Multiple sequence alignment - TraesCS5B01G341500

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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 TraesCS5B01G341500 chr5B 100.000 2255 0 0 1 2255 526582064 526584318 0.000000e+00 4165.0
1 TraesCS5B01G341500 chr5B 80.516 698 103 20 671 1351 528565786 528565105 2.580000e-139 505.0
2 TraesCS5B01G341500 chr5B 79.724 725 98 31 670 1351 528569121 528568403 1.570000e-131 479.0
3 TraesCS5B01G341500 chr5B 80.159 630 100 11 746 1351 528573596 528572968 4.420000e-122 448.0
4 TraesCS5B01G341500 chr5B 82.661 496 68 7 869 1351 528561715 528561225 7.450000e-115 424.0
5 TraesCS5B01G341500 chr5B 86.415 265 32 3 1904 2165 528546896 528546633 1.020000e-73 287.0
6 TraesCS5B01G341500 chr5B 94.012 167 10 0 92 258 95064413 95064579 1.030000e-63 254.0
7 TraesCS5B01G341500 chr5B 86.344 227 22 5 1903 2122 528543629 528543405 2.890000e-59 239.0
8 TraesCS5B01G341500 chr5B 84.729 203 26 2 1987 2184 527051573 527051775 4.910000e-47 198.0
9 TraesCS5B01G341500 chr5B 92.593 54 4 0 1486 1539 526583361 526583414 6.680000e-11 78.7
10 TraesCS5B01G341500 chr5B 88.710 62 5 1 1486 1545 528565158 528565097 8.640000e-10 75.0
11 TraesCS5B01G341500 chr5D 93.290 2012 107 13 257 2255 433016134 433018130 0.000000e+00 2942.0
12 TraesCS5B01G341500 chr5D 80.604 629 98 12 746 1351 435262401 435261774 4.390000e-127 464.0
13 TraesCS5B01G341500 chr5D 85.338 266 36 3 1921 2184 434325703 434325439 2.850000e-69 272.0
14 TraesCS5B01G341500 chr5D 84.083 289 32 9 1903 2182 434328271 434327988 1.330000e-67 267.0
15 TraesCS5B01G341500 chr5D 83.624 287 36 6 1903 2184 434395462 434395742 2.220000e-65 259.0
16 TraesCS5B01G341500 chr5D 90.099 101 7 1 1350 1450 433017442 433017539 6.540000e-26 128.0
17 TraesCS5B01G341500 chr5D 94.444 54 3 0 1486 1539 433017178 433017231 1.440000e-12 84.2
18 TraesCS5B01G341500 chr5A 91.349 1075 59 11 280 1351 547637746 547638789 0.000000e+00 1439.0
19 TraesCS5B01G341500 chr5A 88.807 679 48 9 257 933 547641982 547642634 0.000000e+00 808.0
20 TraesCS5B01G341500 chr5A 87.901 686 42 11 1144 1819 547642628 547643282 0.000000e+00 769.0
21 TraesCS5B01G341500 chr5A 80.635 630 97 11 746 1351 549199676 549199048 4.390000e-127 464.0
22 TraesCS5B01G341500 chr5A 88.743 382 20 13 1808 2184 547639079 547639442 1.590000e-121 446.0
23 TraesCS5B01G341500 chr5A 78.873 710 112 19 670 1351 549195168 549194469 1.590000e-121 446.0
24 TraesCS5B01G341500 chr5A 89.086 339 26 3 1486 1822 547638736 547639065 5.800000e-111 411.0
25 TraesCS5B01G341500 chr5A 83.162 291 39 4 1903 2184 548232532 548232821 7.990000e-65 257.0
26 TraesCS5B01G341500 chr5A 82.847 274 34 7 1903 2167 549165198 549164929 1.350000e-57 233.0
27 TraesCS5B01G341500 chr4A 92.718 412 25 5 420 827 677178203 677177793 6.940000e-165 590.0
28 TraesCS5B01G341500 chr4A 97.561 164 4 0 93 256 728784504 728784341 4.740000e-72 281.0
29 TraesCS5B01G341500 chr4A 91.071 56 1 3 37 92 677178320 677178269 3.110000e-09 73.1
30 TraesCS5B01G341500 chr4B 94.643 168 8 1 93 259 637355265 637355098 2.220000e-65 259.0
31 TraesCS5B01G341500 chr2B 94.152 171 9 1 93 262 584472853 584473023 2.220000e-65 259.0
32 TraesCS5B01G341500 chr7A 94.578 166 9 0 93 258 665996682 665996847 7.990000e-65 257.0
33 TraesCS5B01G341500 chr7A 94.012 167 9 1 93 259 268798205 268798370 3.720000e-63 252.0
