Multiple sequence alignment - TraesCS1B01G170000

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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 TraesCS1B01G170000 chr1B 100.000 2981 0 0 1 2981 301567964 301564984 0.000000e+00 5505.0
1 TraesCS1B01G170000 chr1B 88.525 183 21 0 2211 2393 551496087 551496269 3.870000e-54 222.0
2 TraesCS1B01G170000 chr1D 94.739 2205 97 12 1 2201 205765449 205763260 0.000000e+00 3411.0
3 TraesCS1B01G170000 chr1D 93.178 557 35 2 2427 2981 205761128 205760573 0.000000e+00 815.0
4 TraesCS1B01G170000 chr1D 93.056 72 3 2 2912 2981 42287584 42287513 1.460000e-18 104.0
5 TraesCS1B01G170000 chr1A 96.169 1540 53 3 664 2201 262289764 262291299 0.000000e+00 2512.0
6 TraesCS1B01G170000 chr1A 92.000 500 40 0 2427 2926 262296322 262296821 0.000000e+00 702.0
7 TraesCS1B01G170000 chr1A 92.667 450 27 6 174 622 262284594 262285038 0.000000e+00 643.0
8 TraesCS1B01G170000 chr5B 90.164 183 18 0 2211 2393 257022845 257023027 3.840000e-59 239.0
9 TraesCS1B01G170000 chr2A 90.164 183 18 0 2211 2393 158882263 158882445 3.840000e-59 239.0
10 TraesCS1B01G170000 chr2A 92.063 63 3 1 341 401 707110802 707110740 1.470000e-13 87.9
11 TraesCS1B01G170000 chr7A 89.617 183 19 0 2211 2393 708775546 708775728 1.790000e-57 233.0
12 TraesCS1B01G170000 chr7A 88.525 183 20 1 2211 2393 64598818 64598999 1.390000e-53 220.0
13 TraesCS1B01G170000 chr3D 89.071 183 20 0 2211 2393 436020083 436020265 8.310000e-56 228.0
14 TraesCS1B01G170000 chr3A 88.587 184 20 1 2211 2393 212744072 212743889 3.870000e-54 222.0
15 TraesCS1B01G170000 chr3A 81.707 164 20 7 2828 2981 709500094 709499931 8.670000e-26 128.0
16 TraesCS1B01G170000 chr2D 87.978 183 22 0 2211 2393 128025778 128025960 1.800000e-52 217.0
17 TraesCS1B01G170000 chr2D 88.235 187 14 7 2211 2393 311550186 311550368 1.800000e-52 217.0
18 TraesCS1B01G170000 chr2D 91.667 72 4 2 2912 2981 73581043 73580972 6.800000e-17 99.0
19 TraesCS1B01G170000 chr6A 79.710 207 38 2 2430 2632 60016268 60016062 2.390000e-31 147.0
20 TraesCS1B01G170000 chr4D 95.312 64 1 2 2917 2978 235509025 235509088 1.890000e-17 100.0
21 TraesCS1B01G170000 chr4B 91.667 72 4 2 2912 2981 638008046 638007975 6.800000e-17 99.0
22 TraesCS1B01G170000 chr6B 86.364 88 10 2 2828 2913 14254289 14254376 8.800000e-16 95.3
23 TraesCS1B01G170000 chr6B 89.189 74 6 1 2909 2980 22713418 22713491 1.140000e-14 91.6
24 TraesCS1B01G170000 chr6D 88.000 75 7 2 2909 2981 392614539 392614613 1.470000e-13 87.9
25 TraesCS1B01G170000 chr4A 88.889 72 5 2 2912 2981 609081937 609081867 5.290000e-13 86.1


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 TraesCS1B01G170000 chr1B 301564984 301567964 2980 True 5505 5505 100.0000 1 2981 1 chr1B.!!$R1 2980
1 TraesCS1B01G170000 chr1D 205760573 205765449 4876 True 2113 3411 93.9585 1 2981 2 chr1D.!!$R2 2980
2 TraesCS1B01G170000 chr1A 262289764 262291299 1535 False 2512 2512 96.1690 664 2201 1 chr1A.!!$F2 1537

