Multiple sequence alignment - TraesCS3B01G449400
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 | TraesCS3B01G449400 | chr3B | 100.000 | 2037 | 0 | 0 | 1 | 2037 | 689987807 | 689985771 | 0.000000e+00 | 3762.0 |
1 | TraesCS3B01G449400 | chr3B | 85.255 | 373 | 53 | 2 | 1255 | 1626 | 131567592 | 131567963 | 1.370000e-102 | 383.0 |
2 | TraesCS3B01G449400 | chr3B | 100.000 | 187 | 0 | 0 | 2263 | 2449 | 689985545 | 689985359 | 1.800000e-91 | 346.0 |
3 | TraesCS3B01G449400 | chr3B | 93.333 | 150 | 9 | 1 | 2300 | 2449 | 690112959 | 690112811 | 1.140000e-53 | 220.0 |
4 | TraesCS3B01G449400 | chr3B | 89.873 | 79 | 5 | 1 | 2335 | 2410 | 690104532 | 690104454 | 5.570000e-17 | 99.0 |
5 | TraesCS3B01G449400 | chr2A | 99.362 | 2038 | 11 | 2 | 1 | 2037 | 682560615 | 682558579 | 0.000000e+00 | 3690.0 |
6 | TraesCS3B01G449400 | chr2A | 98.331 | 2037 | 33 | 1 | 1 | 2037 | 509973528 | 509971493 | 0.000000e+00 | 3572.0 |
7 | TraesCS3B01G449400 | chr2A | 100.000 | 43 | 0 | 0 | 2263 | 2305 | 509971471 | 509971429 | 2.020000e-11 | 80.5 |
8 | TraesCS3B01G449400 | chr1B | 98.871 | 2037 | 23 | 0 | 1 | 2037 | 222287286 | 222285250 | 0.000000e+00 | 3635.0 |
9 | TraesCS3B01G449400 | chr1B | 100.000 | 43 | 0 | 0 | 2263 | 2305 | 222285224 | 222285182 | 2.020000e-11 | 80.5 |
10 | TraesCS3B01G449400 | chr7B | 98.184 | 2037 | 37 | 0 | 1 | 2037 | 204459304 | 204461340 | 0.000000e+00 | 3557.0 |
11 | TraesCS3B01G449400 | chr7B | 99.333 | 1499 | 10 | 0 | 1 | 1499 | 13054141 | 13052643 | 0.000000e+00 | 2713.0 |
12 | TraesCS3B01G449400 | chr7B | 97.787 | 497 | 10 | 1 | 1479 | 1974 | 13052579 | 13052083 | 0.000000e+00 | 856.0 |
13 | TraesCS3B01G449400 | chr7B | 100.000 | 41 | 0 | 0 | 2263 | 2303 | 204461408 | 204461448 | 2.610000e-10 | 76.8 |
14 | TraesCS3B01G449400 | chr3A | 99.600 | 1501 | 4 | 1 | 1 | 1499 | 210126907 | 210125407 | 0.000000e+00 | 2737.0 |
15 | TraesCS3B01G449400 | chr3A | 98.036 | 560 | 10 | 1 | 1479 | 2037 | 210125343 | 210124784 | 0.000000e+00 | 972.0 |
16 | TraesCS3B01G449400 | chr3A | 95.395 | 152 | 6 | 1 | 2299 | 2449 | 658094483 | 658094332 | 8.750000e-60 | 241.0 |
17 | TraesCS3B01G449400 | chr1A | 79.768 | 1206 | 180 | 50 | 865 | 2037 | 537147174 | 537146000 | 0.000000e+00 | 817.0 |
18 | TraesCS3B01G449400 | chr1D | 79.797 | 1183 | 177 | 49 | 865 | 2023 | 440875019 | 440876163 | 0.000000e+00 | 804.0 |