34 TraesCS5B01G341500 chr3A 93.567 171 11 0 92 262 37458055 37457885 2.870000e-64 255.0
35 TraesCS5B01G341500 chr1D 93.529 170 10 1 93 262 413947327 413947495 3.720000e-63 252.0
36 TraesCS5B01G341500 chr2A 91.620 179 15 0 87 265 550861310 550861132 4.810000e-62 248.0


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 TraesCS5B01G341500 chr5B 526582064 526584318 2254 False 2121.85 4165 96.2965 1 2255 2 chr5B.!!$F3 2254
1 TraesCS5B01G341500 chr5B 528561225 528573596 12371 True 386.20 505 82.3540 670 1545 5 chr5B.!!$R2 875
2 TraesCS5B01G341500 chr5B 528543405 528546896 3491 True 263.00 287 86.3795 1903 2165 2 chr5B.!!$R1 262
3 TraesCS5B01G341500 chr5D 433016134 433018130 1996 False 1051.40 2942 92.6110 257 2255 3 chr5D.!!$F2 1998
4 TraesCS5B01G341500 chr5D 435261774 435262401 627 True 464.00 464 80.6040 746 1351 1 chr5D.!!$R1 605
5 TraesCS5B01G341500 chr5D 434325439 434328271 2832 True 269.50 272 84.7105 1903 2184 2 chr5D.!!$R2 281
6 TraesCS5B01G341500 chr5A 547637746 547643282 5536 False 774.60 1439 89.1772 257 2184 5 chr5A.!!$F2 1927
7 TraesCS5B01G341500 chr5A 549194469 549199676 5207 True 455.00 464 79.7540 670 1351 2 chr5A.!!$R2 681
8 TraesCS5B01G341500 chr4A 677177793 677178320 527 True 331.55 590 91.8945 37 827 2 chr4A.!!$R2 790

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
154 155 0.031817 CCTGGAATTTCCCCATGGCT 60.032 55.0 12.9 0.0 35.03 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1732 0.918258 TGCCTCCATTAGTGCCATGA 59.082 50.0 0.0 0.0 0.0 3.07 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
20 21 2.426522 CCTGAAAGATGAACGCTTCCA 58.573 47.619 0.00 0.00 34.07 3.53
21 22 2.160417 CCTGAAAGATGAACGCTTCCAC 59.840 50.000 0.00 0.00 34.07 4.02
22 23 2.151202 TGAAAGATGAACGCTTCCACC 58.849 47.619 0.00 0.00 0.00 4.61
23 24 1.128692 GAAAGATGAACGCTTCCACCG 59.871 52.381 0.00 0.00 0.00 4.94
24 25 1.298859 AAGATGAACGCTTCCACCGC 61.299 55.000 0.00 0.00 0.00 5.68
25 26 1.741770 GATGAACGCTTCCACCGCT 60.742 57.895 0.00 0.00 0.00 5.52
26 27 1.970917 GATGAACGCTTCCACCGCTG 61.971 60.000 0.00 0.00 0.00 5.18
27 28 4.090057 GAACGCTTCCACCGCTGC 62.090 66.667 0.00 0.00 0.00 5.25
28 29 4.626081 AACGCTTCCACCGCTGCT 62.626 61.111 0.00 0.00 0.00 4.24
31 32 3.123620 GCTTCCACCGCTGCTGAG 61.124 66.667 0.00 0.00 0.00 3.35
32 33 2.435586 CTTCCACCGCTGCTGAGG 60.436 66.667 11.81 11.81 39.17 3.86
33 34 2.922503 TTCCACCGCTGCTGAGGA 60.923 61.111 19.91 6.16 36.60 3.71
34 35 2.454832 CTTCCACCGCTGCTGAGGAA 62.455 60.000 19.91 18.52 36.60 3.36
35 36 2.435586 CCACCGCTGCTGAGGAAG 60.436 66.667 19.91 11.13 36.60 3.46
68 69 0.808755 GTACCATTTCCCTTGTGCCG 59.191 55.000 0.00 0.00 0.00 5.69
76 77 0.970937 TCCCTTGTGCCGGAGACTAG 60.971 60.000 5.05 7.09 0.00 2.57
77 78 1.153549 CCTTGTGCCGGAGACTAGC 60.154 63.158 5.05 0.00 0.00 3.42
78 79 1.608717 CCTTGTGCCGGAGACTAGCT 61.609 60.000 5.05 0.00 0.00 3.32
79 80 1.103803 CTTGTGCCGGAGACTAGCTA 58.896 55.000 5.05 0.00 0.00 3.32
80 81 0.815734 TTGTGCCGGAGACTAGCTAC 59.184 55.000 5.05 0.00 0.00 3.58
81 82 0.034380 TGTGCCGGAGACTAGCTACT 60.034 55.000 5.05 0.00 0.00 2.57
82 83 1.104630 GTGCCGGAGACTAGCTACTT 58.895 55.000 5.05 0.00 0.00 2.24
83 84 1.103803 TGCCGGAGACTAGCTACTTG 58.896 55.000 5.05 0.00 0.00 3.16
