Multiple sequence alignment - TraesCS7A01G157600

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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 TraesCS7A01G157600 chr7A 100.000 1320 0 0 767 2086 110828267 110826948 0.000000e+00 2438
1 TraesCS7A01G157600 chr7A 100.000 750 0 0 2329 3078 110826705 110825956 0.000000e+00 1386
2 TraesCS7A01G157600 chr7A 100.000 231 0 0 1 231 110829033 110828803 7.890000e-116 427
3 TraesCS7A01G157600 chr2A 93.702 1302 79 3 786 2086 770131387 770132686 0.000000e+00 1947
4 TraesCS7A01G157600 chr2A 93.353 677 45 0 2402 3078 770133008 770133684 0.000000e+00 1002
5 TraesCS7A01G157600 chr2A 93.902 82 5 0 2329 2410 770132730 770132811 1.160000e-24 124
6 TraesCS7A01G157600 chr3A 93.405 1304 84 2 784 2086 730877142 730875840 0.000000e+00 1930
7 TraesCS7A01G157600 chr7D 91.794 1304 96 4 784 2086 22724971 22723678 0.000000e+00 1805
8 TraesCS7A01G157600 chr7D 90.076 1310 113 8 783 2086 76326268 76324970 0.000000e+00 1683
9 TraesCS7A01G157600 chr7D 90.801 674 61 1 2405 3078 22723168 22722496 0.000000e+00 900
10 TraesCS7A01G157600 chr7D 89.911 674 68 0 2405 3078 76324642 76323969 0.000000e+00 869
11 TraesCS7A01G157600 chr7D 89.970 668 66 1 2398 3065 561615317 561614651 0.000000e+00 861
12 TraesCS7A01G157600 chr7D 94.771 153 7 1 1 153 105994895 105994744 1.430000e-58 237
13 TraesCS7A01G157600 chr7D 90.196 153 13 2 1 153 105988231 105988081 6.730000e-47 198
14 TraesCS7A01G157600 chr7D 95.000 80 4 0 2331 2410 22723447 22723368 3.220000e-25 126
15 TraesCS7A01G157600 chr7D 92.683 82 6 0 2329 2410 561615592 561615511 5.390000e-23 119
16 TraesCS7A01G157600 chr4D 91.264 1305 106 7 784 2086 54061103 54062401 0.000000e+00 1772
17 TraesCS7A01G157600 chr4D 90.653 674 63 0 2405 3078 54062727 54063400 0.000000e+00 896
18 TraesCS7A01G157600 chr4D 96.341 82 3 0 2329 2410 54062446 54062527 5.350000e-28 135
19 TraesCS7A01G157600 chr5B 89.901 1307 120 10 783 2085 543287162 543288460 0.000000e+00 1672
20 TraesCS7A01G157600 chr5B 90.237 676 61 5 2406 3078 543288791 543289464 0.000000e+00 878
21 TraesCS7A01G157600 chr7B 89.579 1305 124 10 786 2086 504472265 504470969 0.000000e+00 1646
22 TraesCS7A01G157600 chr7B 90.074 675 63 4 2406 3078 504470470 504469798 0.000000e+00 872
23 TraesCS7A01G157600 chr7B 84.211 133 10 4 19 151 64687147 64687026 5.390000e-23 119
24 TraesCS7A01G157600 chr3D 89.433 1306 127 11 784 2086 591211289 591212586 0.000000e+00 1637
25 TraesCS7A01G157600 chr3D 95.122 82 4 0 2329 2410 591212623 591212704 2.490000e-26 130
26 TraesCS7A01G157600 chr5D 89.051 1306 135 8 784 2086 539853905 539855205 0.000000e+00 1613
27 TraesCS7A01G157600 chr3B 93.620 674 36 3 2405 3078 581643450 581642784 0.000000e+00 1000
28 TraesCS7A01G157600 chr3B 92.683 82 6 0 2329 2410 47735925 47736006 5.390000e-23 119
29 TraesCS7A01G157600 chr3B 92.683 82 6 0 2329 2410 47803476 47803557 5.390000e-23 119
30 TraesCS7A01G157600 chr3B 92.683 82 6 0 2329 2410 47857359 47857440 5.390000e-23 119
31 TraesCS7A01G157600 chr2B 92.878 674 48 0 2405 3078 22594362 22593689 0.000000e+00 979
32 TraesCS7A01G157600 chr1D 92.683 82 6 0 2329 2410 73084063 73084144 5.390000e-23 119


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 TraesCS7A01G157600 chr7A 110825956 110829033 3077 True 1417.000000 2438 100.000000 1 3078 3 chr7A.!!$R1 3077
