Multiple sequence alignment - TraesCS4B01G301000

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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 TraesCS4B01G301000 chr4B 100.000 2484 0 0 1 2484 587428069 587430552 0.000000e+00 4588.0
1 TraesCS4B01G301000 chr4B 96.283 269 7 2 2218 2483 287016012 287016280 2.930000e-119 438.0
2 TraesCS4B01G301000 chr4B 93.706 143 8 1 2343 2484 379021657 379021515 1.940000e-51 213.0
3 TraesCS4B01G301000 chr4B 93.151 73 5 0 2218 2290 379021738 379021666 9.390000e-20 108.0
4 TraesCS4B01G301000 chr4B 89.655 58 6 0 231 288 198951211 198951268 9.530000e-10 75.0
5 TraesCS4B01G301000 chr6D 94.213 1918 95 8 300 2210 401339393 401337485 0.000000e+00 2913.0
6 TraesCS4B01G301000 chr6D 82.468 154 23 4 943 1093 238478019 238478171 5.570000e-27 132.0
7 TraesCS4B01G301000 chr7B 91.919 1918 127 10 300 2210 319265422 319267318 0.000000e+00 2658.0
8 TraesCS4B01G301000 chr7B 97.104 1485 39 3 1003 2484 491904693 491903210 0.000000e+00 2501.0
9 TraesCS4B01G301000 chr7B 93.094 362 11 2 579 926 491905055 491904694 3.660000e-143 518.0
10 TraesCS4B01G301000 chr5B 86.119 2010 225 29 235 2210 40031912 40033901 0.000000e+00 2117.0
11 TraesCS4B01G301000 chr5B 88.398 181 18 3 2031 2210 240822501 240822679 5.380000e-52 215.0
12 TraesCS4B01G301000 chr2A 93.279 1235 69 5 229 1458 645909633 645910858 0.000000e+00 1808.0
13 TraesCS4B01G301000 chr2A 95.623 1028 43 2 1455 2480 645911143 645912170 0.000000e+00 1648.0
14 TraesCS4B01G301000 chr2A 93.089 246 13 4 1 243 549330105 549330349 8.450000e-95 357.0
15 TraesCS4B01G301000 chr2A 87.671 73 7 2 229 299 441306718 441306646 1.580000e-12 84.2
16 TraesCS4B01G301000 chr1D 97.388 268 6 1 2218 2484 212118978 212118711 2.910000e-124 455.0
17 TraesCS4B01G301000 chr1D 95.982 224 8 1 1 223 229299756 229299533 1.820000e-96 363.0
18 TraesCS4B01G301000 chr1D 92.400 250 12 4 1 243 469692455 469692704 1.410000e-92 350.0
19 TraesCS4B01G301000 chr1D 92.308 247 15 3 1 243 41708246 41708492 5.080000e-92 348.0
20 TraesCS4B01G301000 chr7A 97.015 268 7 1 2218 2484 373888137 373887870 1.350000e-122 449.0
21 TraesCS4B01G301000 chr7A 94.403 268 14 1 2218 2484 665590375 665590642 6.390000e-111 411.0
22 TraesCS4B01G301000 chr7A 90.210 143 13 1 2343 2484 373878548 373878406 4.220000e-43 185.0
23 TraesCS4B01G301000 chr7A 96.721 61 2 0 1139 1199 291028381 291028321 4.370000e-18 102.0
24 TraesCS4B01G301000 chr3D 95.473 243 8 3 1 240 345564804 345564562 3.880000e-103 385.0
25 TraesCS4B01G301000 chr4D 94.332 247 10 3 1 243 328338426 328338672 2.330000e-100 375.0
26 TraesCS4B01G301000 chr4D 93.902 246 12 2 1 243 415049069 415048824 3.900000e-98 368.0
27 TraesCS4B01G301000 chr4D 92.683 246 12 3 1 240 435613798 435614043 1.410000e-92 350.0
28 TraesCS4B01G301000 chr7D 94.118 238 12 1 2 237 250899291 250899528 6.530000e-96 361.0
29 TraesCS4B01G301000 chr4A 88.462 182 19 2 2031 2210 283595734 283595553 4.160000e-53 219.0
30 TraesCS4B01G301000 chr4A 88.235 68 8 0 232 299 271441372 271441305 5.690000e-12 82.4
31 TraesCS4B01G301000 chr4A 91.525 59 5 0 230 288 642495795 642495737 5.690000e-12 82.4
32 TraesCS4B01G301000 chr4A 84.932 73 9 2 215 285 231510678 231510750 3.430000e-09 73.1
33 TraesCS4B01G301000 chr3A 88.462 182 19 2 2031 2210 354208209 354208028 4.160000e-53 219.0
34 TraesCS4B01G301000 chr3A 89.655 87 7 2 215 299 220366257 220366343 2.610000e-20 110.0
35 TraesCS4B01G301000 chr3A 79.856 139 28 0 943 1081 411058593 411058731 4.370000e-18 102.0
