Multiple sequence alignment - TraesCS6B01G126300

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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 TraesCS6B01G126300 chr6B 100.000 2747 0 0 1 2747 121791317 121788571 0.000000e+00 5073.0
1 TraesCS6B01G126300 chr6A 94.331 2064 83 10 34 2070 65657241 65655185 0.000000e+00 3133.0
2 TraesCS6B01G126300 chr6A 91.813 342 24 3 2410 2747 65655170 65654829 8.900000e-130 473.0
3 TraesCS6B01G126300 chr6A 88.618 246 23 4 2119 2362 596907414 596907172 7.440000e-76 294.0
4 TraesCS6B01G126300 chr6D 93.907 2035 72 16 34 2033 49272115 49274132 0.000000e+00 3024.0
5 TraesCS6B01G126300 chr6D 91.740 339 27 1 2410 2747 49274154 49274492 1.150000e-128 470.0
6 TraesCS6B01G126300 chr2A 89.540 239 24 1 2124 2361 65676069 65675831 4.450000e-78 302.0
7 TraesCS6B01G126300 chr4B 88.934 244 26 1 2119 2361 71704422 71704665 1.600000e-77 300.0
8 TraesCS6B01G126300 chr4B 89.583 48 3 2 2611 2657 184883316 184883362 2.950000e-05 60.2
9 TraesCS6B01G126300 chr5D 88.142 253 25 4 2112 2360 33053895 33053644 2.070000e-76 296.0
10 TraesCS6B01G126300 chr5D 88.400 250 24 4 2112 2357 37041912 37042160 2.070000e-76 296.0
11 TraesCS6B01G126300 chr5D 86.822 258 31 2 2107 2361 225272684 225272427 4.480000e-73 285.0
12 TraesCS6B01G126300 chr5A 88.843 242 24 2 2123 2361 388578181 388577940 7.440000e-76 294.0
13 TraesCS6B01G126300 chr5A 87.747 253 26 4 2112 2360 22058162 22057911 9.620000e-75 291.0
14 TraesCS6B01G126300 chr4D 87.747 253 28 2 2112 2361 114578954 114579206 2.680000e-75 292.0


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 TraesCS6B01G126300 chr6B 121788571 121791317 2746 True 5073 5073 100.0000 1 2747 1 chr6B.!!$R1 2746
1 TraesCS6B01G126300 chr6A 65654829 65657241 2412 True 1803 3133 93.0720 34 2747 2 chr6A.!!$R2 2713
2 TraesCS6B01G126300 chr6D 49272115 49274492 2377 False 1747 3024 92.8235 34 2747 2 chr6D.!!$F1 2713

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
712 734 1.567357 TGTGCTCTATGGTAGCCACA 58.433 50.0 0.0 0.0 39.3 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2421 0.115745 TGTACTCCCTCCCGTCCTTT 59.884 55.0 0.0 0.0 0.0 3.11 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 5.352643 GTACAACGTTTCTGCCATTAGTT 57.647 39.130 0.00 0.00 0.00 2.24
23 24 4.483476 ACAACGTTTCTGCCATTAGTTC 57.517 40.909 0.00 0.00 0.00 3.01
24 25 3.252458 ACAACGTTTCTGCCATTAGTTCC 59.748 43.478 0.00 0.00 0.00 3.62
25 26 3.418684 ACGTTTCTGCCATTAGTTCCT 57.581 42.857 0.00 0.00 0.00 3.36
26 27 4.546829 ACGTTTCTGCCATTAGTTCCTA 57.453 40.909 0.00 0.00 0.00 2.94
27 28 5.099042 ACGTTTCTGCCATTAGTTCCTAT 57.901 39.130 0.00 0.00 0.00 2.57
28 29 6.229936 ACGTTTCTGCCATTAGTTCCTATA 57.770 37.500 0.00 0.00 0.00 1.31
29 30 6.827727 ACGTTTCTGCCATTAGTTCCTATAT 58.172 36.000 0.00 0.00 0.00 0.86
30 31 7.959175 ACGTTTCTGCCATTAGTTCCTATATA 58.041 34.615 0.00 0.00 0.00 0.86
31 32 8.594550 ACGTTTCTGCCATTAGTTCCTATATAT 58.405 33.333 0.00 0.00 0.00 0.86
75 76 4.849383 CGTGGTTTTATTTGTTCGGACATC 59.151 41.667 0.00 0.00 35.29 3.06
187 191 5.289434 GCTGGAATTTAGCTTGTACAAATGC 59.711 40.000 10.03 10.54 38.14 3.56
307 311 9.467796 TCAGATATGACCAGGAATACAGTATAG 57.532 37.037 0.00 0.00 0.00 1.31
328 332 9.534565 GTATAGTTCTGCATTCTCTGAATGTAA 57.465 33.333 17.90 9.88 0.00 2.41
336 340 9.107177 CTGCATTCTCTGAATGTAACTTAAGAT 57.893 33.333 10.09 0.00 0.00 2.40
383 387 1.761449 TGCTTTGCTTTGTGTCCTGA 58.239 45.000 0.00 0.00 0.00 3.86
394 398 3.517296 TGTGTCCTGAACTCTCTCTCT 57.483 47.619 0.00 0.00 0.00 3.10