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
838 842 0.459759 GTTCCGTCGTCTCCAATCCC 60.46 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 3879 0.106894 GATAAACTGGGGAGGAGGCG 59.893 60.0 0.0 0.0 0.0 5.52 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.647636 AGGATGTGTGTCTATGTAGCCT 58.352 45.455 0.00 0.00 0.00 4.58
49 50 4.804597 AGGATGTGTGTCTATGTAGCCTA 58.195 43.478 0.00 0.00 0.00 3.93
75 77 2.288213 TGCACACGGTTCAAAAACACAA 60.288 40.909 0.00 0.00 37.10 3.33
125 127 3.640592 TGCAAAATGTGTGTGCATGTAG 58.359 40.909 0.00 0.00 43.09 2.74
138 140 4.883006 TGTGCATGTAGTGTATCATTGCAT 59.117 37.500 0.00 0.00 34.03 3.96
140 142 6.711645 TGTGCATGTAGTGTATCATTGCATAT 59.288 34.615 0.00 0.00 34.03 1.78
189 191 4.919774 TCCCTATACAGAGGTTTTGCAA 57.080 40.909 0.00 0.00 34.45 4.08
196 198 9.736023 CCTATACAGAGGTTTTGCAAAAATATC 57.264 33.333 25.40 20.93 0.00 1.63
197 199 9.438291 CTATACAGAGGTTTTGCAAAAATATCG 57.562 33.333 25.40 16.03 0.00 2.92
199 201 4.864247 CAGAGGTTTTGCAAAAATATCGGG 59.136 41.667 25.40 15.67 0.00 5.14
201 203 3.055458 AGGTTTTGCAAAAATATCGGGGG 60.055 43.478 25.40 0.00 0.00 5.40
202 204 3.307129 GGTTTTGCAAAAATATCGGGGGT 60.307 43.478 25.40 0.00 0.00 4.95
203 205 3.601443 TTTGCAAAAATATCGGGGGTG 57.399 42.857 10.02 0.00 0.00 4.61
228 230 1.328680 GAAGCATATCACTGCACACGG 59.671 52.381 0.00 0.00 44.77 4.94
236 238 2.020720 TCACTGCACACGGTTTCAAAT 58.979 42.857 0.00 0.00 31.05 2.32
271 273 5.826586 TGTGATTTCTTGCACACGTTTTAT 58.173 33.333 0.00 0.00 39.86 1.40
319 321 3.121025 GCCATCGCAAGCAGTTTAAAAAC 60.121 43.478 0.00 0.00 35.53 2.43
325 328 4.445351 GCAAGCAGTTTAAAAACGCAATC 58.555 39.130 17.88 7.79 43.51 2.67
326 329 4.676955 CAAGCAGTTTAAAAACGCAATCG 58.323 39.130 17.88 0.00 43.51 3.34
350 353 4.142600 TGTGTGATGTCTGATACGTCTCAG 60.143 45.833 21.48 21.48 44.25 3.35
462 465 6.484364 AACATATTAAGCCAATTCCAAGGG 57.516 37.500 0.00 0.00 0.00 3.95
515 519 5.123979 GGCTTTGAATATTCTCAAACGGACT 59.876 40.000 16.24 0.00 39.74 3.85
622 626 1.134220 GGAGGCGGACCATAAACATGA 60.134 52.381 0.00 0.00 39.06 3.07
637 641 5.520748 AAACATGAACTCTATTGGTCCCT 57.479 39.130 0.00 0.00 0.00 4.20
639 643 4.104086 ACATGAACTCTATTGGTCCCTGA 58.896 43.478 0.00 0.00 0.00 3.86
749 753 2.789208 CGTTGCTTAGTGGATGCAATG 58.211 47.619 0.00 0.00 46.43 2.82
838 842 0.459759 GTTCCGTCGTCTCCAATCCC 60.460 60.000 0.00 0.00 0.00 3.85
1044 1049 1.672030 CAAGCCCACTCATGCACGA 60.672 57.895 0.00 0.00 0.00 4.35
1466 1471 0.878523 CTGCCAAGAACGGACGAACA 60.879 55.000 0.00 0.00 0.00 3.18
1590 1595 1.781025 CGGTGCTCAACTTCGCCAAA 61.781 55.000 0.00 0.00 33.28 3.28
1655 1660 1.584742 GCGTACGGTTCTACGAGGC 60.585 63.158 18.39 0.00 41.75 4.70
1924 1929 1.795768 TGAGATGCAGGACGTGAAAC 58.204 50.000 0.00 0.00 0.00 2.78
1927 1932 0.798776 GATGCAGGACGTGAAACAGG 59.201 55.000 0.00 0.00 35.74 4.00
1950 1955 5.391097 GGAGATCGAATCGAAGATGACGTAT 60.391 44.000 10.12 0.00 45.12 3.06