19 | TraesCS3B01G449400 | chr4D | 83.747 | 726 | 95 | 14 | 841 | 1557 | 278289227 | 278289938 | 0.000000e+00 | 665.0 |
20 | TraesCS3B01G449400 | chr4D | 95.556 | 45 | 2 | 0 | 2263 | 2307 | 365038466 | 365038422 | 3.380000e-09 | 73.1 |
21 | TraesCS3B01G449400 | chr3D | 90.667 | 150 | 13 | 1 | 2300 | 2449 | 523316864 | 523316716 | 5.340000e-47 | 198.0 |
22 | TraesCS3B01G449400 | chr5A | 94.231 | 104 | 5 | 1 | 379 | 481 | 460411016 | 460410913 | 9.070000e-35 | 158.0 |
23 | TraesCS3B01G449400 | chr4A | 94.231 | 104 | 5 | 1 | 379 | 481 | 146663888 | 146663785 | 9.070000e-35 | 158.0 |
24 | TraesCS3B01G449400 | chr6A | 92.523 | 107 | 7 | 1 | 380 | 485 | 601004505 | 601004611 | 4.220000e-33 | 152.0 |
25 | TraesCS3B01G449400 | chr6B | 97.727 | 44 | 1 | 0 | 2263 | 2306 | 460917413 | 460917370 | 2.610000e-10 | 76.8 |
26 | TraesCS3B01G449400 | chr6B | 93.878 | 49 | 2 | 1 | 2263 | 2311 | 9208740 | 9208693 | 3.380000e-09 | 73.1 |
27 | TraesCS3B01G449400 | chrUn | 97.674 | 43 | 1 | 0 | 2267 | 2309 | 90100608 | 90100566 | 9.390000e-10 | 75.0 |
28 | TraesCS3B01G449400 | chr7A | 92.157 | 51 | 2 | 2 | 2267 | 2317 | 11236322 | 11236274 | 1.210000e-08 | 71.3 |
29 | TraesCS3B01G449400 | chr5D | 89.286 | 56 | 4 | 2 | 2263 | 2317 | 466597858 | 466597804 | 4.370000e-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 | TraesCS3B01G449400 | chr3B | 689985359 | 689987807 | 2448 | True | 2054.00 | 3762 | 100.0000 | 1 | 2449 | 2 | chr3B.!!$R3 | 2448 |
1 | TraesCS3B01G449400 | chr2A | 682558579 | 682560615 | 2036 | True | 3690.00 | 3690 | 99.3620 | 1 | 2037 | 1 | chr2A.!!$R1 | 2036 |
2 | TraesCS3B01G449400 | chr2A | 509971429 | 509973528 | 2099 | True | 1826.25 | 3572 | 99.1655 | 1 | 2305 | 2 | chr2A.!!$R2 | 2304 |
3 | TraesCS3B01G449400 | chr1B | 222285182 | 222287286 | 2104 | True | 1857.75 | 3635 | 99.4355 | 1 | 2305 | 2 | chr1B.!!$R1 | 2304 |
4 | TraesCS3B01G449400 | chr7B | 204459304 | 204461448 | 2144 | False | 1816.90 | 3557 | 99.0920 | 1 | 2303 | 2 | chr7B.!!$F1 | 2302 |
5 | TraesCS3B01G449400 | chr7B | 13052083 | 13054141 | 2058 | True | 1784.50 | 2713 | 98.5600 | 1 | 1974 | 2 | chr7B.!!$R1 | 1973 |
6 | TraesCS3B01G449400 | chr3A | 210124784 | 210126907 | 2123 | True | 1854.50 | 2737 | 98.8180 | 1 | 2037 | 2 | chr3A.!!$R2 | 2036 |