444 449 9.499585 CAATGACAGCAAATCTAATCTACAAAG 57.500 33.333 0.00 0.00 0.00 2.77
473 480 6.605594 GGTTGGAATACATGTTGGAATCCTTA 59.394 38.462 2.30 0.00 0.00 2.69
513 520 8.695456 ACTCAAATTGGAAAATACTTTGTCACT 58.305 29.630 0.00 0.00 0.00 3.41
514 521 8.870160 TCAAATTGGAAAATACTTTGTCACTG 57.130 30.769 0.00 0.00 0.00 3.66
518 525 7.397892 TTGGAAAATACTTTGTCACTGTCAA 57.602 32.000 0.00 0.00 0.00 3.18
603 625 7.393515 ACCTTTTGCCTTAATAAGAGTTACTGG 59.606 37.037 0.83 0.00 0.00 4.00
712 734 1.567357 TGTGCTCTATGGTAGCCACA 58.433 50.000 0.00 0.00 39.30 4.17
754 776 7.861630 TGTTTTACTTGATCACTAGTTTGCTC 58.138 34.615 5.40 0.00 34.40 4.26
857 893 6.818644 CAGGCTTCATCTTTTACACTAAGCTA 59.181 38.462 0.00 0.00 38.29 3.32
1080 1116 1.001860 GAAGAGCAGGCTGTGACTTCT 59.998 52.381 26.46 16.46 37.74 2.85
1116 1152 4.603131 TCTTGCCTGCTATTTTGGAATCT 58.397 39.130 0.00 0.00 0.00 2.40
1260 1296 4.051661 TGATTCCCTTCAAGAGCCAATT 57.948 40.909 0.00 0.00 0.00 2.32
1272 1308 0.598065 AGCCAATTGAAGGTTCACGC 59.402 50.000 7.12 0.00 36.83 5.34
1334 1370 1.153289 CAGAGGCGGAATCCCACAG 60.153 63.158 0.00 0.00 0.00 3.66
1354 1390 4.022589 ACAGTCTGCATGTGGAAAAAGATG 60.023 41.667 0.00 0.00 0.00 2.90
1627 1663 3.071747 GGACCTCAAGAAACTCCTCAAGT 59.928 47.826 0.00 0.00 41.10 3.16
1711 1747 0.865111 CGTTGATGAACTTGTGGCGA 59.135 50.000 0.00 0.00 0.00 5.54
1747 1783 1.790387 CTGCAGCGAAACCAGTAGC 59.210 57.895 0.00 0.00 0.00 3.58
1803 1839 2.364324 GCATCTCTACCGTCCAATGGTA 59.636 50.000 0.00 0.00 38.67 3.25
1869 1905 1.996786 GCCGGTCCATTGTGCATCTG 61.997 60.000 1.90 0.00 0.00 2.90
2000 2043 4.067972 TGTCTAGACACCCTTGAAACAC 57.932 45.455 21.74 0.00 36.21 3.32
2033 2076 4.789012 TCAATTCAGGCAGATTTTGGAC 57.211 40.909 0.00 0.00 0.00 4.02
2034 2077 4.410099 TCAATTCAGGCAGATTTTGGACT 58.590 39.130 0.00 0.00 0.00 3.85
2049 2092 1.078567 GACTGCTCCTCAGGCCTTG 60.079 63.158 0.00 0.00 45.36 3.61
2050 2093 1.835927 GACTGCTCCTCAGGCCTTGT 61.836 60.000 0.00 0.00 45.36 3.16
2051 2094 2.290847 CTGCTCCTCAGGCCTTGTA 58.709 57.895 0.00 0.00 39.15 2.41
2055 2100 2.019984 GCTCCTCAGGCCTTGTAAATG 58.980 52.381 0.00 0.00 0.00 2.32
2070 2115 6.885952 TTGTAAATGCAAGGTGCTTAGTAA 57.114 33.333 0.00 0.00 45.31 2.24
2071 2116 6.885952 TGTAAATGCAAGGTGCTTAGTAAA 57.114 33.333 0.00 0.00 45.31 2.01
2072 2117 7.278461 TGTAAATGCAAGGTGCTTAGTAAAA 57.722 32.000 0.00 0.00 45.31 1.52
2073 2118 7.891561 TGTAAATGCAAGGTGCTTAGTAAAAT 58.108 30.769 0.00 0.00 45.31 1.82
2074 2119 9.015367 TGTAAATGCAAGGTGCTTAGTAAAATA 57.985 29.630 0.00 0.00 45.31 1.40
2075 2120 9.849166 GTAAATGCAAGGTGCTTAGTAAAATAA 57.151 29.630 0.00 0.00 45.31 1.40
2077 2122 8.757164 AATGCAAGGTGCTTAGTAAAATAAAC 57.243 30.769 0.00 0.00 45.31 2.01
2078 2123 6.375377 TGCAAGGTGCTTAGTAAAATAAACG 58.625 36.000 1.43 0.00 45.31 3.60
2079 2124 6.205076 TGCAAGGTGCTTAGTAAAATAAACGA 59.795 34.615 1.43 0.00 45.31 3.85
2080 2125 6.741358 GCAAGGTGCTTAGTAAAATAAACGAG 59.259 38.462 0.00 0.00 40.96 4.18
2081 2126 7.572539 GCAAGGTGCTTAGTAAAATAAACGAGT 60.573 37.037 0.00 0.00 40.96 4.18
2082 2127 7.974482 AGGTGCTTAGTAAAATAAACGAGTT 57.026 32.000 0.00 0.00 0.00 3.01
2083 2128 8.387190 AGGTGCTTAGTAAAATAAACGAGTTT 57.613 30.769 6.46 6.46 36.63 2.66
2084 2129 8.843262 AGGTGCTTAGTAAAATAAACGAGTTTT 58.157 29.630 6.53 0.00 34.23 2.43
2085 2130 9.454585 GGTGCTTAGTAAAATAAACGAGTTTTT 57.545 29.630 6.53 0.00 34.23 1.94
2100 2145 3.935371 TTTTTGAAGCACCCCCTGA 57.065 47.368 0.00 0.00 0.00 3.86
2101 2146 1.703411 TTTTTGAAGCACCCCCTGAG 58.297 50.000 0.00 0.00 0.00 3.35
2102 2147 0.827507 TTTTGAAGCACCCCCTGAGC 60.828 55.000 0.00 0.00 0.00 4.26