36 TraesCS4B01G301000 chr3A 90.909 55 5 0 245 299 677560375 677560321 9.530000e-10 75.0
37 TraesCS4B01G301000 chr1B 88.462 182 17 3 2031 2210 143838419 143838240 1.500000e-52 217.0
38 TraesCS4B01G301000 chr5A 93.007 143 9 1 2343 2484 498003338 498003480 9.000000e-50 207.0
39 TraesCS4B01G301000 chr5A 92.982 57 4 0 243 299 21821062 21821118 1.580000e-12 84.2
40 TraesCS4B01G301000 chr6B 90.110 91 7 2 942 1030 388404591 388404681 1.560000e-22 117.0
41 TraesCS4B01G301000 chr6A 79.856 139 28 0 943 1081 390132789 390132651 4.370000e-18 102.0
42 TraesCS4B01G301000 chr1A 79.856 139 27 1 943 1081 380358248 380358385 1.570000e-17 100.0
43 TraesCS4B01G301000 chr1A 90.141 71 7 0 229 299 554696581 554696511 2.630000e-15 93.5


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 TraesCS4B01G301000 chr4B 587428069 587430552 2483 False 4588.0 4588 100.000 1 2484 1 chr4B.!!$F3 2483
1 TraesCS4B01G301000 chr6D 401337485 401339393 1908 True 2913.0 2913 94.213 300 2210 1 chr6D.!!$R1 1910
2 TraesCS4B01G301000 chr7B 319265422 319267318 1896 False 2658.0 2658 91.919 300 2210 1 chr7B.!!$F1 1910
3 TraesCS4B01G301000 chr7B 491903210 491905055 1845 True 1509.5 2501 95.099 579 2484 2 chr7B.!!$R1 1905
4 TraesCS4B01G301000 chr5B 40031912 40033901 1989 False 2117.0 2117 86.119 235 2210 1 chr5B.!!$F1 1975
5 TraesCS4B01G301000 chr2A 645909633 645912170 2537 False 1728.0 1808 94.451 229 2480 2 chr2A.!!$F2 2251

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
78 79 0.107897 TACGCGGTGCCTGAAATCAT 60.108 50.0 12.47 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2206 0.036732 TGCCGCTGAAGTCCAAATCT 59.963 50.0 0.0 0.0 0.0 2.4 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
48 49 4.858965 AGAAATTGATTCTCAGAGCCCT 57.141 40.909 0.00 0.00 45.42 5.19
49 50 5.965033 AGAAATTGATTCTCAGAGCCCTA 57.035 39.130 0.00 0.00 45.42 3.53
50 51 5.679601 AGAAATTGATTCTCAGAGCCCTAC 58.320 41.667 0.00 0.00 45.42 3.18
51 52 3.742433 ATTGATTCTCAGAGCCCTACG 57.258 47.619 0.00 0.00 0.00 3.51
52 53 2.437085 TGATTCTCAGAGCCCTACGA 57.563 50.000 0.00 0.00 0.00 3.43
53 54 2.025155 TGATTCTCAGAGCCCTACGAC 58.975 52.381 0.00 0.00 0.00 4.34
54 55 2.025155 GATTCTCAGAGCCCTACGACA 58.975 52.381 0.00 0.00 0.00 4.35
55 56 1.919240 TTCTCAGAGCCCTACGACAA 58.081 50.000 0.00 0.00 0.00 3.18
56 57 2.145397 TCTCAGAGCCCTACGACAAT 57.855 50.000 0.00 0.00 0.00 2.71
57 58 2.457598 TCTCAGAGCCCTACGACAATT 58.542 47.619 0.00 0.00 0.00 2.32
58 59 2.166459 TCTCAGAGCCCTACGACAATTG 59.834 50.000 3.24 3.24 0.00 2.32
59 60 1.899814 TCAGAGCCCTACGACAATTGT 59.100 47.619 11.78 11.78 0.00 2.71
60 61 3.093814 TCAGAGCCCTACGACAATTGTA 58.906 45.455 11.95 0.00 0.00 2.41
61 62 3.119245 TCAGAGCCCTACGACAATTGTAC 60.119 47.826 11.95 4.61 0.00 2.90
62 63 2.159282 AGAGCCCTACGACAATTGTACG 60.159 50.000 11.95 17.88 0.00 3.67
63 64 0.648958 GCCCTACGACAATTGTACGC 59.351 55.000 22.03 10.94 0.00 4.42
64 65 0.918619 CCCTACGACAATTGTACGCG 59.081 55.000 22.03 18.64 0.00 6.01
65 66 0.918619 CCTACGACAATTGTACGCGG 59.081 55.000 22.03 19.15 0.00 6.46
66 67 1.621107 CTACGACAATTGTACGCGGT 58.379 50.000 22.03 13.68 0.00 5.68
67 68 1.319374 CTACGACAATTGTACGCGGTG 59.681 52.381 22.03 11.73 0.00 4.94
68 69 1.225637 CGACAATTGTACGCGGTGC 60.226 57.895 11.95 0.00 0.00 5.01
69 70 1.133869 GACAATTGTACGCGGTGCC 59.866 57.895 11.95 0.00 0.00 5.01
70 71 1.296056 GACAATTGTACGCGGTGCCT 61.296 55.000 11.95 0.00 0.00 4.75
71 72 1.134487 CAATTGTACGCGGTGCCTG 59.866 57.895 12.47 0.00 0.00 4.85
72 73 1.004320 AATTGTACGCGGTGCCTGA 60.004 52.632 12.47 0.00 0.00 3.86