1 TraesCS7A01G157600 chr2A 770131387 770133684 2297 False 1024.333333 1947 93.652333 786 3078 3 chr2A.!!$F1 2292
2 TraesCS7A01G157600 chr3A 730875840 730877142 1302 True 1930.000000 1930 93.405000 784 2086 1 chr3A.!!$R1 1302
3 TraesCS7A01G157600 chr7D 76323969 76326268 2299 True 1276.000000 1683 89.993500 783 3078 2 chr7D.!!$R4 2295
4 TraesCS7A01G157600 chr7D 22722496 22724971 2475 True 943.666667 1805 92.531667 784 3078 3 chr7D.!!$R3 2294
5 TraesCS7A01G157600 chr7D 561614651 561615592 941 True 490.000000 861 91.326500 2329 3065 2 chr7D.!!$R5 736
6 TraesCS7A01G157600 chr4D 54061103 54063400 2297 False 934.333333 1772 92.752667 784 3078 3 chr4D.!!$F1 2294
7 TraesCS7A01G157600 chr5B 543287162 543289464 2302 False 1275.000000 1672 90.069000 783 3078 2 chr5B.!!$F1 2295
8 TraesCS7A01G157600 chr7B 504469798 504472265 2467 True 1259.000000 1646 89.826500 786 3078 2 chr7B.!!$R2 2292
9 TraesCS7A01G157600 chr3D 591211289 591212704 1415 False 883.500000 1637 92.277500 784 2410 2 chr3D.!!$F1 1626
10 TraesCS7A01G157600 chr5D 539853905 539855205 1300 False 1613.000000 1613 89.051000 784 2086 1 chr5D.!!$F1 1302
11 TraesCS7A01G157600 chr3B 581642784 581643450 666 True 1000.000000 1000 93.620000 2405 3078 1 chr3B.!!$R1 673
12 TraesCS7A01G157600 chr2B 22593689 22594362 673 True 979.000000 979 92.878000 2405 3078 1 chr2B.!!$R1 673

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
183 184 0.106519 GCCAGGGCCTATCACACATT 60.107 55.0 5.28 0.0 34.56 2.71 F
215 216 0.175302 CGTCAGGAGAGCAGAGCAAT 59.825 55.0 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 1968 0.322726 TGTGCACCATCCTCACCATG 60.323 55.000 15.69 0.0 0.00 3.66 R
2379 2401 3.476552 TCGAAGAGGCATGTCTTGTTTT 58.523 40.909 0.00 0.0 36.89 2.43 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
22 23 5.378230 AGAAGATGTCCTGGCATATCAAA 57.622 39.130 4.03 0.00 0.00 2.69
23 24 5.759059 AGAAGATGTCCTGGCATATCAAAA 58.241 37.500 4.03 0.00 0.00 2.44
24 25 6.371278 AGAAGATGTCCTGGCATATCAAAAT 58.629 36.000 4.03 0.00 0.00 1.82
25 26 6.837568 AGAAGATGTCCTGGCATATCAAAATT 59.162 34.615 4.03 0.00 0.00 1.82
26 27 6.401047 AGATGTCCTGGCATATCAAAATTG 57.599 37.500 4.03 0.00 0.00 2.32
27 28 5.895534 AGATGTCCTGGCATATCAAAATTGT 59.104 36.000 4.03 0.00 0.00 2.71
28 29 5.581126 TGTCCTGGCATATCAAAATTGTC 57.419 39.130 0.00 0.00 0.00 3.18
29 30 5.263599 TGTCCTGGCATATCAAAATTGTCT 58.736 37.500 0.00 0.00 0.00 3.41
30 31 6.422333 TGTCCTGGCATATCAAAATTGTCTA 58.578 36.000 0.00 0.00 0.00 2.59
31 32 6.543465 TGTCCTGGCATATCAAAATTGTCTAG 59.457 38.462 0.00 0.00 0.00 2.43
32 33 6.767902 GTCCTGGCATATCAAAATTGTCTAGA 59.232 38.462 0.00 0.00 0.00 2.43
33 34 7.283127 GTCCTGGCATATCAAAATTGTCTAGAA 59.717 37.037 0.00 0.00 0.00 2.10
34 35 7.833682 TCCTGGCATATCAAAATTGTCTAGAAA 59.166 33.333 0.00 0.00 0.00 2.52
35 36 8.469200 CCTGGCATATCAAAATTGTCTAGAAAA 58.531 33.333 0.00 0.00 0.00 2.29
44 45 9.457436 TCAAAATTGTCTAGAAAATACCCTACC 57.543 33.333 8.62 0.00 0.00 3.18
45 46 9.462606 CAAAATTGTCTAGAAAATACCCTACCT 57.537 33.333 8.62 0.00 0.00 3.08
48 49 9.725206 AATTGTCTAGAAAATACCCTACCTAGA 57.275 33.333 8.62 0.00 32.69 2.43
49 50 9.900112 ATTGTCTAGAAAATACCCTACCTAGAT 57.100 33.333 6.34 0.00 36.18 1.98
50 51 9.725206 TTGTCTAGAAAATACCCTACCTAGATT 57.275 33.333 0.00 0.00 36.18 2.40
