Multiple sequence alignment - TraesCS5B01G492900
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 | TraesCS5B01G492900 | chr5B | 100.000 | 1753 | 0 | 0 | 644 | 2396 | 661131157 | 661129405 | 0.000000e+00 | 3238.0 |
1 | TraesCS5B01G492900 | chr5B | 100.000 | 357 | 0 | 0 | 1 | 357 | 661131800 | 661131444 | 0.000000e+00 | 660.0 |
2 | TraesCS5B01G492900 | chr5D | 93.431 | 1644 | 76 | 10 | 776 | 2396 | 526109887 | 526108253 | 0.000000e+00 | 2409.0 |
3 | TraesCS5B01G492900 | chr5D | 93.197 | 294 | 18 | 1 | 2 | 293 | 526110726 | 526110433 | 4.730000e-117 | 431.0 |
4 | TraesCS5B01G492900 | chr5A | 91.588 | 1581 | 74 | 14 | 833 | 2396 | 653134030 | 653132492 | 0.000000e+00 | 2128.0 |
5 | TraesCS5B01G492900 | chr1A | 89.011 | 91 | 10 | 0 | 681 | 771 | 486748831 | 486748741 | 1.950000e-21 | 113.0 |
6 | TraesCS5B01G492900 | chr1A | 78.667 | 150 | 28 | 4 | 1962 | 2108 | 320336591 | 320336443 | 1.960000e-16 | 97.1 |
7 | TraesCS5B01G492900 | chr1A | 76.351 | 148 | 25 | 10 | 1979 | 2123 | 51704527 | 51704667 | 1.190000e-08 | 71.3 |
8 | TraesCS5B01G492900 | chr7B | 90.361 | 83 | 6 | 2 | 1899 | 1979 | 303164603 | 303164521 | 9.060000e-20 | 108.0 |
9 | TraesCS5B01G492900 | chr7B | 100.000 | 28 | 0 | 0 | 2079 | 2106 | 16252740 | 16252767 | 4.000000e-03 | 52.8 |
10 | TraesCS5B01G492900 | chr3D | 85.714 | 98 | 14 | 0 | 679 | 776 | 607227083 | 607226986 | 1.170000e-18 | 104.0 |
11 | TraesCS5B01G492900 | chr3D | 100.000 | 28 | 0 | 0 | 2079 | 2106 | 233290222 | 233290195 | 4.000000e-03 | 52.8 |
12 | TraesCS5B01G492900 | chr7D | 92.188 | 64 | 5 | 0 | 2046 | 2109 | 609236799 | 609236862 | 9.120000e-15 | 91.6 |
13 | TraesCS5B01G492900 | chr7D | 89.062 | 64 | 7 | 0 | 2046 | 2109 | 608875983 | 608875920 | 1.970000e-11 | 80.5 |
14 | TraesCS5B01G492900 | chr1B | 93.333 | 60 | 4 | 0 | 2046 | 2105 | 647533844 | 647533903 | 3.280000e-14 | 89.8 |
15 | TraesCS5B01G492900 | chr2D | 89.706 | 68 | 7 | 0 | 1913 | 1980 | 630017182 | 630017249 | 1.180000e-13 | 87.9 |
16 | TraesCS5B01G492900 | chr2B | 90.164 | 61 | 6 | 0 | 1913 | 1973 | 772985000 | 772985060 | 1.970000e-11 | 80.5 |
17 | TraesCS5B01G492900 | chr3A | 87.143 | 70 | 7 | 2 | 78 | 146 | 235347114 | 235347046 | 7.100000e-11 | 78.7 |
18 | TraesCS5B01G492900 | chr6B | 84.722 | 72 | 8 | 2 | 681 | 750 | 66994347 | 66994417 | 4.270000e-08 | 69.4 |
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 | TraesCS5B01G492900 | chr5B | 661129405 | 661131800 | 2395 | True | 1949 | 3238 | 100.000 | 1 | 2396 | 2 | chr5B.!!$R1 | 2395 |
1 | TraesCS5B01G492900 | chr5D | 526108253 | 526110726 | 2473 | True | 1420 | 2409 | 93.314 | 2 | 2396 | 2 | chr5D.!!$R1 | 2394 |
2 | TraesCS5B01G492900 | chr5A | 653132492 | 653134030 | 1538 | True | 2128 | 2128 | 91.588 | 833 | 2396 | 1 | chr5A.!!$R1 | 1563 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
662 | 702 | 0.596082 | ATGTAGCAAAACCGGTGTGC | 59.404 | 50.0 | 27.98 | 27.98 | 38.59 | 4.57 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1496 | 1577 | 0.322187 | GTCCGGTGGGCTAAACACAT | 60.322 | 55.0 | 0.0 | 0.0 | 40.54 | 3.21 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
75 | 76 | 1.745087 | TCTTGATTTGATCGGGCTTGC | 59.255 | 47.619 | 0.00 | 0.00 | 0.00 | 4.01 |
88 | 89 | 2.644992 | CTTGCGGAACACCTTGGC | 59.355 | 61.111 | 0.00 | 0.00 | 0.00 | 4.52 |