73 74 0.604243 AATTGTACGCGGTGCCTGAA 60.604 50.000 12.47 0.00 0.00 3.02
74 75 0.604243 ATTGTACGCGGTGCCTGAAA 60.604 50.000 12.47 0.00 0.00 2.69
75 76 0.604243 TTGTACGCGGTGCCTGAAAT 60.604 50.000 12.47 0.00 0.00 2.17
76 77 1.017177 TGTACGCGGTGCCTGAAATC 61.017 55.000 12.47 0.00 0.00 2.17
77 78 1.017177 GTACGCGGTGCCTGAAATCA 61.017 55.000 12.47 0.00 0.00 2.57
78 79 0.107897 TACGCGGTGCCTGAAATCAT 60.108 50.000 12.47 0.00 0.00 2.45
79 80 1.353103 CGCGGTGCCTGAAATCATC 59.647 57.895 0.00 0.00 0.00 2.92
80 81 1.368345 CGCGGTGCCTGAAATCATCA 61.368 55.000 0.00 0.00 36.38 3.07
81 82 1.027357 GCGGTGCCTGAAATCATCAT 58.973 50.000 0.00 0.00 37.44 2.45
82 83 1.406539 GCGGTGCCTGAAATCATCATT 59.593 47.619 0.00 0.00 37.44 2.57
83 84 2.542411 GCGGTGCCTGAAATCATCATTC 60.542 50.000 0.00 0.00 37.44 2.67
84 85 2.947652 CGGTGCCTGAAATCATCATTCT 59.052 45.455 0.00 0.00 37.44 2.40
85 86 3.379372 CGGTGCCTGAAATCATCATTCTT 59.621 43.478 0.00 0.00 37.44 2.52
86 87 4.576053 CGGTGCCTGAAATCATCATTCTTA 59.424 41.667 0.00 0.00 37.44 2.10
87 88 5.240183 CGGTGCCTGAAATCATCATTCTTAT 59.760 40.000 0.00 0.00 37.44 1.73
88 89 6.427853 CGGTGCCTGAAATCATCATTCTTATA 59.572 38.462 0.00 0.00 37.44 0.98
89 90 7.571983 CGGTGCCTGAAATCATCATTCTTATAC 60.572 40.741 0.00 0.00 37.44 1.47
90 91 7.293745 GTGCCTGAAATCATCATTCTTATACG 58.706 38.462 0.00 0.00 37.44 3.06
91 92 6.427853 TGCCTGAAATCATCATTCTTATACGG 59.572 38.462 0.00 0.00 37.44 4.02
92 93 6.428159 GCCTGAAATCATCATTCTTATACGGT 59.572 38.462 0.00 0.00 37.44 4.83
93 94 7.571983 GCCTGAAATCATCATTCTTATACGGTG 60.572 40.741 0.00 0.00 37.44 4.94
94 95 7.095060 CCTGAAATCATCATTCTTATACGGTGG 60.095 40.741 0.00 0.00 37.44 4.61
95 96 6.710295 TGAAATCATCATTCTTATACGGTGGG 59.290 38.462 0.00 0.00 31.50 4.61
96 97 5.825593 ATCATCATTCTTATACGGTGGGT 57.174 39.130 0.00 0.00 0.00 4.51
97 98 5.209818 TCATCATTCTTATACGGTGGGTC 57.790 43.478 0.00 0.00 0.00 4.46
98 99 4.651962 TCATCATTCTTATACGGTGGGTCA 59.348 41.667 0.00 0.00 0.00 4.02
99 100 4.395959 TCATTCTTATACGGTGGGTCAC 57.604 45.455 0.00 0.00 0.00 3.67
100 101 2.945447 TTCTTATACGGTGGGTCACG 57.055 50.000 0.00 0.00 34.83 4.35
101 102 0.457035 TCTTATACGGTGGGTCACGC 59.543 55.000 0.00 0.00 34.83 5.34
102 103 0.529119 CTTATACGGTGGGTCACGCC 60.529 60.000 0.00 0.00 46.57 5.68
108 109 3.284449 GTGGGTCACGCCACCAAC 61.284 66.667 5.77 0.63 38.32 3.77
109 110 3.798511 TGGGTCACGCCACCAACA 61.799 61.111 5.77 0.00 38.32 3.33
110 111 2.517402 GGGTCACGCCACCAACAA 60.517 61.111 5.77 0.00 38.32 2.83
111 112 2.122167 GGGTCACGCCACCAACAAA 61.122 57.895 5.77 0.00 38.32 2.83
112 113 1.668101 GGGTCACGCCACCAACAAAA 61.668 55.000 5.77 0.00 38.32 2.44
113 114 0.173708 GGTCACGCCACCAACAAAAA 59.826 50.000 0.00 0.00 36.32 1.94
114 115 1.202475 GGTCACGCCACCAACAAAAAT 60.202 47.619 0.00 0.00 36.32 1.82
115 116 2.545731 GTCACGCCACCAACAAAAATT 58.454 42.857 0.00 0.00 0.00 1.82
116 117 2.283884 GTCACGCCACCAACAAAAATTG 59.716 45.455 0.00 0.00 0.00 2.32
117 118 2.166459 TCACGCCACCAACAAAAATTGA 59.834 40.909 0.00 0.00 0.00 2.57
118 119 2.932614 CACGCCACCAACAAAAATTGAA 59.067 40.909 0.00 0.00 0.00 2.69
119 120 3.372206 CACGCCACCAACAAAAATTGAAA 59.628 39.130 0.00 0.00 0.00 2.69
120 121 4.003648 ACGCCACCAACAAAAATTGAAAA 58.996 34.783 0.00 0.00 0.00 2.29
121 122 4.637977 ACGCCACCAACAAAAATTGAAAAT 59.362 33.333 0.00 0.00 0.00 1.82
122 123 5.204101 CGCCACCAACAAAAATTGAAAATC 58.796 37.500 0.00 0.00 0.00 2.17
123 124 5.007528 CGCCACCAACAAAAATTGAAAATCT 59.992 36.000 0.00 0.00 0.00 2.40
124 125 6.458070 CGCCACCAACAAAAATTGAAAATCTT 60.458 34.615 0.00 0.00 0.00 2.40
