Multiple sequence alignment - TraesCS5B01G050100

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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 TraesCS5B01G050100 chr5B 100.000 1579 0 0 755 2333 55366172 55367750 0.000000e+00 2916
1 TraesCS5B01G050100 chr5B 100.000 455 0 0 1 455 55365418 55365872 0.000000e+00 841
2 TraesCS5B01G050100 chr5D 95.442 1448 52 9 755 2196 52276983 52278422 0.000000e+00 2296
3 TraesCS5B01G050100 chr5D 97.333 450 11 1 1 450 52276521 52276969 0.000000e+00 763
4 TraesCS5B01G050100 chr7D 87.586 435 48 5 1765 2196 592567823 592567392 1.240000e-137 499
5 TraesCS5B01G050100 chr3B 87.298 433 45 8 1765 2196 482988654 482988231 9.690000e-134 486
6 TraesCS5B01G050100 chr6B 86.747 415 50 4 1765 2177 142818176 142817765 7.600000e-125 457
7 TraesCS5B01G050100 chr1A 85.912 433 55 6 1765 2196 305605035 305605462 7.600000e-125 457
8 TraesCS5B01G050100 chr5A 89.096 376 28 7 1029 1391 41419244 41419619 2.730000e-124 455
9 TraesCS5B01G050100 chr5A 83.641 434 61 8 1765 2196 674542360 674542785 1.300000e-107 399
10 TraesCS5B01G050100 chr5A 88.102 353 19 8 1397 1742 41419661 41419997 4.670000e-107 398
11 TraesCS5B01G050100 chr5A 88.966 290 22 7 755 1034 41413127 41413416 1.330000e-92 350
12 TraesCS5B01G050100 chr5A 89.855 207 21 0 190 396 41412798 41413004 1.370000e-67 267
13 TraesCS5B01G050100 chr1D 85.747 435 54 8 1765 2196 240984818 240985247 9.830000e-124 453
14 TraesCS5B01G050100 chr1D 85.484 434 56 7 1765 2196 240983239 240983667 1.640000e-121 446
15 TraesCS5B01G050100 chr1D 82.781 453 66 10 1752 2196 40807701 40807253 6.040000e-106 394
16 TraesCS5B01G050100 chr2A 96.269 134 5 0 2198 2331 387636065 387635932 1.090000e-53 220
17 TraesCS5B01G050100 chr2A 94.891 137 7 0 2195 2331 748873572 748873708 5.050000e-52 215
18 TraesCS5B01G050100 chr3D 91.241 137 12 0 2195 2331 525743033 525743169 1.100000e-43 187


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 TraesCS5B01G050100 chr5B 55365418 55367750 2332 False 1878.5 2916 100.0000 1 2333 2 chr5B.!!$F1 2332
1 TraesCS5B01G050100 chr5D 52276521 52278422 1901 False 1529.5 2296 96.3875 1 2196 2 chr5D.!!$F1 2195
2 TraesCS5B01G050100 chr5A 41419244 41419997 753 False 426.5 455 88.5990 1029 1742 2 chr5A.!!$F3 713
3 TraesCS5B01G050100 chr5A 41412798 41413416 618 False 308.5 350 89.4105 190 1034 2 chr5A.!!$F2 844
4 TraesCS5B01G050100 chr1D 240983239 240985247 2008 False 449.5 453 85.6155 1765 2196 2 chr1D.!!$F1 431

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
273 274 0.036022 AAAGCACCTGAGACTGGAGC 59.964 55.0 8.44 8.44 38.75 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1673 0.107703 CCGCATTGCCCTCAACTCTA 60.108 55.0 2.41 0.0 34.6 2.43 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.127845 TGTGTCCTTCTCTGGAATACATCTC 59.872 44.000 0.00 0.00 37.93 2.75
100 101 1.998315 CTCTTCATTGCACCGAGTCAG 59.002 52.381 0.00 0.00 0.00 3.51
110 111 0.600255 ACCGAGTCAGAAGGTTTGCG 60.600 55.000 0.00 0.00 33.96 4.85
113 114 1.656095 CGAGTCAGAAGGTTTGCGATC 59.344 52.381 0.00 0.00 0.00 3.69