95 | 96 | 1.632589 | GGAACACCTTGGCATTCCTT | 58.367 | 50.000 | 9.11 | 0.00 | 38.08 | 3.36 |
106 | 107 | 2.433604 | TGGCATTCCTTTGCTTTCACAA | 59.566 | 40.909 | 0.00 | 0.00 | 42.38 | 3.33 |
118 | 119 | 1.112315 | TTTCACAATGCCCAAGCCGT | 61.112 | 50.000 | 0.00 | 0.00 | 38.69 | 5.68 |
125 | 126 | 2.125106 | GCCCAAGCCGTCTCGATT | 60.125 | 61.111 | 0.00 | 0.00 | 0.00 | 3.34 |
128 | 129 | 0.870307 | CCCAAGCCGTCTCGATTACG | 60.870 | 60.000 | 12.16 | 12.16 | 40.01 | 3.18 |
159 | 160 | 1.227973 | CCTCGCTTATCCTTGCCCC | 60.228 | 63.158 | 0.00 | 0.00 | 0.00 | 5.80 |
164 | 165 | 1.477558 | CGCTTATCCTTGCCCCTGAAT | 60.478 | 52.381 | 0.00 | 0.00 | 0.00 | 2.57 |
192 | 193 | 1.228245 | GCTCTCAGCCACCAACCAA | 60.228 | 57.895 | 0.00 | 0.00 | 34.48 | 3.67 |
214 | 215 | 5.695851 | ATGAATTTGTCTGTCACTTCCAC | 57.304 | 39.130 | 0.00 | 0.00 | 0.00 | 4.02 |
215 | 216 | 4.522114 | TGAATTTGTCTGTCACTTCCACA | 58.478 | 39.130 | 0.00 | 0.00 | 0.00 | 4.17 |
223 | 224 | 5.700832 | TGTCTGTCACTTCCACAATATTGAC | 59.299 | 40.000 | 22.16 | 7.62 | 35.08 | 3.18 |
238 | 239 | 7.846107 | CACAATATTGACGTTAATCTGCAGTAC | 59.154 | 37.037 | 22.16 | 7.22 | 0.00 | 2.73 |
246 | 247 | 7.116662 | TGACGTTAATCTGCAGTACGTTAAATT | 59.883 | 33.333 | 26.43 | 15.38 | 44.44 | 1.82 |
268 | 271 | 2.050691 | CGTGTGCCACAAAAATGCTAC | 58.949 | 47.619 | 0.00 | 0.00 | 33.40 | 3.58 |
287 | 290 | 4.809426 | GCTACATACACGGACTAAAGCAAT | 59.191 | 41.667 | 0.00 | 0.00 | 0.00 | 3.56 |
293 | 296 | 3.074412 | CACGGACTAAAGCAATGGAACT | 58.926 | 45.455 | 0.00 | 0.00 | 0.00 | 3.01 |
294 | 297 | 3.502211 | CACGGACTAAAGCAATGGAACTT | 59.498 | 43.478 | 0.00 | 0.00 | 0.00 | 2.66 |
295 | 298 | 4.023193 | CACGGACTAAAGCAATGGAACTTT | 60.023 | 41.667 | 0.00 | 0.00 | 0.00 | 2.66 |
296 | 299 | 5.180492 | CACGGACTAAAGCAATGGAACTTTA | 59.820 | 40.000 | 0.00 | 0.00 | 0.00 | 1.85 |
297 | 300 | 5.180680 | ACGGACTAAAGCAATGGAACTTTAC | 59.819 | 40.000 | 0.00 | 0.00 | 0.00 | 2.01 |
298 | 301 | 5.180492 | CGGACTAAAGCAATGGAACTTTACA | 59.820 | 40.000 | 0.00 | 0.00 | 0.00 | 2.41 |
299 | 302 | 6.612306 | GGACTAAAGCAATGGAACTTTACAG | 58.388 | 40.000 | 0.00 | 0.00 | 0.00 | 2.74 |
300 | 303 | 6.430000 | GGACTAAAGCAATGGAACTTTACAGA | 59.570 | 38.462 | 0.00 | 0.00 | 0.00 | 3.41 |
301 | 304 | 7.121315 | GGACTAAAGCAATGGAACTTTACAGAT | 59.879 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
302 | 305 | 8.045176 | ACTAAAGCAATGGAACTTTACAGATC | 57.955 | 34.615 | 0.00 | 0.00 | 0.00 | 2.75 |
303 | 306 | 6.899393 | AAAGCAATGGAACTTTACAGATCA | 57.101 | 33.333 | 0.00 | 0.00 | 0.00 | 2.92 |
304 | 307 | 6.506500 | AAGCAATGGAACTTTACAGATCAG | 57.493 | 37.500 | 0.00 | 0.00 | 0.00 | 2.90 |
305 | 308 | 4.397417 | AGCAATGGAACTTTACAGATCAGC | 59.603 | 41.667 | 0.00 | 0.00 | 0.00 | 4.26 |
306 | 309 | 4.397417 | GCAATGGAACTTTACAGATCAGCT | 59.603 | 41.667 | 0.00 | 0.00 | 0.00 | 4.24 |
319 | 322 | 4.822685 | AGATCAGCTGACATGTCTCTTT | 57.177 | 40.909 | 25.55 | 12.27 | 0.00 | 2.52 |
320 | 323 | 5.163281 | AGATCAGCTGACATGTCTCTTTT | 57.837 | 39.130 | 25.55 | 11.97 | 0.00 | 2.27 |
321 | 324 | 5.558818 | AGATCAGCTGACATGTCTCTTTTT | 58.441 | 37.500 | 25.55 | 7.84 | 0.00 | 1.94 |
322 | 325 | 6.705302 | AGATCAGCTGACATGTCTCTTTTTA | 58.295 | 36.000 | 25.55 | 3.59 | 0.00 | 1.52 |
323 | 326 | 7.164122 | AGATCAGCTGACATGTCTCTTTTTAA | 58.836 | 34.615 | 25.55 | 2.85 | 0.00 | 1.52 |