7 | TraesCS3B01G449400 | chr1A | 537146000 | 537147174 | 1174 | True | 817.00 | 817 | 79.7680 | 865 | 2037 | 1 | chr1A.!!$R1 | 1172 |
8 | TraesCS3B01G449400 | chr1D | 440875019 | 440876163 | 1144 | False | 804.00 | 804 | 79.7970 | 865 | 2023 | 1 | chr1D.!!$F1 | 1158 |
9 | TraesCS3B01G449400 | chr4D | 278289227 | 278289938 | 711 | False | 665.00 | 665 | 83.7470 | 841 | 1557 | 1 | chr4D.!!$F1 | 716 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
346 | 347 | 0.324923 | TACTAGGTGACACCCCGCAT | 60.325 | 55.0 | 21.32 | 4.74 | 39.75 | 4.73 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2345 | 2564 | 1.152546 | GGTGCCCCAACCAGAACTT | 60.153 | 57.895 | 0.0 | 0.0 | 40.22 | 2.66 | 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 |
---|---|---|---|---|---|---|---|---|---|
306 | 307 | 9.491675 | TGTAACTTCGGAAATTAAGTATGTTGA | 57.508 | 29.630 | 0.00 | 0.00 | 34.91 | 3.18 |
346 | 347 | 0.324923 | TACTAGGTGACACCCCGCAT | 60.325 | 55.000 | 21.32 | 4.74 | 39.75 | 4.73 |
985 | 989 | 1.403972 | GCACGAAGAACGCTACCGAG | 61.404 | 60.000 | 0.00 | 0.00 | 46.94 | 4.63 |
2305 | 2524 | 5.409520 | CACGGGCGTTCTACTAGTATATGTA | 59.590 | 44.000 | 2.33 | 0.00 | 0.00 | 2.29 |
2306 | 2525 | 5.997746 | ACGGGCGTTCTACTAGTATATGTAA | 59.002 | 40.000 | 2.33 | 0.00 | 0.00 | 2.41 |
2307 | 2526 | 6.486657 | ACGGGCGTTCTACTAGTATATGTAAA | 59.513 | 38.462 | 2.33 | 0.00 | 0.00 | 2.01 |
2308 | 2527 | 7.020010 | CGGGCGTTCTACTAGTATATGTAAAG | 58.980 | 42.308 | 2.33 | 0.00 | 0.00 | 1.85 |
2309 | 2528 | 7.311408 | GGGCGTTCTACTAGTATATGTAAAGG | 58.689 | 42.308 | 2.33 | 0.00 | 0.00 | 3.11 |
2310 | 2529 | 7.040132 | GGGCGTTCTACTAGTATATGTAAAGGT | 60.040 | 40.741 | 2.33 | 0.00 | 0.00 | 3.50 |
2311 | 2530 | 8.020244 | GGCGTTCTACTAGTATATGTAAAGGTC | 58.980 | 40.741 | 2.33 | 0.00 | 0.00 | 3.85 |
2312 | 2531 | 7.743838 | GCGTTCTACTAGTATATGTAAAGGTCG | 59.256 | 40.741 | 2.33 | 1.77 | 0.00 | 4.79 |
2313 | 2532 | 8.982685 | CGTTCTACTAGTATATGTAAAGGTCGA | 58.017 | 37.037 | 2.33 | 0.00 | 0.00 | 4.20 |
2316 | 2535 | 9.486497 | TCTACTAGTATATGTAAAGGTCGACTG | 57.514 | 37.037 | 16.46 | 0.00 | 0.00 | 3.51 |
2317 | 2536 | 7.507733 | ACTAGTATATGTAAAGGTCGACTGG | 57.492 | 40.000 | 16.46 | 0.00 | 0.00 | 4.00 |
2318 | 2537 | 5.197682 | AGTATATGTAAAGGTCGACTGGC | 57.802 | 43.478 | 16.46 | 0.00 | 0.00 | 4.85 |
2319 | 2538 | 4.894114 | AGTATATGTAAAGGTCGACTGGCT | 59.106 | 41.667 | 16.46 | 0.67 | 0.00 | 4.75 |
