Multiple sequence alignment - TraesCS2B01G240700

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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 TraesCS2B01G240700 chr2B 100.000 2701 0 0 1 2701 244883215 244880515 0.000000e+00 4988
1 TraesCS2B01G240700 chr2B 96.809 188 6 0 5 192 782101400 782101587 5.610000e-82 315
2 TraesCS2B01G240700 chr2D 95.627 1372 35 9 362 1727 188814073 188812721 0.000000e+00 2178
3 TraesCS2B01G240700 chr2D 88.772 668 46 11 2049 2696 188811893 188811235 0.000000e+00 791
4 TraesCS2B01G240700 chr2D 83.121 314 25 12 1702 2005 188812690 188812395 7.420000e-66 261
5 TraesCS2B01G240700 chr2D 95.294 85 4 0 281 365 188814298 188814214 4.690000e-28 135
6 TraesCS2B01G240700 chr2D 93.023 86 6 0 187 272 188815481 188815396 2.820000e-25 126
7 TraesCS2B01G240700 chr2A 94.044 1192 41 12 550 1727 202879796 202878621 0.000000e+00 1781
8 TraesCS2B01G240700 chr2A 86.471 680 48 18 2049 2696 202877834 202877167 0.000000e+00 706
9 TraesCS2B01G240700 chr2A 90.000 210 15 6 1702 1908 202878590 202878384 1.590000e-67 267
10 TraesCS2B01G240700 chr2A 91.477 176 8 1 187 362 202880126 202879958 4.500000e-58 235
11 TraesCS2B01G240700 chr1D 96.257 187 7 0 6 192 15293461 15293275 9.390000e-80 307
12 TraesCS2B01G240700 chr1B 97.253 182 4 1 5 186 640451271 640451451 9.390000e-80 307
13 TraesCS2B01G240700 chr1B 95.789 190 8 0 5 194 654508441 654508630 9.390000e-80 307
14 TraesCS2B01G240700 chr1B 95.312 192 9 0 5 196 676078500 676078309 3.380000e-79 305
15 TraesCS2B01G240700 chr1B 94.388 196 9 1 5 200 90922946 90922753 1.570000e-77 300
16 TraesCS2B01G240700 chr3D 95.312 192 9 0 5 196 108291030 108290839 3.380000e-79 305
17 TraesCS2B01G240700 chr3D 92.647 204 15 0 5 208 524311861 524311658 7.310000e-76 294
18 TraesCS2B01G240700 chr3B 95.767 189 8 0 5 193 813188485 813188297 3.380000e-79 305


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 TraesCS2B01G240700 chr2B 244880515 244883215 2700 True 4988.00 4988 100.0000 1 2701 1 chr2B.!!$R1 2700
1 TraesCS2B01G240700 chr2D 188811235 188815481 4246 True 698.20 2178 91.1674 187 2696 5 chr2D.!!$R1 2509
2 TraesCS2B01G240700 chr2A 202877167 202880126 2959 True 747.25 1781 90.4980 187 2696 4 chr2A.!!$R1 2509

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
161 162 0.386476 TGGCAACCTAGGTATACGCG 59.614 55.0 16.67 3.53 0.0 6.01 F
162 163 0.386838 GGCAACCTAGGTATACGCGT 59.613 55.0 19.17 19.17 0.0 6.01 F
1269 2521 0.521867 CATCAACATGGCAGCGTTCG 60.522 55.0 0.00 0.57 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 2372 1.440938 TTTTGTCGGCGGTCCACTTG 61.441 55.000 7.21 0.0 0.00 3.16 R
1490 2742 2.048603 GGCCGCTGCTTCTTCCATT 61.049 57.895 0.00 0.0 37.74 3.16 R
2635 4502 0.110644 CAAGAACCGAACTGAAGCGC 60.111 55.000 0.00 0.0 0.00 5.92 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
18 19 2.113767 GTCTGCGTACCCCTAGGTC 58.886 63.158 8.29 0.00 46.45 3.85
19 20 1.452651 TCTGCGTACCCCTAGGTCG 60.453 63.158 8.29 8.12 46.45 4.79
20 21 1.751927 CTGCGTACCCCTAGGTCGT 60.752 63.158 8.29 6.00 46.45 4.34
21 22 1.722636 CTGCGTACCCCTAGGTCGTC 61.723 65.000 8.29 4.71 46.45 4.20
22 23 1.750399 GCGTACCCCTAGGTCGTCA 60.750 63.158 8.29 0.00 46.45 4.35
23 24 1.315257 GCGTACCCCTAGGTCGTCAA 61.315 60.000 8.29 0.00 46.45 3.18
24 25 1.396653 CGTACCCCTAGGTCGTCAAT 58.603 55.000 8.29 0.00 46.45 2.57
25 26 1.753073 CGTACCCCTAGGTCGTCAATT 59.247 52.381 8.29 0.00 46.45 2.32
26 27 2.167075 CGTACCCCTAGGTCGTCAATTT 59.833 50.000 8.29 0.00 46.45 1.82