51 52 9.725206 TGTCTAGAAAATACCCTACCTAGATTT 57.275 33.333 0.00 0.00 36.18 2.17
60 61 9.503369 AATACCCTACCTAGATTTTCTACAAGT 57.497 33.333 0.00 0.00 0.00 3.16
62 63 8.536340 ACCCTACCTAGATTTTCTACAAGTAG 57.464 38.462 0.77 0.77 30.01 2.57
63 64 7.069702 ACCCTACCTAGATTTTCTACAAGTAGC 59.930 40.741 2.37 0.00 33.32 3.58
64 65 7.288158 CCCTACCTAGATTTTCTACAAGTAGCT 59.712 40.741 2.37 0.00 33.32 3.32
65 66 8.354426 CCTACCTAGATTTTCTACAAGTAGCTC 58.646 40.741 0.00 0.00 33.32 4.09
66 67 6.797454 ACCTAGATTTTCTACAAGTAGCTCG 58.203 40.000 0.00 0.00 33.32 5.03
67 68 6.602406 ACCTAGATTTTCTACAAGTAGCTCGA 59.398 38.462 0.00 0.00 33.32 4.04
68 69 7.136119 CCTAGATTTTCTACAAGTAGCTCGAG 58.864 42.308 8.45 8.45 33.32 4.04
69 70 5.344884 AGATTTTCTACAAGTAGCTCGAGC 58.655 41.667 30.01 30.01 42.49 5.03
81 82 2.505608 GCTCGAGCTTTAAACGTTCC 57.494 50.000 29.88 0.00 38.21 3.62
82 83 2.067013 GCTCGAGCTTTAAACGTTCCT 58.933 47.619 29.88 0.00 38.21 3.36
83 84 2.479275 GCTCGAGCTTTAAACGTTCCTT 59.521 45.455 29.88 0.00 38.21 3.36
84 85 3.664537 GCTCGAGCTTTAAACGTTCCTTG 60.665 47.826 29.88 0.00 38.21 3.61
85 86 3.460103 TCGAGCTTTAAACGTTCCTTGT 58.540 40.909 0.00 0.00 0.00 3.16
86 87 3.492011 TCGAGCTTTAAACGTTCCTTGTC 59.508 43.478 0.00 0.00 0.00 3.18
87 88 3.493503 CGAGCTTTAAACGTTCCTTGTCT 59.506 43.478 0.00 0.00 0.00 3.41
88 89 4.682860 CGAGCTTTAAACGTTCCTTGTCTA 59.317 41.667 0.00 0.00 0.00 2.59
89 90 5.176223 CGAGCTTTAAACGTTCCTTGTCTAA 59.824 40.000 0.00 0.00 0.00 2.10
90 91 6.128634 CGAGCTTTAAACGTTCCTTGTCTAAT 60.129 38.462 0.00 0.00 0.00 1.73
91 92 7.506328 AGCTTTAAACGTTCCTTGTCTAATT 57.494 32.000 0.00 0.00 0.00 1.40
92 93 8.611654 AGCTTTAAACGTTCCTTGTCTAATTA 57.388 30.769 0.00 0.00 0.00 1.40
93 94 9.227777 AGCTTTAAACGTTCCTTGTCTAATTAT 57.772 29.630 0.00 0.00 0.00 1.28
94 95 9.486857 GCTTTAAACGTTCCTTGTCTAATTATC 57.513 33.333 0.00 0.00 0.00 1.75
145 146 9.460019 TTGATTTATCATGTATGAAGTGAACCA 57.540 29.630 0.00 0.00 40.69 3.67
146 147 9.631257 TGATTTATCATGTATGAAGTGAACCAT 57.369 29.630 0.00 0.00 40.69 3.55
147 148 9.888878 GATTTATCATGTATGAAGTGAACCATG 57.111 33.333 0.00 0.00 40.69 3.66
148 149 8.806429 TTTATCATGTATGAAGTGAACCATGT 57.194 30.769 0.00 0.00 40.69 3.21
149 150 9.898152 TTTATCATGTATGAAGTGAACCATGTA 57.102 29.630 0.00 0.00 40.69 2.29
152 153 8.887036 TCATGTATGAAGTGAACCATGTATAC 57.113 34.615 0.00 0.00 33.08 1.47
153 154 8.482128 TCATGTATGAAGTGAACCATGTATACA 58.518 33.333 8.27 8.27 35.17 2.29
154 155 9.276590 CATGTATGAAGTGAACCATGTATACAT 57.723 33.333 12.75 12.75 39.64 2.29
155 156 9.851686 ATGTATGAAGTGAACCATGTATACATT 57.148 29.630 15.85 2.66 37.25 2.71
156 157 9.108284 TGTATGAAGTGAACCATGTATACATTG 57.892 33.333 15.85 14.76 33.61 2.82
157 158 9.109393 GTATGAAGTGAACCATGTATACATTGT 57.891 33.333 15.85 15.42 34.19 2.71
158 159 7.994425 TGAAGTGAACCATGTATACATTGTT 57.006 32.000 26.81 26.81 42.57 2.83
159 160 9.679661 ATGAAGTGAACCATGTATACATTGTTA 57.320 29.630 26.63 15.39 40.77 2.41
160 161 9.679661 TGAAGTGAACCATGTATACATTGTTAT 57.320 29.630 26.63 16.79 40.77 1.89
162 163 8.365399 AGTGAACCATGTATACATTGTTATCG 57.635 34.615 26.63 11.28 40.77 2.92
163 164 7.441157 AGTGAACCATGTATACATTGTTATCGG 59.559 37.037 26.63 19.59 40.77 4.18
164 165 6.708502 TGAACCATGTATACATTGTTATCGGG 59.291 38.462 26.63 19.02 40.77 5.14