216 217 9.739276 ATTTATTTATCTGTGTGTTTCAGAGGA 57.261 29.630 0.00 0.00 43.66 3.71
221 222 2.797156 CTGTGTGTTTCAGAGGACTTCG 59.203 50.000 0.00 0.00 34.34 3.79
254 255 8.028938 GGAAAGCTGCACAAATTTTCTTATCTA 58.971 33.333 1.02 0.00 0.00 1.98
273 274 0.036022 AAAGCACCTGAGACTGGAGC 59.964 55.000 8.44 8.44 38.75 4.70
314 315 4.202202 CCGAGAAGCAAGAGTGATATCCTT 60.202 45.833 0.00 0.00 0.00 3.36
373 374 5.067936 TGGAAAAGCTGGAATTTCACGTAAA 59.932 36.000 10.06 0.00 37.29 2.01
450 505 6.010850 GGAAATAAAGGGGAAACAGTCTTCT 58.989 40.000 0.00 0.00 0.00 2.85
451 506 6.493802 GGAAATAAAGGGGAAACAGTCTTCTT 59.506 38.462 0.00 0.00 0.00 2.52
452 507 7.309255 GGAAATAAAGGGGAAACAGTCTTCTTC 60.309 40.741 0.00 0.00 0.00 2.87
453 508 4.797912 AAAGGGGAAACAGTCTTCTTCT 57.202 40.909 0.00 0.00 0.00 2.85
786 841 7.989826 AGTCATGAACTAACCATTAGCAAATC 58.010 34.615 0.00 0.00 36.07 2.17
791 846 6.312918 TGAACTAACCATTAGCAAATCGAGTC 59.687 38.462 0.00 0.00 36.71 3.36
807 862 0.763035 AGTCCGTACTGTTTTGGGCT 59.237 50.000 0.00 0.00 33.57 5.19
909 966 3.809905 AGTTCTTCACTTCACCAAGTCC 58.190 45.455 0.00 0.00 41.24 3.85
976 1043 4.986659 ACTGACGATGCGTAAAAAGTAGTT 59.013 37.500 0.00 0.00 41.37 2.24
1065 1132 1.381327 CCTACGGAGCCTTCCCTCA 60.381 63.158 0.00 0.00 40.67 3.86
1122 1189 0.242825 GGTTTTACGGCTGGAAAGGC 59.757 55.000 2.51 0.94 0.00 4.35
1147 1214 2.816958 AGCTGGCGCTTCACATCG 60.817 61.111 7.64 0.00 46.47 3.84
1230 1300 2.237643 TGGTTCCGATTTTAGGCTGCTA 59.762 45.455 0.00 0.00 0.00 3.49
1236 1306 2.481952 CGATTTTAGGCTGCTAGGATGC 59.518 50.000 0.00 0.00 0.00 3.91
1237 1307 2.348411 TTTTAGGCTGCTAGGATGCC 57.652 50.000 14.15 14.15 46.42 4.40
1241 1311 3.550431 GCTGCTAGGATGCCCGGA 61.550 66.667 0.73 0.00 37.58 5.14
1271 1345 0.461339 TTTTCGGATGGCTACGAGGC 60.461 55.000 0.00 0.00 40.51 4.70
1377 1458 4.727507 ATGTATCTCTCTCACACACACC 57.272 45.455 0.00 0.00 0.00 4.16
1547 1673 4.202641 ACCACCATTCATATCTGGCATGAT 60.203 41.667 0.00 0.00 35.88 2.45
1548 1674 5.014438 ACCACCATTCATATCTGGCATGATA 59.986 40.000 0.00 8.44 35.88 2.15
1549 1675 5.589050 CCACCATTCATATCTGGCATGATAG 59.411 44.000 0.00 0.00 35.88 2.08
1550 1676 6.412214 CACCATTCATATCTGGCATGATAGA 58.588 40.000 0.00 0.00 35.88 1.98
1566 1692 0.107703 TAGAGTTGAGGGCAATGCGG 60.108 55.000 0.00 0.00 36.22 5.69
1594 1720 7.870509 TGATGATTTTCCCTTATCTGTTCAG 57.129 36.000 0.00 0.00 0.00 3.02
1638 1766 6.209391 CCATGATGAATAATTTGTAGGGACCC 59.791 42.308 0.59 0.59 0.00 4.46
1773 1901 5.722441 TGTATCACATGTACTAAGGGTTGGA 59.278 40.000 0.00 0.00 0.00 3.53
1774 1902 4.819105 TCACATGTACTAAGGGTTGGAG 57.181 45.455 0.00 0.00 0.00 3.86
1775 1903 4.422057 TCACATGTACTAAGGGTTGGAGA 58.578 43.478 0.00 0.00 0.00 3.71
1804 3509 2.103340 GCGCCGTTGGTGTTGTTT 59.897 55.556 0.00 0.00 35.34 2.83
2004 3711 6.529125 GTGGATGTTGATATTTTTGCTGTGAG 59.471 38.462 0.00 0.00 0.00 3.51
2019 3726 4.906423 GCTGTGAGCATGATCAAAGTTAG 58.094 43.478 27.47 16.04 41.89 2.34
2091 3799 5.478679 TGTGGAATATTTAGTTTGGTGGGTG 59.521 40.000 0.00 0.00 0.00 4.61
2096 3804 1.000041 TTAGTTTGGTGGGTGGGGGT 61.000 55.000 0.00 0.00 0.00 4.95
2196 3904 6.373216 TGTGCTAACCAACCTATGTTTATGTC 59.627 38.462 0.00 0.00 30.42 3.06