125 126 6.912051 GCCACCAACAAAAATTGAAAATCTTC 59.088 34.615 0.00 0.00 0.00 2.87
126 127 7.414984 GCCACCAACAAAAATTGAAAATCTTCA 60.415 33.333 0.00 0.00 39.87 3.02
166 167 8.877808 AAATTCCTCAGTTGTTCAATTTCTTC 57.122 30.769 0.00 0.00 0.00 2.87
167 168 7.587037 ATTCCTCAGTTGTTCAATTTCTTCA 57.413 32.000 0.00 0.00 0.00 3.02
168 169 7.403312 TTCCTCAGTTGTTCAATTTCTTCAA 57.597 32.000 0.00 0.00 0.00 2.69
169 170 6.795399 TCCTCAGTTGTTCAATTTCTTCAAC 58.205 36.000 0.00 0.00 38.69 3.18
170 171 6.603201 TCCTCAGTTGTTCAATTTCTTCAACT 59.397 34.615 0.00 0.00 45.93 3.16
171 172 7.122650 TCCTCAGTTGTTCAATTTCTTCAACTT 59.877 33.333 6.19 0.00 43.68 2.66
172 173 7.761249 CCTCAGTTGTTCAATTTCTTCAACTTT 59.239 33.333 6.19 0.00 43.68 2.66
173 174 8.464770 TCAGTTGTTCAATTTCTTCAACTTTG 57.535 30.769 6.19 0.00 43.68 2.77
174 175 7.063308 TCAGTTGTTCAATTTCTTCAACTTTGC 59.937 33.333 6.19 0.00 43.68 3.68
175 176 6.873076 AGTTGTTCAATTTCTTCAACTTTGCA 59.127 30.769 0.00 0.00 43.68 4.08
176 177 7.550196 AGTTGTTCAATTTCTTCAACTTTGCAT 59.450 29.630 0.00 0.00 43.68 3.96
177 178 7.846644 TGTTCAATTTCTTCAACTTTGCATT 57.153 28.000 0.00 0.00 0.00 3.56
178 179 8.939201 TGTTCAATTTCTTCAACTTTGCATTA 57.061 26.923 0.00 0.00 0.00 1.90
179 180 9.545105 TGTTCAATTTCTTCAACTTTGCATTAT 57.455 25.926 0.00 0.00 0.00 1.28
181 182 9.985730 TTCAATTTCTTCAACTTTGCATTATCT 57.014 25.926 0.00 0.00 0.00 1.98
182 183 9.985730 TCAATTTCTTCAACTTTGCATTATCTT 57.014 25.926 0.00 0.00 0.00 2.40
184 185 9.985730 AATTTCTTCAACTTTGCATTATCTTCA 57.014 25.926 0.00 0.00 0.00 3.02
185 186 8.801715 TTTCTTCAACTTTGCATTATCTTCAC 57.198 30.769 0.00 0.00 0.00 3.18
186 187 7.750229 TCTTCAACTTTGCATTATCTTCACT 57.250 32.000 0.00 0.00 0.00 3.41
187 188 7.587629 TCTTCAACTTTGCATTATCTTCACTG 58.412 34.615 0.00 0.00 0.00 3.66
188 189 7.445096 TCTTCAACTTTGCATTATCTTCACTGA 59.555 33.333 0.00 0.00 0.00 3.41
189 190 7.692460 TCAACTTTGCATTATCTTCACTGAT 57.308 32.000 0.00 0.00 0.00 2.90
190 191 8.114331 TCAACTTTGCATTATCTTCACTGATT 57.886 30.769 0.00 0.00 0.00 2.57
191 192 8.239314 TCAACTTTGCATTATCTTCACTGATTC 58.761 33.333 0.00 0.00 0.00 2.52
192 193 7.093322 ACTTTGCATTATCTTCACTGATTCC 57.907 36.000 0.00 0.00 0.00 3.01
193 194 5.739752 TTGCATTATCTTCACTGATTCCG 57.260 39.130 0.00 0.00 0.00 4.30
194 195 4.769688 TGCATTATCTTCACTGATTCCGT 58.230 39.130 0.00 0.00 0.00 4.69
195 196 4.811024 TGCATTATCTTCACTGATTCCGTC 59.189 41.667 0.00 0.00 0.00 4.79
196 197 4.811024 GCATTATCTTCACTGATTCCGTCA 59.189 41.667 0.00 0.00 35.05 4.35
197 198 5.468072 GCATTATCTTCACTGATTCCGTCAT 59.532 40.000 0.00 0.00 35.97 3.06
198 199 6.017605 GCATTATCTTCACTGATTCCGTCATT 60.018 38.462 0.00 0.00 35.97 2.57
199 200 7.467811 GCATTATCTTCACTGATTCCGTCATTT 60.468 37.037 0.00 0.00 35.97 2.32
200 201 7.921786 TTATCTTCACTGATTCCGTCATTTT 57.078 32.000 0.00 0.00 35.97 1.82
201 202 6.824305 ATCTTCACTGATTCCGTCATTTTT 57.176 33.333 0.00 0.00 35.97 1.94
202 203 6.241207 TCTTCACTGATTCCGTCATTTTTC 57.759 37.500 0.00 0.00 35.97 2.29
203 204 5.997746 TCTTCACTGATTCCGTCATTTTTCT 59.002 36.000 0.00 0.00 35.97 2.52
204 205 6.486657 TCTTCACTGATTCCGTCATTTTTCTT 59.513 34.615 0.00 0.00 35.97 2.52
205 206 6.241207 TCACTGATTCCGTCATTTTTCTTC 57.759 37.500 0.00 0.00 35.97 2.87
206 207 5.762711 TCACTGATTCCGTCATTTTTCTTCA 59.237 36.000 0.00 0.00 35.97 3.02
207 208 6.430925 TCACTGATTCCGTCATTTTTCTTCAT 59.569 34.615 0.00 0.00 35.97 2.57
208 209 7.040478 TCACTGATTCCGTCATTTTTCTTCATT 60.040 33.333 0.00 0.00 35.97 2.57
209 210 7.061441 CACTGATTCCGTCATTTTTCTTCATTG 59.939 37.037 0.00 0.00 35.97 2.82