27 28 2.781681 ACCCCTAGGTCGTCAATTTG 57.218 50.000 8.29 0.00 46.45 2.32
28 29 2.262637 ACCCCTAGGTCGTCAATTTGA 58.737 47.619 8.29 0.00 46.45 2.69
29 30 2.844348 ACCCCTAGGTCGTCAATTTGAT 59.156 45.455 8.29 0.00 46.45 2.57
30 31 3.118371 ACCCCTAGGTCGTCAATTTGATC 60.118 47.826 8.29 0.00 46.45 2.92
31 32 3.118408 CCCCTAGGTCGTCAATTTGATCA 60.118 47.826 8.29 0.00 0.00 2.92
32 33 4.513442 CCCTAGGTCGTCAATTTGATCAA 58.487 43.478 8.29 3.38 0.00 2.57
33 34 4.332819 CCCTAGGTCGTCAATTTGATCAAC 59.667 45.833 7.89 0.00 0.00 3.18
34 35 4.332819 CCTAGGTCGTCAATTTGATCAACC 59.667 45.833 7.89 14.93 0.00 3.77
35 36 4.021102 AGGTCGTCAATTTGATCAACCT 57.979 40.909 7.89 17.69 33.46 3.50
36 37 5.160607 AGGTCGTCAATTTGATCAACCTA 57.839 39.130 20.14 0.00 35.24 3.08
37 38 5.556915 AGGTCGTCAATTTGATCAACCTAA 58.443 37.500 20.14 0.00 35.24 2.69
38 39 6.180472 AGGTCGTCAATTTGATCAACCTAAT 58.820 36.000 20.14 0.00 35.24 1.73
39 40 7.335627 AGGTCGTCAATTTGATCAACCTAATA 58.664 34.615 20.14 0.00 35.24 0.98
40 41 7.280205 AGGTCGTCAATTTGATCAACCTAATAC 59.720 37.037 20.14 1.91 35.24 1.89
41 42 7.065324 GGTCGTCAATTTGATCAACCTAATACA 59.935 37.037 7.89 0.00 0.00 2.29
42 43 8.447833 GTCGTCAATTTGATCAACCTAATACAA 58.552 33.333 7.89 0.00 0.00 2.41
43 44 8.664798 TCGTCAATTTGATCAACCTAATACAAG 58.335 33.333 7.89 0.00 0.00 3.16
44 45 8.450964 CGTCAATTTGATCAACCTAATACAAGT 58.549 33.333 7.89 0.00 0.00 3.16
45 46 9.774742 GTCAATTTGATCAACCTAATACAAGTC 57.225 33.333 7.89 0.00 0.00 3.01
46 47 9.513906 TCAATTTGATCAACCTAATACAAGTCA 57.486 29.630 7.89 0.00 0.00 3.41
90 91 9.479549 ACCAATATAAACTTCAGATGTTCCATT 57.520 29.630 2.28 1.23 0.00 3.16
98 99 8.652810 AACTTCAGATGTTCCATTTTCAAAAG 57.347 30.769 0.00 0.00 0.00 2.27
99 100 7.212274 ACTTCAGATGTTCCATTTTCAAAAGG 58.788 34.615 0.00 0.00 0.00 3.11
100 101 6.729690 TCAGATGTTCCATTTTCAAAAGGT 57.270 33.333 0.00 0.00 0.00 3.50
101 102 7.831691 TCAGATGTTCCATTTTCAAAAGGTA 57.168 32.000 0.00 0.00 0.00 3.08
102 103 8.421249 TCAGATGTTCCATTTTCAAAAGGTAT 57.579 30.769 0.00 0.00 0.00 2.73
103 104 9.527157 TCAGATGTTCCATTTTCAAAAGGTATA 57.473 29.630 0.00 0.00 0.00 1.47
149 150 5.669164 TTAGGGTGATAAAATTGGCAACC 57.331 39.130 0.00 0.00 38.39 3.77
150 151 3.790126 AGGGTGATAAAATTGGCAACCT 58.210 40.909 0.00 0.00 43.35 3.50
151 152 4.941713 AGGGTGATAAAATTGGCAACCTA 58.058 39.130 0.00 0.00 46.13 3.08
152 153 4.956075 AGGGTGATAAAATTGGCAACCTAG 59.044 41.667 0.00 0.00 46.13 3.02
153 154 4.099419 GGGTGATAAAATTGGCAACCTAGG 59.901 45.833 7.41 7.41 35.26 3.02
154 155 4.709886 GGTGATAAAATTGGCAACCTAGGT 59.290 41.667 9.21 9.21 0.00 3.08
155 156 5.889289 GGTGATAAAATTGGCAACCTAGGTA 59.111 40.000 16.67 0.00 0.00 3.08
156 157 6.549736 GGTGATAAAATTGGCAACCTAGGTAT 59.450 38.462 16.67 0.83 0.00 2.73
157 158 7.722285 GGTGATAAAATTGGCAACCTAGGTATA 59.278 37.037 16.67 0.00 0.00 1.47
158 159 8.565416 GTGATAAAATTGGCAACCTAGGTATAC 58.435 37.037 16.67 8.74 0.00 1.47
159 160 7.442969 TGATAAAATTGGCAACCTAGGTATACG 59.557 37.037 16.67 5.52 0.00 3.06
160 161 2.607631 TTGGCAACCTAGGTATACGC 57.392 50.000 16.67 15.11 0.00 4.42
161 162 0.386476 TGGCAACCTAGGTATACGCG 59.614 55.000 16.67 3.53 0.00 6.01
162 163 0.386838 GGCAACCTAGGTATACGCGT 59.613 55.000 19.17 19.17 0.00 6.01
163 164 1.608590 GGCAACCTAGGTATACGCGTA 59.391 52.381 22.94 22.94 0.00 4.42
164 165 2.351157 GGCAACCTAGGTATACGCGTAG 60.351 54.545 24.78 11.28 0.00 3.51
165 166 2.351157 GCAACCTAGGTATACGCGTAGG 60.351 54.545 24.78 21.85 46.64 3.18
166 167 3.141398 CAACCTAGGTATACGCGTAGGA 58.859 50.000 25.95 14.03 45.08 2.94