2197 3905 6.598064 GTGCTAACCAACCTATGTTTATGTCT 59.402 38.462 0.00 0.00 30.42 3.41
2198 3906 6.821665 TGCTAACCAACCTATGTTTATGTCTC 59.178 38.462 0.00 0.00 30.42 3.36
2199 3907 6.018994 GCTAACCAACCTATGTTTATGTCTCG 60.019 42.308 0.00 0.00 30.42 4.04
2200 3908 5.416271 ACCAACCTATGTTTATGTCTCGT 57.584 39.130 0.00 0.00 30.42 4.18
2201 3909 5.175859 ACCAACCTATGTTTATGTCTCGTG 58.824 41.667 0.00 0.00 30.42 4.35
2202 3910 4.034048 CCAACCTATGTTTATGTCTCGTGC 59.966 45.833 0.00 0.00 30.42 5.34
2203 3911 4.737855 ACCTATGTTTATGTCTCGTGCT 57.262 40.909 0.00 0.00 0.00 4.40
2204 3912 4.683832 ACCTATGTTTATGTCTCGTGCTC 58.316 43.478 0.00 0.00 0.00 4.26
2205 3913 4.402793 ACCTATGTTTATGTCTCGTGCTCT 59.597 41.667 0.00 0.00 0.00 4.09
2206 3914 5.105310 ACCTATGTTTATGTCTCGTGCTCTT 60.105 40.000 0.00 0.00 0.00 2.85
2207 3915 5.812642 CCTATGTTTATGTCTCGTGCTCTTT 59.187 40.000 0.00 0.00 0.00 2.52
2208 3916 5.786401 ATGTTTATGTCTCGTGCTCTTTC 57.214 39.130 0.00 0.00 0.00 2.62
2209 3917 4.883083 TGTTTATGTCTCGTGCTCTTTCT 58.117 39.130 0.00 0.00 0.00 2.52
2210 3918 5.297547 TGTTTATGTCTCGTGCTCTTTCTT 58.702 37.500 0.00 0.00 0.00 2.52
2211 3919 5.177511 TGTTTATGTCTCGTGCTCTTTCTTG 59.822 40.000 0.00 0.00 0.00 3.02
2212 3920 2.154854 TGTCTCGTGCTCTTTCTTGG 57.845 50.000 0.00 0.00 0.00 3.61
2213 3921 1.412710 TGTCTCGTGCTCTTTCTTGGT 59.587 47.619 0.00 0.00 0.00 3.67
2214 3922 2.062519 GTCTCGTGCTCTTTCTTGGTC 58.937 52.381 0.00 0.00 0.00 4.02
2215 3923 1.686587 TCTCGTGCTCTTTCTTGGTCA 59.313 47.619 0.00 0.00 0.00 4.02
2216 3924 2.064762 CTCGTGCTCTTTCTTGGTCAG 58.935 52.381 0.00 0.00 0.00 3.51
2217 3925 0.514691 CGTGCTCTTTCTTGGTCAGC 59.485 55.000 0.00 0.00 0.00 4.26
2218 3926 1.875576 CGTGCTCTTTCTTGGTCAGCT 60.876 52.381 0.00 0.00 0.00 4.24
2219 3927 2.610479 CGTGCTCTTTCTTGGTCAGCTA 60.610 50.000 0.00 0.00 0.00 3.32
2220 3928 2.739379 GTGCTCTTTCTTGGTCAGCTAC 59.261 50.000 0.00 0.00 0.00 3.58
2221 3929 2.634940 TGCTCTTTCTTGGTCAGCTACT 59.365 45.455 0.00 0.00 0.00 2.57
2222 3930 3.832490 TGCTCTTTCTTGGTCAGCTACTA 59.168 43.478 0.00 0.00 0.00 1.82
2223 3931 4.177783 GCTCTTTCTTGGTCAGCTACTAC 58.822 47.826 0.00 0.00 0.00 2.73
2224 3932 4.322049 GCTCTTTCTTGGTCAGCTACTACA 60.322 45.833 0.00 0.00 0.00 2.74
2225 3933 5.784177 CTCTTTCTTGGTCAGCTACTACAA 58.216 41.667 0.00 0.00 0.00 2.41
2226 3934 6.360370 TCTTTCTTGGTCAGCTACTACAAT 57.640 37.500 0.00 0.00 0.00 2.71
2227 3935 6.769512 TCTTTCTTGGTCAGCTACTACAATT 58.230 36.000 0.00 0.00 0.00 2.32
2228 3936 6.874134 TCTTTCTTGGTCAGCTACTACAATTC 59.126 38.462 0.00 0.00 0.00 2.17
2229 3937 5.086104 TCTTGGTCAGCTACTACAATTCC 57.914 43.478 0.00 0.00 0.00 3.01
2230 3938 4.777896 TCTTGGTCAGCTACTACAATTCCT 59.222 41.667 0.00 0.00 0.00 3.36
2231 3939 5.955959 TCTTGGTCAGCTACTACAATTCCTA 59.044 40.000 0.00 0.00 0.00 2.94
2232 3940 5.593679 TGGTCAGCTACTACAATTCCTAC 57.406 43.478 0.00 0.00 0.00 3.18
2233 3941 5.020795 TGGTCAGCTACTACAATTCCTACA 58.979 41.667 0.00 0.00 0.00 2.74
2234 3942 5.482526 TGGTCAGCTACTACAATTCCTACAA 59.517 40.000 0.00 0.00 0.00 2.41
2235 3943 5.811100 GGTCAGCTACTACAATTCCTACAAC 59.189 44.000 0.00 0.00 0.00 3.32