210 211 7.040478 ACTGATTCCGTCATTTTTCTTCATTGA 60.040 33.333 0.00 0.00 35.97 2.57
211 212 7.083858 TGATTCCGTCATTTTTCTTCATTGAC 58.916 34.615 0.00 0.00 34.70 3.18
212 213 6.633500 TTCCGTCATTTTTCTTCATTGACT 57.367 33.333 0.00 0.00 35.64 3.41
213 214 6.633500 TCCGTCATTTTTCTTCATTGACTT 57.367 33.333 0.00 0.00 35.64 3.01
214 215 7.038154 TCCGTCATTTTTCTTCATTGACTTT 57.962 32.000 0.00 0.00 35.64 2.66
215 216 8.160521 TCCGTCATTTTTCTTCATTGACTTTA 57.839 30.769 0.00 0.00 35.64 1.85
216 217 8.792633 TCCGTCATTTTTCTTCATTGACTTTAT 58.207 29.630 0.00 0.00 35.64 1.40
275 276 8.423906 TCTAATCCCAGGATCAGAATAGTTAC 57.576 38.462 0.00 0.00 33.08 2.50
286 287 7.655328 GGATCAGAATAGTTACTTGGATCACAG 59.345 40.741 0.00 0.00 33.38 3.66
288 289 5.233050 CAGAATAGTTACTTGGATCACAGCG 59.767 44.000 0.00 0.00 0.00 5.18
290 291 1.623811 AGTTACTTGGATCACAGCGGT 59.376 47.619 0.00 0.00 0.00 5.68
292 293 1.557099 TACTTGGATCACAGCGGTCT 58.443 50.000 0.00 0.00 0.00 3.85
293 294 1.557099 ACTTGGATCACAGCGGTCTA 58.443 50.000 0.00 0.00 0.00 2.59
294 295 2.111384 ACTTGGATCACAGCGGTCTAT 58.889 47.619 0.00 0.00 0.00 1.98
295 296 3.296854 ACTTGGATCACAGCGGTCTATA 58.703 45.455 0.00 0.00 0.00 1.31
296 297 3.898123 ACTTGGATCACAGCGGTCTATAT 59.102 43.478 0.00 0.00 0.00 0.86
297 298 5.077564 ACTTGGATCACAGCGGTCTATATA 58.922 41.667 0.00 0.00 0.00 0.86
312 313 7.337167 CGGTCTATATAGTATATAGGGGCGAT 58.663 42.308 26.48 0.77 0.00 4.58
343 344 2.614481 CCCGAGATCTGAAAACCCGAAA 60.614 50.000 0.00 0.00 0.00 3.46
622 637 1.753463 CTACCTTCCCGACGGCTCT 60.753 63.158 8.86 0.00 0.00 4.09
773 802 2.659016 CTGCTCTCCAACGCCTGA 59.341 61.111 0.00 0.00 0.00 3.86
887 916 3.083997 GTCCATCCCCAGACGCCT 61.084 66.667 0.00 0.00 0.00 5.52
929 958 2.591429 CACCAGACAAGCACCGCA 60.591 61.111 0.00 0.00 0.00 5.69
960 989 2.264480 CGGCCACATCGACCTTCA 59.736 61.111 2.24 0.00 0.00 3.02
1074 1103 2.609299 TCCGCCCTCCATCACCAA 60.609 61.111 0.00 0.00 0.00 3.67
1080 1109 1.750018 CCTCCATCACCAATGCGCA 60.750 57.895 14.96 14.96 33.71 6.09
1135 1164 3.064958 CCTTGTGCATCATCAGCTACAAG 59.935 47.826 12.69 12.69 43.10 3.16
1235 1264 8.934543 CTGAAATTCAGTAAGTTGCCTTGGGC 62.935 46.154 14.47 1.07 43.34 5.36
1245 1274 3.063704 CCTTGGGCGAATGCTGCA 61.064 61.111 4.13 4.13 42.25 4.41
1298 1327 4.513442 TGCTGTTGTTGTCTGTCTACTTT 58.487 39.130 0.00 0.00 0.00 2.66
1498 1821 3.895232 AGATGATCCGTACTTTGCAGT 57.105 42.857 0.00 0.00 36.99 4.40
1825 2150 2.665000 CTCCGCTTCCTCCTTGCA 59.335 61.111 0.00 0.00 0.00 4.08
1928 2254 4.003788 ACTTCGGGAGCACGTGGG 62.004 66.667 18.88 0.00 34.94 4.61
2010 2338 3.071206 ATCCCACTGCTCGTCGCT 61.071 61.111 0.00 0.00 40.11 4.93
2344 2676 3.119463 GCACGTTGAACAAAATGGATTCG 59.881 43.478 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.025155 TGTCGTAGGGCTCTGAGAATC 58.975 52.381 9.28 0.00 0.00 2.52
35 36 2.145397 TGTCGTAGGGCTCTGAGAAT 57.855 50.000 9.28 0.00 0.00 2.40
36 37 1.919240 TTGTCGTAGGGCTCTGAGAA 58.081 50.000 9.28 0.00 0.00 2.87
37 38 2.145397 ATTGTCGTAGGGCTCTGAGA 57.855 50.000 9.28 0.00 0.00 3.27
38 39 2.093973 ACAATTGTCGTAGGGCTCTGAG 60.094 50.000 4.92 0.00 0.00 3.35
39 40 1.899814 ACAATTGTCGTAGGGCTCTGA 59.100 47.619 4.92 0.00 0.00 3.27
40 41 2.386661 ACAATTGTCGTAGGGCTCTG 57.613 50.000 4.92 0.00 0.00 3.35
41 42 2.159282 CGTACAATTGTCGTAGGGCTCT 60.159 50.000 15.85 0.00 0.00 4.09
42 43 2.190981 CGTACAATTGTCGTAGGGCTC 58.809 52.381 15.85 0.00 0.00 4.70
43 44 1.738030 GCGTACAATTGTCGTAGGGCT 60.738 52.381 15.85 0.00 0.00 5.19
44 45 0.648958 GCGTACAATTGTCGTAGGGC 59.351 55.000 15.85 6.98 0.00 5.19