2320 | 2539 | 6.066690 | AGTATATGTAAAGGTCGACTGGCTA | 58.933 | 40.000 | 16.46 | 0.00 | 0.00 | 3.93 |
2321 | 2540 | 5.864418 | ATATGTAAAGGTCGACTGGCTAA | 57.136 | 39.130 | 16.46 | 0.00 | 0.00 | 3.09 |
2322 | 2541 | 4.755266 | ATGTAAAGGTCGACTGGCTAAT | 57.245 | 40.909 | 16.46 | 0.68 | 0.00 | 1.73 |
2323 | 2542 | 5.864418 | ATGTAAAGGTCGACTGGCTAATA | 57.136 | 39.130 | 16.46 | 0.00 | 0.00 | 0.98 |
2324 | 2543 | 5.864418 | TGTAAAGGTCGACTGGCTAATAT | 57.136 | 39.130 | 16.46 | 0.00 | 0.00 | 1.28 |
2325 | 2544 | 6.229936 | TGTAAAGGTCGACTGGCTAATATT | 57.770 | 37.500 | 16.46 | 0.00 | 0.00 | 1.28 |
2326 | 2545 | 7.350744 | TGTAAAGGTCGACTGGCTAATATTA | 57.649 | 36.000 | 16.46 | 0.00 | 0.00 | 0.98 |
2327 | 2546 | 7.784037 | TGTAAAGGTCGACTGGCTAATATTAA | 58.216 | 34.615 | 16.46 | 0.00 | 0.00 | 1.40 |
2328 | 2547 | 7.707893 | TGTAAAGGTCGACTGGCTAATATTAAC | 59.292 | 37.037 | 16.46 | 0.00 | 0.00 | 2.01 |
2329 | 2548 | 5.211174 | AGGTCGACTGGCTAATATTAACC | 57.789 | 43.478 | 16.46 | 7.82 | 0.00 | 2.85 |
2330 | 2549 | 4.040095 | AGGTCGACTGGCTAATATTAACCC | 59.960 | 45.833 | 16.46 | 8.24 | 0.00 | 4.11 |
2331 | 2550 | 4.202284 | GGTCGACTGGCTAATATTAACCCA | 60.202 | 45.833 | 16.46 | 11.72 | 0.00 | 4.51 |
2332 | 2551 | 5.512576 | GGTCGACTGGCTAATATTAACCCAT | 60.513 | 44.000 | 16.46 | 1.04 | 0.00 | 4.00 |
2333 | 2552 | 5.408604 | GTCGACTGGCTAATATTAACCCATG | 59.591 | 44.000 | 8.70 | 9.56 | 0.00 | 3.66 |
2334 | 2553 | 5.305902 | TCGACTGGCTAATATTAACCCATGA | 59.694 | 40.000 | 11.56 | 8.85 | 0.00 | 3.07 |
2335 | 2554 | 5.995282 | CGACTGGCTAATATTAACCCATGAA | 59.005 | 40.000 | 11.56 | 0.00 | 0.00 | 2.57 |
2336 | 2555 | 6.655003 | CGACTGGCTAATATTAACCCATGAAT | 59.345 | 38.462 | 11.56 | 0.00 | 0.00 | 2.57 |
2337 | 2556 | 7.361201 | CGACTGGCTAATATTAACCCATGAATG | 60.361 | 40.741 | 11.56 | 5.07 | 0.00 | 2.67 |
2338 | 2557 | 7.526041 | ACTGGCTAATATTAACCCATGAATGA | 58.474 | 34.615 | 11.56 | 0.00 | 0.00 | 2.57 |
2339 | 2558 | 7.667219 | ACTGGCTAATATTAACCCATGAATGAG | 59.333 | 37.037 | 11.56 | 3.61 | 0.00 | 2.90 |
2340 | 2559 | 7.754624 | TGGCTAATATTAACCCATGAATGAGA | 58.245 | 34.615 | 11.56 | 0.00 | 0.00 | 3.27 |
2341 | 2560 | 8.224025 | TGGCTAATATTAACCCATGAATGAGAA | 58.776 | 33.333 | 11.56 | 0.00 | 0.00 | 2.87 |
2342 | 2561 | 8.515414 | GGCTAATATTAACCCATGAATGAGAAC | 58.485 | 37.037 | 3.83 | 0.00 | 0.00 | 3.01 |