2236 3944 5.811100 GTCAGCTACTACAATTCCTACAACC 59.189 44.000 0.00 0.00 0.00 3.77
2237 3945 5.482526 TCAGCTACTACAATTCCTACAACCA 59.517 40.000 0.00 0.00 0.00 3.67
2238 3946 5.812642 CAGCTACTACAATTCCTACAACCAG 59.187 44.000 0.00 0.00 0.00 4.00
2239 3947 5.720041 AGCTACTACAATTCCTACAACCAGA 59.280 40.000 0.00 0.00 0.00 3.86
2240 3948 6.384305 AGCTACTACAATTCCTACAACCAGAT 59.616 38.462 0.00 0.00 0.00 2.90
2241 3949 7.048512 GCTACTACAATTCCTACAACCAGATT 58.951 38.462 0.00 0.00 0.00 2.40
2242 3950 7.553044 GCTACTACAATTCCTACAACCAGATTT 59.447 37.037 0.00 0.00 0.00 2.17
2243 3951 7.923414 ACTACAATTCCTACAACCAGATTTC 57.077 36.000 0.00 0.00 0.00 2.17
2244 3952 6.884836 ACTACAATTCCTACAACCAGATTTCC 59.115 38.462 0.00 0.00 0.00 3.13
2245 3953 5.016831 ACAATTCCTACAACCAGATTTCCC 58.983 41.667 0.00 0.00 0.00 3.97
2246 3954 5.222337 ACAATTCCTACAACCAGATTTCCCT 60.222 40.000 0.00 0.00 0.00 4.20
2247 3955 4.301072 TTCCTACAACCAGATTTCCCTG 57.699 45.455 0.00 0.00 0.00 4.45
2248 3956 3.256704 TCCTACAACCAGATTTCCCTGT 58.743 45.455 0.00 0.00 32.43 4.00
2249 3957 3.263425 TCCTACAACCAGATTTCCCTGTC 59.737 47.826 0.00 0.00 32.43 3.51
2250 3958 3.009033 CCTACAACCAGATTTCCCTGTCA 59.991 47.826 0.00 0.00 32.43 3.58
2251 3959 3.146104 ACAACCAGATTTCCCTGTCAG 57.854 47.619 0.00 0.00 32.43 3.51
2252 3960 2.443255 ACAACCAGATTTCCCTGTCAGT 59.557 45.455 0.00 0.00 32.43 3.41
2253 3961 2.816087 CAACCAGATTTCCCTGTCAGTG 59.184 50.000 0.00 0.00 32.43 3.66
2254 3962 1.352352 ACCAGATTTCCCTGTCAGTGG 59.648 52.381 0.00 0.62 32.43 4.00
2255 3963 1.630369 CCAGATTTCCCTGTCAGTGGA 59.370 52.381 6.08 6.08 32.43 4.02
2256 3964 2.240667 CCAGATTTCCCTGTCAGTGGAT 59.759 50.000 9.95 0.00 32.43 3.41
2257 3965 3.276857 CAGATTTCCCTGTCAGTGGATG 58.723 50.000 9.95 3.68 0.00 3.51
2258 3966 3.054875 CAGATTTCCCTGTCAGTGGATGA 60.055 47.826 9.95 4.50 34.79 2.92
2259 3967 3.588842 AGATTTCCCTGTCAGTGGATGAA 59.411 43.478 9.95 4.64 40.43 2.57
2260 3968 3.874383 TTTCCCTGTCAGTGGATGAAA 57.126 42.857 9.95 3.79 40.43 2.69
2261 3969 4.387026 TTTCCCTGTCAGTGGATGAAAT 57.613 40.909 9.95 0.00 40.43 2.17
2262 3970 3.634397 TCCCTGTCAGTGGATGAAATC 57.366 47.619 6.08 0.00 44.55 2.17
2277 3985 5.859205 ATGAAATCATCAAGGGTAAAGCC 57.141 39.130 0.00 0.00 42.54 4.35
2278 3986 4.023291 TGAAATCATCAAGGGTAAAGCCC 58.977 43.478 0.00 0.00 45.33 5.19
2279 3987 5.117772 TGAAATCATCAAGGGTAAAGCCCC 61.118 45.833 0.00 0.00 45.80 5.80
2289 3997 3.497297 GGTAAAGCCCCGTTAATGTTG 57.503 47.619 0.00 0.00 0.00 3.33
2290 3998 3.083293 GGTAAAGCCCCGTTAATGTTGA 58.917 45.455 0.00 0.00 0.00 3.18
2291 3999 3.506844 GGTAAAGCCCCGTTAATGTTGAA 59.493 43.478 0.00 0.00 0.00 2.69
2292 4000 3.653539 AAAGCCCCGTTAATGTTGAAC 57.346 42.857 0.00 0.00 0.00 3.18
2293 4001 1.541379 AGCCCCGTTAATGTTGAACC 58.459 50.000 0.00 0.00 0.00 3.62
2294 4002 0.528924 GCCCCGTTAATGTTGAACCC 59.471 55.000 0.00 0.00 0.00 4.11
2295 4003 1.912417 CCCCGTTAATGTTGAACCCA 58.088 50.000 0.00 0.00 0.00 4.51
2296 4004 1.542472 CCCCGTTAATGTTGAACCCAC 59.458 52.381 0.00 0.00 0.00 4.61
2297 4005 1.542472 CCCGTTAATGTTGAACCCACC 59.458 52.381 0.00 0.00 0.00 4.61