324 | 327 | 7.828223 | AGATCAGCTGACATGTCTCTTTTTAAT | 59.172 | 33.333 | 25.55 | 9.61 | 0.00 | 1.40 |
325 | 328 | 7.369803 | TCAGCTGACATGTCTCTTTTTAATC | 57.630 | 36.000 | 25.55 | 0.00 | 0.00 | 1.75 |
326 | 329 | 6.091305 | TCAGCTGACATGTCTCTTTTTAATCG | 59.909 | 38.462 | 25.55 | 8.97 | 0.00 | 3.34 |
327 | 330 | 5.352569 | AGCTGACATGTCTCTTTTTAATCGG | 59.647 | 40.000 | 25.55 | 2.55 | 0.00 | 4.18 |
328 | 331 | 5.447818 | GCTGACATGTCTCTTTTTAATCGGG | 60.448 | 44.000 | 25.55 | 0.00 | 0.00 | 5.14 |
329 | 332 | 4.394920 | TGACATGTCTCTTTTTAATCGGGC | 59.605 | 41.667 | 25.55 | 0.00 | 0.00 | 6.13 |
330 | 333 | 4.589908 | ACATGTCTCTTTTTAATCGGGCT | 58.410 | 39.130 | 0.00 | 0.00 | 0.00 | 5.19 |
331 | 334 | 5.741011 | ACATGTCTCTTTTTAATCGGGCTA | 58.259 | 37.500 | 0.00 | 0.00 | 0.00 | 3.93 |
332 | 335 | 6.177610 | ACATGTCTCTTTTTAATCGGGCTAA | 58.822 | 36.000 | 0.00 | 0.00 | 0.00 | 3.09 |
333 | 336 | 6.657541 | ACATGTCTCTTTTTAATCGGGCTAAA | 59.342 | 34.615 | 0.00 | 0.00 | 0.00 | 1.85 |
334 | 337 | 7.339466 | ACATGTCTCTTTTTAATCGGGCTAAAT | 59.661 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
335 | 338 | 8.836413 | CATGTCTCTTTTTAATCGGGCTAAATA | 58.164 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
336 | 339 | 8.795842 | TGTCTCTTTTTAATCGGGCTAAATAA | 57.204 | 30.769 | 0.00 | 0.00 | 0.00 | 1.40 |
337 | 340 | 8.671028 | TGTCTCTTTTTAATCGGGCTAAATAAC | 58.329 | 33.333 | 0.00 | 0.00 | 0.00 | 1.89 |
338 | 341 | 8.127327 | GTCTCTTTTTAATCGGGCTAAATAACC | 58.873 | 37.037 | 0.00 | 0.00 | 0.00 | 2.85 |
339 | 342 | 7.830201 | TCTCTTTTTAATCGGGCTAAATAACCA | 59.170 | 33.333 | 0.00 | 0.00 | 0.00 | 3.67 |
340 | 343 | 8.528044 | TCTTTTTAATCGGGCTAAATAACCAT | 57.472 | 30.769 | 0.00 | 0.00 | 0.00 | 3.55 |
341 | 344 | 8.626526 | TCTTTTTAATCGGGCTAAATAACCATC | 58.373 | 33.333 | 0.00 | 0.00 | 0.00 | 3.51 |
342 | 345 | 8.528044 | TTTTTAATCGGGCTAAATAACCATCT | 57.472 | 30.769 | 0.00 | 0.00 | 0.00 | 2.90 |
343 | 346 | 7.739498 | TTTAATCGGGCTAAATAACCATCTC | 57.261 | 36.000 | 0.00 | 0.00 | 0.00 | 2.75 |
344 | 347 | 3.764237 | TCGGGCTAAATAACCATCTCC | 57.236 | 47.619 | 0.00 | 0.00 | 0.00 | 3.71 |
345 | 348 | 2.370849 | TCGGGCTAAATAACCATCTCCC | 59.629 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
346 | 349 | 2.552373 | CGGGCTAAATAACCATCTCCCC | 60.552 | 54.545 | 0.00 | 0.00 | 0.00 | 4.81 |
347 | 350 | 2.225041 | GGGCTAAATAACCATCTCCCCC | 60.225 | 54.545 | 0.00 | 0.00 | 0.00 | 5.40 |
348 | 351 | 2.552373 | GGCTAAATAACCATCTCCCCCG | 60.552 | 54.545 | 0.00 | 0.00 | 0.00 | 5.73 |
349 | 352 | 2.370849 | GCTAAATAACCATCTCCCCCGA | 59.629 | 50.000 | 0.00 | 0.00 | 0.00 | 5.14 |
350 | 353 | 3.181448 | GCTAAATAACCATCTCCCCCGAA | 60.181 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
351 | 354 | 4.506802 | GCTAAATAACCATCTCCCCCGAAT | 60.507 | 45.833 | 0.00 | 0.00 | 0.00 | 3.34 |
352 | 355 | 4.536295 | AAATAACCATCTCCCCCGAATT | 57.464 | 40.909 | 0.00 | 0.00 | 0.00 | 2.17 |
353 | 356 | 5.656549 | AAATAACCATCTCCCCCGAATTA | 57.343 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
354 | 357 | 5.656549 | AATAACCATCTCCCCCGAATTAA | 57.343 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
355 | 358 | 3.292492 | AACCATCTCCCCCGAATTAAC | 57.708 | 47.619 | 0.00 | 0.00 | 0.00 | 2.01 |
356 | 359 | 2.201830 | ACCATCTCCCCCGAATTAACA | 58.798 | 47.619 | 0.00 | 0.00 | 0.00 | 2.41 |
662 | 702 | 0.596082 | ATGTAGCAAAACCGGTGTGC | 59.404 | 50.000 | 27.98 | 27.98 | 38.59 | 4.57 |