2343 | 2562 | 8.515414 | GCTAATATTAACCCATGAATGAGAACC | 58.485 | 37.037 | 0.00 | 0.00 | 0.00 | 3.62 |
2344 | 2563 | 7.839680 | AATATTAACCCATGAATGAGAACCC | 57.160 | 36.000 | 0.00 | 0.00 | 0.00 | 4.11 |
2345 | 2564 | 4.666412 | TTAACCCATGAATGAGAACCCA | 57.334 | 40.909 | 0.00 | 0.00 | 0.00 | 4.51 |
2346 | 2565 | 3.541242 | AACCCATGAATGAGAACCCAA | 57.459 | 42.857 | 0.00 | 0.00 | 0.00 | 4.12 |
2347 | 2566 | 3.091633 | ACCCATGAATGAGAACCCAAG | 57.908 | 47.619 | 0.00 | 0.00 | 0.00 | 3.61 |
2348 | 2567 | 2.379907 | ACCCATGAATGAGAACCCAAGT | 59.620 | 45.455 | 0.00 | 0.00 | 0.00 | 3.16 |
2349 | 2568 | 3.181418 | ACCCATGAATGAGAACCCAAGTT | 60.181 | 43.478 | 0.00 | 0.00 | 39.54 | 2.66 |
2360 | 2579 | 3.777556 | CCAAGTTCTGGTTGGGGC | 58.222 | 61.111 | 0.00 | 0.00 | 40.83 | 5.80 |
2361 | 2580 | 1.152567 | CCAAGTTCTGGTTGGGGCA | 60.153 | 57.895 | 0.00 | 0.00 | 40.83 | 5.36 |
2362 | 2581 | 1.463553 | CCAAGTTCTGGTTGGGGCAC | 61.464 | 60.000 | 0.00 | 0.00 | 40.83 | 5.01 |
2379 | 2598 | 3.214696 | GCACCTGCCTTATATTGGACT | 57.785 | 47.619 | 0.00 | 0.00 | 34.31 | 3.85 |
2380 | 2599 | 4.351874 | GCACCTGCCTTATATTGGACTA | 57.648 | 45.455 | 0.00 | 0.00 | 34.31 | 2.59 |
2381 | 2600 | 4.911390 | GCACCTGCCTTATATTGGACTAT | 58.089 | 43.478 | 0.00 | 0.00 | 34.31 | 2.12 |
2382 | 2601 | 5.316987 | GCACCTGCCTTATATTGGACTATT | 58.683 | 41.667 | 0.00 | 0.00 | 34.31 | 1.73 |
2383 | 2602 | 5.770162 | GCACCTGCCTTATATTGGACTATTT | 59.230 | 40.000 | 0.00 | 0.00 | 34.31 | 1.40 |
2384 | 2603 | 6.294176 | GCACCTGCCTTATATTGGACTATTTG | 60.294 | 42.308 | 0.00 | 0.00 | 34.31 | 2.32 |
2385 | 2604 | 6.207417 | CACCTGCCTTATATTGGACTATTTGG | 59.793 | 42.308 | 0.00 | 0.00 | 0.00 | 3.28 |
2386 | 2605 | 5.183904 | CCTGCCTTATATTGGACTATTTGGC | 59.816 | 44.000 | 0.00 | 0.00 | 37.38 | 4.52 |
2387 | 2606 | 5.952387 | TGCCTTATATTGGACTATTTGGCT | 58.048 | 37.500 | 0.00 | 0.00 | 37.69 | 4.75 |
2388 | 2607 | 7.085476 | TGCCTTATATTGGACTATTTGGCTA | 57.915 | 36.000 | 0.00 | 0.00 | 37.69 | 3.93 |
2389 | 2608 | 7.522542 | TGCCTTATATTGGACTATTTGGCTAA | 58.477 | 34.615 | 0.00 | 0.00 | 37.69 | 3.09 |
2390 | 2609 | 7.447238 | TGCCTTATATTGGACTATTTGGCTAAC | 59.553 | 37.037 | 0.00 | 0.00 | 37.69 | 2.34 |
2391 | 2610 | 7.665974 | GCCTTATATTGGACTATTTGGCTAACT | 59.334 | 37.037 | 0.00 | 0.00 | 34.42 | 2.24 |