2298 4006 2.231529 CCGTTAATGTTGAACCCACCA 58.768 47.619 0.00 0.00 0.00 4.17
2299 4007 2.227865 CCGTTAATGTTGAACCCACCAG 59.772 50.000 0.00 0.00 0.00 4.00
2300 4008 2.227865 CGTTAATGTTGAACCCACCAGG 59.772 50.000 0.00 0.00 43.78 4.45
2301 4009 3.492337 GTTAATGTTGAACCCACCAGGA 58.508 45.455 0.00 0.00 39.89 3.86
2302 4010 2.765689 AATGTTGAACCCACCAGGAA 57.234 45.000 0.00 0.00 39.89 3.36
2303 4011 1.995376 ATGTTGAACCCACCAGGAAC 58.005 50.000 0.00 0.00 39.89 3.62
2304 4012 0.923358 TGTTGAACCCACCAGGAACT 59.077 50.000 0.00 0.00 43.88 3.01
2305 4013 1.133915 TGTTGAACCCACCAGGAACTC 60.134 52.381 0.00 0.00 34.60 3.01
2306 4014 1.133915 GTTGAACCCACCAGGAACTCA 60.134 52.381 0.00 0.00 34.60 3.41
2307 4015 1.217916 TGAACCCACCAGGAACTCAA 58.782 50.000 0.00 0.00 34.60 3.02
2308 4016 1.142870 TGAACCCACCAGGAACTCAAG 59.857 52.381 0.00 0.00 34.60 3.02
2309 4017 1.420138 GAACCCACCAGGAACTCAAGA 59.580 52.381 0.00 0.00 34.60 3.02
2310 4018 1.059913 ACCCACCAGGAACTCAAGAG 58.940 55.000 0.00 0.00 34.60 2.85
2311 4019 0.322008 CCCACCAGGAACTCAAGAGC 60.322 60.000 0.00 0.00 34.60 4.09
2312 4020 0.397941 CCACCAGGAACTCAAGAGCA 59.602 55.000 0.00 0.00 34.60 4.26
2313 4021 1.202806 CCACCAGGAACTCAAGAGCAA 60.203 52.381 0.00 0.00 34.60 3.91
2314 4022 1.876156 CACCAGGAACTCAAGAGCAAC 59.124 52.381 0.00 0.00 34.60 4.17
2315 4023 1.202818 ACCAGGAACTCAAGAGCAACC 60.203 52.381 0.00 0.00 34.60 3.77
2316 4024 1.151668 CAGGAACTCAAGAGCAACCG 58.848 55.000 0.00 0.00 34.60 4.44
2317 4025 0.603975 AGGAACTCAAGAGCAACCGC 60.604 55.000 0.00 0.00 38.99 5.68
2318 4026 0.884704 GGAACTCAAGAGCAACCGCA 60.885 55.000 0.00 0.00 42.27 5.69
2319 4027 0.514691 GAACTCAAGAGCAACCGCAG 59.485 55.000 0.00 0.00 42.27 5.18
2320 4028 1.510480 AACTCAAGAGCAACCGCAGC 61.510 55.000 0.00 0.00 42.27 5.25
2321 4029 2.669569 TCAAGAGCAACCGCAGCC 60.670 61.111 0.00 0.00 42.27 4.85
2322 4030 2.670934 CAAGAGCAACCGCAGCCT 60.671 61.111 0.00 0.00 42.27 4.58
2323 4031 1.375908 CAAGAGCAACCGCAGCCTA 60.376 57.895 0.00 0.00 42.27 3.93
2324 4032 0.955428 CAAGAGCAACCGCAGCCTAA 60.955 55.000 0.00 0.00 42.27 2.69
2325 4033 0.035056 AAGAGCAACCGCAGCCTAAT 60.035 50.000 0.00 0.00 42.27 1.73
2326 4034 0.830648 AGAGCAACCGCAGCCTAATA 59.169 50.000 0.00 0.00 42.27 0.98
2327 4035 0.938008 GAGCAACCGCAGCCTAATAC 59.062 55.000 0.00 0.00 42.27 1.89
2328 4036 0.251916 AGCAACCGCAGCCTAATACA 59.748 50.000 0.00 0.00 42.27 2.29
2329 4037 1.091537 GCAACCGCAGCCTAATACAA 58.908 50.000 0.00 0.00 38.36 2.41
2330 4038 1.676006 GCAACCGCAGCCTAATACAAT 59.324 47.619 0.00 0.00 38.36 2.71
2331 4039 2.099098 GCAACCGCAGCCTAATACAATT 59.901 45.455 0.00 0.00 38.36 2.32
2332 4040 3.792124 GCAACCGCAGCCTAATACAATTC 60.792 47.826 0.00 0.00 38.36 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.255020 AGGCACGTTATTATCAAGTTTCGTAG 59.745 38.462 0.00 0.00 0.00 3.51
100 101 0.953960 ACGGTGGATCGCAAACCTTC 60.954 55.000 0.00 0.00 0.00 3.46
110 111 3.118371 ACTGGAAATAGGAACGGTGGATC 60.118 47.826 0.00 0.00 0.00 3.36
113 114 2.781681 ACTGGAAATAGGAACGGTGG 57.218 50.000 0.00 0.00 0.00 4.61
216 217 2.416850 CAGCTTTCCTGGCAACGAAGT 61.417 52.381 0.00 0.00 39.66 3.01
