508 1536 3.393687 TGTATCAGCCCTTAGGTGGAAT 58.606 45.455 0.00 0.00 44.42 3.01
1560 1591 3.575805 TCAGCCCTTCAAACAAGGAAAT 58.424 40.909 1.71 0.00 39.81 2.17
1580 1611 7.995488 AGGAAATAAGCAATCATGTTAGCTAGT 59.005 33.333 8.49 0.00 36.07 2.57
1629 1660 3.182182 CTGACTCGAGATCGCATGAAAA 58.818 45.455 21.68 0.00 39.60 2.29
1630 1661 3.584834 TGACTCGAGATCGCATGAAAAA 58.415 40.909 21.68 0.00 39.60 1.94
1674 1708 5.833131 TGGAATTCTAACCTTTTGCTTCACT 59.167 36.000 5.23 0.00 0.00 3.41
1735 1769 6.017440 GTGTGTTTGAGCCAGTGTTATTAGAA 60.017 38.462 0.00 0.00 0.00 2.10
1759 1793 5.878406 AGATAACAATGTACTAGCAGGCT 57.122 39.130 0.00 0.00 0.00 4.58
1799 1833 6.878317 TCTGATAGCTGTTACAACTTATGCT 58.122 36.000 0.00 0.00 0.00 3.79
2020 2055 9.783256 GTGTACTTTTGAGTTAATTGTTTCTGT 57.217 29.630 0.00 0.00 0.00 3.41
2036 2075 7.801716 TGTTTCTGTAGCTAATTGTTTCTGT 57.198 32.000 0.00 0.00 0.00 3.41
2184 6688 5.463286 ACATATGTGTTGACATGTTTGCTG 58.537 37.500 7.78 0.00 43.03 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.364142 GCAAAGCTTTCTATCTAGAATCTAGGA 58.636 37.037 16.47 4.32 41.52 2.94
40 41 7.602265 GGCAAAGCTTTCTATCTAGAATCTAGG 59.398 40.741 16.47 2.02 41.52 3.02
41 42 8.147058 TGGCAAAGCTTTCTATCTAGAATCTAG 58.853 37.037 9.23 10.93 41.52 2.43
42 43 7.928706 GTGGCAAAGCTTTCTATCTAGAATCTA 59.071 37.037 9.23 0.00 41.52 1.98
43 44 6.765512 GTGGCAAAGCTTTCTATCTAGAATCT 59.234 38.462 9.23 0.00 41.52 2.40
44 45 6.292596 CGTGGCAAAGCTTTCTATCTAGAATC 60.293 42.308 9.23 0.00 41.52 2.52
45 46 5.525378 CGTGGCAAAGCTTTCTATCTAGAAT 59.475 40.000 9.23 0.00 41.52 2.40
46 47 4.870426 CGTGGCAAAGCTTTCTATCTAGAA 59.130 41.667 9.23 0.00 40.33 2.10
47 48 4.433615 CGTGGCAAAGCTTTCTATCTAGA 58.566 43.478 9.23 0.00 0.00 2.43
48 49 3.001736 GCGTGGCAAAGCTTTCTATCTAG 59.998 47.826 9.23 0.00 0.00 2.43
49 50 2.936498 GCGTGGCAAAGCTTTCTATCTA 59.064 45.455 9.23 0.00 0.00 1.98
50 51 1.740025 GCGTGGCAAAGCTTTCTATCT 59.260 47.619 9.23 0.00 0.00 1.98
51 52 1.740025 AGCGTGGCAAAGCTTTCTATC 59.260 47.619 9.23 0.00 37.97 2.08
52 53 1.470098 CAGCGTGGCAAAGCTTTCTAT 59.530 47.619 9.23 0.00 39.27 1.98
53 54 0.874390 CAGCGTGGCAAAGCTTTCTA 59.126 50.000 9.23 0.00 39.27 2.10
54 55 1.656441 CAGCGTGGCAAAGCTTTCT 59.344 52.632 9.23 0.00 39.27 2.52
55 56 2.018324 GCAGCGTGGCAAAGCTTTC 61.018 57.895 9.23 4.47 39.27 2.62