1962 1967 3.859961 AGATGACGTATCTGCGTTTCAAG 59.140 43.478 6.70 0.00 44.46 3.02
1973 1978 5.510671 TCTGCGTTTCAAGAAACATTCTTC 58.489 37.500 21.48 7.09 46.62 2.87
2012 2017 0.747255 ATAGATCTCGCAACACGCCT 59.253 50.000 0.00 0.00 43.23 5.52
2035 2040 3.378427 GGCTAGGATTCCATGACAAACAC 59.622 47.826 5.29 0.00 0.00 3.32
2074 2079 1.118033 CGCGTACATGACATACGGTC 58.882 55.000 14.06 0.00 44.40 4.79
2195 2200 5.633601 CGTTACATCATACTTCACACACAGT 59.366 40.000 0.00 0.00 0.00 3.55
2242 3888 1.763968 AAAAATAAGCCGCCTCCTCC 58.236 50.000 0.00 0.00 0.00 4.30
2243 3889 0.106669 AAAATAAGCCGCCTCCTCCC 60.107 55.000 0.00 0.00 0.00 4.30
2249 3895 3.330720 CCGCCTCCTCCCCAGTTT 61.331 66.667 0.00 0.00 0.00 2.66
2250 3896 1.993391 CCGCCTCCTCCCCAGTTTA 60.993 63.158 0.00 0.00 0.00 2.01
2253 3899 0.474614 GCCTCCTCCCCAGTTTATCC 59.525 60.000 0.00 0.00 0.00 2.59
2254 3900 0.759346 CCTCCTCCCCAGTTTATCCG 59.241 60.000 0.00 0.00 0.00 4.18
2255 3901 1.691482 CCTCCTCCCCAGTTTATCCGA 60.691 57.143 0.00 0.00 0.00 4.55
2258 3904 3.901844 CTCCTCCCCAGTTTATCCGATAA 59.098 47.826 0.00 0.00 0.00 1.75
2259 3905 3.901844 TCCTCCCCAGTTTATCCGATAAG 59.098 47.826 1.21 0.00 0.00 1.73
2260 3906 3.557264 CCTCCCCAGTTTATCCGATAAGC 60.557 52.174 6.84 6.84 0.00 3.09
2261 3907 2.370849 TCCCCAGTTTATCCGATAAGCC 59.629 50.000 10.44 2.68 0.00 4.35
2263 3909 3.139077 CCCAGTTTATCCGATAAGCCAC 58.861 50.000 10.44 3.19 0.00 5.01
2264 3910 3.139077 CCAGTTTATCCGATAAGCCACC 58.861 50.000 10.44 0.00 0.00 4.61
2265 3911 3.181454 CCAGTTTATCCGATAAGCCACCT 60.181 47.826 10.44 0.00 0.00 4.00
2266 3912 4.058817 CAGTTTATCCGATAAGCCACCTC 58.941 47.826 10.44 0.00 0.00 3.85
2268 3914 4.039366 AGTTTATCCGATAAGCCACCTCTC 59.961 45.833 10.44 0.00 0.00 3.20
2270 3916 2.160721 TCCGATAAGCCACCTCTCTT 57.839 50.000 0.00 0.00 0.00 2.85
2271 3917 3.308035 TCCGATAAGCCACCTCTCTTA 57.692 47.619 0.00 0.00 0.00 2.10
2272 3918 3.845860 TCCGATAAGCCACCTCTCTTAT 58.154 45.455 0.00 0.00 37.98 1.73
2274 3920 5.391256 TCCGATAAGCCACCTCTCTTATTA 58.609 41.667 0.00 0.00 36.09 0.98
2275 3921 5.836898 TCCGATAAGCCACCTCTCTTATTAA 59.163 40.000 0.00 0.00 36.09 1.40
2276 3922 6.497259 TCCGATAAGCCACCTCTCTTATTAAT 59.503 38.462 0.00 0.00 36.09 1.40
2277 3923 7.016268 TCCGATAAGCCACCTCTCTTATTAATT 59.984 37.037 0.00 0.00 36.09 1.40
2278 3924 7.118390 CCGATAAGCCACCTCTCTTATTAATTG 59.882 40.741 0.00 0.00 36.09 2.32
2279 3925 7.118390 CGATAAGCCACCTCTCTTATTAATTGG 59.882 40.741 0.00 0.00 36.09 3.16
2280 3926 5.053978 AGCCACCTCTCTTATTAATTGGG 57.946 43.478 0.00 0.00 0.00 4.12
2281 3927 4.141158 AGCCACCTCTCTTATTAATTGGGG 60.141 45.833 0.00 0.00 0.00 4.96
2282 3928 4.145052 CCACCTCTCTTATTAATTGGGGC 58.855 47.826 0.00 0.00 0.00 5.80
2283 3929 4.141158 CCACCTCTCTTATTAATTGGGGCT 60.141 45.833 0.00 0.00 0.00 5.19
2284 3930 5.449553 CACCTCTCTTATTAATTGGGGCTT 58.550 41.667 0.00 0.00 0.00 4.35
2285 3931 5.532779 CACCTCTCTTATTAATTGGGGCTTC 59.467 44.000 0.00 0.00 0.00 3.86