221 222 1.006922 GTGCAGCTTTCCTGGCAAC 60.007 57.895 0.00 0.00 42.03 4.17
254 255 0.036022 GCTCCAGTCTCAGGTGCTTT 59.964 55.000 0.00 0.00 41.24 3.51
314 315 2.779755 TTAGAAGGCAGGCGAAATCA 57.220 45.000 0.00 0.00 0.00 2.57
786 841 1.425412 CCCAAAACAGTACGGACTCG 58.575 55.000 0.00 0.00 43.02 4.18
791 846 3.340034 TGATAAGCCCAAAACAGTACGG 58.660 45.455 0.00 0.00 0.00 4.02
807 862 9.952030 TTATTCCACAAGTACAACTGATGATAA 57.048 29.630 0.00 0.00 0.00 1.75
1065 1132 0.616964 TGAGATGCAGGTGAGGCTCT 60.617 55.000 16.72 0.00 0.00 4.09
1147 1214 2.089349 GCGCGACAGAGTTCCTCAC 61.089 63.158 12.10 0.00 32.06 3.51
1230 1300 1.201429 AAGTGAACTCCGGGCATCCT 61.201 55.000 0.00 0.00 0.00 3.24
1236 1306 2.152016 GAAAAGGAAGTGAACTCCGGG 58.848 52.381 0.00 0.00 0.00 5.73
1237 1307 1.798813 CGAAAAGGAAGTGAACTCCGG 59.201 52.381 0.00 0.00 0.00 5.14
1377 1458 1.376037 GTCTGGAGGAAGTTGCGGG 60.376 63.158 0.00 0.00 0.00 6.13
1547 1673 0.107703 CCGCATTGCCCTCAACTCTA 60.108 55.000 2.41 0.00 34.60 2.43
1548 1674 1.377725 CCGCATTGCCCTCAACTCT 60.378 57.895 2.41 0.00 34.60 3.24
1549 1675 3.056313 GCCGCATTGCCCTCAACTC 62.056 63.158 2.41 0.00 34.60 3.01
1550 1676 3.064324 GCCGCATTGCCCTCAACT 61.064 61.111 2.41 0.00 34.60 3.16
1566 1692 5.537674 ACAGATAAGGGAAAATCATCATGGC 59.462 40.000 0.00 0.00 0.00 4.40
1638 1766 3.179443 TCGCCTTAGCCTGATTAGTTG 57.821 47.619 0.00 0.00 34.57 3.16
1761 1889 1.590147 CGCGTCTCCAACCCTTAGT 59.410 57.895 0.00 0.00 0.00 2.24
1762 1890 1.810030 GCGCGTCTCCAACCCTTAG 60.810 63.158 8.43 0.00 0.00 2.18
1763 1891 1.823169 AAGCGCGTCTCCAACCCTTA 61.823 55.000 8.43 0.00 0.00 2.69
1904 3611 9.838339 AAATACCGAGATGATATTATGAATCCC 57.162 33.333 0.00 0.00 0.00 3.85
2004 3711 9.070149 GTCAAATTTCTCTAACTTTGATCATGC 57.930 33.333 0.00 0.00 39.15 4.06
2009 3716 7.394641 GGAGGGTCAAATTTCTCTAACTTTGAT 59.605 37.037 6.84 0.00 39.15 2.57
2047 3755 5.351458 CACAAGCTCCAAAATATAAAGGGC 58.649 41.667 0.00 0.00 0.00 5.19
2091 3799 2.683768 ACTCACTCTATCATCACCCCC 58.316 52.381 0.00 0.00 0.00 5.40
2196 3904 2.064762 CTGACCAAGAAAGAGCACGAG 58.935 52.381 0.00 0.00 0.00 4.18
2197 3905 1.873903 GCTGACCAAGAAAGAGCACGA 60.874 52.381 0.00 0.00 0.00 4.35
2198 3906 0.514691 GCTGACCAAGAAAGAGCACG 59.485 55.000 0.00 0.00 0.00 5.34
2199 3907 1.889545 AGCTGACCAAGAAAGAGCAC 58.110 50.000 0.00 0.00 31.80 4.40
2200 3908 2.634940 AGTAGCTGACCAAGAAAGAGCA 59.365 45.455 0.00 0.00 31.80 4.26
2201 3909 3.326836 AGTAGCTGACCAAGAAAGAGC 57.673 47.619 0.00 0.00 0.00 4.09
2202 3910 5.392767 TGTAGTAGCTGACCAAGAAAGAG 57.607 43.478 0.00 0.00 0.00 2.85
2203 3911 5.801531 TTGTAGTAGCTGACCAAGAAAGA 57.198 39.130 0.00 0.00 0.00 2.52
2204 3912 6.092807 GGAATTGTAGTAGCTGACCAAGAAAG 59.907 42.308 0.00 0.00 0.00 2.62
2205 3913 5.938125 GGAATTGTAGTAGCTGACCAAGAAA 59.062 40.000 0.00 0.00 0.00 2.52
2206 3914 5.248477 AGGAATTGTAGTAGCTGACCAAGAA 59.752 40.000 0.00 0.00 0.00 2.52
2207 3915 4.777896 AGGAATTGTAGTAGCTGACCAAGA 59.222 41.667 0.00 0.00 0.00 3.02
2208 3916 5.091261 AGGAATTGTAGTAGCTGACCAAG 57.909 43.478 0.00 0.00 0.00 3.61
2209 3917 5.482526 TGTAGGAATTGTAGTAGCTGACCAA 59.517 40.000 0.00 0.00 0.00 3.67