663 | 703 | 1.284715 | GTAGCAAAACCGGTGTGCC | 59.715 | 57.895 | 30.21 | 17.74 | 39.13 | 5.01 |
707 | 747 | 5.520288 | CGTTGTACAATGCTAGATGCTTAGT | 59.480 | 40.000 | 14.61 | 0.00 | 43.37 | 2.24 |
708 | 748 | 6.508563 | CGTTGTACAATGCTAGATGCTTAGTG | 60.509 | 42.308 | 14.61 | 0.00 | 43.37 | 2.74 |
713 | 753 | 5.363868 | ACAATGCTAGATGCTTAGTGAGGTA | 59.636 | 40.000 | 0.00 | 0.00 | 43.37 | 3.08 |
723 | 763 | 8.594550 | AGATGCTTAGTGAGGTACTTAGAAAAA | 58.405 | 33.333 | 0.00 | 0.00 | 41.55 | 1.94 |
750 | 790 | 5.376854 | TCTGATTTTTCTAAAGCACCAGC | 57.623 | 39.130 | 0.00 | 0.00 | 34.92 | 4.85 |
763 | 803 | 1.004927 | GCACCAGCGCTTATTTCTACG | 60.005 | 52.381 | 7.50 | 0.00 | 0.00 | 3.51 |
764 | 804 | 1.593006 | CACCAGCGCTTATTTCTACGG | 59.407 | 52.381 | 7.50 | 4.89 | 0.00 | 4.02 |
771 | 811 | 4.038162 | AGCGCTTATTTCTACGGAAGAGAT | 59.962 | 41.667 | 2.64 | 0.00 | 35.05 | 2.75 |
773 | 813 | 4.149046 | CGCTTATTTCTACGGAAGAGATGC | 59.851 | 45.833 | 4.06 | 0.45 | 35.05 | 3.91 |
803 | 869 | 7.765695 | AAAAAGGCTGATTCATTTCTCTACA | 57.234 | 32.000 | 0.00 | 0.00 | 0.00 | 2.74 |
805 | 871 | 4.775236 | AGGCTGATTCATTTCTCTACACC | 58.225 | 43.478 | 0.00 | 0.00 | 0.00 | 4.16 |
806 | 872 | 4.472833 | AGGCTGATTCATTTCTCTACACCT | 59.527 | 41.667 | 0.00 | 0.00 | 0.00 | 4.00 |
825 | 893 | 3.099141 | CCTCCCCTAAACATGTTGCATT | 58.901 | 45.455 | 12.82 | 0.00 | 0.00 | 3.56 |
826 | 894 | 3.515104 | CCTCCCCTAAACATGTTGCATTT | 59.485 | 43.478 | 12.82 | 0.00 | 0.00 | 2.32 |
856 | 926 | 2.124011 | AAACGCATTGCACAGAGTTG | 57.876 | 45.000 | 9.69 | 0.00 | 0.00 | 3.16 |
876 | 946 | 1.933853 | GTTGTTCTTGAGTCGCACAGT | 59.066 | 47.619 | 0.00 | 0.00 | 0.00 | 3.55 |
884 | 954 | 3.106407 | GTCGCACAGTCTCCACGC | 61.106 | 66.667 | 0.00 | 0.00 | 0.00 | 5.34 |
897 | 967 | 4.953868 | CACGCCGTGACCCGACAA | 62.954 | 66.667 | 12.85 | 0.00 | 39.56 | 3.18 |
1400 | 1470 | 4.363990 | CGCGCTCCTGTGAGTGGT | 62.364 | 66.667 | 5.56 | 0.00 | 46.92 | 4.16 |
1465 | 1543 | 9.759259 | GCTTTGCAAAACATTTCCTAATTATTC | 57.241 | 29.630 | 13.84 | 0.00 | 0.00 | 1.75 |
1529 | 1610 | 1.001633 | ACCGGACTAAACTGCGTCAAT | 59.998 | 47.619 | 9.46 | 0.00 | 31.88 | 2.57 |
1533 | 1614 | 4.331717 | CCGGACTAAACTGCGTCAATATTT | 59.668 | 41.667 | 0.00 | 0.00 | 31.88 | 1.40 |
1626 | 1707 | 6.694877 | AGGACTAAGGACTTGTTTTGAAAC | 57.305 | 37.500 | 0.00 | 0.00 | 39.33 | 2.78 |
1713 | 1794 | 2.443887 | TGCGTGGTACTTACAAGGTC | 57.556 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
1749 | 1830 | 8.807667 | AAAGAAAACAGATGATTGTGATTGTC | 57.192 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
1756 | 1837 | 9.896645 | AACAGATGATTGTGATTGTCTATAAGT | 57.103 | 29.630 | 0.00 | 0.00 | 0.00 | 2.24 |
1796 | 1877 | 7.996644 | AGTGGACCAATTGAAGAAGTTAACTTA | 59.003 | 33.333 | 20.58 | 5.55 | 36.11 | 2.24 |
1866 | 1947 | 9.273016 | GAGAAATCCGATAAACATAGAAATCCA | 57.727 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
1891 | 1972 | 1.746220 | CGGCCAAACATTCGGGATTTA | 59.254 | 47.619 | 2.24 | 0.00 | 0.00 | 1.40 |
1892 | 1973 | 2.360801 | CGGCCAAACATTCGGGATTTAT | 59.639 | 45.455 | 2.24 | 0.00 | 0.00 | 1.40 |
1893 | 1974 | 3.550030 | CGGCCAAACATTCGGGATTTATC | 60.550 | 47.826 | 2.24 | 0.00 | 0.00 | 1.75 |
1894 | 1975 | 3.383185 | GGCCAAACATTCGGGATTTATCA | 59.617 | 43.478 | 0.00 | 0.00 | 0.00 | 2.15 |