2286 3932 5.433381 ACCTCTCTTATTAATTGGGGCTTCT 59.567 40.000 0.00 0.00 0.00 2.85
2287 3933 6.619852 ACCTCTCTTATTAATTGGGGCTTCTA 59.380 38.462 0.00 0.00 0.00 2.10
2288 3934 7.128883 ACCTCTCTTATTAATTGGGGCTTCTAA 59.871 37.037 0.00 0.00 0.00 2.10
2289 3935 7.998964 CCTCTCTTATTAATTGGGGCTTCTAAA 59.001 37.037 0.00 0.00 0.00 1.85
2290 3936 8.747538 TCTCTTATTAATTGGGGCTTCTAAAC 57.252 34.615 0.00 0.00 0.00 2.01
2291 3937 8.557450 TCTCTTATTAATTGGGGCTTCTAAACT 58.443 33.333 0.00 0.00 0.00 2.66
2292 3938 9.847224 CTCTTATTAATTGGGGCTTCTAAACTA 57.153 33.333 0.00 0.00 0.00 2.24
2293 3939 9.847224 TCTTATTAATTGGGGCTTCTAAACTAG 57.153 33.333 0.00 0.00 0.00 2.57
2294 3940 9.628500 CTTATTAATTGGGGCTTCTAAACTAGT 57.372 33.333 0.00 0.00 0.00 2.57
2300 3946 6.742559 TGGGGCTTCTAAACTAGTTATAGG 57.257 41.667 8.92 0.00 32.90 2.57
2301 3947 6.446451 TGGGGCTTCTAAACTAGTTATAGGA 58.554 40.000 8.92 7.02 32.90 2.94
2302 3948 7.080353 TGGGGCTTCTAAACTAGTTATAGGAT 58.920 38.462 8.92 0.00 32.90 3.24
2304 3950 9.097946 GGGGCTTCTAAACTAGTTATAGGATAA 57.902 37.037 8.92 3.80 32.90 1.75
2305 3951 9.926158 GGGCTTCTAAACTAGTTATAGGATAAC 57.074 37.037 8.92 1.82 32.90 1.89
2340 3986 8.546597 AATTTTAACAAATTTTATGAGCGGCT 57.453 26.923 0.00 0.00 39.19 5.52
2341 3987 7.954788 TTTTAACAAATTTTATGAGCGGCTT 57.045 28.000 2.97 0.00 0.00 4.35
2343 3989 9.477484 TTTTAACAAATTTTATGAGCGGCTTAA 57.523 25.926 2.97 0.00 0.00 1.85
2344 3990 9.646427 TTTAACAAATTTTATGAGCGGCTTAAT 57.354 25.926 2.97 4.10 0.00 1.40
2346 3992 8.546597 AACAAATTTTATGAGCGGCTTAATTT 57.453 26.923 2.97 8.90 0.00 1.82
2348 3994 8.998377 ACAAATTTTATGAGCGGCTTAATTTTT 58.002 25.926 2.97 3.25 0.00 1.94
2352 3998 7.749539 TTTATGAGCGGCTTAATTTTTAAGC 57.250 32.000 19.02 19.02 46.64 3.09
2355 4001 6.503589 TGAGCGGCTTAATTTTTAAGCTAA 57.496 33.333 23.68 8.99 46.58 3.09
2356 4002 6.551736 TGAGCGGCTTAATTTTTAAGCTAAG 58.448 36.000 23.68 17.91 46.58 2.18
2357 4003 6.373216 TGAGCGGCTTAATTTTTAAGCTAAGA 59.627 34.615 23.68 8.57 46.58 2.10
2358 4004 7.094549 TGAGCGGCTTAATTTTTAAGCTAAGAA 60.095 33.333 23.68 10.52 46.58 2.52
2360 4006 7.120726 AGCGGCTTAATTTTTAAGCTAAGAAGA 59.879 33.333 23.68 0.00 46.58 2.87
2361 4007 7.429630 GCGGCTTAATTTTTAAGCTAAGAAGAG 59.570 37.037 23.68 11.27 46.58 2.85
2363 4009 9.776158 GGCTTAATTTTTAAGCTAAGAAGAGAC 57.224 33.333 23.68 6.80 46.58 3.36
2392 4057 2.804697 TTTAAGCCGCCCAAAAGAAC 57.195 45.000 0.00 0.00 0.00 3.01
2394 4059 1.917872 TAAGCCGCCCAAAAGAACAT 58.082 45.000 0.00 0.00 0.00 2.71
2396 4061 1.154035 GCCGCCCAAAAGAACATCG 60.154 57.895 0.00 0.00 0.00 3.84
2398 4063 0.168128 CCGCCCAAAAGAACATCGTC 59.832 55.000 0.00 0.00 0.00 4.20
2399 4064 0.871722 CGCCCAAAAGAACATCGTCA 59.128 50.000 0.00 0.00 0.00 4.35
2400 4065 1.135972 CGCCCAAAAGAACATCGTCAG 60.136 52.381 0.00 0.00 0.00 3.51
2401 4066 2.151202 GCCCAAAAGAACATCGTCAGA 58.849 47.619 0.00 0.00 0.00 3.27
2403 4068 2.484264 CCCAAAAGAACATCGTCAGACC 59.516 50.000 0.00 0.00 0.00 3.85