167 168 2.772287 ACCTAGGTATACGCGTAGGAC 58.228 52.381 25.95 22.99 45.08 3.85
168 169 2.370189 ACCTAGGTATACGCGTAGGACT 59.630 50.000 25.95 22.11 45.08 3.85
169 170 3.181450 ACCTAGGTATACGCGTAGGACTT 60.181 47.826 25.95 21.88 45.08 3.01
170 171 3.188048 CCTAGGTATACGCGTAGGACTTG 59.812 52.174 24.78 19.23 45.08 3.16
171 172 2.648059 AGGTATACGCGTAGGACTTGT 58.352 47.619 24.78 8.30 0.00 3.16
172 173 3.808728 AGGTATACGCGTAGGACTTGTA 58.191 45.455 24.78 7.25 0.00 2.41
173 174 4.199310 AGGTATACGCGTAGGACTTGTAA 58.801 43.478 24.78 0.00 0.00 2.41
174 175 4.640201 AGGTATACGCGTAGGACTTGTAAA 59.360 41.667 24.78 0.00 0.00 2.01
175 176 4.735338 GGTATACGCGTAGGACTTGTAAAC 59.265 45.833 24.78 6.78 0.00 2.01
176 177 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
177 178 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
178 179 2.294233 ACGCGTAGGACTTGTAAACTGA 59.706 45.455 11.67 0.00 0.00 3.41
179 180 2.915463 CGCGTAGGACTTGTAAACTGAG 59.085 50.000 0.00 0.00 0.00 3.35
180 181 3.365666 CGCGTAGGACTTGTAAACTGAGA 60.366 47.826 0.00 0.00 0.00 3.27
181 182 3.919197 GCGTAGGACTTGTAAACTGAGAC 59.081 47.826 0.00 0.00 0.00 3.36
182 183 4.156915 CGTAGGACTTGTAAACTGAGACG 58.843 47.826 0.00 0.00 0.00 4.18
183 184 3.662247 AGGACTTGTAAACTGAGACGG 57.338 47.619 0.00 0.00 0.00 4.79
184 185 3.228453 AGGACTTGTAAACTGAGACGGA 58.772 45.455 0.00 0.00 0.00 4.69
185 186 3.256136 AGGACTTGTAAACTGAGACGGAG 59.744 47.826 0.00 0.00 0.00 4.63
189 190 5.290386 ACTTGTAAACTGAGACGGAGAAAG 58.710 41.667 0.00 0.00 0.00 2.62
256 257 2.649331 AAGCAAGATCTGTGCAATGC 57.351 45.000 23.08 16.27 44.74 3.56
407 1645 8.916628 TGGCTGTCAATATGCATAAACTATAA 57.083 30.769 11.13 0.00 0.00 0.98
408 1646 9.002600 TGGCTGTCAATATGCATAAACTATAAG 57.997 33.333 11.13 4.48 0.00 1.73
439 1677 4.270325 GTGTTGGCCGAGCTAGTTAATTAG 59.730 45.833 0.00 0.76 0.00 1.73
440 1678 3.746045 TGGCCGAGCTAGTTAATTAGG 57.254 47.619 7.08 0.00 0.00 2.69
445 1683 3.060602 CGAGCTAGTTAATTAGGCCTGC 58.939 50.000 17.99 6.67 0.00 4.85
556 1794 8.430431 ACCCATTTCGGTTTCCTTTTTAAAATA 58.570 29.630 0.55 0.00 29.19 1.40
780 2018 2.271800 CTACTCGAATCACCCTGCAAC 58.728 52.381 0.00 0.00 0.00 4.17
794 2032 0.693049 TGCAACCTCTCCTCTTTCCC 59.307 55.000 0.00 0.00 0.00 3.97
928 2178 0.883153 TGGTTGTAGCAGCAGCATTG 59.117 50.000 3.17 0.00 45.49 2.82
936 2186 0.879765 GCAGCAGCATTGTTCAGACT 59.120 50.000 0.00 0.00 41.58 3.24
938 2188 2.159599 GCAGCAGCATTGTTCAGACTAC 60.160 50.000 0.00 0.00 41.58 2.73
941 2191 2.417933 GCAGCATTGTTCAGACTACCAG 59.582 50.000 0.00 0.00 0.00 4.00
964 2214 1.039856 ACCAAGCATCCACCAACAAC 58.960 50.000 0.00 0.00 0.00 3.32
1079 2329 1.226575 CGCTGGCGATCGACTACAA 60.227 57.895 23.76 0.00 42.83 2.41
1193 2443 5.580691 CGTGCACAAACTTCCTATGATCTAA 59.419 40.000 18.64 0.00 0.00 2.10
1194 2444 6.092122 CGTGCACAAACTTCCTATGATCTAAA 59.908 38.462 18.64 0.00 0.00 1.85
1216 2466 9.809096 CTAAATACTCTACATGCTTTCTTCTCA 57.191 33.333 0.00 0.00 0.00 3.27
1269 2521 0.521867 CATCAACATGGCAGCGTTCG 60.522 55.000 0.00 0.57 0.00 3.95
1376 2628 1.301401 CGGCAAGACCACCTTCGAA 60.301 57.895 0.00 0.00 39.03 3.71
1389 2641 2.196382 CTTCGAACTCGGCGAGACCA 62.196 60.000 40.35 20.35 39.14 4.02
1572 2824 4.124351 CCTACGCGGACGCCAAGA 62.124 66.667 12.47 0.00 45.53 3.02
1608 2860 4.742201 CGACCACCTCCACGCCTG 62.742 72.222 0.00 0.00 0.00 4.85
1643 2907 2.029666 GCTCCGCGGTATCAGCAT 59.970 61.111 26.44 0.00 34.19 3.79
1773 3093 1.850441 CGAGGCGTGGTTAACTATTCG 59.150 52.381 5.42 1.61 0.00 3.34