1895 | 1976 | 4.359706 | GCCAAACATTCGGGATTTATCAC | 58.640 | 43.478 | 0.00 | 0.00 | 0.00 | 3.06 |
1896 | 1977 | 4.736464 | GCCAAACATTCGGGATTTATCACC | 60.736 | 45.833 | 0.00 | 0.00 | 0.00 | 4.02 |
1897 | 1978 | 4.202111 | CCAAACATTCGGGATTTATCACCC | 60.202 | 45.833 | 0.00 | 0.00 | 42.43 | 4.61 |
1917 | 1998 | 2.287308 | CCTGGCAAATCGAACGTTTTCA | 60.287 | 45.455 | 0.46 | 0.00 | 0.00 | 2.69 |
1977 | 2058 | 1.002468 | GCAAGCATGTCAACTTCGTGT | 60.002 | 47.619 | 0.00 | 0.00 | 0.00 | 4.49 |
2004 | 2085 | 8.729805 | TCAGTTTAATTTTGCCAGAAAATTGT | 57.270 | 26.923 | 13.43 | 0.00 | 39.40 | 2.71 |
2005 | 2086 | 9.171877 | TCAGTTTAATTTTGCCAGAAAATTGTT | 57.828 | 25.926 | 13.43 | 0.00 | 39.40 | 2.83 |
2017 | 2098 | 5.636965 | CCAGAAAATTGTTGTGTGTGTCAAA | 59.363 | 36.000 | 0.00 | 0.00 | 0.00 | 2.69 |
2039 | 2120 | 1.730501 | ACTTGTCATCCATGCGTCAG | 58.269 | 50.000 | 0.00 | 0.00 | 0.00 | 3.51 |
2052 | 2133 | 3.535280 | TGCGTCAGTAGAATTGCCATA | 57.465 | 42.857 | 0.00 | 0.00 | 0.00 | 2.74 |
2053 | 2134 | 3.867857 | TGCGTCAGTAGAATTGCCATAA | 58.132 | 40.909 | 0.00 | 0.00 | 0.00 | 1.90 |
2108 | 2189 | 6.238621 | CGAACATTCGGGATTTATCATTTCCA | 60.239 | 38.462 | 6.11 | 0.00 | 46.30 | 3.53 |
2111 | 2192 | 8.884124 | ACATTCGGGATTTATCATTTCCATAT | 57.116 | 30.769 | 0.00 | 0.00 | 0.00 | 1.78 |
2214 | 2295 | 7.312154 | TGTTAACTTGATGTGTTGAATATGGC | 58.688 | 34.615 | 7.22 | 0.00 | 0.00 | 4.40 |
2233 | 2314 | 4.269183 | TGGCGATCCAACAAATATTGAGT | 58.731 | 39.130 | 0.00 | 0.00 | 39.99 | 3.41 |
2239 | 2320 | 6.852853 | CGATCCAACAAATATTGAGTGCATAC | 59.147 | 38.462 | 0.00 | 0.00 | 0.00 | 2.39 |
2282 | 2365 | 5.667539 | TTCACCTGGACATTGAACAAAAA | 57.332 | 34.783 | 0.00 | 0.00 | 0.00 | 1.94 |
2331 | 2418 | 5.905903 | CAACTTTTTGCACGTTTGTTTACA | 58.094 | 33.333 | 0.00 | 0.00 | 0.00 | 2.41 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 5.476945 | AGGAAATTAAAGATTGGAAGCGTGT | 59.523 | 36.000 | 0.00 | 0.00 | 0.00 | 4.49 |
75 | 76 | 0.609131 | AGGAATGCCAAGGTGTTCCG | 60.609 | 55.000 | 14.61 | 0.00 | 43.75 | 4.30 |
88 | 89 | 3.434299 | GGCATTGTGAAAGCAAAGGAATG | 59.566 | 43.478 | 0.00 | 0.00 | 31.63 | 2.67 |
95 | 96 | 1.540797 | GCTTGGGCATTGTGAAAGCAA | 60.541 | 47.619 | 11.81 | 0.00 | 42.19 | 3.91 |
106 | 107 | 2.257409 | AATCGAGACGGCTTGGGCAT | 62.257 | 55.000 | 5.45 | 0.00 | 40.87 | 4.40 |
144 | 145 | 0.107214 | TTCAGGGGCAAGGATAAGCG | 60.107 | 55.000 | 0.00 | 0.00 | 0.00 | 4.68 |
159 | 160 | 3.295093 | TGAGAGCTAGGACAGGATTCAG | 58.705 | 50.000 | 0.00 | 0.00 | 0.00 | 3.02 |
164 | 165 | 0.396417 | GGCTGAGAGCTAGGACAGGA | 60.396 | 60.000 | 0.00 | 0.00 | 41.99 | 3.86 |
192 | 193 | 5.132502 | TGTGGAAGTGACAGACAAATTCAT | 58.867 | 37.500 | 0.00 | 0.00 | 31.89 | 2.57 |
214 | 215 | 7.057402 | CGTACTGCAGATTAACGTCAATATTG | 58.943 | 38.462 | 23.35 | 9.29 | 0.00 | 1.90 |
215 | 216 | 6.755141 | ACGTACTGCAGATTAACGTCAATATT | 59.245 | 34.615 | 23.35 | 4.18 | 42.62 | 1.28 |
223 | 224 | 7.159818 | CGAAATTTAACGTACTGCAGATTAACG | 59.840 | 37.037 | 23.35 | 23.47 | 39.37 | 3.18 |
268 | 271 | 4.188462 | TCCATTGCTTTAGTCCGTGTATG | 58.812 | 43.478 | 0.00 | 0.00 | 0.00 | 2.39 |
287 | 290 | 4.040339 | TGTCAGCTGATCTGTAAAGTTCCA | 59.960 | 41.667 | 21.47 | 5.17 | 43.32 | 3.53 |
293 | 296 | 5.186603 | AGAGACATGTCAGCTGATCTGTAAA | 59.813 | 40.000 | 27.02 | 7.26 | 43.32 | 2.01 |
294 | 297 | 4.708909 | AGAGACATGTCAGCTGATCTGTAA | 59.291 | 41.667 | 27.02 | 8.71 | 43.32 | 2.41 |