45 46 0.918619 CGCGTACAATTGTCGTAGGG 59.081 55.000 15.85 9.37 0.00 3.53
46 47 0.918619 CCGCGTACAATTGTCGTAGG 59.081 55.000 15.85 18.80 0.00 3.18
47 48 1.319374 CACCGCGTACAATTGTCGTAG 59.681 52.381 15.85 14.64 0.00 3.51
48 49 1.338765 CACCGCGTACAATTGTCGTA 58.661 50.000 15.85 0.00 0.00 3.43
49 50 1.893168 GCACCGCGTACAATTGTCGT 61.893 55.000 15.85 2.05 0.00 4.34
50 51 1.225637 GCACCGCGTACAATTGTCG 60.226 57.895 15.85 18.19 0.00 4.35
51 52 1.133869 GGCACCGCGTACAATTGTC 59.866 57.895 15.85 6.18 0.00 3.18
52 53 1.302192 AGGCACCGCGTACAATTGT 60.302 52.632 16.68 16.68 0.00 2.71
53 54 1.134487 CAGGCACCGCGTACAATTG 59.866 57.895 4.92 3.24 0.00 2.32
54 55 0.604243 TTCAGGCACCGCGTACAATT 60.604 50.000 4.92 0.00 0.00 2.32
55 56 0.604243 TTTCAGGCACCGCGTACAAT 60.604 50.000 4.92 0.00 0.00 2.71
56 57 0.604243 ATTTCAGGCACCGCGTACAA 60.604 50.000 4.92 0.00 0.00 2.41
57 58 1.004320 ATTTCAGGCACCGCGTACA 60.004 52.632 4.92 0.00 0.00 2.90
58 59 1.017177 TGATTTCAGGCACCGCGTAC 61.017 55.000 4.92 0.00 0.00 3.67
59 60 0.107897 ATGATTTCAGGCACCGCGTA 60.108 50.000 4.92 0.00 0.00 4.42
60 61 1.369091 GATGATTTCAGGCACCGCGT 61.369 55.000 4.92 0.00 0.00 6.01
61 62 1.353103 GATGATTTCAGGCACCGCG 59.647 57.895 0.00 0.00 0.00 6.46
62 63 1.027357 ATGATGATTTCAGGCACCGC 58.973 50.000 0.00 0.00 37.89 5.68
63 64 2.947652 AGAATGATGATTTCAGGCACCG 59.052 45.455 0.00 0.00 37.89 4.94
64 65 4.996788 AAGAATGATGATTTCAGGCACC 57.003 40.909 0.00 0.00 37.89 5.01
65 66 7.293745 CGTATAAGAATGATGATTTCAGGCAC 58.706 38.462 0.00 0.00 37.89 5.01
66 67 6.427853 CCGTATAAGAATGATGATTTCAGGCA 59.572 38.462 0.00 0.00 37.89 4.75
67 68 6.428159 ACCGTATAAGAATGATGATTTCAGGC 59.572 38.462 0.00 0.00 37.89 4.85
68 69 7.095060 CCACCGTATAAGAATGATGATTTCAGG 60.095 40.741 0.00 0.00 37.89 3.86
69 70 7.095060 CCCACCGTATAAGAATGATGATTTCAG 60.095 40.741 0.00 0.00 37.89 3.02
70 71 6.710295 CCCACCGTATAAGAATGATGATTTCA 59.290 38.462 0.00 0.00 39.12 2.69
71 72 6.710744 ACCCACCGTATAAGAATGATGATTTC 59.289 38.462 0.00 0.00 0.00 2.17
72 73 6.601332 ACCCACCGTATAAGAATGATGATTT 58.399 36.000 0.00 0.00 0.00 2.17
73 74 6.183361 TGACCCACCGTATAAGAATGATGATT 60.183 38.462 0.00 0.00 0.00 2.57
74 75 5.306937 TGACCCACCGTATAAGAATGATGAT 59.693 40.000 0.00 0.00 0.00 2.45
75 76 4.651962 TGACCCACCGTATAAGAATGATGA 59.348 41.667 0.00 0.00 0.00 2.92
76 77 4.750098 GTGACCCACCGTATAAGAATGATG 59.250 45.833 0.00 0.00 0.00 3.07
77 78 4.500887 CGTGACCCACCGTATAAGAATGAT 60.501 45.833 0.00 0.00 0.00 2.45
78 79 3.181484 CGTGACCCACCGTATAAGAATGA 60.181 47.826 0.00 0.00 0.00 2.57
79 80 3.120792 CGTGACCCACCGTATAAGAATG 58.879 50.000 0.00 0.00 0.00 2.67
80 81 2.482490 GCGTGACCCACCGTATAAGAAT 60.482 50.000 0.00 0.00 0.00 2.40
81 82 1.135024 GCGTGACCCACCGTATAAGAA 60.135 52.381 0.00 0.00 0.00 2.52
82 83 0.457035 GCGTGACCCACCGTATAAGA 59.543 55.000 0.00 0.00 0.00 2.10
83 84 0.529119 GGCGTGACCCACCGTATAAG 60.529 60.000 0.00 0.00 0.00 1.73
84 85 1.256361 TGGCGTGACCCACCGTATAA 61.256 55.000 0.00 0.00 37.83 0.98
85 86 1.681666 TGGCGTGACCCACCGTATA 60.682 57.895 0.00 0.00 37.83 1.47
86 87 2.998480 TGGCGTGACCCACCGTAT 60.998 61.111 0.00 0.00 37.83 3.06
92 93 2.838748 TTTGTTGGTGGCGTGACCCA 62.839 55.000 2.93 0.00 37.83 4.51
93 94 1.668101 TTTTGTTGGTGGCGTGACCC 61.668 55.000 2.93 0.00 37.83 4.46
94 95 0.173708 TTTTTGTTGGTGGCGTGACC 59.826 50.000 0.00 0.00 39.84 4.02
95 96 2.217429 ATTTTTGTTGGTGGCGTGAC 57.783 45.000 0.00 0.00 0.00 3.67
96 97 2.166459 TCAATTTTTGTTGGTGGCGTGA 59.834 40.909 0.00 0.00 0.00 4.35
97 98 2.544685 TCAATTTTTGTTGGTGGCGTG 58.455 42.857 0.00 0.00 0.00 5.34