165 166 5.001232 ACCATGTATACATTGTTATCGGGC 58.999 41.667 15.85 0.00 33.61 6.13
166 167 4.394920 CCATGTATACATTGTTATCGGGCC 59.605 45.833 15.85 0.00 33.61 5.80
167 168 4.691326 TGTATACATTGTTATCGGGCCA 57.309 40.909 4.39 0.00 0.00 5.36
168 169 4.637276 TGTATACATTGTTATCGGGCCAG 58.363 43.478 4.39 0.00 0.00 4.85
169 170 2.631160 TACATTGTTATCGGGCCAGG 57.369 50.000 4.39 0.00 0.00 4.45
170 171 0.106719 ACATTGTTATCGGGCCAGGG 60.107 55.000 4.39 0.00 0.00 4.45
171 172 1.152756 ATTGTTATCGGGCCAGGGC 60.153 57.895 4.39 3.77 41.06 5.19
181 182 2.998097 GCCAGGGCCTATCACACA 59.002 61.111 5.28 0.00 34.56 3.72
182 183 1.533711 GCCAGGGCCTATCACACAT 59.466 57.895 5.28 0.00 34.56 3.21
183 184 0.106519 GCCAGGGCCTATCACACATT 60.107 55.000 5.28 0.00 34.56 2.71
184 185 1.972872 CCAGGGCCTATCACACATTC 58.027 55.000 5.28 0.00 0.00 2.67
185 186 1.492176 CCAGGGCCTATCACACATTCT 59.508 52.381 5.28 0.00 0.00 2.40
186 187 2.569059 CAGGGCCTATCACACATTCTG 58.431 52.381 5.28 0.00 0.00 3.02
187 188 1.492176 AGGGCCTATCACACATTCTGG 59.508 52.381 2.82 0.00 0.00 3.86
188 189 1.312815 GGCCTATCACACATTCTGGC 58.687 55.000 0.00 0.00 38.28 4.85
189 190 0.940126 GCCTATCACACATTCTGGCG 59.060 55.000 0.00 0.00 0.00 5.69
190 191 1.743772 GCCTATCACACATTCTGGCGT 60.744 52.381 0.00 0.00 0.00 5.68
191 192 1.935873 CCTATCACACATTCTGGCGTG 59.064 52.381 0.00 0.00 39.10 5.34
192 193 2.418609 CCTATCACACATTCTGGCGTGA 60.419 50.000 0.00 0.00 37.96 4.35
193 194 1.730501 ATCACACATTCTGGCGTGAG 58.269 50.000 0.00 0.00 37.34 3.51
205 206 3.579685 CGTGAGCTCGTCAGGAGA 58.420 61.111 9.64 0.00 46.23 3.71
206 207 1.427419 CGTGAGCTCGTCAGGAGAG 59.573 63.158 9.64 0.00 46.23 3.20
212 213 1.433064 CTCGTCAGGAGAGCAGAGC 59.567 63.158 0.00 0.00 46.23 4.09
213 214 1.303643 TCGTCAGGAGAGCAGAGCA 60.304 57.895 0.00 0.00 0.00 4.26
214 215 0.895559 TCGTCAGGAGAGCAGAGCAA 60.896 55.000 0.00 0.00 0.00 3.91
215 216 0.175302 CGTCAGGAGAGCAGAGCAAT 59.825 55.000 0.00 0.00 0.00 3.56
216 217 1.406898 CGTCAGGAGAGCAGAGCAATA 59.593 52.381 0.00 0.00 0.00 1.90
217 218 2.159184 CGTCAGGAGAGCAGAGCAATAA 60.159 50.000 0.00 0.00 0.00 1.40
218 219 3.677148 CGTCAGGAGAGCAGAGCAATAAA 60.677 47.826 0.00 0.00 0.00 1.40
219 220 3.620821 GTCAGGAGAGCAGAGCAATAAAC 59.379 47.826 0.00 0.00 0.00 2.01
220 221 3.517100 TCAGGAGAGCAGAGCAATAAACT 59.483 43.478 0.00 0.00 0.00 2.66
221 222 3.870419 CAGGAGAGCAGAGCAATAAACTC 59.130 47.826 0.00 0.00 0.00 3.01
222 223 3.118445 AGGAGAGCAGAGCAATAAACTCC 60.118 47.826 0.00 0.00 41.74 3.85
223 224 3.369892 GGAGAGCAGAGCAATAAACTCCA 60.370 47.826 0.00 0.00 41.28 3.86
224 225 4.450053 GAGAGCAGAGCAATAAACTCCAT 58.550 43.478 0.00 0.00 34.56 3.41
225 226 4.197750 AGAGCAGAGCAATAAACTCCATG 58.802 43.478 0.00 0.00 34.56 3.66
226 227 4.080695 AGAGCAGAGCAATAAACTCCATGA 60.081 41.667 0.00 0.00 34.56 3.07
227 228 4.197750 AGCAGAGCAATAAACTCCATGAG 58.802 43.478 0.00 0.00 34.56 2.90
228 229 4.080695 AGCAGAGCAATAAACTCCATGAGA 60.081 41.667 0.00 0.00 34.56 3.27
230 231 5.668471 CAGAGCAATAAACTCCATGAGAGA 58.332 41.667 15.51 0.00 46.50 3.10
818 822 3.261083 AGGCTAGGGTTTCTTTCCTCTT 58.739 45.455 0.00 0.00 34.75 2.85
904 911 4.035102 GGCCAACCCTCGCTCCTT 62.035 66.667 0.00 0.00 0.00 3.36
908 915 1.679898 CAACCCTCGCTCCTTCCTT 59.320 57.895 0.00 0.00 0.00 3.36
958 965 3.392228 CCCTGTCAGGCACTAGCA 58.608 61.111 13.99 0.00 44.61 3.49