2392 | 2611 | 9.574516 | CCTTATATTGGACTATTTGGCTAACTT | 57.425 | 33.333 | 0.00 | 0.00 | 0.00 | 2.66 |
2396 | 2615 | 7.775053 | ATTGGACTATTTGGCTAACTTGAAA | 57.225 | 32.000 | 0.00 | 0.00 | 0.00 | 2.69 |
2397 | 2616 | 7.775053 | TTGGACTATTTGGCTAACTTGAAAT | 57.225 | 32.000 | 0.00 | 0.00 | 0.00 | 2.17 |
2398 | 2617 | 7.156876 | TGGACTATTTGGCTAACTTGAAATG | 57.843 | 36.000 | 0.00 | 0.00 | 0.00 | 2.32 |
2399 | 2618 | 6.152661 | TGGACTATTTGGCTAACTTGAAATGG | 59.847 | 38.462 | 0.00 | 0.00 | 0.00 | 3.16 |
2400 | 2619 | 6.152831 | GGACTATTTGGCTAACTTGAAATGGT | 59.847 | 38.462 | 0.00 | 0.00 | 33.67 | 3.55 |
2401 | 2620 | 7.338449 | GGACTATTTGGCTAACTTGAAATGGTA | 59.662 | 37.037 | 0.00 | 0.00 | 31.85 | 3.25 |
2402 | 2621 | 8.823220 | ACTATTTGGCTAACTTGAAATGGTAT | 57.177 | 30.769 | 0.00 | 0.00 | 30.45 | 2.73 |
2403 | 2622 | 9.255029 | ACTATTTGGCTAACTTGAAATGGTATT | 57.745 | 29.630 | 0.00 | 0.00 | 30.45 | 1.89 |
2404 | 2623 | 9.520204 | CTATTTGGCTAACTTGAAATGGTATTG | 57.480 | 33.333 | 0.00 | 0.00 | 0.00 | 1.90 |
2405 | 2624 | 6.909550 | TTGGCTAACTTGAAATGGTATTGT | 57.090 | 33.333 | 0.00 | 0.00 | 0.00 | 2.71 |
2406 | 2625 | 6.909550 | TGGCTAACTTGAAATGGTATTGTT | 57.090 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
2407 | 2626 | 7.296628 | TGGCTAACTTGAAATGGTATTGTTT | 57.703 | 32.000 | 0.00 | 0.00 | 0.00 | 2.83 |
2408 | 2627 | 7.731054 | TGGCTAACTTGAAATGGTATTGTTTT | 58.269 | 30.769 | 0.00 | 0.00 | 0.00 | 2.43 |
2409 | 2628 | 8.207545 | TGGCTAACTTGAAATGGTATTGTTTTT | 58.792 | 29.630 | 0.00 | 0.00 | 0.00 | 1.94 |
2410 | 2629 | 9.699703 | GGCTAACTTGAAATGGTATTGTTTTTA | 57.300 | 29.630 | 0.00 | 0.00 | 0.00 | 1.52 |
2414 | 2633 | 9.830975 | AACTTGAAATGGTATTGTTTTTAAGCT | 57.169 | 25.926 | 0.00 | 0.00 | 32.34 | 3.74 |
2415 | 2634 | 9.260002 | ACTTGAAATGGTATTGTTTTTAAGCTG | 57.740 | 29.630 | 0.00 | 0.00 | 32.34 | 4.24 |
2416 | 2635 | 9.474920 | CTTGAAATGGTATTGTTTTTAAGCTGA | 57.525 | 29.630 | 0.00 | 0.00 | 0.00 | 4.26 |
2417 | 2636 | 8.810652 | TGAAATGGTATTGTTTTTAAGCTGAC | 57.189 | 30.769 | 0.00 | 0.00 | 0.00 | 3.51 |
2418 | 2637 | 8.417106 | TGAAATGGTATTGTTTTTAAGCTGACA | 58.583 | 29.630 | 0.00 | 0.00 | 0.00 | 3.58 |
2419 | 2638 | 9.255304 | GAAATGGTATTGTTTTTAAGCTGACAA | 57.745 | 29.630 | 0.00 | 0.00 | 36.55 | 3.18 |
2420 | 2639 | 9.606631 | AAATGGTATTGTTTTTAAGCTGACAAA | 57.393 | 25.926 | 0.00 | 0.00 | 35.83 | 2.83 |