98 99 2.969628 TCAATTTTTGTTGGTGGCGT 57.030 40.000 0.00 0.00 0.00 5.68
99 100 4.606457 TTTTCAATTTTTGTTGGTGGCG 57.394 36.364 0.00 0.00 0.00 5.69
100 101 6.375945 AGATTTTCAATTTTTGTTGGTGGC 57.624 33.333 0.00 0.00 0.00 5.01
101 102 7.983307 TGAAGATTTTCAATTTTTGTTGGTGG 58.017 30.769 0.00 0.00 40.26 4.61
140 141 9.965824 GAAGAAATTGAACAACTGAGGAATTTA 57.034 29.630 0.00 0.00 0.00 1.40
141 142 8.477256 TGAAGAAATTGAACAACTGAGGAATTT 58.523 29.630 0.00 0.00 0.00 1.82
142 143 8.010733 TGAAGAAATTGAACAACTGAGGAATT 57.989 30.769 0.00 0.00 0.00 2.17
143 144 7.587037 TGAAGAAATTGAACAACTGAGGAAT 57.413 32.000 0.00 0.00 0.00 3.01
144 145 7.122650 AGTTGAAGAAATTGAACAACTGAGGAA 59.877 33.333 14.93 0.00 45.70 3.36
145 146 6.603201 AGTTGAAGAAATTGAACAACTGAGGA 59.397 34.615 14.93 0.00 45.70 3.71
146 147 6.799512 AGTTGAAGAAATTGAACAACTGAGG 58.200 36.000 14.93 0.00 45.70 3.86
147 148 8.589629 CAAAGTTGAAGAAATTGAACAACTGAG 58.410 33.333 15.81 10.58 46.37 3.35
148 149 7.063308 GCAAAGTTGAAGAAATTGAACAACTGA 59.937 33.333 15.81 0.00 46.37 3.41
149 150 7.148606 TGCAAAGTTGAAGAAATTGAACAACTG 60.149 33.333 15.81 9.89 46.37 3.16
151 152 7.059448 TGCAAAGTTGAAGAAATTGAACAAC 57.941 32.000 0.00 0.00 40.37 3.32
152 153 7.846644 ATGCAAAGTTGAAGAAATTGAACAA 57.153 28.000 0.00 0.00 0.00 2.83
153 154 7.846644 AATGCAAAGTTGAAGAAATTGAACA 57.153 28.000 0.00 0.00 0.00 3.18
155 156 9.985730 AGATAATGCAAAGTTGAAGAAATTGAA 57.014 25.926 0.00 0.00 0.00 2.69
156 157 9.985730 AAGATAATGCAAAGTTGAAGAAATTGA 57.014 25.926 0.00 0.00 0.00 2.57
158 159 9.985730 TGAAGATAATGCAAAGTTGAAGAAATT 57.014 25.926 0.00 0.00 0.00 1.82
159 160 9.415544 GTGAAGATAATGCAAAGTTGAAGAAAT 57.584 29.630 0.00 0.00 0.00 2.17
160 161 8.632679 AGTGAAGATAATGCAAAGTTGAAGAAA 58.367 29.630 0.00 0.00 0.00 2.52
161 162 8.077991 CAGTGAAGATAATGCAAAGTTGAAGAA 58.922 33.333 0.00 0.00 0.00 2.52
162 163 7.445096 TCAGTGAAGATAATGCAAAGTTGAAGA 59.555 33.333 0.00 0.00 0.00 2.87
163 164 7.587629 TCAGTGAAGATAATGCAAAGTTGAAG 58.412 34.615 0.00 0.00 0.00 3.02
164 165 7.509141 TCAGTGAAGATAATGCAAAGTTGAA 57.491 32.000 0.00 0.00 0.00 2.69
165 166 7.692460 ATCAGTGAAGATAATGCAAAGTTGA 57.308 32.000 0.00 0.00 0.00 3.18
166 167 7.487189 GGAATCAGTGAAGATAATGCAAAGTTG 59.513 37.037 0.00 0.00 0.00 3.16
167 168 7.542025 GGAATCAGTGAAGATAATGCAAAGTT 58.458 34.615 0.00 0.00 0.00 2.66
168 169 6.183360 CGGAATCAGTGAAGATAATGCAAAGT 60.183 38.462 0.00 0.00 0.00 2.66
169 170 6.183360 ACGGAATCAGTGAAGATAATGCAAAG 60.183 38.462 0.00 0.00 0.00 2.77
170 171 5.647658 ACGGAATCAGTGAAGATAATGCAAA 59.352 36.000 0.00 0.00 0.00 3.68
171 172 5.185454 ACGGAATCAGTGAAGATAATGCAA 58.815 37.500 0.00 0.00 0.00 4.08
172 173 4.769688 ACGGAATCAGTGAAGATAATGCA 58.230 39.130 0.00 0.00 0.00 3.96
173 174 4.811024 TGACGGAATCAGTGAAGATAATGC 59.189 41.667 0.00 0.00 31.91 3.56
174 175 7.488187 AATGACGGAATCAGTGAAGATAATG 57.512 36.000 0.00 0.00 41.91 1.90
175 176 8.511604 AAAATGACGGAATCAGTGAAGATAAT 57.488 30.769 0.00 0.00 41.91 1.28
176 177 7.921786 AAAATGACGGAATCAGTGAAGATAA 57.078 32.000 0.00 0.00 41.91 1.75
177 178 7.824289 AGAAAAATGACGGAATCAGTGAAGATA 59.176 33.333 0.00 0.00 41.91 1.98
178 179 6.656693 AGAAAAATGACGGAATCAGTGAAGAT 59.343 34.615 0.00 0.00 41.91 2.40
179 180 5.997746 AGAAAAATGACGGAATCAGTGAAGA 59.002 36.000 0.00 0.00 41.91 2.87
180 181 6.246420 AGAAAAATGACGGAATCAGTGAAG 57.754 37.500 0.00 0.00 41.91 3.02
181 182 6.262049 TGAAGAAAAATGACGGAATCAGTGAA 59.738 34.615 0.00 0.00 41.91 3.18
182 183 5.762711 TGAAGAAAAATGACGGAATCAGTGA 59.237 36.000 0.00 0.00 41.91 3.41