56 57 2.028043 GCAGCGTGGCAAAGCTTT 59.972 55.556 14.91 5.69 39.27 3.51
57 58 3.218470 TGCAGCGTGGCAAAGCTT 61.218 55.556 14.91 0.00 39.27 3.74
63 64 0.875040 CAAACATTTGCAGCGTGGCA 60.875 50.000 0.00 0.00 43.19 4.92
64 65 0.597118 TCAAACATTTGCAGCGTGGC 60.597 50.000 0.00 0.00 38.05 5.01
65 66 1.522258 GTTCAAACATTTGCAGCGTGG 59.478 47.619 0.00 0.00 38.05 4.94
66 67 2.462889 AGTTCAAACATTTGCAGCGTG 58.537 42.857 0.00 0.00 38.05 5.34
67 68 2.869233 AGTTCAAACATTTGCAGCGT 57.131 40.000 0.00 0.00 38.05 5.07
68 69 3.114809 TGAAGTTCAAACATTTGCAGCG 58.885 40.909 2.20 0.00 38.05 5.18
69 70 5.467902 TTTGAAGTTCAAACATTTGCAGC 57.532 34.783 23.91 0.00 41.02 5.25
70 71 6.829703 TGTTTTGAAGTTCAAACATTTGCAG 58.170 32.000 26.72 0.00 45.03 4.41
71 72 6.791887 TGTTTTGAAGTTCAAACATTTGCA 57.208 29.167 26.72 16.35 45.03 4.08
72 73 7.242783 ACATGTTTTGAAGTTCAAACATTTGC 58.757 30.769 26.72 14.50 45.03 3.68
73 74 9.609950 AAACATGTTTTGAAGTTCAAACATTTG 57.390 25.926 26.72 22.15 45.03 2.32
78 79 9.209297 GCATAAAACATGTTTTGAAGTTCAAAC 57.791 29.630 35.69 21.13 45.03 2.93
79 80 8.113062 CGCATAAAACATGTTTTGAAGTTCAAA 58.887 29.630 35.69 23.91 43.84 2.69
80 81 7.489435 TCGCATAAAACATGTTTTGAAGTTCAA 59.511 29.630 35.69 19.92 42.18 2.69
81 82 6.975197 TCGCATAAAACATGTTTTGAAGTTCA 59.025 30.769 35.69 20.54 42.18 3.18
82 83 7.378461 TCTCGCATAAAACATGTTTTGAAGTTC 59.622 33.333 35.69 20.87 42.18 3.01
83 84 7.199766 TCTCGCATAAAACATGTTTTGAAGTT 58.800 30.769 35.69 18.40 42.18 2.66
84 85 6.734137 TCTCGCATAAAACATGTTTTGAAGT 58.266 32.000 35.69 20.83 42.18 3.01
85 86 7.077605 TCTCTCGCATAAAACATGTTTTGAAG 58.922 34.615 35.69 26.79 42.18 3.02
86 87 6.964908 TCTCTCGCATAAAACATGTTTTGAA 58.035 32.000 35.69 23.00 42.18 2.69
87 88 6.552859 TCTCTCGCATAAAACATGTTTTGA 57.447 33.333 35.69 25.63 42.18 2.69
88 89 7.167302 TGTTTCTCTCGCATAAAACATGTTTTG 59.833 33.333 35.69 25.85 42.18 2.44
89 90 7.199766 TGTTTCTCTCGCATAAAACATGTTTT 58.800 30.769 32.63 32.63 44.16 2.43
90 91 6.734137 TGTTTCTCTCGCATAAAACATGTTT 58.266 32.000 18.13 18.13 36.86 2.83
91 92 6.312399 TGTTTCTCTCGCATAAAACATGTT 57.688 33.333 4.92 4.92 36.86 2.71
92 93 5.940192 TGTTTCTCTCGCATAAAACATGT 57.060 34.783 0.00 0.00 36.86 3.21
93 94 7.621832 TTTTGTTTCTCTCGCATAAAACATG 57.378 32.000 0.00 0.00 40.25 3.21