2103 2148 2.005606 TTTGAAGCACCCCCTGAGCA 62.006 55.000 0.00 0.00 0.00 4.26
2104 2149 2.360475 GAAGCACCCCCTGAGCAC 60.360 66.667 0.00 0.00 0.00 4.40
2105 2150 3.927481 GAAGCACCCCCTGAGCACC 62.927 68.421 0.00 0.00 0.00 5.01
2106 2151 4.990910 AGCACCCCCTGAGCACCT 62.991 66.667 0.00 0.00 0.00 4.00
2107 2152 3.971702 GCACCCCCTGAGCACCTT 61.972 66.667 0.00 0.00 0.00 3.50
2108 2153 2.034687 CACCCCCTGAGCACCTTG 59.965 66.667 0.00 0.00 0.00 3.61
2109 2154 2.450502 ACCCCCTGAGCACCTTGT 60.451 61.111 0.00 0.00 0.00 3.16
2110 2155 1.151899 ACCCCCTGAGCACCTTGTA 60.152 57.895 0.00 0.00 0.00 2.41
2111 2156 0.550147 ACCCCCTGAGCACCTTGTAT 60.550 55.000 0.00 0.00 0.00 2.29
2112 2157 0.625849 CCCCCTGAGCACCTTGTATT 59.374 55.000 0.00 0.00 0.00 1.89
2113 2158 1.683011 CCCCCTGAGCACCTTGTATTG 60.683 57.143 0.00 0.00 0.00 1.90
2114 2159 1.004745 CCCCTGAGCACCTTGTATTGT 59.995 52.381 0.00 0.00 0.00 2.71
2115 2160 2.238646 CCCCTGAGCACCTTGTATTGTA 59.761 50.000 0.00 0.00 0.00 2.41
2116 2161 3.270877 CCCTGAGCACCTTGTATTGTAC 58.729 50.000 0.00 0.00 0.00 2.90
2117 2162 3.055094 CCCTGAGCACCTTGTATTGTACT 60.055 47.826 0.00 0.00 0.00 2.73
2118 2163 4.184629 CCTGAGCACCTTGTATTGTACTC 58.815 47.826 0.00 0.00 0.00 2.59
2119 2164 4.081420 CCTGAGCACCTTGTATTGTACTCT 60.081 45.833 0.00 0.00 0.00 3.24
2120 2165 5.073311 TGAGCACCTTGTATTGTACTCTC 57.927 43.478 0.00 0.00 0.00 3.20
2121 2166 4.772624 TGAGCACCTTGTATTGTACTCTCT 59.227 41.667 0.00 0.00 0.00 3.10
2122 2167 5.078411 AGCACCTTGTATTGTACTCTCTG 57.922 43.478 0.00 0.00 0.00 3.35
2123 2168 4.081420 AGCACCTTGTATTGTACTCTCTGG 60.081 45.833 0.00 0.00 0.00 3.86
2124 2169 4.322801 GCACCTTGTATTGTACTCTCTGGT 60.323 45.833 0.00 0.00 0.00 4.00
2125 2170 5.411781 CACCTTGTATTGTACTCTCTGGTC 58.588 45.833 0.00 0.00 0.00 4.02
2126 2171 5.186021 CACCTTGTATTGTACTCTCTGGTCT 59.814 44.000 0.00 0.00 0.00 3.85
2127 2172 5.780793 ACCTTGTATTGTACTCTCTGGTCTT 59.219 40.000 0.00 0.00 0.00 3.01
2128 2173 6.270231 ACCTTGTATTGTACTCTCTGGTCTTT 59.730 38.462 0.00 0.00 0.00 2.52
2129 2174 7.162082 CCTTGTATTGTACTCTCTGGTCTTTT 58.838 38.462 0.00 0.00 0.00 2.27
2130 2175 7.661847 CCTTGTATTGTACTCTCTGGTCTTTTT 59.338 37.037 0.00 0.00 0.00 1.94
2152 2197 7.987268 TTTTACTCTGCGTATTAGATCTGTG 57.013 36.000 5.18 0.00 0.00 3.66
2153 2198 6.694877 TTACTCTGCGTATTAGATCTGTGT 57.305 37.500 5.18 0.00 0.00 3.72
2154 2199 5.584253 ACTCTGCGTATTAGATCTGTGTT 57.416 39.130 5.18 0.00 0.00 3.32
2155 2200 6.694877 ACTCTGCGTATTAGATCTGTGTTA 57.305 37.500 5.18 0.00 0.00 2.41
2156 2201 7.096884 ACTCTGCGTATTAGATCTGTGTTAA 57.903 36.000 5.18 0.00 0.00 2.01
2157 2202 7.197017 ACTCTGCGTATTAGATCTGTGTTAAG 58.803 38.462 5.18 0.00 0.00 1.85
2158 2203 7.096884 TCTGCGTATTAGATCTGTGTTAAGT 57.903 36.000 5.18 0.00 0.00 2.24
2159 2204 7.194278 TCTGCGTATTAGATCTGTGTTAAGTC 58.806 38.462 5.18 0.00 0.00 3.01
2160 2205 6.859017 TGCGTATTAGATCTGTGTTAAGTCA 58.141 36.000 5.18 0.00 0.00 3.41
2161 2206 7.317390 TGCGTATTAGATCTGTGTTAAGTCAA 58.683 34.615 5.18 0.00 0.00 3.18
2162 2207 7.815549 TGCGTATTAGATCTGTGTTAAGTCAAA 59.184 33.333 5.18 0.00 0.00 2.69
2163 2208 8.108782 GCGTATTAGATCTGTGTTAAGTCAAAC 58.891 37.037 5.18 0.00 0.00 2.93
2164 2209 9.135843 CGTATTAGATCTGTGTTAAGTCAAACA 57.864 33.333 5.18 0.00 37.03 2.83
2168 2213 6.672147 AGATCTGTGTTAAGTCAAACATTGC 58.328 36.000 0.00 0.00 41.18 3.56
2169 2214 5.826601 TCTGTGTTAAGTCAAACATTGCA 57.173 34.783 0.00 0.00 41.18 4.08
2170 2215 6.201226 TCTGTGTTAAGTCAAACATTGCAA 57.799 33.333 0.00 0.00 41.18 4.08
2171 2216 6.625362 TCTGTGTTAAGTCAAACATTGCAAA 58.375 32.000 1.71 0.00 41.18 3.68