183 184 6.000891 TGAAGAAAAATGACGGAATCAGTG 57.999 37.500 0.00 0.00 41.91 3.66
184 185 6.824305 ATGAAGAAAAATGACGGAATCAGT 57.176 33.333 0.00 0.00 41.91 3.41
185 186 7.272084 GTCAATGAAGAAAAATGACGGAATCAG 59.728 37.037 0.00 0.00 41.91 2.90
186 187 7.040478 AGTCAATGAAGAAAAATGACGGAATCA 60.040 33.333 0.00 0.00 43.85 2.57
187 188 7.308435 AGTCAATGAAGAAAAATGACGGAATC 58.692 34.615 0.00 0.00 43.85 2.52
188 189 7.219484 AGTCAATGAAGAAAAATGACGGAAT 57.781 32.000 0.00 0.00 43.85 3.01
189 190 6.633500 AGTCAATGAAGAAAAATGACGGAA 57.367 33.333 0.00 0.00 43.85 4.30
190 191 6.633500 AAGTCAATGAAGAAAAATGACGGA 57.367 33.333 0.00 0.00 43.85 4.69
191 192 8.970691 ATAAAGTCAATGAAGAAAAATGACGG 57.029 30.769 0.00 0.00 43.85 4.79
240 241 8.742125 TGATCCTGGGATTAGAATAGTGTTAT 57.258 34.615 3.45 0.00 34.60 1.89
253 254 7.420680 CCAAGTAACTATTCTGATCCTGGGATT 60.421 40.741 3.45 0.00 34.60 3.01
259 260 7.345653 TGTGATCCAAGTAACTATTCTGATCCT 59.654 37.037 0.00 0.00 0.00 3.24
261 262 7.170658 GCTGTGATCCAAGTAACTATTCTGATC 59.829 40.741 0.00 0.00 0.00 2.92
264 265 5.233050 CGCTGTGATCCAAGTAACTATTCTG 59.767 44.000 0.00 0.00 0.00 3.02
275 276 2.898729 ATAGACCGCTGTGATCCAAG 57.101 50.000 0.00 0.00 0.00 3.61
286 287 5.353678 CGCCCCTATATACTATATAGACCGC 59.646 48.000 16.79 15.63 30.99 5.68
288 289 7.556996 CCATCGCCCCTATATACTATATAGACC 59.443 44.444 16.79 9.41 30.99 3.85
290 291 8.458951 TCCATCGCCCCTATATACTATATAGA 57.541 38.462 16.79 0.91 30.99 1.98
292 293 7.241251 ACCTCCATCGCCCCTATATACTATATA 59.759 40.741 0.00 0.00 0.00 0.86
293 294 6.046881 ACCTCCATCGCCCCTATATACTATAT 59.953 42.308 0.00 0.00 0.00 0.86
294 295 5.374753 ACCTCCATCGCCCCTATATACTATA 59.625 44.000 0.00 0.00 0.00 1.31
295 296 4.170251 ACCTCCATCGCCCCTATATACTAT 59.830 45.833 0.00 0.00 0.00 2.12
296 297 3.530564 ACCTCCATCGCCCCTATATACTA 59.469 47.826 0.00 0.00 0.00 1.82
297 298 2.315155 ACCTCCATCGCCCCTATATACT 59.685 50.000 0.00 0.00 0.00 2.12
377 378 2.683933 GGAAGAGAGTCGGGGCCA 60.684 66.667 4.39 0.00 0.00 5.36
773 802 2.660552 CGGTTGACTGCGTCGGTT 60.661 61.111 0.00 0.00 34.95 4.44
810 839 2.753701 CGGGTTCCATGGTGACCA 59.246 61.111 28.91 6.84 38.19 4.02
903 932 0.764890 CTTGTCTGGTGGTCAGGGAA 59.235 55.000 0.00 0.00 43.53 3.97
960 989 0.984995 GGTCAAGGTAGCCCTCTTGT 59.015 55.000 9.38 0.00 41.56 3.16
1034 1063 3.286751 GCGGCAAGTCAGGCACAA 61.287 61.111 0.00 0.00 0.00 3.33
1135 1164 2.579684 AAGTAGCCACGCAGCCTAGC 62.580 60.000 0.00 0.00 0.00 3.42
1235 1264 1.063616 CTGAACCAGATGCAGCATTCG 59.936 52.381 9.90 3.64 32.44 3.34
1245 1274 2.146342 CGACTTGCAACTGAACCAGAT 58.854 47.619 0.00 0.00 35.18 2.90
1263 1292 1.939934 CAACAGCAAAACAGAGGACGA 59.060 47.619 0.00 0.00 0.00 4.20
1487 1810 3.131396 ACAGCACACTACTGCAAAGTAC 58.869 45.455 1.27 0.00 39.86 2.73
1498 1821 1.268625 CTCCACACGTACAGCACACTA 59.731 52.381 0.00 0.00 0.00 2.74
1554 1877 5.050972 GCAAGCGAGCTTAATAAGTTACGAT 60.051 40.000 10.22 9.03 34.50 3.73
1825 2150 3.789290 GGGTGGGGGCGATAACGT 61.789 66.667 0.00 0.00 41.98 3.99
1875 2201 3.600388 CGCTGAAGTCCAAATCTACCTT 58.400 45.455 0.00 0.00 0.00 3.50
1880 2206 0.036732 TGCCGCTGAAGTCCAAATCT 59.963 50.000 0.00 0.00 0.00 2.40
1928 2254 0.884514 GGCCAGTTTTTCTGAGCTCC 59.115 55.000 12.15 0.00 46.27 4.70
2010 2338 2.279851 CTCACGCCGTTGTGGTCA 60.280 61.111 0.00 0.00 40.31 4.02
2222 2553 4.472691 TCTGCAAGATGTTTCAAACTCG 57.527 40.909 1.10 0.00 38.67 4.18
2344 2676 3.678072 TCGATCAGAAACAACCGATCAAC 59.322 43.478 0.00 0.00 35.11 3.18


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

AutoCloner maintained by Alex Coulton.