2404 4069 3.403038 CCAAAAGAACATCGTCAGACCT 58.597 45.455 0.00 0.00 0.00 3.85
2406 4071 5.178797 CCAAAAGAACATCGTCAGACCTAT 58.821 41.667 0.00 0.00 0.00 2.57
2407 4072 5.643777 CCAAAAGAACATCGTCAGACCTATT 59.356 40.000 0.00 0.00 0.00 1.73
2408 4073 6.816640 CCAAAAGAACATCGTCAGACCTATTA 59.183 38.462 0.00 0.00 0.00 0.98
2409 4074 7.495934 CCAAAAGAACATCGTCAGACCTATTAT 59.504 37.037 0.00 0.00 0.00 1.28
2410 4075 8.543774 CAAAAGAACATCGTCAGACCTATTATC 58.456 37.037 0.00 0.00 0.00 1.75
2411 4076 7.589958 AAGAACATCGTCAGACCTATTATCT 57.410 36.000 0.00 0.00 0.00 1.98
2475 4386 5.359576 TGGCAAGCCGATTAATTTTAGACAT 59.640 36.000 6.60 0.00 39.42 3.06
2503 4414 5.839517 AATTATGGAGCAGCCTAGAGATT 57.160 39.130 0.00 0.00 37.63 2.40
2506 4417 2.315176 TGGAGCAGCCTAGAGATTCTC 58.685 52.381 5.49 5.49 37.63 2.87
2535 4446 2.278857 CGGATCAACGAGAGGCGG 60.279 66.667 0.00 0.00 46.49 6.13
2556 4467 5.815740 GCGGTCTATCAAGGTTCTTATTTGA 59.184 40.000 0.00 0.00 35.52 2.69
2557 4468 6.238130 GCGGTCTATCAAGGTTCTTATTTGAC 60.238 42.308 0.00 0.00 34.04 3.18
2558 4469 6.816640 CGGTCTATCAAGGTTCTTATTTGACA 59.183 38.462 0.00 0.00 34.04 3.58
2567 4478 5.833131 AGGTTCTTATTTGACAGGAAAGCAA 59.167 36.000 0.00 0.00 0.00 3.91
2632 4543 3.924686 GTGTGATACCGATATAAAGCCCG 59.075 47.826 0.00 0.00 0.00 6.13
2637 4548 1.000938 ACCGATATAAAGCCCGACGAC 60.001 52.381 0.00 0.00 0.00 4.34
2640 4551 2.059541 GATATAAAGCCCGACGACTGC 58.940 52.381 0.00 0.00 0.00 4.40
2673 4584 2.946329 TCATTAACACTTGCACACCGTT 59.054 40.909 0.00 0.00 0.00 4.44
2684 4595 2.952978 TGCACACCGTTCAATAAAACCT 59.047 40.909 0.00 0.00 0.00 3.50
2709 4620 7.552459 TCATGAAAAGATGATGACATTGCAAT 58.448 30.769 5.99 5.99 36.82 3.56
2743 4654 2.200373 ACAACCCTCATGTTAGTGGC 57.800 50.000 0.00 0.00 0.00 5.01
2757 4668 2.109126 GTGGCGCTGATGTTCTCCC 61.109 63.158 7.64 0.00 0.00 4.30
2765 4676 2.229784 GCTGATGTTCTCCCCAAAACTG 59.770 50.000 0.00 0.00 0.00 3.16
2783 4694 6.469782 AAACTGGTGTCAACATTGATCTTT 57.530 33.333 0.00 0.00 39.73 2.52
2804 4715 8.814448 TCTTTATATAATCAGAAAGGGGAGGT 57.186 34.615 0.00 0.00 31.24 3.85
2823 4734 5.279456 GGAGGTTGCCAAAACACATTATCTT 60.279 40.000 0.00 0.00 0.00 2.40
2855 4766 9.928618 TTATGTTGGATCCCAATTCAAGTATAA 57.071 29.630 9.90 1.95 45.80 0.98
2880 4791 7.200434 AGATAAAGCCTAACTTCCAATGAGA 57.800 36.000 0.00 0.00 37.75 3.27
2884 4795 3.118445 AGCCTAACTTCCAATGAGAGAGC 60.118 47.826 0.00 0.00 0.00 4.09
2917 4828 1.745489 CGCTGGAGGCTTGGTAACC 60.745 63.158 0.00 0.00 39.13 2.85
2974 4887 6.095021 GGGGTAAGTTGATCAGTTGTAAATCC 59.905 42.308 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.514330 AGACACACATCCTTTTGTAAAAACTA 57.486 30.769 0.00 0.00 0.00 2.24
28 29 5.243954 TGATAGGCTACATAGACACACATCC 59.756 44.000 0.00 0.00 32.29 3.51
48 49 4.837896 TTTTGAACCGTGTGCAATGATA 57.162 36.364 0.00 0.00 30.44 2.15
49 50 3.724508 TTTTGAACCGTGTGCAATGAT 57.275 38.095 0.00 0.00 30.44 2.45