2172 2217 6.751425 TCTGTGTTAAGTCAAACATTGCAAAG 59.249 34.615 1.71 0.19 41.18 2.77
2173 2218 6.393990 TGTGTTAAGTCAAACATTGCAAAGT 58.606 32.000 1.71 1.06 41.18 2.66
2174 2219 6.870965 TGTGTTAAGTCAAACATTGCAAAGTT 59.129 30.769 13.99 13.99 41.18 2.66
2175 2220 7.386299 TGTGTTAAGTCAAACATTGCAAAGTTT 59.614 29.630 23.21 23.21 41.18 2.66
2271 2316 8.500753 ACGAATCTAACAATATTTACTTGGCA 57.499 30.769 0.00 0.00 0.00 4.92
2272 2317 9.120538 ACGAATCTAACAATATTTACTTGGCAT 57.879 29.630 0.00 0.00 0.00 4.40
2273 2318 9.950680 CGAATCTAACAATATTTACTTGGCATT 57.049 29.630 0.00 0.00 0.00 3.56
2277 2322 8.465999 TCTAACAATATTTACTTGGCATTGTGG 58.534 33.333 0.15 0.00 39.20 4.17
2278 2323 6.849085 ACAATATTTACTTGGCATTGTGGA 57.151 33.333 0.00 0.00 38.16 4.02
2279 2324 7.422465 ACAATATTTACTTGGCATTGTGGAT 57.578 32.000 0.00 0.00 38.16 3.41
2280 2325 7.267128 ACAATATTTACTTGGCATTGTGGATG 58.733 34.615 0.00 0.00 38.16 3.51
2281 2326 7.093377 ACAATATTTACTTGGCATTGTGGATGT 60.093 33.333 0.00 0.00 38.16 3.06
2282 2327 5.743636 ATTTACTTGGCATTGTGGATGTT 57.256 34.783 0.00 0.00 38.07 2.71
2283 2328 4.517952 TTACTTGGCATTGTGGATGTTG 57.482 40.909 0.00 0.00 38.07 3.33
2284 2329 2.596346 ACTTGGCATTGTGGATGTTGA 58.404 42.857 0.00 0.00 38.07 3.18
2285 2330 3.167485 ACTTGGCATTGTGGATGTTGAT 58.833 40.909 0.00 0.00 38.07 2.57
2286 2331 4.343231 ACTTGGCATTGTGGATGTTGATA 58.657 39.130 0.00 0.00 38.07 2.15
2287 2332 4.158394 ACTTGGCATTGTGGATGTTGATAC 59.842 41.667 0.00 0.00 38.07 2.24
2288 2333 3.966979 TGGCATTGTGGATGTTGATACT 58.033 40.909 0.00 0.00 38.07 2.12
2289 2334 4.343231 TGGCATTGTGGATGTTGATACTT 58.657 39.130 0.00 0.00 38.07 2.24
2290 2335 4.771577 TGGCATTGTGGATGTTGATACTTT 59.228 37.500 0.00 0.00 38.07 2.66
2291 2336 5.245751 TGGCATTGTGGATGTTGATACTTTT 59.754 36.000 0.00 0.00 38.07 2.27
2292 2337 6.165577 GGCATTGTGGATGTTGATACTTTTT 58.834 36.000 0.00 0.00 38.07 1.94
2384 2429 9.460906 GACTTATATGTAGACTAAAAAGGACGG 57.539 37.037 0.00 0.00 0.00 4.79
2385 2430 8.419442 ACTTATATGTAGACTAAAAAGGACGGG 58.581 37.037 0.00 0.00 0.00 5.28
2386 2431 8.537728 TTATATGTAGACTAAAAAGGACGGGA 57.462 34.615 0.00 0.00 0.00 5.14
2387 2432 4.796038 TGTAGACTAAAAAGGACGGGAG 57.204 45.455 0.00 0.00 0.00 4.30
2388 2433 3.512724 TGTAGACTAAAAAGGACGGGAGG 59.487 47.826 0.00 0.00 0.00 4.30
2389 2434 1.907255 AGACTAAAAAGGACGGGAGGG 59.093 52.381 0.00 0.00 0.00 4.30
2390 2435 1.904537 GACTAAAAAGGACGGGAGGGA 59.095 52.381 0.00 0.00 0.00 4.20
2391 2436 1.907255 ACTAAAAAGGACGGGAGGGAG 59.093 52.381 0.00 0.00 0.00 4.30
2392 2437 1.907255 CTAAAAAGGACGGGAGGGAGT 59.093 52.381 0.00 0.00 0.00 3.85
2393 2438 2.034436 AAAAAGGACGGGAGGGAGTA 57.966 50.000 0.00 0.00 0.00 2.59
2394 2439 1.273759 AAAAGGACGGGAGGGAGTAC 58.726 55.000 0.00 0.00 0.00 2.73
2395 2440 0.115745 AAAGGACGGGAGGGAGTACA 59.884 55.000 0.00 0.00 0.00 2.90
2396 2441 0.115745 AAGGACGGGAGGGAGTACAA 59.884 55.000 0.00 0.00 0.00 2.41
2403 2448 0.325765 GGAGGGAGTACAAGGCCTCT 60.326 60.000 5.23 0.00 0.00 3.69
2422 2474 0.260230 TTCAGGGTGCCAGTTTTCCA 59.740 50.000 0.00 0.00 0.00 3.53
2431 2483 0.178992 CCAGTTTTCCACCTGGCTCA 60.179 55.000 0.00 0.00 41.65 4.26
2518 2570 0.183492 TGGCTTGCTCACCTTGACTT 59.817 50.000 0.00 0.00 0.00 3.01
2537 2589 1.444553 CAGACCTCTCGCGTTGACC 60.445 63.158 5.77 0.00 0.00 4.02
2574 2626 8.645730 AATTTCCAAATTTGAAACCATTTTGC 57.354 26.923 19.86 0.00 35.16 3.68
2575 2627 6.764308 TTCCAAATTTGAAACCATTTTGCA 57.236 29.167 19.86 0.00 0.00 4.08
2576 2628 6.374565 TCCAAATTTGAAACCATTTTGCAG 57.625 33.333 19.86 0.00 0.00 4.41