295 | 298 | 4.276642 | AGAGACATGTCAGCTGATCTGTA | 58.723 | 43.478 | 27.02 | 10.72 | 43.32 | 2.74 |
296 | 299 | 3.098377 | AGAGACATGTCAGCTGATCTGT | 58.902 | 45.455 | 27.02 | 25.46 | 43.32 | 3.41 |
297 | 300 | 3.804786 | AGAGACATGTCAGCTGATCTG | 57.195 | 47.619 | 27.02 | 21.02 | 44.21 | 2.90 |
298 | 301 | 4.822685 | AAAGAGACATGTCAGCTGATCT | 57.177 | 40.909 | 27.02 | 18.21 | 0.00 | 2.75 |
299 | 302 | 5.876612 | AAAAAGAGACATGTCAGCTGATC | 57.123 | 39.130 | 27.02 | 13.34 | 0.00 | 2.92 |
300 | 303 | 7.201591 | CGATTAAAAAGAGACATGTCAGCTGAT | 60.202 | 37.037 | 27.02 | 2.86 | 0.00 | 2.90 |
301 | 304 | 6.091305 | CGATTAAAAAGAGACATGTCAGCTGA | 59.909 | 38.462 | 27.02 | 13.74 | 0.00 | 4.26 |
302 | 305 | 6.246449 | CGATTAAAAAGAGACATGTCAGCTG | 58.754 | 40.000 | 27.02 | 7.63 | 0.00 | 4.24 |
303 | 306 | 5.352569 | CCGATTAAAAAGAGACATGTCAGCT | 59.647 | 40.000 | 27.02 | 19.77 | 0.00 | 4.24 |
304 | 307 | 5.447818 | CCCGATTAAAAAGAGACATGTCAGC | 60.448 | 44.000 | 27.02 | 17.91 | 0.00 | 4.26 |
305 | 308 | 5.447818 | GCCCGATTAAAAAGAGACATGTCAG | 60.448 | 44.000 | 27.02 | 4.14 | 0.00 | 3.51 |
306 | 309 | 4.394920 | GCCCGATTAAAAAGAGACATGTCA | 59.605 | 41.667 | 27.02 | 4.65 | 0.00 | 3.58 |
307 | 310 | 4.636206 | AGCCCGATTAAAAAGAGACATGTC | 59.364 | 41.667 | 18.47 | 18.47 | 0.00 | 3.06 |
308 | 311 | 4.589908 | AGCCCGATTAAAAAGAGACATGT | 58.410 | 39.130 | 0.00 | 0.00 | 0.00 | 3.21 |
309 | 312 | 6.677781 | TTAGCCCGATTAAAAAGAGACATG | 57.322 | 37.500 | 0.00 | 0.00 | 0.00 | 3.21 |
310 | 313 | 7.881775 | ATTTAGCCCGATTAAAAAGAGACAT | 57.118 | 32.000 | 0.00 | 0.00 | 0.00 | 3.06 |
311 | 314 | 8.671028 | GTTATTTAGCCCGATTAAAAAGAGACA | 58.329 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
312 | 315 | 8.127327 | GGTTATTTAGCCCGATTAAAAAGAGAC | 58.873 | 37.037 | 0.00 | 0.00 | 0.00 | 3.36 |
313 | 316 | 7.830201 | TGGTTATTTAGCCCGATTAAAAAGAGA | 59.170 | 33.333 | 0.00 | 0.00 | 0.00 | 3.10 |
314 | 317 | 7.992008 | TGGTTATTTAGCCCGATTAAAAAGAG | 58.008 | 34.615 | 0.00 | 0.00 | 0.00 | 2.85 |
315 | 318 | 7.941431 | TGGTTATTTAGCCCGATTAAAAAGA | 57.059 | 32.000 | 0.00 | 0.00 | 0.00 | 2.52 |
316 | 319 | 8.630037 | AGATGGTTATTTAGCCCGATTAAAAAG | 58.370 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
317 | 320 | 8.528044 | AGATGGTTATTTAGCCCGATTAAAAA | 57.472 | 30.769 | 0.00 | 0.00 | 0.00 | 1.94 |
318 | 321 | 7.229907 | GGAGATGGTTATTTAGCCCGATTAAAA | 59.770 | 37.037 | 0.00 | 0.00 | 0.00 | 1.52 |
319 | 322 | 6.713450 | GGAGATGGTTATTTAGCCCGATTAAA | 59.287 | 38.462 | 0.00 | 0.00 | 0.00 | 1.52 |
320 | 323 | 6.235664 | GGAGATGGTTATTTAGCCCGATTAA | 58.764 | 40.000 | 0.00 | 0.00 | 0.00 | 1.40 |
321 | 324 | 5.280317 | GGGAGATGGTTATTTAGCCCGATTA | 60.280 | 44.000 | 0.00 | 0.00 | 0.00 | 1.75 |
322 | 325 | 4.506802 | GGGAGATGGTTATTTAGCCCGATT | 60.507 | 45.833 | 0.00 | 0.00 | 0.00 | 3.34 |
323 | 326 | 3.009143 | GGGAGATGGTTATTTAGCCCGAT | 59.991 | 47.826 | 0.00 | 0.00 | 0.00 | 4.18 |
324 | 327 | 2.370849 | GGGAGATGGTTATTTAGCCCGA | 59.629 | 50.000 | 0.00 | 0.00 | 0.00 | 5.14 |
325 | 328 | 2.552373 | GGGGAGATGGTTATTTAGCCCG | 60.552 | 54.545 | 0.00 | 0.00 | 35.15 | 6.13 |
326 | 329 | 2.225041 | GGGGGAGATGGTTATTTAGCCC | 60.225 | 54.545 | 0.00 | 0.00 | 0.00 | 5.19 |
327 | 330 | 2.552373 | CGGGGGAGATGGTTATTTAGCC | 60.552 | 54.545 | 0.00 | 0.00 | 0.00 | 3.93 |
328 | 331 | 2.370849 | TCGGGGGAGATGGTTATTTAGC | 59.629 | 50.000 | 0.00 | 0.00 | 0.00 | 3.09 |