128 129 0.383737 TTCGCGATTCGTGCAAACAC 60.384 50.000 10.88 0.00 43.76 3.32
129 130 0.110867 CTTCGCGATTCGTGCAAACA 60.111 50.000 10.88 0.00 37.28 2.83
130 131 1.388475 GCTTCGCGATTCGTGCAAAC 61.388 55.000 10.88 2.90 37.28 2.93
131 132 1.154488 GCTTCGCGATTCGTGCAAA 60.154 52.632 10.88 4.39 37.28 3.68
132 133 2.474266 GCTTCGCGATTCGTGCAA 59.526 55.556 10.88 8.96 37.28 4.08
144 145 0.811219 TCCATCCATTCTGCGCTTCG 60.811 55.000 9.73 0.00 0.00 3.79
145 146 1.602311 ATCCATCCATTCTGCGCTTC 58.398 50.000 9.73 0.00 0.00 3.86
146 147 2.369860 TCTATCCATCCATTCTGCGCTT 59.630 45.455 9.73 0.00 0.00 4.68
147 148 1.973515 TCTATCCATCCATTCTGCGCT 59.026 47.619 9.73 0.00 0.00 5.92
148 149 2.462456 TCTATCCATCCATTCTGCGC 57.538 50.000 0.00 0.00 0.00 6.09
149 150 4.403752 TCCTATCTATCCATCCATTCTGCG 59.596 45.833 0.00 0.00 0.00 5.18
150 151 5.946942 TCCTATCTATCCATCCATTCTGC 57.053 43.478 0.00 0.00 0.00 4.26
151 152 6.126825 CCCTTCCTATCTATCCATCCATTCTG 60.127 46.154 0.00 0.00 0.00 3.02
152 153 5.969402 CCCTTCCTATCTATCCATCCATTCT 59.031 44.000 0.00 0.00 0.00 2.40
153 154 5.397334 GCCCTTCCTATCTATCCATCCATTC 60.397 48.000 0.00 0.00 0.00 2.67
154 155 4.476479 GCCCTTCCTATCTATCCATCCATT 59.524 45.833 0.00 0.00 0.00 3.16
155 156 4.043596 GCCCTTCCTATCTATCCATCCAT 58.956 47.826 0.00 0.00 0.00 3.41
156 157 3.454858 GCCCTTCCTATCTATCCATCCA 58.545 50.000 0.00 0.00 0.00 3.41
157 158 2.774809 GGCCCTTCCTATCTATCCATCC 59.225 54.545 0.00 0.00 0.00 3.51
158 159 3.454082 CAGGCCCTTCCTATCTATCCATC 59.546 52.174 0.00 0.00 45.52 3.51
159 160 3.458831 CAGGCCCTTCCTATCTATCCAT 58.541 50.000 0.00 0.00 45.52 3.41
160 161 2.495383 CCAGGCCCTTCCTATCTATCCA 60.495 54.545 0.00 0.00 45.52 3.41
161 162 2.192263 CCAGGCCCTTCCTATCTATCC 58.808 57.143 0.00 0.00 45.52 2.59
162 163 2.192263 CCCAGGCCCTTCCTATCTATC 58.808 57.143 0.00 0.00 45.52 2.08
163 164 1.514442 ACCCAGGCCCTTCCTATCTAT 59.486 52.381 0.00 0.00 45.52 1.98
164 165 0.949582 ACCCAGGCCCTTCCTATCTA 59.050 55.000 0.00 0.00 45.52 1.98
165 166 0.695803 CACCCAGGCCCTTCCTATCT 60.696 60.000 0.00 0.00 45.52 1.98
166 167 1.839894 CACCCAGGCCCTTCCTATC 59.160 63.158 0.00 0.00 45.52 2.08
167 168 2.386935 GCACCCAGGCCCTTCCTAT 61.387 63.158 0.00 0.00 45.52 2.57
168 169 3.015145 GCACCCAGGCCCTTCCTA 61.015 66.667 0.00 0.00 45.52 2.94
170 171 4.748144 CTGCACCCAGGCCCTTCC 62.748 72.222 0.00 0.00 35.38 3.46