2581 2634 9.303537 CAAATTTGAAACCATTTTGCAGAAAAT 57.696 25.926 13.08 0.00 41.58 1.82
2626 2679 5.577835 TCACGGATTTGAAAAACTGTTCAG 58.422 37.500 0.00 0.00 38.69 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.352643 AACTAATGGCAGAAACGTTGTAC 57.647 39.130 0.00 0.00 0.00 2.90
1 2 4.453136 GGAACTAATGGCAGAAACGTTGTA 59.547 41.667 0.00 0.00 0.00 2.41
2 3 3.252458 GGAACTAATGGCAGAAACGTTGT 59.748 43.478 0.00 0.00 0.00 3.32
3 4 3.502211 AGGAACTAATGGCAGAAACGTTG 59.498 43.478 0.00 0.00 36.02 4.10
4 5 3.751518 AGGAACTAATGGCAGAAACGTT 58.248 40.909 0.00 0.00 36.02 3.99
5 6 3.418684 AGGAACTAATGGCAGAAACGT 57.581 42.857 0.00 0.00 36.02 3.99
19 20 6.389278 TCCGAGCCCTAGTATATATAGGAACT 59.611 42.308 13.15 10.44 42.15 3.01
20 21 6.599445 TCCGAGCCCTAGTATATATAGGAAC 58.401 44.000 13.15 7.01 42.15 3.62
21 22 6.836714 TCCGAGCCCTAGTATATATAGGAA 57.163 41.667 13.15 0.00 42.15 3.36
22 23 6.599445 GTTCCGAGCCCTAGTATATATAGGA 58.401 44.000 13.15 0.00 42.15 2.94
23 24 5.469421 CGTTCCGAGCCCTAGTATATATAGG 59.531 48.000 6.90 6.90 39.71 2.57
24 25 5.049543 GCGTTCCGAGCCCTAGTATATATAG 60.050 48.000 0.00 0.00 0.00 1.31
25 26 4.818546 GCGTTCCGAGCCCTAGTATATATA 59.181 45.833 0.00 0.00 0.00 0.86
26 27 3.631227 GCGTTCCGAGCCCTAGTATATAT 59.369 47.826 0.00 0.00 0.00 0.86
27 28 3.012518 GCGTTCCGAGCCCTAGTATATA 58.987 50.000 0.00 0.00 0.00 0.86
28 29 1.817447 GCGTTCCGAGCCCTAGTATAT 59.183 52.381 0.00 0.00 0.00 0.86
29 30 1.242076 GCGTTCCGAGCCCTAGTATA 58.758 55.000 0.00 0.00 0.00 1.47
30 31 2.039509 GCGTTCCGAGCCCTAGTAT 58.960 57.895 0.00 0.00 0.00 2.12
31 32 3.518003 GCGTTCCGAGCCCTAGTA 58.482 61.111 0.00 0.00 0.00 1.82
75 76 2.481185 GTGCCATTGCCATTTCAAACTG 59.519 45.455 0.00 0.00 36.33 3.16
187 191 0.108945 TCAGTCAGTGCTCAGCATCG 60.109 55.000 0.54 0.00 41.91 3.84
307 311 6.734104 AGTTACATTCAGAGAATGCAGAAC 57.266 37.500 17.12 16.87 0.00 3.01
360 364 1.594397 GGACACAAAGCAAAGCAAAGC 59.406 47.619 0.00 0.00 0.00 3.51
361 365 2.861935 CAGGACACAAAGCAAAGCAAAG 59.138 45.455 0.00 0.00 0.00 2.77
383 387 4.985538 ACAAGTCTGAGAGAGAGAGAGTT 58.014 43.478 0.00 0.00 30.93 3.01
444 449 5.461032 TCCAACATGTATTCCAACCAAAC 57.539 39.130 0.00 0.00 0.00 2.93
493 500 7.581213 TGACAGTGACAAAGTATTTTCCAAT 57.419 32.000 0.00 0.00 35.03 3.16
538 545 4.875578 TCTCTAAGAGGGTAGCCTACAA 57.124 45.455 14.87 0.80 0.00 2.41
541 548 7.337167 CGTATAATCTCTAAGAGGGTAGCCTA 58.663 42.308 14.87 0.00 0.00 3.93
547 555 5.336491 ACCCGTATAATCTCTAAGAGGGT 57.664 43.478 1.67 1.67 44.06 4.34
550 558 5.535406 ACCACACCCGTATAATCTCTAAGAG 59.465 44.000 0.00 0.00 0.00 2.85
582 604 8.599792 ACTTACCAGTAACTCTTATTAAGGCAA 58.400 33.333 3.66 0.00 0.00 4.52
603 625 4.700213 AGGCACACACCAAATGATACTTAC 59.300 41.667 0.00 0.00 0.00 2.34
712 734 5.343307 AAAACAAAATGAGCTGGTCAAGT 57.657 34.783 14.08 7.57 39.19 3.16
778 800 8.722394 CAAAGACAAAAGAGGGAAGTAGTTATC 58.278 37.037 0.00 0.00 0.00 1.75
1080 1116 2.173356 AGGCAAGAAATCATCGGATCCA 59.827 45.455 13.41 0.00 31.88 3.41
1116 1152 7.652909 TCGACTTCCTTTTCGTTTGACTTAATA 59.347 33.333 0.00 0.00 36.60 0.98
1128 1164 4.515432 GTGAAAGTTCGACTTCCTTTTCG 58.485 43.478 0.00 0.00 37.47 3.46
1260 1296 0.604073 TGGTATCGCGTGAACCTTCA 59.396 50.000 22.26 8.54 34.23 3.02
1310 1346 1.373570 GGATTCCGCCTCTGAAAGTG 58.626 55.000 0.00 0.00 33.76 3.16
1334 1370 3.057033 AGCATCTTTTTCCACATGCAGAC 60.057 43.478 5.60 0.00 43.48 3.51
1354 1390 6.154192 TCCATCTCTACATTATCATCCTGAGC 59.846 42.308 0.00 0.00 0.00 4.26
1374 1410 2.223665 GCTATTGCCTTGTTGCTCCATC 60.224 50.000 0.00 0.00 0.00 3.51
1711 1747 2.408050 CAGCGACAAGTTACTCAAGCT 58.592 47.619 0.00 0.00 0.00 3.74