84 85 0.249114 GCCGGAGACTAGCTACTTGC 60.249 60.000 5.05 0.00 43.29 4.01
101 102 4.476410 CGTGAGCTCAGCGGCGTA 62.476 66.667 18.89 0.00 37.29 4.42
102 103 2.580867 GTGAGCTCAGCGGCGTAG 60.581 66.667 18.89 5.18 37.29 3.51
115 116 3.547513 CGTAGCTAGGGGGTGGCC 61.548 72.222 5.50 0.00 31.44 5.36
116 117 2.366435 GTAGCTAGGGGGTGGCCA 60.366 66.667 0.00 0.00 31.44 5.36
117 118 2.040884 TAGCTAGGGGGTGGCCAG 60.041 66.667 5.11 0.00 31.44 4.85
118 119 3.714078 TAGCTAGGGGGTGGCCAGG 62.714 68.421 5.11 0.00 31.44 4.45
120 121 4.760220 CTAGGGGGTGGCCAGGGT 62.760 72.222 5.11 0.00 0.00 4.34
121 122 3.294217 TAGGGGGTGGCCAGGGTA 61.294 66.667 5.11 0.00 0.00 3.69
122 123 3.341469 TAGGGGGTGGCCAGGGTAG 62.341 68.421 5.11 0.00 0.00 3.18
124 125 3.408853 GGGGTGGCCAGGGTAGTC 61.409 72.222 5.11 0.00 0.00 2.59
125 126 3.408853 GGGTGGCCAGGGTAGTCC 61.409 72.222 5.11 0.44 0.00 3.85
126 127 2.609610 GGTGGCCAGGGTAGTCCA 60.610 66.667 5.11 0.00 38.24 4.02
127 128 2.001269 GGTGGCCAGGGTAGTCCAT 61.001 63.158 5.11 0.00 38.24 3.41
128 129 1.224592 GTGGCCAGGGTAGTCCATG 59.775 63.158 5.11 0.00 44.12 3.66
133 134 3.006061 CAGGGTAGTCCATGGACCA 57.994 57.895 36.09 24.31 45.59 4.02
134 135 0.541863 CAGGGTAGTCCATGGACCAC 59.458 60.000 36.09 32.47 45.59 4.16
136 137 1.912971 GGTAGTCCATGGACCACCC 59.087 63.158 38.40 30.27 46.36 4.61
137 138 0.620700 GGTAGTCCATGGACCACCCT 60.621 60.000 38.40 24.76 46.36 4.34
138 139 0.541863 GTAGTCCATGGACCACCCTG 59.458 60.000 36.09 0.00 45.59 4.45
144 145 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
145 146 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
146 147 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
147 148 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
148 149 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
149 150 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
150 151 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
151 152 1.488390 CACCCTGGAATTTCCCCATG 58.512 55.000 12.90 2.87 35.03 3.66
152 153 0.339510 ACCCTGGAATTTCCCCATGG 59.660 55.000 12.90 4.14 42.81 3.66
153 154 1.050421 CCCTGGAATTTCCCCATGGC 61.050 60.000 12.90 0.00 35.03 4.40
154 155 0.031817 CCTGGAATTTCCCCATGGCT 60.032 55.000 12.90 0.00 35.03 4.75
155 156 1.623279 CCTGGAATTTCCCCATGGCTT 60.623 52.381 12.90 0.00 35.03 4.35
156 157 2.190538 CTGGAATTTCCCCATGGCTTT 58.809 47.619 12.90 0.00 35.03 3.51
157 158 2.573009 CTGGAATTTCCCCATGGCTTTT 59.427 45.455 12.90 0.00 35.03 2.27
158 159 3.774216 CTGGAATTTCCCCATGGCTTTTA 59.226 43.478 12.90 0.00 35.03 1.52
159 160 4.369872 TGGAATTTCCCCATGGCTTTTAT 58.630 39.130 12.90 0.00 35.03 1.40
160 161 5.533112 TGGAATTTCCCCATGGCTTTTATA 58.467 37.500 12.90 0.00 35.03 0.98
161 162 6.149616 TGGAATTTCCCCATGGCTTTTATAT 58.850 36.000 12.90 0.00 35.03 0.86
162 163 7.309091 TGGAATTTCCCCATGGCTTTTATATA 58.691 34.615 12.90 0.00 35.03 0.86
163 164 7.454380 TGGAATTTCCCCATGGCTTTTATATAG 59.546 37.037 12.90 0.00 35.03 1.31
164 165 7.454694 GGAATTTCCCCATGGCTTTTATATAGT 59.545 37.037 6.09 0.00 0.00 2.12
165 166 7.781324 ATTTCCCCATGGCTTTTATATAGTG 57.219 36.000 6.09 0.00 0.00 2.74
166 167 5.922960 TCCCCATGGCTTTTATATAGTGT 57.077 39.130 6.09 0.00 0.00 3.55
167 168 7.395525 TTCCCCATGGCTTTTATATAGTGTA 57.604 36.000 6.09 0.00 0.00 2.90
168 169 7.016153 TCCCCATGGCTTTTATATAGTGTAG 57.984 40.000 6.09 0.00 0.00 2.74