1784 3104 7.518052 CGTGGTTAACTATTCGTTGTACCAAAA 60.518 37.037 5.42 0.00 45.23 2.44
1786 3106 7.041235 TGGTTAACTATTCGTTGTACCAAAAGG 60.041 37.037 5.42 0.00 43.05 3.11
1787 3107 5.366829 AACTATTCGTTGTACCAAAAGGC 57.633 39.130 0.00 0.00 33.72 4.35
1873 3201 3.362870 ACAGCTCCCTACTACGTAACT 57.637 47.619 0.00 0.00 0.00 2.24
1874 3202 3.277715 ACAGCTCCCTACTACGTAACTC 58.722 50.000 0.00 0.00 0.00 3.01
1886 3214 5.302360 ACTACGTAACTCCATTTTGAAGCA 58.698 37.500 0.00 0.00 0.00 3.91
1890 3218 5.473504 ACGTAACTCCATTTTGAAGCAGATT 59.526 36.000 0.00 0.00 0.00 2.40
1909 3237 7.449027 GCAGATTTTCGTAATATGCTACTAGC 58.551 38.462 18.48 0.61 40.55 3.42
1910 3238 7.329717 GCAGATTTTCGTAATATGCTACTAGCT 59.670 37.037 18.48 0.00 42.97 3.32
1911 3239 9.197694 CAGATTTTCGTAATATGCTACTAGCTT 57.802 33.333 9.49 5.73 42.97 3.74
1912 3240 9.765795 AGATTTTCGTAATATGCTACTAGCTTT 57.234 29.630 9.49 3.81 42.97 3.51
1923 3251 9.726438 ATATGCTACTAGCTTTATACTTTTGGG 57.274 33.333 9.49 0.00 42.97 4.12
1924 3252 5.820947 TGCTACTAGCTTTATACTTTTGGGC 59.179 40.000 9.49 0.00 42.97 5.36
1925 3253 5.050295 GCTACTAGCTTTATACTTTTGGGCG 60.050 44.000 0.00 0.00 38.45 6.13
1926 3254 5.093849 ACTAGCTTTATACTTTTGGGCGA 57.906 39.130 0.00 0.00 0.00 5.54
1927 3255 5.116882 ACTAGCTTTATACTTTTGGGCGAG 58.883 41.667 0.00 0.00 0.00 5.03
1928 3256 2.683362 AGCTTTATACTTTTGGGCGAGC 59.317 45.455 0.00 0.00 0.00 5.03
1929 3257 2.422127 GCTTTATACTTTTGGGCGAGCA 59.578 45.455 0.00 0.00 0.00 4.26
1930 3258 3.119637 GCTTTATACTTTTGGGCGAGCAA 60.120 43.478 0.00 0.00 0.00 3.91
1931 3259 4.617298 GCTTTATACTTTTGGGCGAGCAAA 60.617 41.667 0.00 0.00 0.00 3.68
1932 3260 5.455056 TTTATACTTTTGGGCGAGCAAAA 57.545 34.783 0.00 0.00 0.00 2.44
1933 3261 5.652994 TTATACTTTTGGGCGAGCAAAAT 57.347 34.783 0.00 0.00 31.07 1.82
1967 3295 7.009815 CGAGCAATTTGATACTGCATTTTGATT 59.990 33.333 0.00 0.00 38.58 2.57
1980 3308 4.142838 GCATTTTGATTAGCTTTGGTTGCC 60.143 41.667 0.00 0.00 0.00 4.52
1991 3319 3.734902 GCTTTGGTTGCCTCAATTATCCG 60.735 47.826 0.00 0.00 0.00 4.18
1995 3323 4.277476 TGGTTGCCTCAATTATCCGAAAT 58.723 39.130 0.00 0.00 0.00 2.17
2023 3799 7.619050 TCTCAGAGAAATTATGAGTGCTTTCT 58.381 34.615 0.00 0.00 43.92 2.52
2029 3805 6.312426 AGAAATTATGAGTGCTTTCTGTCTCG 59.688 38.462 0.00 0.00 36.77 4.04
2040 3816 5.142962 GCTTTCTGTCTCGTCTTTTTGATG 58.857 41.667 0.00 0.00 0.00 3.07
2044 3820 4.389992 TCTGTCTCGTCTTTTTGATGATGC 59.610 41.667 0.00 0.00 39.69 3.91
2045 3821 4.064388 TGTCTCGTCTTTTTGATGATGCA 58.936 39.130 0.00 0.00 39.69 3.96
2047 3823 4.848299 GTCTCGTCTTTTTGATGATGCAAC 59.152 41.667 0.00 0.00 39.69 4.17
2048 3824 4.514816 TCTCGTCTTTTTGATGATGCAACA 59.485 37.500 0.00 0.00 39.69 3.33
2050 3826 5.155643 TCGTCTTTTTGATGATGCAACATG 58.844 37.500 14.87 0.00 35.91 3.21
2051 3827 4.201551 CGTCTTTTTGATGATGCAACATGC 60.202 41.667 14.87 6.80 37.62 4.06
2091 3930 0.609957 CACATTTGCTCCTGGAGGCA 60.610 55.000 24.43 18.81 36.62 4.75
2115 3954 8.629158 GCACCAAGTATAAATAATGGACATGAA 58.371 33.333 0.00 0.00 0.00 2.57
2118 3957 8.289618 CCAAGTATAAATAATGGACATGAACCG 58.710 37.037 0.00 0.00 0.00 4.44
2140 3979 8.845942 ACCGATTTAGTTTTATAAAATTCGCC 57.154 30.769 13.54 1.22 30.94 5.54
2148 3987 8.113173 AGTTTTATAAAATTCGCCCACTACAA 57.887 30.769 13.54 0.00 0.00 2.41
2149 3988 8.024865 AGTTTTATAAAATTCGCCCACTACAAC 58.975 33.333 13.54 0.00 0.00 3.32
2160 3999 4.319622 CGCCCACTACAACAAAACGAAATA 60.320 41.667 0.00 0.00 0.00 1.40
2162 4001 5.571357 GCCCACTACAACAAAACGAAATATG 59.429 40.000 0.00 0.00 0.00 1.78