1747 1783 4.489679 GGAACCAAGAACAAACTGCTAG 57.510 45.455 0.00 0.00 0.00 3.42
1803 1839 0.464870 TGCTTTGCTGCCACAACATT 59.535 45.000 0.00 0.00 0.00 2.71
1858 1894 2.651455 CTGATGGTCCAGATGCACAAT 58.349 47.619 0.00 0.00 36.29 2.71
1859 1895 1.340308 CCTGATGGTCCAGATGCACAA 60.340 52.381 0.00 0.00 36.29 3.33
1972 2015 6.961360 TCAAGGGTGTCTAGACATATACTG 57.039 41.667 27.54 19.50 43.97 2.74
1973 2016 7.399191 TGTTTCAAGGGTGTCTAGACATATACT 59.601 37.037 27.54 18.93 43.97 2.12
1974 2017 7.491696 GTGTTTCAAGGGTGTCTAGACATATAC 59.508 40.741 27.54 17.33 43.97 1.47
1975 2018 7.553334 GTGTTTCAAGGGTGTCTAGACATATA 58.447 38.462 27.54 8.68 43.97 0.86
1976 2019 6.407202 GTGTTTCAAGGGTGTCTAGACATAT 58.593 40.000 27.54 14.12 43.97 1.78
1984 2027 0.818040 GGCGTGTTTCAAGGGTGTCT 60.818 55.000 0.00 0.00 0.00 3.41
2000 2043 2.574322 CTGAATTGAACTCAAACGGCG 58.426 47.619 4.80 4.80 39.55 6.46
2033 2076 0.615331 TTACAAGGCCTGAGGAGCAG 59.385 55.000 5.69 0.00 44.49 4.24
2034 2077 1.064003 TTTACAAGGCCTGAGGAGCA 58.936 50.000 5.69 0.00 0.00 4.26
2055 2100 6.604930 TCGTTTATTTTACTAAGCACCTTGC 58.395 36.000 0.00 0.00 45.46 4.01
2082 2127 1.703411 CTCAGGGGGTGCTTCAAAAA 58.297 50.000 0.00 0.00 0.00 1.94
2083 2128 0.827507 GCTCAGGGGGTGCTTCAAAA 60.828 55.000 0.00 0.00 33.29 2.44
2084 2129 1.228552 GCTCAGGGGGTGCTTCAAA 60.229 57.895 0.00 0.00 33.29 2.69
2085 2130 2.436109 GCTCAGGGGGTGCTTCAA 59.564 61.111 0.00 0.00 33.29 2.69
2086 2131 2.853542 TGCTCAGGGGGTGCTTCA 60.854 61.111 0.00 0.00 36.94 3.02
2087 2132 2.360475 GTGCTCAGGGGGTGCTTC 60.360 66.667 0.00 0.00 36.94 3.86
2088 2133 3.971702 GGTGCTCAGGGGGTGCTT 61.972 66.667 0.00 0.00 36.94 3.91
2089 2134 4.990910 AGGTGCTCAGGGGGTGCT 62.991 66.667 0.00 0.00 36.94 4.40
2090 2135 3.971702 AAGGTGCTCAGGGGGTGC 61.972 66.667 0.00 0.00 36.55 5.01
2091 2136 1.488705 TACAAGGTGCTCAGGGGGTG 61.489 60.000 0.00 0.00 0.00 4.61
2092 2137 0.550147 ATACAAGGTGCTCAGGGGGT 60.550 55.000 0.00 0.00 0.00 4.95
2093 2138 0.625849 AATACAAGGTGCTCAGGGGG 59.374 55.000 0.00 0.00 0.00 5.40
2094 2139 1.004745 ACAATACAAGGTGCTCAGGGG 59.995 52.381 0.00 0.00 0.00 4.79
2095 2140 2.496899 ACAATACAAGGTGCTCAGGG 57.503 50.000 0.00 0.00 0.00 4.45
2096 2141 4.081420 AGAGTACAATACAAGGTGCTCAGG 60.081 45.833 11.41 0.00 45.52 3.86
2097 2142 5.078411 AGAGTACAATACAAGGTGCTCAG 57.922 43.478 11.41 0.00 45.52 3.35
2098 2143 4.772624 AGAGAGTACAATACAAGGTGCTCA 59.227 41.667 11.41 0.00 45.52 4.26
2099 2144 5.105752 CAGAGAGTACAATACAAGGTGCTC 58.894 45.833 0.00 0.00 44.08 4.26
2100 2145 4.081420 CCAGAGAGTACAATACAAGGTGCT 60.081 45.833 0.00 0.00 32.48 4.40
2101 2146 4.184629 CCAGAGAGTACAATACAAGGTGC 58.815 47.826 0.00 0.00 0.00 5.01
2102 2147 5.186021 AGACCAGAGAGTACAATACAAGGTG 59.814 44.000 0.00 0.00 0.00 4.00
2103 2148 5.334421 AGACCAGAGAGTACAATACAAGGT 58.666 41.667 0.00 0.00 0.00 3.50
2104 2149 5.923733 AGACCAGAGAGTACAATACAAGG 57.076 43.478 0.00 0.00 0.00 3.61
2105 2150 8.608844 AAAAAGACCAGAGAGTACAATACAAG 57.391 34.615 0.00 0.00 0.00 3.16
2127 2172 8.033038 ACACAGATCTAATACGCAGAGTAAAAA 58.967 33.333 0.00 0.00 39.04 1.94
2128 2173 7.544622 ACACAGATCTAATACGCAGAGTAAAA 58.455 34.615 0.00 0.00 39.04 1.52
2129 2174 7.096884 ACACAGATCTAATACGCAGAGTAAA 57.903 36.000 0.00 0.00 39.04 2.01
2130 2175 6.694877 ACACAGATCTAATACGCAGAGTAA 57.305 37.500 0.00 0.00 39.04 2.24
2131 2176 6.694877 AACACAGATCTAATACGCAGAGTA 57.305 37.500 0.00 0.00 40.03 2.59
2132 2177 5.584253 AACACAGATCTAATACGCAGAGT 57.416 39.130 0.00 0.00 0.00 3.24
2133 2178 7.197017 ACTTAACACAGATCTAATACGCAGAG 58.803 38.462 0.00 0.00 0.00 3.35