2421 | 2640 | 9.777297 | AATGGTATTGTTTTTAAGCTGACAAAT | 57.223 | 25.926 | 0.00 | 0.00 | 35.83 | 2.32 |
2422 | 2641 | 9.777297 | ATGGTATTGTTTTTAAGCTGACAAATT | 57.223 | 25.926 | 0.00 | 0.00 | 35.83 | 1.82 |
2423 | 2642 | 9.255304 | TGGTATTGTTTTTAAGCTGACAAATTC | 57.745 | 29.630 | 0.00 | 0.00 | 35.83 | 2.17 |
2424 | 2643 | 9.255304 | GGTATTGTTTTTAAGCTGACAAATTCA | 57.745 | 29.630 | 0.00 | 0.00 | 35.83 | 2.57 |
2436 | 2655 | 8.613060 | AGCTGACAAATTCATATATGTAGGTG | 57.387 | 34.615 | 12.42 | 9.37 | 32.17 | 4.00 |
2437 | 2656 | 8.432013 | AGCTGACAAATTCATATATGTAGGTGA | 58.568 | 33.333 | 12.42 | 0.18 | 32.17 | 4.02 |
2438 | 2657 | 9.224267 | GCTGACAAATTCATATATGTAGGTGAT | 57.776 | 33.333 | 12.42 | 0.00 | 32.17 | 3.06 |
2440 | 2659 | 9.725019 | TGACAAATTCATATATGTAGGTGATCC | 57.275 | 33.333 | 12.42 | 4.40 | 0.00 | 3.36 |
2442 | 2661 | 9.950496 | ACAAATTCATATATGTAGGTGATCCTC | 57.050 | 33.333 | 12.42 | 0.00 | 43.94 | 3.71 |
2443 | 2662 | 9.091784 | CAAATTCATATATGTAGGTGATCCTCG | 57.908 | 37.037 | 12.42 | 0.00 | 43.94 | 4.63 |
2444 | 2663 | 6.775594 | TTCATATATGTAGGTGATCCTCGG | 57.224 | 41.667 | 12.42 | 0.00 | 43.94 | 4.63 |
2445 | 2664 | 5.827756 | TCATATATGTAGGTGATCCTCGGT | 58.172 | 41.667 | 12.42 | 0.00 | 43.94 | 4.69 |
2446 | 2665 | 5.652452 | TCATATATGTAGGTGATCCTCGGTG | 59.348 | 44.000 | 12.42 | 0.00 | 43.94 | 4.94 |
2447 | 2666 | 1.414158 | ATGTAGGTGATCCTCGGTGG | 58.586 | 55.000 | 0.00 | 0.00 | 43.94 | 4.61 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
346 | 347 | 8.628630 | TCCAAAGTTACATACAATCATCAACA | 57.371 | 30.769 | 0.00 | 0.00 | 0.00 | 3.33 |
985 | 989 | 3.633235 | ACGACATCTATGCTCATCGAAC | 58.367 | 45.455 | 7.44 | 0.00 | 33.88 | 3.95 |
1531 | 1713 | 8.367156 | GCCCATTAAGAAATGAAATATGCCTAA | 58.633 | 33.333 | 0.00 | 0.00 | 44.50 | 2.69 |
2305 | 2524 | 6.053650 | GGTTAATATTAGCCAGTCGACCTTT | 58.946 | 40.000 | 20.16 | 0.00 | 34.54 | 3.11 |
2306 | 2525 | 5.454329 | GGGTTAATATTAGCCAGTCGACCTT | 60.454 | 44.000 | 24.62 | 0.00 | 35.92 | 3.50 |
2307 | 2526 | 4.040095 | GGGTTAATATTAGCCAGTCGACCT | 59.960 | 45.833 | 24.62 | 4.91 | 35.92 | 3.85 |
2308 | 2527 | 4.202284 | TGGGTTAATATTAGCCAGTCGACC | 60.202 | 45.833 | 24.62 | 13.33 | 38.19 | 4.79 |
2309 | 2528 | 4.952460 | TGGGTTAATATTAGCCAGTCGAC | 58.048 | 43.478 | 24.62 | 7.70 | 38.19 | 4.20 |
2310 | 2529 | 5.305902 | TCATGGGTTAATATTAGCCAGTCGA | 59.694 | 40.000 | 24.62 | 14.47 | 45.45 | 4.20 |