2169 4008 9.658475 CTACAACAAAACGAAATATGAAAGACA 57.342 29.630 0.00 0.00 0.00 3.41
2192 4031 5.296813 GTGTAACTGGCTGGAAATTACAG 57.703 43.478 0.00 0.00 36.65 2.74
2195 4034 4.373156 AACTGGCTGGAAATTACAGAGT 57.627 40.909 9.83 1.38 38.20 3.24
2198 4037 5.876357 ACTGGCTGGAAATTACAGAGTTAA 58.124 37.500 9.83 0.00 38.20 2.01
2200 4039 6.948309 ACTGGCTGGAAATTACAGAGTTAAAT 59.052 34.615 9.83 0.00 38.20 1.40
2203 4042 8.902806 TGGCTGGAAATTACAGAGTTAAATATG 58.097 33.333 9.83 0.00 38.20 1.78
2204 4043 9.120538 GGCTGGAAATTACAGAGTTAAATATGA 57.879 33.333 9.83 0.00 38.20 2.15
2248 4087 4.265073 ACTATTGCAGGAGAACATGAACC 58.735 43.478 0.00 0.00 0.00 3.62
2271 4110 9.847224 AACCAATTTAGTATAACATCACTAGGG 57.153 33.333 0.00 0.00 0.00 3.53
2296 4147 1.016653 GTCTTGCCAAGAGAGGTCGC 61.017 60.000 7.55 0.00 38.41 5.19
2306 4157 0.038892 GAGAGGTCGCCACGTTGTAA 60.039 55.000 0.00 0.00 0.00 2.41
2481 4343 7.773224 TGCAGCACAACCTATTTATGTTATAGT 59.227 33.333 0.00 0.00 0.00 2.12
2482 4344 9.268268 GCAGCACAACCTATTTATGTTATAGTA 57.732 33.333 0.00 0.00 0.00 1.82
2499 4366 2.365582 AGTACATCAAAATCACGGGCC 58.634 47.619 0.00 0.00 0.00 5.80
2617 4484 6.150976 GGTGTCACAAGATAATCAAATGTCCA 59.849 38.462 5.12 0.00 0.00 4.02
2635 4502 1.074319 CACGGGTGATACAACGACGG 61.074 60.000 0.00 0.00 0.00 4.79
2696 4565 4.267928 CACTAAACGGCTTCTGCATAGTAC 59.732 45.833 0.00 0.00 41.91 2.73
2697 4566 3.611766 AAACGGCTTCTGCATAGTACT 57.388 42.857 0.00 0.00 41.91 2.73
2698 4567 2.873133 ACGGCTTCTGCATAGTACTC 57.127 50.000 0.00 0.00 41.91 2.59
2699 4568 1.409427 ACGGCTTCTGCATAGTACTCC 59.591 52.381 0.00 0.00 41.91 3.85
2700 4569 1.269831 CGGCTTCTGCATAGTACTCCC 60.270 57.143 0.00 0.00 41.91 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.351502 ACCTAGGGGTACGCAGAC 57.648 61.111 14.81 0.00 45.32 3.51
9 10 3.118408 TGATCAAATTGACGACCTAGGGG 60.118 47.826 14.81 7.16 38.88 4.79
10 11 4.137116 TGATCAAATTGACGACCTAGGG 57.863 45.455 14.81 0.00 0.00 3.53
11 12 4.332819 GGTTGATCAAATTGACGACCTAGG 59.667 45.833 10.35 7.41 33.24 3.02
12 13 5.178797 AGGTTGATCAAATTGACGACCTAG 58.821 41.667 23.65 0.00 38.91 3.02
13 14 5.160607 AGGTTGATCAAATTGACGACCTA 57.839 39.130 23.65 2.75 38.91 3.08
14 15 4.021102 AGGTTGATCAAATTGACGACCT 57.979 40.909 21.35 21.35 37.41 3.85
15 16 5.873179 TTAGGTTGATCAAATTGACGACC 57.127 39.130 10.35 18.82 34.74 4.79
16 17 7.970384 TGTATTAGGTTGATCAAATTGACGAC 58.030 34.615 10.35 4.41 0.00 4.34
17 18 8.554835 TTGTATTAGGTTGATCAAATTGACGA 57.445 30.769 10.35 1.53 0.00 4.20
18 19 8.450964 ACTTGTATTAGGTTGATCAAATTGACG 58.549 33.333 10.35 0.00 0.00 4.35
19 20 9.774742 GACTTGTATTAGGTTGATCAAATTGAC 57.225 33.333 10.35 4.82 0.00 3.18
20 21 9.513906 TGACTTGTATTAGGTTGATCAAATTGA 57.486 29.630 10.35 0.00 0.00 2.57
123 124 9.084533 GGTTGCCAATTTTATCACCCTAATATA 57.915 33.333 0.00 0.00 0.00 0.86
124 125 7.789349 AGGTTGCCAATTTTATCACCCTAATAT 59.211 33.333 0.00 0.00 0.00 1.28
125 126 7.129425 AGGTTGCCAATTTTATCACCCTAATA 58.871 34.615 0.00 0.00 0.00 0.98
126 127 5.963865 AGGTTGCCAATTTTATCACCCTAAT 59.036 36.000 0.00 0.00 0.00 1.73
127 128 5.337788 AGGTTGCCAATTTTATCACCCTAA 58.662 37.500 0.00 0.00 0.00 2.69
128 129 4.941713 AGGTTGCCAATTTTATCACCCTA 58.058 39.130 0.00 0.00 0.00 3.53
129 130 3.790126 AGGTTGCCAATTTTATCACCCT 58.210 40.909 0.00 0.00 0.00 4.34
130 131 4.099419 CCTAGGTTGCCAATTTTATCACCC 59.901 45.833 0.00 0.00 0.00 4.61
131 132 4.709886 ACCTAGGTTGCCAATTTTATCACC 59.290 41.667 9.21 0.00 0.00 4.02
132 133 5.914898 ACCTAGGTTGCCAATTTTATCAC 57.085 39.130 9.21 0.00 0.00 3.06