1026 1033 4.647564 ACAACTGAACCTGGAAGATGAT 57.352 40.909 0.00 0.00 34.07 2.45
1050 1057 6.577103 TGACTTTGATGATCTGGTGATAGAC 58.423 40.000 0.00 0.00 32.19 2.59
1097 1112 2.285773 TGAGATGGCTCACGCTGGT 61.286 57.895 0.00 0.00 45.88 4.00
1261 1276 1.597742 ACGCATGATGTATCAAGGGC 58.402 50.000 12.21 9.22 40.61 5.19
1308 1323 4.576053 CGTGTTGATGGTTCCATATGATGT 59.424 41.667 3.65 0.00 0.00 3.06
1581 1596 1.736645 GCTACGAGAAACTGGCGCA 60.737 57.895 10.83 0.00 0.00 6.09
1622 1637 3.615496 GCTCATTGGTCATGATTGCAAAC 59.385 43.478 1.71 0.04 41.35 2.93
1907 1926 3.053768 TGATGTTGGACCAGATGCCAATA 60.054 43.478 0.00 0.00 45.13 1.90
1909 1928 2.040947 TGTTGGACCAGATGCCAATACA 59.959 45.455 0.00 0.00 45.13 2.29
1928 1947 1.205460 ATTGGTAGGGCCGAGTGGTT 61.205 55.000 0.00 0.00 41.21 3.67
1949 1968 3.462199 CTAGCGCTTACCCAGGGGC 62.462 68.421 18.68 2.51 40.85 5.80
2379 2401 1.335496 CGGGGCTTGTTTTTCTTTCGA 59.665 47.619 0.00 0.00 0.00 3.71
2408 2635 3.529533 ACATGCCTCTTCGAAGATGAAG 58.470 45.455 28.03 17.20 45.37 3.02
2415 2642 2.531206 CTTCGAAGATGAAGACCGTCC 58.469 52.381 20.74 0.00 46.64 4.79
2523 2750 4.561123 GCAGCATGAGCATATGTCTAGAGT 60.561 45.833 4.29 0.00 45.49 3.24
2533 2760 0.322546 TGTCTAGAGTCCAGCGCTCA 60.323 55.000 7.13 0.00 35.55 4.26
2745 2974 4.828939 TGCTTCTTCATGTTCTGACCATTT 59.171 37.500 0.00 0.00 32.17 2.32
2773 3002 1.940613 GTGGTTCGACTTGCTCTTGTT 59.059 47.619 0.00 0.00 0.00 2.83
2794 3023 2.173782 TGATTCGAGGAGGACTAGAGCT 59.826 50.000 0.00 0.00 32.23 4.09
2997 3229 0.613777 AAGTTAAGGTCCGAGCTGGG 59.386 55.000 8.78 8.78 38.76 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.378230 TTTGATATGCCAGGACATCTTCT 57.622 39.130 0.00 0.00 0.00 2.85
1 2 6.645790 ATTTTGATATGCCAGGACATCTTC 57.354 37.500 0.00 0.00 0.00 2.87
2 3 6.381994 ACAATTTTGATATGCCAGGACATCTT 59.618 34.615 0.00 0.00 0.00 2.40
3 4 5.895534 ACAATTTTGATATGCCAGGACATCT 59.104 36.000 0.00 0.00 0.00 2.90
4 5 6.040166 AGACAATTTTGATATGCCAGGACATC 59.960 38.462 0.00 0.00 0.00 3.06
5 6 5.895534 AGACAATTTTGATATGCCAGGACAT 59.104 36.000 0.00 0.00 0.00 3.06
6 7 5.263599 AGACAATTTTGATATGCCAGGACA 58.736 37.500 0.00 0.00 0.00 4.02
7 8 5.841957 AGACAATTTTGATATGCCAGGAC 57.158 39.130 0.00 0.00 0.00 3.85
8 9 6.899089 TCTAGACAATTTTGATATGCCAGGA 58.101 36.000 0.00 0.00 0.00 3.86
9 10 7.572523 TTCTAGACAATTTTGATATGCCAGG 57.427 36.000 0.00 0.00 0.00 4.45
18 19 9.457436 GGTAGGGTATTTTCTAGACAATTTTGA 57.543 33.333 9.33 0.00 0.00 2.69
19 20 9.462606 AGGTAGGGTATTTTCTAGACAATTTTG 57.537 33.333 9.33 0.00 0.00 2.44
22 23 9.725206 TCTAGGTAGGGTATTTTCTAGACAATT 57.275 33.333 9.33 0.00 31.40 2.32
23 24 9.900112 ATCTAGGTAGGGTATTTTCTAGACAAT 57.100 33.333 9.04 9.04 36.89 2.71
24 25 9.725206 AATCTAGGTAGGGTATTTTCTAGACAA 57.275 33.333 0.00 0.00 36.89 3.18
25 26 9.725206 AAATCTAGGTAGGGTATTTTCTAGACA 57.275 33.333 0.00 0.00 36.89 3.41
34 35 9.503369 ACTTGTAGAAAATCTAGGTAGGGTATT 57.497 33.333 0.00 0.00 28.01 1.89
36 37 9.638176 CTACTTGTAGAAAATCTAGGTAGGGTA 57.362 37.037 1.81 0.00 31.57 3.69
37 38 7.069702 GCTACTTGTAGAAAATCTAGGTAGGGT 59.930 40.741 11.54 0.00 33.43 4.34
38 39 7.288158 AGCTACTTGTAGAAAATCTAGGTAGGG 59.712 40.741 11.54 0.00 33.43 3.53
39 40 8.240267 AGCTACTTGTAGAAAATCTAGGTAGG 57.760 38.462 11.54 1.95 33.43 3.18