2134 2179 7.096884 ACTTAACACAGATCTAATACGCAGA 57.903 36.000 0.00 0.00 0.00 4.26
2135 2180 6.972901 TGACTTAACACAGATCTAATACGCAG 59.027 38.462 0.00 0.00 0.00 5.18
2136 2181 6.859017 TGACTTAACACAGATCTAATACGCA 58.141 36.000 0.00 0.00 0.00 5.24
2137 2182 7.751047 TTGACTTAACACAGATCTAATACGC 57.249 36.000 0.00 0.00 0.00 4.42
2138 2183 9.135843 TGTTTGACTTAACACAGATCTAATACG 57.864 33.333 0.00 0.00 33.31 3.06
2142 2187 8.289618 GCAATGTTTGACTTAACACAGATCTAA 58.710 33.333 0.00 0.00 40.53 2.10
2143 2188 7.443879 TGCAATGTTTGACTTAACACAGATCTA 59.556 33.333 0.00 0.00 40.53 1.98
2144 2189 6.262944 TGCAATGTTTGACTTAACACAGATCT 59.737 34.615 0.00 0.00 40.53 2.75
2145 2190 6.437928 TGCAATGTTTGACTTAACACAGATC 58.562 36.000 0.00 0.00 40.53 2.75
2146 2191 6.389830 TGCAATGTTTGACTTAACACAGAT 57.610 33.333 0.00 0.00 40.53 2.90
2147 2192 5.826601 TGCAATGTTTGACTTAACACAGA 57.173 34.783 0.00 0.00 40.53 3.41
2148 2193 6.531240 ACTTTGCAATGTTTGACTTAACACAG 59.469 34.615 11.92 0.00 40.53 3.66
2149 2194 6.393990 ACTTTGCAATGTTTGACTTAACACA 58.606 32.000 11.92 0.00 40.53 3.72
2150 2195 6.885735 ACTTTGCAATGTTTGACTTAACAC 57.114 33.333 11.92 0.00 40.53 3.32
2151 2196 7.897575 AAACTTTGCAATGTTTGACTTAACA 57.102 28.000 31.27 0.69 41.81 2.41
2159 2204 9.771915 AAATTTAGTCAAACTTTGCAATGTTTG 57.228 25.926 39.20 39.20 46.71 2.93
2245 2290 8.952278 TGCCAAGTAAATATTGTTAGATTCGTT 58.048 29.630 0.00 0.00 0.00 3.85
2246 2291 8.500753 TGCCAAGTAAATATTGTTAGATTCGT 57.499 30.769 0.00 0.00 0.00 3.85
2247 2292 9.950680 AATGCCAAGTAAATATTGTTAGATTCG 57.049 29.630 0.00 0.00 0.00 3.34
2251 2296 8.465999 CCACAATGCCAAGTAAATATTGTTAGA 58.534 33.333 0.00 0.00 39.25 2.10
2252 2297 8.465999 TCCACAATGCCAAGTAAATATTGTTAG 58.534 33.333 0.00 0.00 39.25 2.34
2253 2298 8.354711 TCCACAATGCCAAGTAAATATTGTTA 57.645 30.769 0.00 0.00 39.25 2.41
2254 2299 7.238486 TCCACAATGCCAAGTAAATATTGTT 57.762 32.000 0.00 0.00 39.25 2.83
2255 2300 6.849085 TCCACAATGCCAAGTAAATATTGT 57.151 33.333 0.00 0.00 41.23 2.71
2256 2301 7.267128 ACATCCACAATGCCAAGTAAATATTG 58.733 34.615 0.00 0.00 39.12 1.90
2257 2302 7.422465 ACATCCACAATGCCAAGTAAATATT 57.578 32.000 0.00 0.00 39.12 1.28
2258 2303 7.123997 TCAACATCCACAATGCCAAGTAAATAT 59.876 33.333 0.00 0.00 39.12 1.28
2259 2304 6.435591 TCAACATCCACAATGCCAAGTAAATA 59.564 34.615 0.00 0.00 39.12 1.40
2260 2305 5.245751 TCAACATCCACAATGCCAAGTAAAT 59.754 36.000 0.00 0.00 39.12 1.40
2261 2306 4.586421 TCAACATCCACAATGCCAAGTAAA 59.414 37.500 0.00 0.00 39.12 2.01
2262 2307 4.148079 TCAACATCCACAATGCCAAGTAA 58.852 39.130 0.00 0.00 39.12 2.24
2263 2308 3.760738 TCAACATCCACAATGCCAAGTA 58.239 40.909 0.00 0.00 39.12 2.24
2264 2309 2.596346 TCAACATCCACAATGCCAAGT 58.404 42.857 0.00 0.00 39.12 3.16
2265 2310 3.880047 ATCAACATCCACAATGCCAAG 57.120 42.857 0.00 0.00 39.12 3.61
2266 2311 4.343231 AGTATCAACATCCACAATGCCAA 58.657 39.130 0.00 0.00 39.12 4.52
2267 2312 3.966979 AGTATCAACATCCACAATGCCA 58.033 40.909 0.00 0.00 39.12 4.92
2268 2313 4.989279 AAGTATCAACATCCACAATGCC 57.011 40.909 0.00 0.00 39.12 4.40
2358 2403 9.460906 CCGTCCTTTTTAGTCTACATATAAGTC 57.539 37.037 0.00 0.00 0.00 3.01
2359 2404 8.419442 CCCGTCCTTTTTAGTCTACATATAAGT 58.581 37.037 0.00 0.00 0.00 2.24
2360 2405 8.636213 TCCCGTCCTTTTTAGTCTACATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
2361 2406 8.537728 TCCCGTCCTTTTTAGTCTACATATAA 57.462 34.615 0.00 0.00 0.00 0.98
2362 2407 7.232127 CCTCCCGTCCTTTTTAGTCTACATATA 59.768 40.741 0.00 0.00 0.00 0.86
2363 2408 6.041751 CCTCCCGTCCTTTTTAGTCTACATAT 59.958 42.308 0.00 0.00 0.00 1.78