169 170 6.561070 TCCCCATGGCTTTTATATAGTGTAGT 59.439 38.462 6.09 0.00 0.00 2.73
170 171 7.735777 TCCCCATGGCTTTTATATAGTGTAGTA 59.264 37.037 6.09 0.00 0.00 1.82
171 172 8.380099 CCCCATGGCTTTTATATAGTGTAGTAA 58.620 37.037 6.09 0.00 0.00 2.24
172 173 9.787435 CCCATGGCTTTTATATAGTGTAGTAAA 57.213 33.333 6.09 0.00 0.00 2.01
229 230 9.349713 TGTAAATATTTCTATTGATGGACCACC 57.650 33.333 3.39 0.00 0.00 4.61
230 231 7.839680 AAATATTTCTATTGATGGACCACCC 57.160 36.000 0.00 0.00 34.81 4.61
231 232 6.786843 ATATTTCTATTGATGGACCACCCT 57.213 37.500 0.00 0.00 35.38 4.34
232 233 3.931907 TTCTATTGATGGACCACCCTG 57.068 47.619 0.00 0.00 35.38 4.45
233 234 2.126882 TCTATTGATGGACCACCCTGG 58.873 52.381 0.00 0.00 45.02 4.45
234 235 0.550914 TATTGATGGACCACCCTGGC 59.449 55.000 0.00 0.00 42.67 4.85
235 236 1.217057 ATTGATGGACCACCCTGGCT 61.217 55.000 0.00 0.00 42.67 4.75
236 237 1.434513 TTGATGGACCACCCTGGCTT 61.435 55.000 0.00 0.00 42.67 4.35
237 238 0.548926 TGATGGACCACCCTGGCTTA 60.549 55.000 0.00 0.00 42.67 3.09
238 239 0.846693 GATGGACCACCCTGGCTTAT 59.153 55.000 0.00 0.00 42.67 1.73
239 240 1.215423 GATGGACCACCCTGGCTTATT 59.785 52.381 0.00 0.00 42.67 1.40
240 241 0.331278 TGGACCACCCTGGCTTATTG 59.669 55.000 0.00 0.00 42.67 1.90
241 242 0.395724 GGACCACCCTGGCTTATTGG 60.396 60.000 0.00 0.00 42.67 3.16
242 243 0.395724 GACCACCCTGGCTTATTGGG 60.396 60.000 0.00 0.00 42.67 4.12
243 244 1.758122 CCACCCTGGCTTATTGGGC 60.758 63.158 0.00 0.00 44.56 5.36
244 245 1.307647 CACCCTGGCTTATTGGGCT 59.692 57.895 0.00 0.00 44.56 5.19
245 246 1.039233 CACCCTGGCTTATTGGGCTG 61.039 60.000 0.00 0.00 44.56 4.85
246 247 1.456331 CCCTGGCTTATTGGGCTGG 60.456 63.158 6.91 6.91 45.62 4.85
247 248 2.129785 CCTGGCTTATTGGGCTGGC 61.130 63.158 0.00 0.00 41.95 4.85
248 249 1.076485 CTGGCTTATTGGGCTGGCT 60.076 57.895 0.00 0.00 0.00 4.75
249 250 0.183492 CTGGCTTATTGGGCTGGCTA 59.817 55.000 0.00 0.00 0.00 3.93
250 251 0.106719 TGGCTTATTGGGCTGGCTAC 60.107 55.000 0.00 0.00 0.00 3.58
251 252 1.166531 GGCTTATTGGGCTGGCTACG 61.167 60.000 0.00 0.00 0.00 3.51
252 253 1.786049 GCTTATTGGGCTGGCTACGC 61.786 60.000 0.00 0.00 0.00 4.42
281 282 2.878429 CTGGGTGTCCTCTCGTCG 59.122 66.667 0.00 0.00 0.00 5.12
313 314 3.181434 ACTCCAAGTGAAAATACAGGCCA 60.181 43.478 5.01 0.00 0.00 5.36
314 315 3.420893 TCCAAGTGAAAATACAGGCCAG 58.579 45.455 5.01 0.00 0.00 4.85
315 316 3.073798 TCCAAGTGAAAATACAGGCCAGA 59.926 43.478 5.01 0.00 0.00 3.86
316 317 3.826157 CCAAGTGAAAATACAGGCCAGAA 59.174 43.478 5.01 0.00 0.00 3.02
335 336 3.718956 AGAAGGAATATGCCCTAACTGCT 59.281 43.478 0.00 0.00 32.77 4.24
773 783 6.958767 AGTTTATGGTACTTTGTAGGATGCT 58.041 36.000 0.00 0.00 0.00 3.79
786 797 8.430573 TTTGTAGGATGCTATAAGCTGGTATA 57.569 34.615 3.78 0.00 42.97 1.47
832 843 5.508224 GCAGTGTTGAACTATTTTACATCGC 59.492 40.000 0.00 0.00 36.83 4.58
843 858 7.309920 ACTATTTTACATCGCGGAAAAACATT 58.690 30.769 6.13 0.00 0.00 2.71
865 880 4.379652 TCAAAATTGAGGGAAAAGCTTGC 58.620 39.130 0.00 0.00 32.50 4.01
866 881 4.101430 TCAAAATTGAGGGAAAAGCTTGCT 59.899 37.500 0.00 0.00 32.50 3.91
885 909 6.756074 GCTTGCTATATATTCAGGAGCTACAG 59.244 42.308 0.00 0.00 34.19 2.74
926 959 1.337728 TGACACCGTACTGCTTGGATG 60.338 52.381 0.00 0.00 0.00 3.51
1034 1068 3.126879 CGCTGCATCGAAGGGCAA 61.127 61.111 3.33 0.00 37.71 4.52
1062 1096 0.034574 TGCCATCGCATGTAAACCCT 60.035 50.000 0.00 0.00 41.12 4.34