133 134 7.442969 CGTATACCTAGGTTGCCAATTTTATCA 59.557 37.037 22.11 0.00 0.00 2.15
134 135 7.572539 GCGTATACCTAGGTTGCCAATTTTATC 60.573 40.741 22.11 0.00 0.00 1.75
135 136 6.206048 GCGTATACCTAGGTTGCCAATTTTAT 59.794 38.462 22.11 5.71 0.00 1.40
136 137 5.528320 GCGTATACCTAGGTTGCCAATTTTA 59.472 40.000 22.11 0.00 0.00 1.52
137 138 4.337274 GCGTATACCTAGGTTGCCAATTTT 59.663 41.667 22.11 0.00 0.00 1.82
138 139 3.881089 GCGTATACCTAGGTTGCCAATTT 59.119 43.478 22.11 0.00 0.00 1.82
139 140 3.473625 GCGTATACCTAGGTTGCCAATT 58.526 45.455 22.11 0.00 0.00 2.32
140 141 2.547218 CGCGTATACCTAGGTTGCCAAT 60.547 50.000 22.11 9.64 0.00 3.16
141 142 1.202440 CGCGTATACCTAGGTTGCCAA 60.202 52.381 22.11 0.75 0.00 4.52
142 143 0.386476 CGCGTATACCTAGGTTGCCA 59.614 55.000 22.11 1.21 0.00 4.92
143 144 0.386838 ACGCGTATACCTAGGTTGCC 59.613 55.000 22.11 7.02 0.00 4.52
144 145 2.351157 CCTACGCGTATACCTAGGTTGC 60.351 54.545 22.11 17.41 0.00 4.17
145 146 3.058639 GTCCTACGCGTATACCTAGGTTG 60.059 52.174 22.11 9.15 0.00 3.77
146 147 3.142174 GTCCTACGCGTATACCTAGGTT 58.858 50.000 22.11 10.62 0.00 3.50
147 148 2.370189 AGTCCTACGCGTATACCTAGGT 59.630 50.000 20.91 20.57 0.00 3.08
148 149 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
149 150 3.812053 ACAAGTCCTACGCGTATACCTAG 59.188 47.826 20.91 8.56 0.00 3.02
150 151 3.808728 ACAAGTCCTACGCGTATACCTA 58.191 45.455 20.91 0.00 0.00 3.08
151 152 2.648059 ACAAGTCCTACGCGTATACCT 58.352 47.619 20.91 12.19 0.00 3.08
152 153 4.552166 TTACAAGTCCTACGCGTATACC 57.448 45.455 20.91 10.04 0.00 2.73
153 154 5.453587 CAGTTTACAAGTCCTACGCGTATAC 59.546 44.000 20.91 19.74 0.00 1.47
154 155 5.353956 TCAGTTTACAAGTCCTACGCGTATA 59.646 40.000 20.91 8.44 0.00 1.47
155 156 4.156556 TCAGTTTACAAGTCCTACGCGTAT 59.843 41.667 20.91 5.41 0.00 3.06
156 157 3.501828 TCAGTTTACAAGTCCTACGCGTA 59.498 43.478 19.40 19.40 0.00 4.42
157 158 2.294233 TCAGTTTACAAGTCCTACGCGT 59.706 45.455 19.17 19.17 0.00 6.01
158 159 2.915463 CTCAGTTTACAAGTCCTACGCG 59.085 50.000 3.53 3.53 0.00 6.01
159 160 3.919197 GTCTCAGTTTACAAGTCCTACGC 59.081 47.826 0.00 0.00 0.00 4.42
160 161 4.156915 CGTCTCAGTTTACAAGTCCTACG 58.843 47.826 0.00 0.00 0.00 3.51
161 162 4.217118 TCCGTCTCAGTTTACAAGTCCTAC 59.783 45.833 0.00 0.00 0.00 3.18
162 163 4.401022 TCCGTCTCAGTTTACAAGTCCTA 58.599 43.478 0.00 0.00 0.00 2.94
163 164 3.228453 TCCGTCTCAGTTTACAAGTCCT 58.772 45.455 0.00 0.00 0.00 3.85
164 165 3.255149 TCTCCGTCTCAGTTTACAAGTCC 59.745 47.826 0.00 0.00 0.00 3.85
165 166 4.500603 TCTCCGTCTCAGTTTACAAGTC 57.499 45.455 0.00 0.00 0.00 3.01
166 167 4.931661 TTCTCCGTCTCAGTTTACAAGT 57.068 40.909 0.00 0.00 0.00 3.16
167 168 5.290386 ACTTTCTCCGTCTCAGTTTACAAG 58.710 41.667 0.00 0.00 0.00 3.16
168 169 5.272283 ACTTTCTCCGTCTCAGTTTACAA 57.728 39.130 0.00 0.00 0.00 2.41
169 170 4.931661 ACTTTCTCCGTCTCAGTTTACA 57.068 40.909 0.00 0.00 0.00 2.41
170 171 5.766222 TGTACTTTCTCCGTCTCAGTTTAC 58.234 41.667 0.00 0.00 0.00 2.01
171 172 6.395426 TTGTACTTTCTCCGTCTCAGTTTA 57.605 37.500 0.00 0.00 0.00 2.01
172 173 4.931661 TGTACTTTCTCCGTCTCAGTTT 57.068 40.909 0.00 0.00 0.00 2.66
173 174 4.931661 TTGTACTTTCTCCGTCTCAGTT 57.068 40.909 0.00 0.00 0.00 3.16
174 175 5.470047 AATTGTACTTTCTCCGTCTCAGT 57.530 39.130 0.00 0.00 0.00 3.41
175 176 7.884816 TTTAATTGTACTTTCTCCGTCTCAG 57.115 36.000 0.00 0.00 0.00 3.35
176 177 8.665643 TTTTTAATTGTACTTTCTCCGTCTCA 57.334 30.769 0.00 0.00 0.00 3.27
177 178 9.543018 CATTTTTAATTGTACTTTCTCCGTCTC 57.457 33.333 0.00 0.00 0.00 3.36