40 41 8.071368 CGAGCTACTTGTAGAAAATCTAGGTAG 58.929 40.741 11.54 12.63 34.53 3.18
41 42 7.772292 TCGAGCTACTTGTAGAAAATCTAGGTA 59.228 37.037 11.54 0.00 28.01 3.08
42 43 6.602406 TCGAGCTACTTGTAGAAAATCTAGGT 59.398 38.462 11.54 0.00 28.01 3.08
43 44 7.028926 TCGAGCTACTTGTAGAAAATCTAGG 57.971 40.000 11.54 0.00 28.01 3.02
44 45 6.635239 GCTCGAGCTACTTGTAGAAAATCTAG 59.365 42.308 29.88 6.15 38.21 2.43
45 46 6.496571 GCTCGAGCTACTTGTAGAAAATCTA 58.503 40.000 29.88 0.00 38.21 1.98
46 47 5.344884 GCTCGAGCTACTTGTAGAAAATCT 58.655 41.667 29.88 0.00 38.21 2.40
47 48 5.629348 GCTCGAGCTACTTGTAGAAAATC 57.371 43.478 29.88 0.00 38.21 2.17
62 63 2.067013 AGGAACGTTTAAAGCTCGAGC 58.933 47.619 30.01 30.01 42.49 5.03
63 64 3.493503 ACAAGGAACGTTTAAAGCTCGAG 59.506 43.478 8.45 8.45 0.00 4.04
64 65 3.460103 ACAAGGAACGTTTAAAGCTCGA 58.540 40.909 0.46 0.00 0.00 4.04
65 66 3.493503 AGACAAGGAACGTTTAAAGCTCG 59.506 43.478 0.46 0.00 0.00 5.03
66 67 6.535274 TTAGACAAGGAACGTTTAAAGCTC 57.465 37.500 0.46 0.00 0.00 4.09
67 68 7.506328 AATTAGACAAGGAACGTTTAAAGCT 57.494 32.000 0.46 0.00 0.00 3.74
68 69 9.486857 GATAATTAGACAAGGAACGTTTAAAGC 57.513 33.333 0.46 0.00 0.00 3.51
119 120 9.460019 TGGTTCACTTCATACATGATAAATCAA 57.540 29.630 0.00 0.00 40.69 2.57
120 121 9.631257 ATGGTTCACTTCATACATGATAAATCA 57.369 29.630 0.00 0.00 41.70 2.57
121 122 9.888878 CATGGTTCACTTCATACATGATAAATC 57.111 33.333 0.00 0.00 38.29 2.17
122 123 9.412460 ACATGGTTCACTTCATACATGATAAAT 57.588 29.630 0.00 0.00 39.08 1.40
123 124 8.806429 ACATGGTTCACTTCATACATGATAAA 57.194 30.769 0.00 0.00 39.08 1.40
126 127 9.494271 GTATACATGGTTCACTTCATACATGAT 57.506 33.333 0.00 2.40 39.08 2.45
127 128 8.482128 TGTATACATGGTTCACTTCATACATGA 58.518 33.333 0.08 0.00 39.08 3.07
128 129 8.661352 TGTATACATGGTTCACTTCATACATG 57.339 34.615 0.08 0.00 40.94 3.21
129 130 9.851686 AATGTATACATGGTTCACTTCATACAT 57.148 29.630 18.94 0.00 39.04 2.29
130 131 9.108284 CAATGTATACATGGTTCACTTCATACA 57.892 33.333 18.94 0.00 36.56 2.29
131 132 9.109393 ACAATGTATACATGGTTCACTTCATAC 57.891 33.333 18.58 0.00 37.20 2.39
132 133 9.679661 AACAATGTATACATGGTTCACTTCATA 57.320 29.630 26.48 0.00 44.85 2.15
133 134 8.579850 AACAATGTATACATGGTTCACTTCAT 57.420 30.769 26.48 8.13 44.85 2.57
134 135 7.994425 AACAATGTATACATGGTTCACTTCA 57.006 32.000 26.48 0.00 44.85 3.02
136 137 8.826710 CGATAACAATGTATACATGGTTCACTT 58.173 33.333 32.53 19.93 44.85 3.16
137 138 7.441157 CCGATAACAATGTATACATGGTTCACT 59.559 37.037 32.53 21.73 44.85 3.41
138 139 7.307751 CCCGATAACAATGTATACATGGTTCAC 60.308 40.741 32.53 25.78 44.85 3.18
139 140 6.708502 CCCGATAACAATGTATACATGGTTCA 59.291 38.462 32.53 21.88 44.85 3.18
140 141 6.348213 GCCCGATAACAATGTATACATGGTTC 60.348 42.308 32.53 22.17 44.85 3.62
142 143 5.001232 GCCCGATAACAATGTATACATGGT 58.999 41.667 18.58 18.58 42.08 3.55
143 144 4.394920 GGCCCGATAACAATGTATACATGG 59.605 45.833 18.94 18.07 36.56 3.66
144 145 5.000591 TGGCCCGATAACAATGTATACATG 58.999 41.667 18.94 14.50 36.56 3.21
145 146 5.235850 TGGCCCGATAACAATGTATACAT 57.764 39.130 12.75 12.75 38.41 2.29
146 147 4.504165 CCTGGCCCGATAACAATGTATACA 60.504 45.833 8.27 8.27 0.00 2.29
147 148 4.000988 CCTGGCCCGATAACAATGTATAC 58.999 47.826 0.00 0.00 0.00 1.47
148 149 3.008594 CCCTGGCCCGATAACAATGTATA 59.991 47.826 0.00 0.00 0.00 1.47
149 150 2.224769 CCCTGGCCCGATAACAATGTAT 60.225 50.000 0.00 0.00 0.00 2.29