178 179 2.496899 AATAGAACACCTGCACCCAG 57.503 50.000 0.00 0.00 38.85 4.45
179 180 5.904984 ATATAATAGAACACCTGCACCCA 57.095 39.130 0.00 0.00 0.00 4.51
180 181 8.863872 AAATATATAATAGAACACCTGCACCC 57.136 34.615 0.00 0.00 0.00 4.61
183 184 9.214957 CCGAAAATATATAATAGAACACCTGCA 57.785 33.333 0.00 0.00 0.00 4.41
184 185 9.216117 ACCGAAAATATATAATAGAACACCTGC 57.784 33.333 0.00 0.00 0.00 4.85
186 187 9.939802 GGACCGAAAATATATAATAGAACACCT 57.060 33.333 0.00 0.00 0.00 4.00
187 188 9.715121 TGGACCGAAAATATATAATAGAACACC 57.285 33.333 0.00 0.00 0.00 4.16
189 190 9.938280 CCTGGACCGAAAATATATAATAGAACA 57.062 33.333 0.00 0.00 0.00 3.18
190 191 8.880750 GCCTGGACCGAAAATATATAATAGAAC 58.119 37.037 0.00 0.00 0.00 3.01
191 192 7.762615 CGCCTGGACCGAAAATATATAATAGAA 59.237 37.037 0.00 0.00 0.00 2.10
192 193 7.093640 ACGCCTGGACCGAAAATATATAATAGA 60.094 37.037 0.00 0.00 0.00 1.98
193 194 7.039882 ACGCCTGGACCGAAAATATATAATAG 58.960 38.462 0.00 0.00 0.00 1.73
194 195 6.938507 ACGCCTGGACCGAAAATATATAATA 58.061 36.000 0.00 0.00 0.00 0.98
195 196 5.801380 ACGCCTGGACCGAAAATATATAAT 58.199 37.500 0.00 0.00 0.00 1.28
196 197 5.217978 ACGCCTGGACCGAAAATATATAA 57.782 39.130 0.00 0.00 0.00 0.98
197 198 4.322198 GGACGCCTGGACCGAAAATATATA 60.322 45.833 0.00 0.00 0.00 0.86
198 199 3.556423 GGACGCCTGGACCGAAAATATAT 60.556 47.826 0.00 0.00 0.00 0.86
199 200 2.224113 GGACGCCTGGACCGAAAATATA 60.224 50.000 0.00 0.00 0.00 0.86
200 201 1.474498 GGACGCCTGGACCGAAAATAT 60.474 52.381 0.00 0.00 0.00 1.28
201 202 0.108041 GGACGCCTGGACCGAAAATA 60.108 55.000 0.00 0.00 0.00 1.40
202 203 1.376812 GGACGCCTGGACCGAAAAT 60.377 57.895 0.00 0.00 0.00 1.82
203 204 2.031465 GGACGCCTGGACCGAAAA 59.969 61.111 0.00 0.00 0.00 2.29
243 244 4.078516 AAGGCTACCCGACACGGC 62.079 66.667 4.57 0.00 46.86 5.68
245 246 2.813908 GCAAGGCTACCCGACACG 60.814 66.667 0.00 0.00 35.76 4.49
246 247 1.741770 CTGCAAGGCTACCCGACAC 60.742 63.158 0.00 0.00 35.76 3.67
247 248 1.476845 TTCTGCAAGGCTACCCGACA 61.477 55.000 0.00 0.00 35.76 4.35
308 309 5.415077 CCGAAGATCCTATAGTTGTCGGTAT 59.585 44.000 14.58 0.00 41.38 2.73
317 318 2.823154 GAGCTGCCGAAGATCCTATAGT 59.177 50.000 0.00 0.00 35.13 2.12
483 487 1.928199 AGGATGCACATGCCATCCT 59.072 52.632 29.36 29.36 45.44 3.24