2210 3918 5.020795 TGTAGGAATTGTAGTAGCTGACCA 58.979 41.667 0.00 0.00 0.00 4.02
2211 3919 5.593679 TGTAGGAATTGTAGTAGCTGACC 57.406 43.478 0.00 0.00 0.00 4.02
2212 3920 5.811100 GGTTGTAGGAATTGTAGTAGCTGAC 59.189 44.000 0.00 0.00 0.00 3.51
2213 3921 5.482526 TGGTTGTAGGAATTGTAGTAGCTGA 59.517 40.000 0.00 0.00 0.00 4.26
2214 3922 5.730550 TGGTTGTAGGAATTGTAGTAGCTG 58.269 41.667 0.00 0.00 0.00 4.24
2215 3923 5.720041 TCTGGTTGTAGGAATTGTAGTAGCT 59.280 40.000 0.00 0.00 0.00 3.32
2216 3924 5.974108 TCTGGTTGTAGGAATTGTAGTAGC 58.026 41.667 0.00 0.00 0.00 3.58
2217 3925 9.099454 GAAATCTGGTTGTAGGAATTGTAGTAG 57.901 37.037 0.00 0.00 0.00 2.57
2218 3926 8.044908 GGAAATCTGGTTGTAGGAATTGTAGTA 58.955 37.037 0.00 0.00 0.00 1.82
2219 3927 6.884836 GGAAATCTGGTTGTAGGAATTGTAGT 59.115 38.462 0.00 0.00 0.00 2.73
2220 3928 6.318900 GGGAAATCTGGTTGTAGGAATTGTAG 59.681 42.308 0.00 0.00 0.00 2.74
2221 3929 6.011981 AGGGAAATCTGGTTGTAGGAATTGTA 60.012 38.462 0.00 0.00 0.00 2.41
2222 3930 5.016831 GGGAAATCTGGTTGTAGGAATTGT 58.983 41.667 0.00 0.00 0.00 2.71
2223 3931 5.126061 CAGGGAAATCTGGTTGTAGGAATTG 59.874 44.000 0.00 0.00 0.00 2.32
2224 3932 5.222337 ACAGGGAAATCTGGTTGTAGGAATT 60.222 40.000 0.00 0.00 38.98 2.17
2225 3933 4.292306 ACAGGGAAATCTGGTTGTAGGAAT 59.708 41.667 0.00 0.00 38.98 3.01
2226 3934 3.655777 ACAGGGAAATCTGGTTGTAGGAA 59.344 43.478 0.00 0.00 38.98 3.36
2227 3935 3.256704 ACAGGGAAATCTGGTTGTAGGA 58.743 45.455 0.00 0.00 38.98 2.94
2228 3936 3.009033 TGACAGGGAAATCTGGTTGTAGG 59.991 47.826 0.00 0.00 38.98 3.18
2229 3937 4.256920 CTGACAGGGAAATCTGGTTGTAG 58.743 47.826 0.00 0.00 38.98 2.74
2230 3938 3.650942 ACTGACAGGGAAATCTGGTTGTA 59.349 43.478 7.51 0.00 38.98 2.41
2231 3939 2.443255 ACTGACAGGGAAATCTGGTTGT 59.557 45.455 7.51 0.00 38.98 3.32
2232 3940 2.816087 CACTGACAGGGAAATCTGGTTG 59.184 50.000 7.51 0.00 38.98 3.77
2233 3941 2.224867 CCACTGACAGGGAAATCTGGTT 60.225 50.000 6.19 0.00 38.98 3.67
2234 3942 1.352352 CCACTGACAGGGAAATCTGGT 59.648 52.381 6.19 0.00 38.98 4.00
2235 3943 1.630369 TCCACTGACAGGGAAATCTGG 59.370 52.381 6.19 2.86 38.98 3.86
2236 3944 3.054875 TCATCCACTGACAGGGAAATCTG 60.055 47.826 6.19 5.77 36.62 2.90
2237 3945 3.184628 TCATCCACTGACAGGGAAATCT 58.815 45.455 6.19 0.00 36.62 2.40
2238 3946 3.634397 TCATCCACTGACAGGGAAATC 57.366 47.619 6.19 0.00 36.62 2.17
2239 3947 4.387026 TTTCATCCACTGACAGGGAAAT 57.613 40.909 6.19 0.00 36.62 2.17
2240 3948 3.874383 TTTCATCCACTGACAGGGAAA 57.126 42.857 6.19 5.50 36.62 3.13
2241 3949 3.330405 TGATTTCATCCACTGACAGGGAA 59.670 43.478 6.19 0.00 36.62 3.97
2242 3950 2.912295 TGATTTCATCCACTGACAGGGA 59.088 45.455 6.19 10.54 37.64 4.20
2243 3951 3.354948 TGATTTCATCCACTGACAGGG 57.645 47.619 7.51 1.67 32.17 4.45
2255 3963 5.859205 GGCTTTACCCTTGATGATTTCAT 57.141 39.130 0.00 0.00 39.70 2.57
2269 3977 3.083293 TCAACATTAACGGGGCTTTACC 58.917 45.455 0.00 0.00 37.93 2.85
2270 3978 4.478699 GTTCAACATTAACGGGGCTTTAC 58.521 43.478 0.00 0.00 0.00 2.01
2271 3979 3.506844 GGTTCAACATTAACGGGGCTTTA 59.493 43.478 0.00 0.00 0.00 1.85