150 151 1.142060 CCCTGGCCCGATAACAATGTA 59.858 52.381 0.00 0.00 0.00 2.29
151 152 0.106719 CCCTGGCCCGATAACAATGT 60.107 55.000 0.00 0.00 0.00 2.71
152 153 1.455383 GCCCTGGCCCGATAACAATG 61.455 60.000 0.00 0.00 34.56 2.82
153 154 1.152756 GCCCTGGCCCGATAACAAT 60.153 57.895 0.00 0.00 34.56 2.71
154 155 2.274104 GCCCTGGCCCGATAACAA 59.726 61.111 0.00 0.00 34.56 2.83
164 165 0.106519 AATGTGTGATAGGCCCTGGC 60.107 55.000 0.00 0.00 41.06 4.85
165 166 1.492176 AGAATGTGTGATAGGCCCTGG 59.508 52.381 0.00 0.00 0.00 4.45
166 167 2.569059 CAGAATGTGTGATAGGCCCTG 58.431 52.381 0.00 0.00 0.00 4.45
167 168 1.492176 CCAGAATGTGTGATAGGCCCT 59.508 52.381 0.00 0.00 0.00 5.19
168 169 1.972872 CCAGAATGTGTGATAGGCCC 58.027 55.000 0.00 0.00 0.00 5.80
169 170 1.312815 GCCAGAATGTGTGATAGGCC 58.687 55.000 0.00 0.00 34.71 5.19
170 171 0.940126 CGCCAGAATGTGTGATAGGC 59.060 55.000 0.00 0.00 37.32 3.93
171 172 1.935873 CACGCCAGAATGTGTGATAGG 59.064 52.381 0.00 0.00 41.40 2.57
172 173 2.862536 CTCACGCCAGAATGTGTGATAG 59.137 50.000 7.75 0.00 44.78 2.08
173 174 2.892374 CTCACGCCAGAATGTGTGATA 58.108 47.619 7.75 0.00 44.78 2.15
174 175 1.730501 CTCACGCCAGAATGTGTGAT 58.269 50.000 7.75 0.00 44.78 3.06
175 176 0.950555 GCTCACGCCAGAATGTGTGA 60.951 55.000 7.16 7.16 44.06 3.58
176 177 0.952497 AGCTCACGCCAGAATGTGTG 60.952 55.000 0.00 0.00 40.58 3.82
177 178 0.671781 GAGCTCACGCCAGAATGTGT 60.672 55.000 9.40 0.00 37.38 3.72
178 179 1.690283 CGAGCTCACGCCAGAATGTG 61.690 60.000 15.40 0.00 36.60 3.21
179 180 1.446792 CGAGCTCACGCCAGAATGT 60.447 57.895 15.40 0.00 36.60 2.71
180 181 1.416813 GACGAGCTCACGCCAGAATG 61.417 60.000 15.40 0.00 36.60 2.67
181 182 1.153745 GACGAGCTCACGCCAGAAT 60.154 57.895 15.40 0.00 36.60 2.40
182 183 2.258591 GACGAGCTCACGCCAGAA 59.741 61.111 15.40 0.00 36.60 3.02
183 184 2.982744 CTGACGAGCTCACGCCAGA 61.983 63.158 15.40 0.00 44.07 3.86
184 185 2.505777 CTGACGAGCTCACGCCAG 60.506 66.667 15.40 5.60 37.41 4.85
185 186 4.056125 CCTGACGAGCTCACGCCA 62.056 66.667 15.40 0.00 36.60 5.69
186 187 3.691744 CTCCTGACGAGCTCACGCC 62.692 68.421 15.40 0.00 36.60 5.68
187 188 2.202544 CTCCTGACGAGCTCACGC 60.203 66.667 15.40 2.41 36.70 5.34
188 189 1.427419 CTCTCCTGACGAGCTCACG 59.573 63.158 15.40 3.56 38.62 4.35
194 195 1.311651 TGCTCTGCTCTCCTGACGAG 61.312 60.000 0.00 0.00 40.30 4.18
195 196 0.895559 TTGCTCTGCTCTCCTGACGA 60.896 55.000 0.00 0.00 0.00 4.20
196 197 0.175302 ATTGCTCTGCTCTCCTGACG 59.825 55.000 0.00 0.00 0.00 4.35
197 198 3.533606 TTATTGCTCTGCTCTCCTGAC 57.466 47.619 0.00 0.00 0.00 3.51
198 199 3.517100 AGTTTATTGCTCTGCTCTCCTGA 59.483 43.478 0.00 0.00 0.00 3.86
199 200 3.870419 GAGTTTATTGCTCTGCTCTCCTG 59.130 47.826 0.00 0.00 0.00 3.86
200 201 3.118445 GGAGTTTATTGCTCTGCTCTCCT 60.118 47.826 0.00 0.00 37.71 3.69
201 202 3.202097 GGAGTTTATTGCTCTGCTCTCC 58.798 50.000 0.00 0.00 34.48 3.71
202 203 3.866651 TGGAGTTTATTGCTCTGCTCTC 58.133 45.455 0.00 0.00 33.73 3.20
203 204 3.988976 TGGAGTTTATTGCTCTGCTCT 57.011 42.857 0.00 0.00 33.73 4.09
204 205 4.194640 TCATGGAGTTTATTGCTCTGCTC 58.805 43.478 0.00 0.00 33.73 4.26
205 206 4.080695 TCTCATGGAGTTTATTGCTCTGCT 60.081 41.667 0.00 0.00 33.73 4.24
206 207 4.194640 TCTCATGGAGTTTATTGCTCTGC 58.805 43.478 0.00 0.00 33.73 4.26