75 77 6.689554 TCATGTGCAAAACATCACATACATT 58.310 32.000 7.43 0.00 45.56 2.71
111 113 4.264460 TGATACACTACATGCACACACA 57.736 40.909 0.00 0.00 0.00 3.72
112 114 5.562917 CAATGATACACTACATGCACACAC 58.437 41.667 0.00 0.00 0.00 3.82
153 155 2.859165 AGGGAATCACACACGATTGT 57.141 45.000 0.00 0.00 35.74 2.71
157 159 4.274978 TCTGTATAGGGAATCACACACGA 58.725 43.478 0.00 0.00 0.00 4.35
164 166 5.045213 TGCAAAACCTCTGTATAGGGAATCA 60.045 40.000 0.00 0.00 41.32 2.57
189 191 3.943671 TCATCACACCCCCGATATTTT 57.056 42.857 0.00 0.00 0.00 1.82
196 198 0.180171 TATGCTTCATCACACCCCCG 59.820 55.000 0.00 0.00 0.00 5.73
197 199 2.158623 TGATATGCTTCATCACACCCCC 60.159 50.000 0.00 0.00 0.00 5.40
228 230 6.781138 TCACACACAGTTAGACATTTGAAAC 58.219 36.000 0.00 0.00 0.00 2.78
236 238 5.007626 GCAAGAAATCACACACAGTTAGACA 59.992 40.000 0.00 0.00 0.00 3.41
294 296 8.501919 GTTTTTAAACTGCTTGCGATGGCATC 62.502 42.308 17.58 17.58 41.31 3.91
295 297 6.806684 GTTTTTAAACTGCTTGCGATGGCAT 61.807 40.000 2.27 0.00 41.31 4.40
319 321 1.070821 AGACATCACACACGATTGCG 58.929 50.000 0.00 0.00 44.79 4.85
325 328 2.846550 GACGTATCAGACATCACACACG 59.153 50.000 0.00 0.00 0.00 4.49
326 329 4.098055 AGACGTATCAGACATCACACAC 57.902 45.455 0.00 0.00 0.00 3.82
489 493 4.157656 CCGTTTGAGAATATTCAAAGCCCA 59.842 41.667 17.56 3.13 45.00 5.36
501 505 9.893305 CTAAAATTTTACAGTCCGTTTGAGAAT 57.107 29.630 6.54 0.00 0.00 2.40
584 588 4.947388 GCCTCCACAATACTTTTCCATACA 59.053 41.667 0.00 0.00 0.00 2.29
585 589 4.035208 CGCCTCCACAATACTTTTCCATAC 59.965 45.833 0.00 0.00 0.00 2.39
594 598 0.907704 TGGTCCGCCTCCACAATACT 60.908 55.000 0.00 0.00 35.27 2.12
600 604 0.035820 TGTTTATGGTCCGCCTCCAC 60.036 55.000 0.00 0.00 37.81 4.02
749 753 6.073167 GGACAGAAAGGCTTTAGTAACTTGTC 60.073 42.308 13.37 15.44 0.00 3.18
838 842 1.732259 CTACAGTTGCTAAAGGCGGTG 59.268 52.381 0.00 0.00 45.43 4.94
998 1003 2.499205 CTGACGGGGCTCGCATTA 59.501 61.111 6.72 0.00 43.89 1.90
1219 1224 1.374252 GCTCCGAGGAAACGAGCAA 60.374 57.895 3.51 0.00 36.88 3.91
1590 1595 2.283966 AGCACCTGGTACTCGGCT 60.284 61.111 0.00 0.03 0.00 5.52
1655 1660 1.418342 CCGTATCTTGGACAACGCCG 61.418 60.000 0.00 0.00 34.13 6.46
1924 1929 4.225984 GTCATCTTCGATTCGATCTCCTG 58.774 47.826 9.96 4.33 35.23 3.86
1927 1932 3.879427 ACGTCATCTTCGATTCGATCTC 58.121 45.455 9.96 0.00 35.23 2.75
2012 2017 3.010027 TGTTTGTCATGGAATCCTAGCCA 59.990 43.478 0.00 0.00 38.78 4.75
2021 2026 2.929641 TGAGCTGTGTTTGTCATGGAA 58.070 42.857 0.00 0.00 0.00 3.53
2035 2040 3.667960 GCGGACTTACAACATTTGAGCTG 60.668 47.826 0.00 0.00 0.00 4.24
2101 2106 5.260140 TCAAAAGAAAAGTGACGCTTTACG 58.740 37.500 14.13 1.13 45.91 3.18
2113 2118 9.919348 CATATGTGGTGTTTTTCAAAAGAAAAG 57.081 29.630 0.00 0.00 35.74 2.27
2166 2171 6.312672 TGTGTGAAGTATGATGTAACGAATGG 59.687 38.462 0.00 0.00 0.00 3.16
2195 2200 2.609244 GCCAAAATAGCTTTTCGCACCA 60.609 45.455 0.00 0.00 38.07 4.17
2232 3878 1.345715 ATAAACTGGGGAGGAGGCGG 61.346 60.000 0.00 0.00 0.00 6.13