329 | 332 | 4.699925 | TTCGGGGGAGATGGTTATTTAG | 57.300 | 45.455 | 0.00 | 0.00 | 0.00 | 1.85 |
330 | 333 | 5.656549 | AATTCGGGGGAGATGGTTATTTA | 57.343 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
331 | 334 | 4.536295 | AATTCGGGGGAGATGGTTATTT | 57.464 | 40.909 | 0.00 | 0.00 | 0.00 | 1.40 |
332 | 335 | 5.103855 | TGTTAATTCGGGGGAGATGGTTATT | 60.104 | 40.000 | 0.00 | 0.00 | 0.00 | 1.40 |
333 | 336 | 4.414182 | TGTTAATTCGGGGGAGATGGTTAT | 59.586 | 41.667 | 0.00 | 0.00 | 0.00 | 1.89 |
334 | 337 | 3.781407 | TGTTAATTCGGGGGAGATGGTTA | 59.219 | 43.478 | 0.00 | 0.00 | 0.00 | 2.85 |
335 | 338 | 2.578940 | TGTTAATTCGGGGGAGATGGTT | 59.421 | 45.455 | 0.00 | 0.00 | 0.00 | 3.67 |
336 | 339 | 2.201830 | TGTTAATTCGGGGGAGATGGT | 58.798 | 47.619 | 0.00 | 0.00 | 0.00 | 3.55 |
662 | 702 | 2.870435 | GCCTTATGCCGTATAGGTGTGG | 60.870 | 54.545 | 0.00 | 0.00 | 43.70 | 4.17 |
663 | 703 | 2.413837 | GCCTTATGCCGTATAGGTGTG | 58.586 | 52.381 | 0.00 | 0.00 | 43.70 | 3.82 |
672 | 712 | 0.037139 | TGTACAACGCCTTATGCCGT | 60.037 | 50.000 | 0.00 | 0.00 | 36.24 | 5.68 |
692 | 732 | 5.144100 | AGTACCTCACTAAGCATCTAGCAT | 58.856 | 41.667 | 0.00 | 0.00 | 40.28 | 3.79 |
698 | 738 | 8.773404 | TTTTTCTAAGTACCTCACTAAGCATC | 57.227 | 34.615 | 0.00 | 0.00 | 36.04 | 3.91 |
728 | 768 | 4.083324 | CGCTGGTGCTTTAGAAAAATCAGA | 60.083 | 41.667 | 0.00 | 0.00 | 36.97 | 3.27 |
730 | 770 | 3.611530 | GCGCTGGTGCTTTAGAAAAATCA | 60.612 | 43.478 | 0.00 | 0.00 | 36.97 | 2.57 |
732 | 772 | 2.558359 | AGCGCTGGTGCTTTAGAAAAAT | 59.442 | 40.909 | 10.39 | 0.00 | 44.46 | 1.82 |
733 | 773 | 1.953686 | AGCGCTGGTGCTTTAGAAAAA | 59.046 | 42.857 | 10.39 | 0.00 | 44.46 | 1.94 |
743 | 783 | 1.004927 | CGTAGAAATAAGCGCTGGTGC | 60.005 | 52.381 | 12.58 | 0.00 | 0.00 | 5.01 |
746 | 786 | 2.218953 | TCCGTAGAAATAAGCGCTGG | 57.781 | 50.000 | 12.58 | 4.11 | 0.00 | 4.85 |
747 | 787 | 3.444916 | TCTTCCGTAGAAATAAGCGCTG | 58.555 | 45.455 | 12.58 | 0.00 | 0.00 | 5.18 |
750 | 790 | 4.149046 | GCATCTCTTCCGTAGAAATAAGCG | 59.851 | 45.833 | 0.00 | 0.00 | 30.91 | 4.68 |
785 | 851 | 4.813697 | GGAGGTGTAGAGAAATGAATCAGC | 59.186 | 45.833 | 0.00 | 0.00 | 0.00 | 4.26 |
802 | 868 | 1.818674 | GCAACATGTTTAGGGGAGGTG | 59.181 | 52.381 | 8.77 | 0.00 | 0.00 | 4.00 |
803 | 869 | 1.427368 | TGCAACATGTTTAGGGGAGGT | 59.573 | 47.619 | 8.77 | 0.00 | 0.00 | 3.85 |
805 | 871 | 4.806640 | AAATGCAACATGTTTAGGGGAG | 57.193 | 40.909 | 8.77 | 0.00 | 0.00 | 4.30 |
806 | 872 | 5.540337 | TGTAAAATGCAACATGTTTAGGGGA | 59.460 | 36.000 | 8.77 | 0.00 | 0.00 | 4.81 |
825 | 893 | 4.276183 | TGCAATGCGTTTAGACCTTGTAAA | 59.724 | 37.500 | 0.00 | 0.00 | 0.00 | 2.01 |
826 | 894 | 3.815962 | TGCAATGCGTTTAGACCTTGTAA | 59.184 | 39.130 | 0.00 | 0.00 | 0.00 | 2.41 |
856 | 926 | 1.933853 | ACTGTGCGACTCAAGAACAAC | 59.066 | 47.619 | 0.00 | 0.00 | 0.00 | 3.32 |
884 | 954 | 0.944311 | CTTGTCTTGTCGGGTCACGG | 60.944 | 60.000 | 0.00 | 0.00 | 44.45 | 4.94 |
893 | 963 | 1.423395 | CACCGAGCTCTTGTCTTGTC | 58.577 | 55.000 | 12.85 | 0.00 | 0.00 | 3.18 |
894 | 964 | 0.034059 | CCACCGAGCTCTTGTCTTGT | 59.966 | 55.000 | 12.85 | 0.00 | 0.00 | 3.16 |
895 | 965 | 0.318441 | TCCACCGAGCTCTTGTCTTG | 59.682 | 55.000 | 12.85 | 0.00 | 0.00 | 3.02 |
896 | 966 | 1.270907 | ATCCACCGAGCTCTTGTCTT | 58.729 | 50.000 | 12.85 | 0.00 | 0.00 | 3.01 |