491 495 2.744166 CGGAGTTGATGAGGATGCACAT 60.744 50.000 0.00 0.00 0.00 3.21
528 532 2.096335 GCGACTGCACAAATCATCATGA 59.904 45.455 0.00 0.00 42.15 3.07
642 646 1.227556 GCCGGTAGCGACATCCAAT 60.228 57.895 17.33 0.00 0.00 3.16
707 711 3.327404 AACGGCCCGGAACCATCT 61.327 61.111 8.57 0.00 0.00 2.90
716 720 1.811266 CATCTGAGTCAACGGCCCG 60.811 63.158 0.00 0.00 0.00 6.13
724 729 5.122707 AGTAGAGGTCATCATCTGAGTCA 57.877 43.478 0.00 0.00 35.43 3.41
844 853 3.483869 GGGCTGGAGGTAGCAGGG 61.484 72.222 0.00 0.00 45.46 4.45
952 962 3.399181 CCGGCCCTCCTGTTGCTA 61.399 66.667 0.00 0.00 0.00 3.49
971 981 2.060980 CGCCAGGACTAGGAAGCCT 61.061 63.158 0.00 0.00 37.71 4.58
980 996 1.680522 CTGGTAGATGCGCCAGGACT 61.681 60.000 4.18 0.00 46.27 3.85
991 1007 2.520536 GCCCGGCCATCTGGTAGAT 61.521 63.158 2.24 0.00 37.01 1.98
1275 1295 2.158623 TGATGCCTCAAACTGAACCTGT 60.159 45.455 0.00 0.00 0.00 4.00
1364 1392 6.560711 ACAACCAAATCAAAGAGTACAACAC 58.439 36.000 0.00 0.00 0.00 3.32
1441 1469 6.863275 AGTTCGGAAACAGACTTCAAATTTT 58.137 32.000 0.00 0.00 37.88 1.82
1459 1487 9.307121 GTATCCATATAGATGAAATGAGTTCGG 57.693 37.037 0.00 0.00 39.30 4.30
1508 1536 8.890472 AGTATCCATGCTACCTGGAATAATTTA 58.110 33.333 0.00 0.00 45.57 1.40
1560 1591 4.816385 GCCACTAGCTAACATGATTGCTTA 59.184 41.667 16.18 3.63 38.99 3.09
1580 1611 1.070134 GTCCCTCAACTATATGCGCCA 59.930 52.381 4.18 0.00 0.00 5.69
1629 1660 5.012893 CCAGCCACCTTTATTCTCTTCTTT 58.987 41.667 0.00 0.00 0.00 2.52
1630 1661 4.289672 TCCAGCCACCTTTATTCTCTTCTT 59.710 41.667 0.00 0.00 0.00 2.52
1635 1669 5.196695 AGAATTCCAGCCACCTTTATTCTC 58.803 41.667 0.65 0.00 0.00 2.87
1735 1769 6.540189 CAGCCTGCTAGTACATTGTTATCTTT 59.460 38.462 0.00 0.00 0.00 2.52
1759 1793 0.171231 CAGATCTCTTCGTGCCGACA 59.829 55.000 0.00 0.00 34.89 4.35
1774 1808 7.504403 AGCATAAGTTGTAACAGCTATCAGAT 58.496 34.615 0.00 0.00 0.00 2.90
2012 2047 7.801716 ACAGAAACAATTAGCTACAGAAACA 57.198 32.000 0.00 0.00 0.00 2.83
2013 2048 7.958025 GCTACAGAAACAATTAGCTACAGAAAC 59.042 37.037 0.00 0.00 35.15 2.78
2015 2050 7.386851 AGCTACAGAAACAATTAGCTACAGAA 58.613 34.615 0.00 0.00 44.33 3.02
2016 2051 6.936279 AGCTACAGAAACAATTAGCTACAGA 58.064 36.000 0.00 0.00 44.33 3.41
2184 6688 6.149308 TGTGAATGATATATGCAATTCCGACC 59.851 38.462 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.