2233 3879 0.106894 GATAAACTGGGGAGGAGGCG 59.893 60.000 0.00 0.00 0.00 5.52
2234 3880 0.474614 GGATAAACTGGGGAGGAGGC 59.525 60.000 0.00 0.00 0.00 4.70
2235 3881 0.759346 CGGATAAACTGGGGAGGAGG 59.241 60.000 0.00 0.00 0.00 4.30
2238 3884 3.557264 GCTTATCGGATAAACTGGGGAGG 60.557 52.174 11.32 0.00 0.00 4.30
2239 3885 3.557264 GGCTTATCGGATAAACTGGGGAG 60.557 52.174 11.32 0.00 0.00 4.30
2241 3887 2.105821 TGGCTTATCGGATAAACTGGGG 59.894 50.000 11.32 0.96 0.00 4.96
2242 3888 3.139077 GTGGCTTATCGGATAAACTGGG 58.861 50.000 11.32 1.59 0.00 4.45
2243 3889 3.139077 GGTGGCTTATCGGATAAACTGG 58.861 50.000 11.32 1.92 0.00 4.00
2246 3892 4.039366 AGAGAGGTGGCTTATCGGATAAAC 59.961 45.833 11.32 7.17 0.00 2.01
2247 3893 4.223953 AGAGAGGTGGCTTATCGGATAAA 58.776 43.478 11.32 0.00 0.00 1.40
2249 3895 3.527507 AGAGAGGTGGCTTATCGGATA 57.472 47.619 0.00 0.00 0.00 2.59
2250 3896 2.390225 AGAGAGGTGGCTTATCGGAT 57.610 50.000 0.00 0.00 0.00 4.18
2253 3899 7.118390 CCAATTAATAAGAGAGGTGGCTTATCG 59.882 40.741 0.00 0.00 36.56 2.92
2254 3900 7.391833 CCCAATTAATAAGAGAGGTGGCTTATC 59.608 40.741 0.00 0.00 36.56 1.75
2255 3901 7.234355 CCCAATTAATAAGAGAGGTGGCTTAT 58.766 38.462 0.00 0.00 38.57 1.73
2258 3904 4.141158 CCCCAATTAATAAGAGAGGTGGCT 60.141 45.833 0.00 0.00 0.00 4.75
2259 3905 4.145052 CCCCAATTAATAAGAGAGGTGGC 58.855 47.826 0.00 0.00 0.00 5.01
2260 3906 4.141158 AGCCCCAATTAATAAGAGAGGTGG 60.141 45.833 0.00 0.00 0.00 4.61
2261 3907 5.053978 AGCCCCAATTAATAAGAGAGGTG 57.946 43.478 0.00 0.00 0.00 4.00
2263 3909 5.946486 AGAAGCCCCAATTAATAAGAGAGG 58.054 41.667 0.00 0.00 0.00 3.69
2264 3910 8.841300 GTTTAGAAGCCCCAATTAATAAGAGAG 58.159 37.037 0.00 0.00 0.00 3.20
2265 3911 8.557450 AGTTTAGAAGCCCCAATTAATAAGAGA 58.443 33.333 0.00 0.00 0.00 3.10
2266 3912 8.753497 AGTTTAGAAGCCCCAATTAATAAGAG 57.247 34.615 0.00 0.00 0.00 2.85
2268 3914 9.628500 ACTAGTTTAGAAGCCCCAATTAATAAG 57.372 33.333 0.00 0.00 0.00 1.73
2274 3920 8.218488 CCTATAACTAGTTTAGAAGCCCCAATT 58.782 37.037 14.49 0.00 0.00 2.32
2275 3921 7.571357 TCCTATAACTAGTTTAGAAGCCCCAAT 59.429 37.037 14.49 0.00 0.00 3.16
2276 3922 6.904654 TCCTATAACTAGTTTAGAAGCCCCAA 59.095 38.462 14.49 0.00 0.00 4.12
2277 3923 6.446451 TCCTATAACTAGTTTAGAAGCCCCA 58.554 40.000 14.49 0.00 0.00 4.96
2278 3924 6.990908 TCCTATAACTAGTTTAGAAGCCCC 57.009 41.667 14.49 0.00 0.00 5.80
2279 3925 9.926158 GTTATCCTATAACTAGTTTAGAAGCCC 57.074 37.037 14.49 2.26 0.00 5.19
2315 3961 8.546597 AGCCGCTCATAAAATTTGTTAAAATT 57.453 26.923 0.00 0.00 45.81 1.82
2316 3962 8.546597 AAGCCGCTCATAAAATTTGTTAAAAT 57.453 26.923 0.00 0.00 37.61 1.82
2317 3963 7.954788 AAGCCGCTCATAAAATTTGTTAAAA 57.045 28.000 0.00 0.00 0.00 1.52
2318 3964 9.646427 ATTAAGCCGCTCATAAAATTTGTTAAA 57.354 25.926 0.00 0.00 0.00 1.52
2319 3965 9.646427 AATTAAGCCGCTCATAAAATTTGTTAA 57.354 25.926 0.00 0.00 0.00 2.01
2320 3966 9.646427 AAATTAAGCCGCTCATAAAATTTGTTA 57.354 25.926 0.00 0.00 0.00 2.41