1080 1114 0.471617 CTAACTCCTCCTGGGGCATG 59.528 60.000 0.00 0.00 37.32 4.06
1108 1142 1.002366 CTCGCCGAAGATTGTCTTGG 58.998 55.000 0.00 0.00 36.73 3.61
1276 1310 5.528690 TGAGCAAATCTTTTAGGATGGATCG 59.471 40.000 0.00 0.00 0.00 3.69
1291 1325 1.709147 GATCGTGGTCATGGCTGTGC 61.709 60.000 0.00 0.00 0.00 4.57
1342 1376 5.471456 AGAAATGCTTAGTCTGTGAGTTTGG 59.529 40.000 0.00 0.00 0.00 3.28
1365 1399 5.413833 GGTGATGAAGCCCATGAATATACAG 59.586 44.000 0.00 0.00 35.17 2.74
1374 1408 5.111989 CCCATGAATATACAGGCATAGACG 58.888 45.833 0.00 0.00 0.00 4.18
1482 1516 4.888239 AGATTCAGATTTCATTCTGCTGGG 59.112 41.667 0.00 0.00 42.37 4.45
1517 1551 7.446931 TGAGGTATGTTGCTCAGAAATGTTTAA 59.553 33.333 0.00 0.00 0.00 1.52
1527 1564 6.514048 GCTCAGAAATGTTTAAGCTGTGAGTT 60.514 38.462 0.00 0.00 33.07 3.01
1562 1601 1.689273 GTGCACTACTAGCTAGCCCAT 59.311 52.381 20.91 3.70 0.00 4.00
1563 1602 1.964223 TGCACTACTAGCTAGCCCATC 59.036 52.381 20.91 8.12 0.00 3.51
1564 1603 2.243810 GCACTACTAGCTAGCCCATCT 58.756 52.381 20.91 2.54 0.00 2.90
1565 1604 2.029470 GCACTACTAGCTAGCCCATCTG 60.029 54.545 20.91 8.53 0.00 2.90
1566 1605 2.029470 CACTACTAGCTAGCCCATCTGC 60.029 54.545 20.91 0.00 0.00 4.26
1567 1606 1.548269 CTACTAGCTAGCCCATCTGCC 59.452 57.143 20.91 0.00 0.00 4.85
1568 1607 1.124477 ACTAGCTAGCCCATCTGCCC 61.124 60.000 20.91 0.00 0.00 5.36
1569 1608 1.074547 TAGCTAGCCCATCTGCCCA 60.075 57.895 12.13 0.00 0.00 5.36
1604 1645 6.537566 GGCATAGACATATGACTAATTTGCG 58.462 40.000 21.78 9.81 43.21 4.85
1631 1672 1.000396 GGGACAAGGCCATGAGCTT 60.000 57.895 16.33 0.00 43.05 3.74
1683 1727 5.415701 AGGCAATGTAATCGTTTGATTCTGT 59.584 36.000 0.00 0.00 43.70 3.41
1688 1732 5.067273 TGTAATCGTTTGATTCTGTTGGGT 58.933 37.500 0.00 0.00 43.70 4.51
1698 1742 1.357137 TCTGTTGGGTCATGGCACTA 58.643 50.000 0.00 0.00 0.00 2.74
1766 1810 1.719600 ACAGTCTTCGCTGCTGAATC 58.280 50.000 0.00 0.98 39.96 2.52
1775 1819 3.712287 TGCTGAATCGGGCAGAGA 58.288 55.556 0.00 0.00 35.39 3.10
1777 1821 1.522580 GCTGAATCGGGCAGAGACC 60.523 63.158 0.00 0.00 35.39 3.85
1806 1852 3.622060 ATCCGGGGTCCAGCGTTTG 62.622 63.158 0.00 0.00 0.00 2.93
1829 1903 2.034053 GGCGGTGTTTCATTCAGTTCAA 59.966 45.455 0.00 0.00 0.00 2.69
1849 1923 7.400339 AGTTCAACCTCCTGTATCAAGAGATTA 59.600 37.037 0.00 0.00 35.67 1.75
1857 1931 7.708051 TCCTGTATCAAGAGATTAGAAGTTCG 58.292 38.462 0.00 0.00 35.67 3.95
1866 1998 5.992217 AGAGATTAGAAGTTCGTGCTTTTGT 59.008 36.000 0.00 0.00 0.00 2.83
1942 2299 3.562343 TGGGTGTACTTTGCACTTACA 57.438 42.857 0.00 0.00 37.07 2.41
1971 2328 3.750371 ACTGCATGTTAGGTGCTTGTTA 58.250 40.909 0.00 0.00 42.92 2.41
2065 2429 3.260380 GGTCTGCATGGTCTCTAGCATAT 59.740 47.826 0.00 0.00 41.85 1.78
2066 2430 4.262808 GGTCTGCATGGTCTCTAGCATATT 60.263 45.833 0.00 0.00 41.85 1.28
2170 2591 5.353394 AGGACTTGTCATTAATTCCGCTA 57.647 39.130 3.08 0.00 35.29 4.26
2185 3347 3.620488 TCCGCTATGGCATTTCTTTTCT 58.380 40.909 4.78 0.00 38.60 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.160417 GTGGAAGCGTTCATCTTTCAGG 59.840 50.000 0.00 0.00 30.22 3.86
2 3 2.151202 GGTGGAAGCGTTCATCTTTCA 58.849 47.619 0.00 0.00 0.00 2.69
14 15 3.123620 CTCAGCAGCGGTGGAAGC 61.124 66.667 17.54 1.01 0.00 3.86
15 16 2.435586 CCTCAGCAGCGGTGGAAG 60.436 66.667 17.54 0.00 0.00 3.46