207 208 5.668471 TCTCTCATGGAGTTTATTGCTCTG 58.332 41.667 9.98 0.00 42.40 3.35
208 209 5.946942 TCTCTCATGGAGTTTATTGCTCT 57.053 39.130 9.98 0.00 42.40 4.09
766 767 3.432326 GGGAAAGTATCGGCAGTTCATCT 60.432 47.826 0.00 0.00 0.00 2.90
767 768 2.872858 GGGAAAGTATCGGCAGTTCATC 59.127 50.000 0.00 0.00 0.00 2.92
768 769 2.421529 GGGGAAAGTATCGGCAGTTCAT 60.422 50.000 0.00 0.00 0.00 2.57
769 770 1.065709 GGGGAAAGTATCGGCAGTTCA 60.066 52.381 0.00 0.00 0.00 3.18
770 771 1.209747 AGGGGAAAGTATCGGCAGTTC 59.790 52.381 0.00 0.00 0.00 3.01
771 772 1.209747 GAGGGGAAAGTATCGGCAGTT 59.790 52.381 0.00 0.00 0.00 3.16
772 773 0.831307 GAGGGGAAAGTATCGGCAGT 59.169 55.000 0.00 0.00 0.00 4.40
773 774 0.249489 CGAGGGGAAAGTATCGGCAG 60.249 60.000 0.00 0.00 0.00 4.85
774 775 1.820581 CGAGGGGAAAGTATCGGCA 59.179 57.895 0.00 0.00 0.00 5.69
775 776 1.594564 GCGAGGGGAAAGTATCGGC 60.595 63.158 0.00 0.00 35.76 5.54
776 777 1.299926 CGCGAGGGGAAAGTATCGG 60.300 63.158 0.00 0.00 35.76 4.18
777 778 1.949631 GCGCGAGGGGAAAGTATCG 60.950 63.158 12.10 0.00 38.19 2.92
778 779 0.461339 TTGCGCGAGGGGAAAGTATC 60.461 55.000 12.10 0.00 0.00 2.24
779 780 0.462047 CTTGCGCGAGGGGAAAGTAT 60.462 55.000 17.45 0.00 0.00 2.12
780 781 1.079405 CTTGCGCGAGGGGAAAGTA 60.079 57.895 17.45 0.00 0.00 2.24
781 782 2.358737 CTTGCGCGAGGGGAAAGT 60.359 61.111 17.45 0.00 0.00 2.66
904 911 2.441532 CGCTACCGAGGGGAAGGA 60.442 66.667 0.00 0.00 36.97 3.36
1011 1018 5.248640 TCAAAGTCATCATCTTCCAGGTTC 58.751 41.667 0.00 0.00 0.00 3.62
1026 1033 6.577103 GTCTATCACCAGATCATCAAAGTCA 58.423 40.000 0.00 0.00 35.67 3.41
1050 1057 1.583986 GATCTCCGGATCAGCCTCG 59.416 63.158 3.57 0.00 45.54 4.63
1097 1112 7.071447 TGAAGGATTTATCGGTATGAACCCTAA 59.929 37.037 0.00 0.00 43.54 2.69
1137 1152 1.476110 GCCGCCCACATATCCTTGTAA 60.476 52.381 0.00 0.00 0.00 2.41
1261 1276 2.521547 AATTCCTGAAGAGCCAAGGG 57.478 50.000 0.00 0.00 0.00 3.95
1308 1323 3.631250 ACTTCCTCTGCCTTTGTGAAAA 58.369 40.909 0.00 0.00 0.00 2.29
1561 1576 1.443872 CGCCAGTTTCTCGTAGCGT 60.444 57.895 0.00 0.00 38.81 5.07
1581 1596 1.611673 GCCCACATACACTGCAGAAGT 60.612 52.381 23.35 19.95 40.93 3.01
1622 1637 2.393768 GCACACCTGATCCGCACTG 61.394 63.158 0.00 0.00 0.00 3.66
1794 1813 4.466827 TGTAGCCGTATCTAGAATGTCCA 58.533 43.478 0.00 0.00 0.00 4.02
1907 1926 1.602237 CACTCGGCCCTACCAATGT 59.398 57.895 0.00 0.00 39.03 2.71
1909 1928 1.205460 AACCACTCGGCCCTACCAAT 61.205 55.000 0.00 0.00 39.03 3.16
1949 1968 0.322726 TGTGCACCATCCTCACCATG 60.323 55.000 15.69 0.00 0.00 3.66
2379 2401 3.476552 TCGAAGAGGCATGTCTTGTTTT 58.523 40.909 0.00 0.00 36.89 2.43
2408 2635 0.457851 CTCCACATGAGAGGACGGTC 59.542 60.000 0.00 0.00 44.42 4.79
2415 2642 4.502962 GGAAAGAGAACTCCACATGAGAG 58.497 47.826 13.65 13.65 44.42 3.20
2523 2750 1.276138 TCTGATTTTCTGAGCGCTGGA 59.724 47.619 18.48 10.53 0.00 3.86
2533 2760 5.133221 CGGAATAACCCCATCTGATTTTCT 58.867 41.667 0.00 0.00 34.64 2.52
2608 2837 8.464404 CCAATCTGCCCATTATCATATGTAAAG 58.536 37.037 1.90 0.00 0.00 1.85
2773 3002 2.173782 AGCTCTAGTCCTCCTCGAATCA 59.826 50.000 0.00 0.00 0.00 2.57
2794 3023 5.243954 CCACATAATCTCATACCGAGGAGAA 59.756 44.000 0.00 0.00 45.13 2.87
2929 3158 2.283388 TCCTTACTCCACGCCCGT 60.283 61.111 0.00 0.00 0.00 5.28
2997 3229 6.837992 TCCGCATCTTTTAGTTGTAAATCAC 58.162 36.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.