2272 3980 2.297880 GGTTCAACATTAACGGGGCTTT 59.702 45.455 0.00 0.00 0.00 3.51
2273 3981 1.890489 GGTTCAACATTAACGGGGCTT 59.110 47.619 0.00 0.00 0.00 4.35
2274 3982 1.541379 GGTTCAACATTAACGGGGCT 58.459 50.000 0.00 0.00 0.00 5.19
2275 3983 0.528924 GGGTTCAACATTAACGGGGC 59.471 55.000 0.00 0.00 0.00 5.80
2276 3984 1.542472 GTGGGTTCAACATTAACGGGG 59.458 52.381 0.00 0.00 0.00 5.73
2277 3985 1.542472 GGTGGGTTCAACATTAACGGG 59.458 52.381 0.00 0.00 0.00 5.28
2278 3986 2.227865 CTGGTGGGTTCAACATTAACGG 59.772 50.000 0.00 0.00 40.22 4.44
2279 3987 2.227865 CCTGGTGGGTTCAACATTAACG 59.772 50.000 0.00 0.00 40.22 3.18
2280 3988 3.492337 TCCTGGTGGGTTCAACATTAAC 58.508 45.455 0.00 0.00 40.22 2.01
2281 3989 3.885976 TCCTGGTGGGTTCAACATTAA 57.114 42.857 0.00 0.00 40.22 1.40
2282 3990 3.139397 AGTTCCTGGTGGGTTCAACATTA 59.861 43.478 0.00 0.00 40.22 1.90
2283 3991 2.091333 AGTTCCTGGTGGGTTCAACATT 60.091 45.455 0.00 0.00 40.22 2.71
2284 3992 1.499007 AGTTCCTGGTGGGTTCAACAT 59.501 47.619 0.00 0.00 40.22 2.71
2285 3993 0.923358 AGTTCCTGGTGGGTTCAACA 59.077 50.000 0.00 0.00 38.45 3.33
2286 3994 1.133915 TGAGTTCCTGGTGGGTTCAAC 60.134 52.381 0.00 0.00 36.25 3.18
2287 3995 1.217916 TGAGTTCCTGGTGGGTTCAA 58.782 50.000 0.00 0.00 36.25 2.69
2288 3996 1.142870 CTTGAGTTCCTGGTGGGTTCA 59.857 52.381 0.00 0.00 36.25 3.18
2289 3997 1.420138 TCTTGAGTTCCTGGTGGGTTC 59.580 52.381 0.00 0.00 36.25 3.62
2290 3998 1.421646 CTCTTGAGTTCCTGGTGGGTT 59.578 52.381 0.00 0.00 36.25 4.11
2291 3999 1.059913 CTCTTGAGTTCCTGGTGGGT 58.940 55.000 0.00 0.00 36.25 4.51
2292 4000 0.322008 GCTCTTGAGTTCCTGGTGGG 60.322 60.000 0.00 0.00 0.00 4.61
2293 4001 0.397941 TGCTCTTGAGTTCCTGGTGG 59.602 55.000 0.00 0.00 0.00 4.61
2294 4002 1.876156 GTTGCTCTTGAGTTCCTGGTG 59.124 52.381 0.00 0.00 0.00 4.17
2295 4003 1.202818 GGTTGCTCTTGAGTTCCTGGT 60.203 52.381 0.00 0.00 0.00 4.00
2296 4004 1.528129 GGTTGCTCTTGAGTTCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
2297 4005 1.151668 CGGTTGCTCTTGAGTTCCTG 58.848 55.000 0.00 0.00 0.00 3.86
2298 4006 0.603975 GCGGTTGCTCTTGAGTTCCT 60.604 55.000 0.00 0.00 38.39 3.36
2299 4007 0.884704 TGCGGTTGCTCTTGAGTTCC 60.885 55.000 0.00 0.10 43.34 3.62
2300 4008 0.514691 CTGCGGTTGCTCTTGAGTTC 59.485 55.000 0.00 0.00 43.34 3.01
2301 4009 1.510480 GCTGCGGTTGCTCTTGAGTT 61.510 55.000 0.00 0.00 43.34 3.01
2302 4010 1.963338 GCTGCGGTTGCTCTTGAGT 60.963 57.895 0.00 0.00 43.34 3.41
2303 4011 2.684843 GGCTGCGGTTGCTCTTGAG 61.685 63.158 0.00 0.00 43.34 3.02
2304 4012 1.826340 TAGGCTGCGGTTGCTCTTGA 61.826 55.000 0.00 0.00 43.34 3.02
2305 4013 0.955428 TTAGGCTGCGGTTGCTCTTG 60.955 55.000 0.00 0.00 43.34 3.02
2306 4014 0.035056 ATTAGGCTGCGGTTGCTCTT 60.035 50.000 0.00 0.00 43.34 2.85
2307 4015 0.830648 TATTAGGCTGCGGTTGCTCT 59.169 50.000 0.00 0.00 43.34 4.09
2308 4016 0.938008 GTATTAGGCTGCGGTTGCTC 59.062 55.000 0.00 0.00 43.34 4.26
2309 4017 0.251916 TGTATTAGGCTGCGGTTGCT 59.748 50.000 0.00 0.00 43.34 3.91
2310 4018 1.091537 TTGTATTAGGCTGCGGTTGC 58.908 50.000 0.00 0.00 43.20 4.17
2311 4019 3.952535 GAATTGTATTAGGCTGCGGTTG 58.047 45.455 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.