16 17 2.454832 CTTCCTCAGCAGCGGTGGAA 62.455 60.000 22.66 22.66 36.70 3.53
17 18 2.922503 TTCCTCAGCAGCGGTGGA 60.923 61.111 17.54 11.80 0.00 4.02
18 19 2.435586 CTTCCTCAGCAGCGGTGG 60.436 66.667 17.54 7.28 0.00 4.61
35 36 2.472909 GGTACCCAGAAGCGCATGC 61.473 63.158 11.47 7.91 43.24 4.06
84 85 4.476410 TACGCCGCTGAGCTCACG 62.476 66.667 23.28 23.28 0.00 4.35
85 86 2.580867 CTACGCCGCTGAGCTCAC 60.581 66.667 13.74 9.19 0.00 3.51
86 87 4.498520 GCTACGCCGCTGAGCTCA 62.499 66.667 17.19 17.19 33.28 4.26
87 88 2.725275 CTAGCTACGCCGCTGAGCTC 62.725 65.000 16.64 6.82 42.97 4.09
89 90 2.354072 CTAGCTACGCCGCTGAGC 60.354 66.667 9.09 0.00 41.12 4.26
90 91 2.333225 CCTAGCTACGCCGCTGAG 59.667 66.667 9.09 3.60 41.12 3.35
91 92 3.217017 CCCTAGCTACGCCGCTGA 61.217 66.667 9.09 0.00 41.12 4.26
92 93 4.286320 CCCCTAGCTACGCCGCTG 62.286 72.222 9.09 0.51 41.12 5.18
95 96 3.912907 CACCCCCTAGCTACGCCG 61.913 72.222 0.00 0.00 0.00 6.46
96 97 3.547513 CCACCCCCTAGCTACGCC 61.548 72.222 0.00 0.00 0.00 5.68
97 98 4.237207 GCCACCCCCTAGCTACGC 62.237 72.222 0.00 0.00 0.00 4.42
98 99 3.547513 GGCCACCCCCTAGCTACG 61.548 72.222 0.00 0.00 0.00 3.51
99 100 2.366435 TGGCCACCCCCTAGCTAC 60.366 66.667 0.00 0.00 0.00 3.58
100 101 2.040884 CTGGCCACCCCCTAGCTA 60.041 66.667 0.00 0.00 0.00 3.32
103 104 3.341469 TACCCTGGCCACCCCCTAG 62.341 68.421 0.00 0.00 0.00 3.02
104 105 3.294217 TACCCTGGCCACCCCCTA 61.294 66.667 0.00 0.00 0.00 3.53
105 106 4.760220 CTACCCTGGCCACCCCCT 62.760 72.222 0.00 0.00 0.00 4.79
107 108 3.408853 GACTACCCTGGCCACCCC 61.409 72.222 0.00 0.00 0.00 4.95
108 109 3.408853 GGACTACCCTGGCCACCC 61.409 72.222 0.00 0.00 0.00 4.61
109 110 2.001269 ATGGACTACCCTGGCCACC 61.001 63.158 0.00 0.00 35.38 4.61
110 111 1.224592 CATGGACTACCCTGGCCAC 59.775 63.158 0.00 0.00 35.38 5.01
111 112 2.000701 CCATGGACTACCCTGGCCA 61.001 63.158 5.56 4.71 43.04 5.36
112 113 1.692749 TCCATGGACTACCCTGGCC 60.693 63.158 11.44 0.00 46.80 5.36
113 114 1.527370 GTCCATGGACTACCCTGGC 59.473 63.158 33.47 7.52 46.80 4.85
114 115 2.859303 GTGGTCCATGGACTACCCTGG 61.859 61.905 38.27 2.59 46.43 4.45
115 116 0.541863 GTGGTCCATGGACTACCCTG 59.458 60.000 38.27 1.91 46.43 4.45
116 117 3.007581 GTGGTCCATGGACTACCCT 57.992 57.895 38.27 0.00 46.43 4.34
120 121 3.006061 CAGGGTGGTCCATGGACTA 57.994 57.895 37.26 31.98 44.04 2.59
121 122 3.826282 CAGGGTGGTCCATGGACT 58.174 61.111 37.26 19.64 44.04 3.85
125 126 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
126 127 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
127 128 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
128 129 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
129 130 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
130 131 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
131 132 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
132 133 1.488390 CATGGGGAAATTCCAGGGTG 58.512 55.000 14.68 3.26 38.64 4.61
135 136 0.031817 AGCCATGGGGAAATTCCAGG 60.032 55.000 15.13 10.46 38.64 4.45
136 137 1.870064 AAGCCATGGGGAAATTCCAG 58.130 50.000 15.13 0.51 38.64 3.86
137 138 2.340721 AAAGCCATGGGGAAATTCCA 57.659 45.000 15.13 0.00 38.64 3.53
138 139 6.686484 ATATAAAAGCCATGGGGAAATTCC 57.314 37.500 15.13 2.79 35.59 3.01
139 140 8.306761 CACTATATAAAAGCCATGGGGAAATTC 58.693 37.037 15.13 0.00 35.59 2.17
140 141 7.789349 ACACTATATAAAAGCCATGGGGAAATT 59.211 33.333 15.13 0.00 35.59 1.82