2364 2409 5.361857 CCTCCCGTCCTTTTTAGTCTACATA 59.638 44.000 0.00 0.00 0.00 2.29
2365 2410 4.161754 CCTCCCGTCCTTTTTAGTCTACAT 59.838 45.833 0.00 0.00 0.00 2.29
2366 2411 3.512724 CCTCCCGTCCTTTTTAGTCTACA 59.487 47.826 0.00 0.00 0.00 2.74
2367 2412 3.118847 CCCTCCCGTCCTTTTTAGTCTAC 60.119 52.174 0.00 0.00 0.00 2.59
2368 2413 3.102204 CCCTCCCGTCCTTTTTAGTCTA 58.898 50.000 0.00 0.00 0.00 2.59
2369 2414 1.907255 CCCTCCCGTCCTTTTTAGTCT 59.093 52.381 0.00 0.00 0.00 3.24
2370 2415 1.904537 TCCCTCCCGTCCTTTTTAGTC 59.095 52.381 0.00 0.00 0.00 2.59
2371 2416 1.907255 CTCCCTCCCGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
2372 2417 1.907255 ACTCCCTCCCGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
2373 2418 2.034436 ACTCCCTCCCGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2374 2419 1.627329 GTACTCCCTCCCGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2375 2420 1.273759 GTACTCCCTCCCGTCCTTTT 58.726 55.000 0.00 0.00 0.00 2.27
2376 2421 0.115745 TGTACTCCCTCCCGTCCTTT 59.884 55.000 0.00 0.00 0.00 3.11
2377 2422 0.115745 TTGTACTCCCTCCCGTCCTT 59.884 55.000 0.00 0.00 0.00 3.36
2378 2423 0.324460 CTTGTACTCCCTCCCGTCCT 60.324 60.000 0.00 0.00 0.00 3.85
2379 2424 1.328430 CCTTGTACTCCCTCCCGTCC 61.328 65.000 0.00 0.00 0.00 4.79
2380 2425 1.957765 GCCTTGTACTCCCTCCCGTC 61.958 65.000 0.00 0.00 0.00 4.79
2381 2426 1.988406 GCCTTGTACTCCCTCCCGT 60.988 63.158 0.00 0.00 0.00 5.28
2382 2427 2.732619 GGCCTTGTACTCCCTCCCG 61.733 68.421 0.00 0.00 0.00 5.14
2383 2428 1.307084 AGGCCTTGTACTCCCTCCC 60.307 63.158 0.00 0.00 0.00 4.30
2384 2429 0.325765 AGAGGCCTTGTACTCCCTCC 60.326 60.000 6.77 0.00 43.86 4.30
2385 2430 1.483004 GAAGAGGCCTTGTACTCCCTC 59.517 57.143 6.77 11.32 43.29 4.30
2386 2431 1.203313 TGAAGAGGCCTTGTACTCCCT 60.203 52.381 6.77 0.00 34.27 4.20
2387 2432 1.208293 CTGAAGAGGCCTTGTACTCCC 59.792 57.143 6.77 0.00 34.27 4.30
2388 2433 1.208293 CCTGAAGAGGCCTTGTACTCC 59.792 57.143 6.77 0.00 34.27 3.85
2389 2434 1.208293 CCCTGAAGAGGCCTTGTACTC 59.792 57.143 6.77 0.00 38.17 2.59
2390 2435 1.280457 CCCTGAAGAGGCCTTGTACT 58.720 55.000 6.77 0.00 38.17 2.73
2391 2436 0.984995 ACCCTGAAGAGGCCTTGTAC 59.015 55.000 6.77 0.00 38.17 2.90
2392 2437 0.984230 CACCCTGAAGAGGCCTTGTA 59.016 55.000 6.77 0.00 38.17 2.41
2393 2438 1.763770 CACCCTGAAGAGGCCTTGT 59.236 57.895 6.77 0.00 38.17 3.16
2394 2439 1.676967 GCACCCTGAAGAGGCCTTG 60.677 63.158 6.77 0.00 38.17 3.61
2395 2440 2.759795 GCACCCTGAAGAGGCCTT 59.240 61.111 6.77 0.00 38.17 4.35
2396 2441 3.334054 GGCACCCTGAAGAGGCCT 61.334 66.667 3.86 3.86 41.39 5.19
2403 2448 0.260230 TGGAAAACTGGCACCCTGAA 59.740 50.000 0.00 0.00 0.00 3.02
2422 2474 1.944177 ATCAGTAGTGTGAGCCAGGT 58.056 50.000 0.00 0.00 0.00 4.00
2431 2483 1.279271 GCCCAGGTCAATCAGTAGTGT 59.721 52.381 0.00 0.00 0.00 3.55
2498 2550 0.183492 AGTCAAGGTGAGCAAGCCAA 59.817 50.000 0.00 0.00 0.00 4.52
2518 2570 1.579932 GTCAACGCGAGAGGTCTGA 59.420 57.895 15.93 0.37 0.00 3.27
2606 2659 5.181690 TCCTGAACAGTTTTTCAAATCCG 57.818 39.130 1.18 0.00 35.07 4.18
2626 2679 7.552458 AATCCACAAACTGTTTTGAAATTCC 57.448 32.000 2.41 0.00 44.38 3.01
2670 2724 7.835634 TTTTTCAAATTGGTGTACACTTTCC 57.164 32.000 24.55 9.52 30.49 3.13
2698 2752 8.578308 TTGTGAAGTTTCTTTCAAATGCATAG 57.422 30.769 0.00 0.00 38.69 2.23
2699 2753 9.545105 AATTGTGAAGTTTCTTTCAAATGCATA 57.455 25.926 0.00 0.00 38.69 3.14
2700 2754 8.441312 AATTGTGAAGTTTCTTTCAAATGCAT 57.559 26.923 0.00 0.00 38.69 3.96


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

AutoCloner maintained by Alex Coulton.