178 179 9.280174 TCATTTTTAATTGTACTTTCTCCGTCT 57.720 29.630 0.00 0.00 0.00 4.18
218 219 3.363084 GCTTTCTCGTTTTCTCTTCCACG 60.363 47.826 0.00 0.00 0.00 4.94
220 221 3.804036 TGCTTTCTCGTTTTCTCTTCCA 58.196 40.909 0.00 0.00 0.00 3.53
256 257 1.734465 GCCGATCTCAAGACAAGTTGG 59.266 52.381 7.96 0.00 0.00 3.77
345 1435 1.003839 CTTTGCTGCCTCCGTACCA 60.004 57.895 0.00 0.00 0.00 3.25
407 1645 0.971959 TCGGCCAACACCCGTATACT 60.972 55.000 2.24 0.00 45.71 2.12
408 1646 0.529119 CTCGGCCAACACCCGTATAC 60.529 60.000 2.24 0.00 45.71 1.47
410 1648 2.582436 CTCGGCCAACACCCGTAT 59.418 61.111 2.24 0.00 45.71 3.06
411 1649 4.382320 GCTCGGCCAACACCCGTA 62.382 66.667 2.24 0.00 45.71 4.02
413 1651 4.077184 TAGCTCGGCCAACACCCG 62.077 66.667 2.24 0.00 46.88 5.28
445 1683 4.398358 AGATGGACAGAGAATGCATGTTTG 59.602 41.667 0.00 0.00 0.00 2.93
497 1735 6.584954 GTCGCAAGCTCAACATATATACTTG 58.415 40.000 0.00 0.00 36.87 3.16
556 1794 5.016051 AGATATGAGCACGAACAGTTGAT 57.984 39.130 0.00 0.00 0.00 2.57
780 2018 3.728385 AACATTGGGAAAGAGGAGAGG 57.272 47.619 0.00 0.00 0.00 3.69
794 2032 0.609151 TGGCCTGCCATGAAACATTG 59.391 50.000 6.80 0.00 41.89 2.82
928 2178 4.561105 CTTGGTTCTCTGGTAGTCTGAAC 58.439 47.826 0.00 0.00 37.04 3.18
936 2186 2.027192 GTGGATGCTTGGTTCTCTGGTA 60.027 50.000 0.00 0.00 0.00 3.25
938 2188 1.457346 GTGGATGCTTGGTTCTCTGG 58.543 55.000 0.00 0.00 0.00 3.86
941 2191 1.541588 GTTGGTGGATGCTTGGTTCTC 59.458 52.381 0.00 0.00 0.00 2.87
964 2214 1.209621 TCCAAAGGATACGAAGGGGG 58.790 55.000 0.00 0.00 46.39 5.40
1122 2372 1.440938 TTTTGTCGGCGGTCCACTTG 61.441 55.000 7.21 0.00 0.00 3.16
1193 2443 7.276658 CGTTGAGAAGAAAGCATGTAGAGTATT 59.723 37.037 0.00 0.00 0.00 1.89
1194 2444 6.754209 CGTTGAGAAGAAAGCATGTAGAGTAT 59.246 38.462 0.00 0.00 0.00 2.12
1206 2456 3.679824 ACCCTACCGTTGAGAAGAAAG 57.320 47.619 0.00 0.00 0.00 2.62
1216 2466 4.402474 GTGTTATACCACTACCCTACCGTT 59.598 45.833 0.00 0.00 32.50 4.44
1376 2628 4.057428 GTGCTGGTCTCGCCGAGT 62.057 66.667 14.64 0.00 41.21 4.18
1490 2742 2.048603 GGCCGCTGCTTCTTCCATT 61.049 57.895 0.00 0.00 37.74 3.16
1517 2769 4.761058 AGCGAGGCCGGAGAAGGA 62.761 66.667 5.05 0.00 36.06 3.36
1784 3104 9.719355 TTTAAACAAGAAAGAAAGAAAAAGCCT 57.281 25.926 0.00 0.00 0.00 4.58
1867 3195 5.551760 ATCTGCTTCAAAATGGAGTTACG 57.448 39.130 0.00 0.00 0.00 3.18
1873 3201 5.452078 ACGAAAATCTGCTTCAAAATGGA 57.548 34.783 0.00 0.00 0.00 3.41
1874 3202 7.816945 ATTACGAAAATCTGCTTCAAAATGG 57.183 32.000 0.00 0.00 0.00 3.16
1886 3214 9.765795 AAAGCTAGTAGCATATTACGAAAATCT 57.234 29.630 23.77 0.00 45.56 2.40
1905 3233 4.024809 GCTCGCCCAAAAGTATAAAGCTAG 60.025 45.833 0.00 0.00 0.00 3.42
1908 3236 2.422127 TGCTCGCCCAAAAGTATAAAGC 59.578 45.455 0.00 0.00 0.00 3.51
1909 3237 4.695217 TTGCTCGCCCAAAAGTATAAAG 57.305 40.909 0.00 0.00 0.00 1.85
1910 3238 5.455056 TTTTGCTCGCCCAAAAGTATAAA 57.545 34.783 8.37 0.00 39.14 1.40
1911 3239 5.652994 ATTTTGCTCGCCCAAAAGTATAA 57.347 34.783 15.00 0.00 44.89 0.98
1912 3240 5.652994 AATTTTGCTCGCCCAAAAGTATA 57.347 34.783 15.00 0.00 44.89 1.47
1913 3241 4.535526 AATTTTGCTCGCCCAAAAGTAT 57.464 36.364 15.00 5.38 44.89 2.12
1916 3244 4.550577 AAAAATTTTGCTCGCCCAAAAG 57.449 36.364 3.73 0.00 44.89 2.27
1942 3270 7.766219 ATCAAAATGCAGTATCAAATTGCTC 57.234 32.000 0.00 0.00 38.60 4.26
1957 3285 4.142838 GGCAACCAAAGCTAATCAAAATGC 60.143 41.667 0.00 0.00 0.00 3.56
1967 3295 4.644685 GGATAATTGAGGCAACCAAAGCTA 59.355 41.667 0.00 0.00 31.88 3.32
1980 3308 9.920133 TCTCTGAGAATATTTCGGATAATTGAG 57.080 33.333 4.57 0.00 34.02 3.02