141 142 7.305246 ACACTATATAAAAGCCATGGGGAAAT 58.695 34.615 15.13 0.00 35.59 2.17
142 143 6.678547 ACACTATATAAAAGCCATGGGGAAA 58.321 36.000 15.13 0.00 35.59 3.13
143 144 6.274322 ACACTATATAAAAGCCATGGGGAA 57.726 37.500 15.13 0.00 35.59 3.97
144 145 5.922960 ACACTATATAAAAGCCATGGGGA 57.077 39.130 15.13 0.00 35.59 4.81
145 146 6.779860 ACTACACTATATAAAAGCCATGGGG 58.220 40.000 15.13 0.00 37.18 4.96
146 147 9.787435 TTTACTACACTATATAAAAGCCATGGG 57.213 33.333 15.13 0.00 0.00 4.00
203 204 9.349713 GGTGGTCCATCAATAGAAATATTTACA 57.650 33.333 0.00 0.00 0.00 2.41
204 205 8.793592 GGGTGGTCCATCAATAGAAATATTTAC 58.206 37.037 4.07 0.00 35.00 2.01
205 206 8.732854 AGGGTGGTCCATCAATAGAAATATTTA 58.267 33.333 4.07 0.00 38.24 1.40
206 207 7.506938 CAGGGTGGTCCATCAATAGAAATATTT 59.493 37.037 4.07 0.00 38.24 1.40
207 208 7.006509 CAGGGTGGTCCATCAATAGAAATATT 58.993 38.462 4.07 0.00 38.24 1.28
208 209 6.467775 CCAGGGTGGTCCATCAATAGAAATAT 60.468 42.308 4.07 0.00 38.24 1.28
209 210 5.163099 CCAGGGTGGTCCATCAATAGAAATA 60.163 44.000 4.07 0.00 38.24 1.40
210 211 4.386761 CCAGGGTGGTCCATCAATAGAAAT 60.387 45.833 4.07 0.00 38.24 2.17
211 212 3.053693 CCAGGGTGGTCCATCAATAGAAA 60.054 47.826 4.07 0.00 38.24 2.52
212 213 2.509548 CCAGGGTGGTCCATCAATAGAA 59.490 50.000 4.07 0.00 38.24 2.10
213 214 2.126882 CCAGGGTGGTCCATCAATAGA 58.873 52.381 4.07 0.00 38.24 1.98
214 215 1.477558 GCCAGGGTGGTCCATCAATAG 60.478 57.143 4.07 0.00 40.46 1.73
215 216 0.550914 GCCAGGGTGGTCCATCAATA 59.449 55.000 4.07 0.00 40.46 1.90
216 217 1.217057 AGCCAGGGTGGTCCATCAAT 61.217 55.000 4.07 0.00 40.46 2.57
217 218 1.434513 AAGCCAGGGTGGTCCATCAA 61.435 55.000 4.07 0.00 40.46 2.57
218 219 0.548926 TAAGCCAGGGTGGTCCATCA 60.549 55.000 4.07 0.00 40.46 3.07
219 220 0.846693 ATAAGCCAGGGTGGTCCATC 59.153 55.000 0.00 0.00 40.46 3.51
220 221 1.063717 CAATAAGCCAGGGTGGTCCAT 60.064 52.381 0.00 0.00 40.46 3.41
221 222 0.331278 CAATAAGCCAGGGTGGTCCA 59.669 55.000 0.00 0.00 40.46 4.02
222 223 0.395724 CCAATAAGCCAGGGTGGTCC 60.396 60.000 0.00 0.00 40.46 4.46
223 224 0.395724 CCCAATAAGCCAGGGTGGTC 60.396 60.000 0.00 0.00 40.46 4.02
224 225 1.697297 CCCAATAAGCCAGGGTGGT 59.303 57.895 0.00 0.00 40.46 4.16
225 226 1.758122 GCCCAATAAGCCAGGGTGG 60.758 63.158 0.00 0.00 44.69 4.61
226 227 1.039233 CAGCCCAATAAGCCAGGGTG 61.039 60.000 0.00 0.00 44.69 4.61
227 228 1.307647 CAGCCCAATAAGCCAGGGT 59.692 57.895 0.00 0.00 44.69 4.34
228 229 1.456331 CCAGCCCAATAAGCCAGGG 60.456 63.158 0.00 0.00 45.68 4.45
229 230 2.129785 GCCAGCCCAATAAGCCAGG 61.130 63.158 0.00 0.00 0.00 4.45
230 231 0.183492 TAGCCAGCCCAATAAGCCAG 59.817 55.000 0.00 0.00 0.00 4.85
231 232 0.106719 GTAGCCAGCCCAATAAGCCA 60.107 55.000 0.00 0.00 0.00 4.75
232 233 1.166531 CGTAGCCAGCCCAATAAGCC 61.167 60.000 0.00 0.00 0.00 4.35
233 234 2.321213 CGTAGCCAGCCCAATAAGC 58.679 57.895 0.00 0.00 0.00 3.09
255 256 2.740055 GACACCCAGCTCACGCAG 60.740 66.667 0.00 0.00 39.10 5.18
281 282 2.743928 CTTGGAGTGTGGCGAGCC 60.744 66.667 7.26 7.26 0.00 4.70
306 307 1.133668 GGCATATTCCTTCTGGCCTGT 60.134 52.381 3.32 0.00 38.37 4.00
313 314 3.718956 AGCAGTTAGGGCATATTCCTTCT 59.281 43.478 0.18 0.00 35.92 2.85
314 315 4.092116 AGCAGTTAGGGCATATTCCTTC 57.908 45.455 0.18 0.00 35.92 3.46
315 316 4.526438 AAGCAGTTAGGGCATATTCCTT 57.474 40.909 0.18 0.00 35.92 3.36