897 | 967 | 1.066573 | CAATCCACCGAGCTCTTGTCT | 60.067 | 52.381 | 12.85 | 0.00 | 0.00 | 3.41 |
1368 | 1438 | 1.429825 | CGCGATGAGGACGAAGAGT | 59.570 | 57.895 | 0.00 | 0.00 | 0.00 | 3.24 |
1400 | 1470 | 2.604686 | AGAAGGAGGGAGCACGCA | 60.605 | 61.111 | 0.36 | 0.00 | 0.00 | 5.24 |
1447 | 1525 | 9.920946 | TCCAGCTAGAATAATTAGGAAATGTTT | 57.079 | 29.630 | 0.00 | 0.00 | 0.00 | 2.83 |
1496 | 1577 | 0.322187 | GTCCGGTGGGCTAAACACAT | 60.322 | 55.000 | 0.00 | 0.00 | 40.54 | 3.21 |
1626 | 1707 | 1.209128 | AAACTGTCAGCGAGTTCACG | 58.791 | 50.000 | 0.00 | 0.00 | 32.33 | 4.35 |
1796 | 1877 | 5.047590 | ACATGACTGTGTGAATGATGCAAAT | 60.048 | 36.000 | 0.00 | 0.00 | 33.22 | 2.32 |
1866 | 1947 | 1.474879 | CCCGAATGTTTGGCCGTTATT | 59.525 | 47.619 | 0.00 | 0.00 | 0.00 | 1.40 |
1891 | 1972 | 1.463674 | GTTCGATTTGCCAGGGTGAT | 58.536 | 50.000 | 0.00 | 0.00 | 0.00 | 3.06 |
1892 | 1973 | 0.953471 | CGTTCGATTTGCCAGGGTGA | 60.953 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 |
1893 | 1974 | 1.234615 | ACGTTCGATTTGCCAGGGTG | 61.235 | 55.000 | 0.00 | 0.00 | 0.00 | 4.61 |
1894 | 1975 | 0.536460 | AACGTTCGATTTGCCAGGGT | 60.536 | 50.000 | 0.00 | 0.00 | 0.00 | 4.34 |
1895 | 1976 | 0.596082 | AAACGTTCGATTTGCCAGGG | 59.404 | 50.000 | 0.00 | 0.00 | 0.00 | 4.45 |
1896 | 1977 | 2.287308 | TGAAAACGTTCGATTTGCCAGG | 60.287 | 45.455 | 0.00 | 0.00 | 36.46 | 4.45 |
1897 | 1978 | 2.993545 | TGAAAACGTTCGATTTGCCAG | 58.006 | 42.857 | 0.00 | 0.00 | 36.46 | 4.85 |
1917 | 1998 | 1.196808 | CGCGTCACTAAACTTGCCATT | 59.803 | 47.619 | 0.00 | 0.00 | 0.00 | 3.16 |
1966 | 2047 | 8.855279 | CAAAATTAAACTGAAACACGAAGTTGA | 58.145 | 29.630 | 0.00 | 0.00 | 41.61 | 3.18 |
2004 | 2085 | 6.502136 | TGACAAGTTATTTGACACACACAA | 57.498 | 33.333 | 0.00 | 0.00 | 39.21 | 3.33 |
2005 | 2086 | 6.238621 | GGATGACAAGTTATTTGACACACACA | 60.239 | 38.462 | 0.00 | 0.00 | 42.58 | 3.72 |
2017 | 2098 | 3.872696 | TGACGCATGGATGACAAGTTAT | 58.127 | 40.909 | 0.00 | 0.00 | 0.00 | 1.89 |
2053 | 2134 | 3.137533 | CCATGGCAAACCGAATGTTTTT | 58.862 | 40.909 | 0.00 | 0.00 | 44.80 | 1.94 |
2063 | 2144 | 3.056465 | TCGGAATTTAACCATGGCAAACC | 60.056 | 43.478 | 13.04 | 9.81 | 0.00 | 3.27 |
2064 | 2145 | 4.181309 | TCGGAATTTAACCATGGCAAAC | 57.819 | 40.909 | 13.04 | 1.90 | 0.00 | 2.93 |
2108 | 2189 | 7.402941 | TGGTGTGTGCCTCCAGAATATATATAT | 59.597 | 37.037 | 0.00 | 0.00 | 0.00 | 0.86 |
2111 | 2192 | 4.904853 | TGGTGTGTGCCTCCAGAATATATA | 59.095 | 41.667 | 0.00 | 0.00 | 0.00 | 0.86 |
2113 | 2194 | 3.111484 | TGGTGTGTGCCTCCAGAATATA | 58.889 | 45.455 | 0.00 | 0.00 | 0.00 | 0.86 |
2191 | 2272 | 6.372937 | TCGCCATATTCAACACATCAAGTTAA | 59.627 | 34.615 | 0.00 | 0.00 | 0.00 | 2.01 |
2214 | 2295 | 5.233957 | TGCACTCAATATTTGTTGGATCG | 57.766 | 39.130 | 0.00 | 0.00 | 0.00 | 3.69 |
2233 | 2314 | 6.839124 | ACAAAAGGAAATCATGAGTATGCA | 57.161 | 33.333 | 0.09 | 0.00 | 34.21 | 3.96 |
2239 | 2320 | 7.383300 | GGTGAAAGAACAAAAGGAAATCATGAG | 59.617 | 37.037 | 0.09 | 0.00 | 0.00 | 2.90 |
2282 | 2365 | 7.392673 | GCAGATGATATGGTTGTTGATTATCCT | 59.607 | 37.037 | 0.00 | 0.00 | 0.00 | 3.24 |
2321 | 2408 | 7.041984 | CCTCTCTTACTGTTCCTGTAAACAAAC | 60.042 | 40.741 | 0.00 | 0.00 | 38.60 | 2.93 |
2331 | 2418 | 1.079658 | AGGCCCTCTCTTACTGTTCCT | 59.920 | 52.381 | 0.00 | 0.00 | 0.00 | 3.36 |
![](/static/images/cyverse_long.png)
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.