1995 3323 9.896645 AAAGCACTCATAATTTCTCTGAGAATA 57.103 29.630 19.93 11.33 38.96 1.75
2011 3787 2.560542 AGACGAGACAGAAAGCACTCAT 59.439 45.455 0.00 0.00 0.00 2.90
2014 3790 3.460857 AAAGACGAGACAGAAAGCACT 57.539 42.857 0.00 0.00 0.00 4.40
2018 3794 6.530913 TCATCAAAAAGACGAGACAGAAAG 57.469 37.500 0.00 0.00 0.00 2.62
2023 3799 4.064388 TGCATCATCAAAAAGACGAGACA 58.936 39.130 0.00 0.00 0.00 3.41
2029 3805 5.199424 GCATGTTGCATCATCAAAAAGAC 57.801 39.130 7.31 0.00 44.26 3.01
2045 3821 4.981806 ACTGTAACACAACTTGCATGTT 57.018 36.364 11.92 11.92 39.75 2.71
2047 3823 5.673337 AGTACTGTAACACAACTTGCATG 57.327 39.130 0.00 0.00 0.00 4.06
2048 3824 5.408604 GCTAGTACTGTAACACAACTTGCAT 59.591 40.000 5.39 0.00 37.51 3.96
2050 3826 4.748102 TGCTAGTACTGTAACACAACTTGC 59.252 41.667 5.39 11.41 37.82 4.01
2051 3827 5.751509 TGTGCTAGTACTGTAACACAACTTG 59.248 40.000 12.42 0.00 35.28 3.16
2091 3930 9.131791 GGTTCATGTCCATTATTTATACTTGGT 57.868 33.333 0.00 0.00 0.00 3.67
2095 3934 9.793259 AATCGGTTCATGTCCATTATTTATACT 57.207 29.630 9.51 0.00 0.00 2.12
2099 3938 9.621629 ACTAAATCGGTTCATGTCCATTATTTA 57.378 29.630 9.51 12.08 0.00 1.40
2101 3940 8.519799 AACTAAATCGGTTCATGTCCATTATT 57.480 30.769 9.51 4.38 0.00 1.40
2102 3941 8.519799 AAACTAAATCGGTTCATGTCCATTAT 57.480 30.769 9.51 0.00 0.00 1.28
2103 3942 7.931578 AAACTAAATCGGTTCATGTCCATTA 57.068 32.000 9.51 5.55 0.00 1.90
2115 3954 7.916977 GGGCGAATTTTATAAAACTAAATCGGT 59.083 33.333 12.74 0.00 0.00 4.69
2118 3957 9.797556 AGTGGGCGAATTTTATAAAACTAAATC 57.202 29.630 12.74 6.23 0.00 2.17
2138 3977 3.423996 TTTCGTTTTGTTGTAGTGGGC 57.576 42.857 0.00 0.00 0.00 5.36
2140 3979 8.789881 TTTCATATTTCGTTTTGTTGTAGTGG 57.210 30.769 0.00 0.00 0.00 4.00
2148 3987 7.703328 ACACTGTCTTTCATATTTCGTTTTGT 58.297 30.769 0.00 0.00 0.00 2.83
2149 3988 9.658475 TTACACTGTCTTTCATATTTCGTTTTG 57.342 29.630 0.00 0.00 0.00 2.44
2160 3999 4.067896 CAGCCAGTTACACTGTCTTTCAT 58.932 43.478 3.30 0.00 44.50 2.57
2162 4001 2.808543 CCAGCCAGTTACACTGTCTTTC 59.191 50.000 3.30 0.00 44.50 2.62
2169 4008 4.980573 TGTAATTTCCAGCCAGTTACACT 58.019 39.130 0.00 0.00 32.21 3.55
2220 4059 6.607600 TCATGTTCTCCTGCAATAGTAGTAGT 59.392 38.462 0.00 0.00 0.00 2.73
2221 4060 7.043961 TCATGTTCTCCTGCAATAGTAGTAG 57.956 40.000 0.00 0.00 0.00 2.57
2222 4061 7.265673 GTTCATGTTCTCCTGCAATAGTAGTA 58.734 38.462 0.00 0.00 0.00 1.82
2248 4087 9.209175 GCTCCCTAGTGATGTTATACTAAATTG 57.791 37.037 0.00 0.00 0.00 2.32
2261 4100 1.107114 AGACGTGCTCCCTAGTGATG 58.893 55.000 0.00 0.00 0.00 3.07
2264 4103 3.425578 CAAGACGTGCTCCCTAGTG 57.574 57.895 0.00 0.00 0.00 2.74
2284 4135 1.006102 AACGTGGCGACCTCTCTTG 60.006 57.895 0.00 0.00 0.00 3.02
2296 4147 2.780714 TGGGTAATGGTTACAACGTGG 58.219 47.619 0.00 0.00 37.88 4.94
2306 4157 1.203001 CCTGTGGTGTTGGGTAATGGT 60.203 52.381 0.00 0.00 0.00 3.55
2351 4213 1.592081 TGTGAAAACGCATTGCAAAGC 59.408 42.857 16.44 16.44 0.00 3.51
2447 4309 0.675633 GGTTGTGCTGCAGGTCAAAT 59.324 50.000 17.12 0.00 0.00 2.32
2481 4343 2.088423 GTGGCCCGTGATTTTGATGTA 58.912 47.619 0.00 0.00 0.00 2.29
2482 4344 0.887933 GTGGCCCGTGATTTTGATGT 59.112 50.000 0.00 0.00 0.00 3.06
2486 4353 0.602562 ACATGTGGCCCGTGATTTTG 59.397 50.000 17.31 0.44 34.01 2.44
2499 4366 5.231991 GGCTTGTTACTTTGTTTGACATGTG 59.768 40.000 1.15 0.00 0.00 3.21
2617 4484 1.213537 CCGTCGTTGTATCACCCGT 59.786 57.895 0.00 0.00 0.00 5.28
2635 4502 0.110644 CAAGAACCGAACTGAAGCGC 60.111 55.000 0.00 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.