2321 3967 8.546597 AAATTAAGCCGCTCATAAAATTTGTT 57.453 26.923 0.00 0.00 0.00 2.83
2322 3968 8.546597 AAAATTAAGCCGCTCATAAAATTTGT 57.453 26.923 0.00 0.00 0.00 2.83
2327 3973 8.180317 GCTTAAAAATTAAGCCGCTCATAAAA 57.820 30.769 19.29 0.00 42.88 1.52
2328 3974 7.749539 GCTTAAAAATTAAGCCGCTCATAAA 57.250 32.000 19.29 0.00 42.88 1.40
2372 4037 2.431057 TGTTCTTTTGGGCGGCTTAAAA 59.569 40.909 9.56 15.26 0.00 1.52
2376 4041 0.603065 GATGTTCTTTTGGGCGGCTT 59.397 50.000 9.56 0.00 0.00 4.35
2378 4043 1.154035 CGATGTTCTTTTGGGCGGC 60.154 57.895 0.00 0.00 0.00 6.53
2380 4045 0.871722 TGACGATGTTCTTTTGGGCG 59.128 50.000 0.00 0.00 0.00 6.13
2386 4051 8.012957 AGATAATAGGTCTGACGATGTTCTTT 57.987 34.615 1.07 0.00 0.00 2.52
2389 4054 7.380065 GTGAAGATAATAGGTCTGACGATGTTC 59.620 40.741 1.07 5.34 0.00 3.18
2392 4057 6.015856 AGGTGAAGATAATAGGTCTGACGATG 60.016 42.308 1.07 0.00 0.00 3.84
2394 4059 5.446860 AGGTGAAGATAATAGGTCTGACGA 58.553 41.667 1.07 0.00 0.00 4.20
2396 4061 9.886132 TTTTTAGGTGAAGATAATAGGTCTGAC 57.114 33.333 0.00 0.00 0.00 3.51
2475 4386 6.186957 TCTAGGCTGCTCCATAATTTCAAAA 58.813 36.000 0.00 0.00 37.29 2.44
2488 4399 4.309099 CATTGAGAATCTCTAGGCTGCTC 58.691 47.826 11.92 0.00 34.92 4.26
2535 4446 8.041323 TCCTGTCAAATAAGAACCTTGATAGAC 58.959 37.037 8.74 0.00 39.38 2.59
2556 4467 2.222027 CTTTCGGAGTTGCTTTCCTGT 58.778 47.619 0.00 0.00 32.34 4.00
2557 4468 1.068954 GCTTTCGGAGTTGCTTTCCTG 60.069 52.381 0.00 0.00 32.34 3.86
2558 4469 1.239347 GCTTTCGGAGTTGCTTTCCT 58.761 50.000 0.00 0.00 32.34 3.36
2632 4543 2.440569 GCTGAGCTTCGCAGTCGTC 61.441 63.158 0.00 0.00 33.92 4.20
2663 4574 2.952978 AGGTTTTATTGAACGGTGTGCA 59.047 40.909 0.00 0.00 0.00 4.57
2684 4595 6.518208 TGCAATGTCATCATCTTTTCATGA 57.482 33.333 0.00 0.00 37.20 3.07
2709 4620 6.891388 TGAGGGTTGTTCTTAGAAACACTTA 58.109 36.000 3.44 0.00 37.67 2.24
2743 4654 1.200020 GTTTTGGGGAGAACATCAGCG 59.800 52.381 0.00 0.00 0.00 5.18
2757 4668 4.383850 TCAATGTTGACACCAGTTTTGG 57.616 40.909 0.00 0.00 40.38 3.28
2783 4694 6.240176 GGCAACCTCCCCTTTCTGATTATATA 60.240 42.308 0.00 0.00 0.00 0.86
2799 4710 2.908688 AATGTGTTTTGGCAACCTCC 57.091 45.000 0.00 0.00 0.00 4.30
2804 4715 9.553064 AACATAAAAGATAATGTGTTTTGGCAA 57.447 25.926 0.00 0.00 36.47 4.52
2823 4734 8.601047 TGAATTGGGATCCAACATAACATAAA 57.399 30.769 15.23 0.00 46.95 1.40
2855 4766 7.633789 TCTCATTGGAAGTTAGGCTTTATCTT 58.366 34.615 0.00 0.00 37.59 2.40
2873 4784 0.594540 CTCGCTCCGCTCTCTCATTG 60.595 60.000 0.00 0.00 0.00 2.82
2874 4785 1.732917 CTCGCTCCGCTCTCTCATT 59.267 57.895 0.00 0.00 0.00 2.57
2901 4812 0.693049 ACAGGTTACCAAGCCTCCAG 59.307 55.000 3.51 0.00 31.73 3.86
2902 4813 0.400213 CACAGGTTACCAAGCCTCCA 59.600 55.000 3.51 0.00 31.73 3.86
2905 4816 5.710409 ATATAACACAGGTTACCAAGCCT 57.290 39.130 3.51 0.00 41.99 4.58
2917 4828 7.360101 GCGGCTTACAAAGGATATATAACACAG 60.360 40.741 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.