316 317 4.526438 AAAGCAGTTAGGGCATATTCCT 57.474 40.909 0.00 0.00 38.36 3.36
335 336 3.130869 ACTGAACTGATGTGCTGCAAAAA 59.869 39.130 2.77 0.00 0.00 1.94
344 345 4.136796 TCTTCCCAAACTGAACTGATGTG 58.863 43.478 0.00 0.00 0.00 3.21
635 645 4.651778 ACAAGCAGCACTACCATTAAGAA 58.348 39.130 0.00 0.00 0.00 2.52
753 763 8.311836 GCTTATAGCATCCTACAAAGTACCATA 58.688 37.037 0.00 0.00 41.89 2.74
786 797 5.301551 TGCGGAATGGAAATTGCATATTAGT 59.698 36.000 0.00 0.00 0.00 2.24
807 818 5.728049 CGATGTAAAATAGTTCAACACTGCG 59.272 40.000 0.00 0.00 35.97 5.18
832 843 5.988561 TCCCTCAATTTTGAATGTTTTTCCG 59.011 36.000 0.00 0.00 36.64 4.30
843 858 4.101430 AGCAAGCTTTTCCCTCAATTTTGA 59.899 37.500 0.00 0.00 35.57 2.69
865 880 7.121907 TGCAGTCTGTAGCTCCTGAATATATAG 59.878 40.741 0.93 0.00 0.00 1.31
866 881 6.948309 TGCAGTCTGTAGCTCCTGAATATATA 59.052 38.462 0.93 0.00 0.00 0.86
926 959 3.808728 TCTATAGTGATGCCTTGCCAAC 58.191 45.455 0.00 0.00 0.00 3.77
1034 1068 1.528339 TGCGATGGCAGGATCACAT 59.472 52.632 0.00 0.00 46.21 3.21
1062 1096 1.635817 GCATGCCCCAGGAGGAGTTA 61.636 60.000 6.36 0.00 38.24 2.24
1108 1142 2.147150 GTTCTCCTTGACTTGCCTCAC 58.853 52.381 0.00 0.00 0.00 3.51
1158 1192 1.815421 AGATAAAGGCCACTGCGCG 60.815 57.895 5.01 0.00 38.85 6.86
1276 1310 2.187599 GAACGCACAGCCATGACCAC 62.188 60.000 0.00 0.00 0.00 4.16
1291 1325 3.926616 ACATACCTCAGAACCAAGAACG 58.073 45.455 0.00 0.00 0.00 3.95
1342 1376 5.413833 CCTGTATATTCATGGGCTTCATCAC 59.586 44.000 0.00 0.00 32.92 3.06
1365 1399 5.465390 TGCAAATTAGTCATACGTCTATGCC 59.535 40.000 0.00 0.00 31.18 4.40
1409 1443 4.457496 ACGCACCGAGCTCATGGG 62.457 66.667 23.00 23.00 42.61 4.00
1482 1516 2.098117 GCAACATACCTCAGAACCATGC 59.902 50.000 0.00 0.00 0.00 4.06
1517 1551 4.202441 ACTTCATCAACAAACTCACAGCT 58.798 39.130 0.00 0.00 0.00 4.24
1527 1564 3.023119 AGTGCACCAACTTCATCAACAA 58.977 40.909 14.63 0.00 0.00 2.83
1604 1645 2.283173 CCTTGTCCCCTGCCCAAC 60.283 66.667 0.00 0.00 0.00 3.77
1631 1672 3.353029 CCACCGTTGCACGCATCA 61.353 61.111 0.00 0.00 40.91 3.07
1683 1727 1.638070 TCCATTAGTGCCATGACCCAA 59.362 47.619 0.00 0.00 0.00 4.12
1688 1732 0.918258 TGCCTCCATTAGTGCCATGA 59.082 50.000 0.00 0.00 0.00 3.07
1698 1742 2.173569 GTCCACTATCCTTGCCTCCATT 59.826 50.000 0.00 0.00 0.00 3.16
1766 1810 2.046892 CCACAAGGTCTCTGCCCG 60.047 66.667 0.00 0.00 0.00 6.13
1775 1819 4.047125 CGGATGGCCCCACAAGGT 62.047 66.667 0.00 0.00 0.00 3.50
1777 1821 4.820744 CCCGGATGGCCCCACAAG 62.821 72.222 0.73 0.00 0.00 3.16
1806 1852 0.951558 ACTGAATGAAACACCGCCAC 59.048 50.000 0.00 0.00 0.00 5.01
1829 1903 7.129425 ACTTCTAATCTCTTGATACAGGAGGT 58.871 38.462 10.13 1.59 38.01 3.85
1888 2178 1.412343 GAGCTCCTCTTCACCTCATCC 59.588 57.143 0.87 0.00 0.00 3.51
1890 2180 1.830477 GTGAGCTCCTCTTCACCTCAT 59.170 52.381 12.15 0.00 35.30 2.90
1971 2328 5.519927 GCAGCAATCAAAACACTGTTAAACT 59.480 36.000 0.00 0.00 0.00 2.66
2065 2429 1.811965 CAGGAAATGATCGGCACACAA 59.188 47.619 0.00 0.00 0.00 3.33
2066 2430 1.452110 CAGGAAATGATCGGCACACA 58.548 50.000 0.00 0.00 0.00 3.72
2170 2591 6.423776 TCTTCCAAAGAAAAGAAATGCCAT 57.576 33.333 0.00 0.00 33.83 4.40
2185 3347 9.793259 AATAGTAAGAGACAATGTTCTTCCAAA 57.207 29.630 11.89 2.07 35.42 3.28


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

AutoCloner maintained by Alex Coulton.