2311 | 2530 | 5.547465 | TCATGGGTTAATATTAGCCAGTCG | 58.453 | 41.667 | 24.62 | 12.83 | 45.45 | 4.18 |
2312 | 2531 | 7.665559 | TCATTCATGGGTTAATATTAGCCAGTC | 59.334 | 37.037 | 24.62 | 11.75 | 45.45 | 3.51 |
2313 | 2532 | 7.526041 | TCATTCATGGGTTAATATTAGCCAGT | 58.474 | 34.615 | 24.62 | 12.79 | 45.45 | 4.00 |
2314 | 2533 | 7.884877 | TCTCATTCATGGGTTAATATTAGCCAG | 59.115 | 37.037 | 24.62 | 15.75 | 45.45 | 4.85 |
2315 | 2534 | 7.754624 | TCTCATTCATGGGTTAATATTAGCCA | 58.245 | 34.615 | 24.62 | 19.06 | 46.21 | 4.75 |
2316 | 2535 | 8.515414 | GTTCTCATTCATGGGTTAATATTAGCC | 58.485 | 37.037 | 17.63 | 17.63 | 33.73 | 3.93 |
2317 | 2536 | 8.515414 | GGTTCTCATTCATGGGTTAATATTAGC | 58.485 | 37.037 | 0.91 | 0.91 | 0.00 | 3.09 |
2318 | 2537 | 9.014297 | GGGTTCTCATTCATGGGTTAATATTAG | 57.986 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
2319 | 2538 | 8.506921 | TGGGTTCTCATTCATGGGTTAATATTA | 58.493 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
2320 | 2539 | 7.361438 | TGGGTTCTCATTCATGGGTTAATATT | 58.639 | 34.615 | 0.00 | 0.00 | 0.00 | 1.28 |
2321 | 2540 | 6.921412 | TGGGTTCTCATTCATGGGTTAATAT | 58.079 | 36.000 | 0.00 | 0.00 | 0.00 | 1.28 |
2322 | 2541 | 6.334378 | TGGGTTCTCATTCATGGGTTAATA | 57.666 | 37.500 | 0.00 | 0.00 | 0.00 | 0.98 |
2323 | 2542 | 5.205517 | TGGGTTCTCATTCATGGGTTAAT | 57.794 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
2324 | 2543 | 4.666412 | TGGGTTCTCATTCATGGGTTAA | 57.334 | 40.909 | 0.00 | 0.00 | 0.00 | 2.01 |
2325 | 2544 | 4.044065 | ACTTGGGTTCTCATTCATGGGTTA | 59.956 | 41.667 | 0.00 | 0.00 | 0.00 | 2.85 |
2326 | 2545 | 3.181418 | ACTTGGGTTCTCATTCATGGGTT | 60.181 | 43.478 | 0.00 | 0.00 | 0.00 | 4.11 |
2327 | 2546 | 2.379907 | ACTTGGGTTCTCATTCATGGGT | 59.620 | 45.455 | 0.00 | 0.00 | 0.00 | 4.51 |
2328 | 2547 | 3.091633 | ACTTGGGTTCTCATTCATGGG | 57.908 | 47.619 | 0.00 | 0.00 | 0.00 | 4.00 |
2329 | 2548 | 4.708726 | GAACTTGGGTTCTCATTCATGG | 57.291 | 45.455 | 0.00 | 0.00 | 45.90 | 3.66 |
2344 | 2563 | 1.463553 | GGTGCCCCAACCAGAACTTG | 61.464 | 60.000 | 0.00 | 0.00 | 40.22 | 3.16 |
2345 | 2564 | 1.152546 | GGTGCCCCAACCAGAACTT | 60.153 | 57.895 | 0.00 | 0.00 | 40.22 | 2.66 |
2346 | 2565 | 2.084930 | AGGTGCCCCAACCAGAACT | 61.085 | 57.895 | 0.00 | 0.00 | 43.20 | 3.01 |
2347 | 2566 | 1.903404 | CAGGTGCCCCAACCAGAAC | 60.903 | 63.158 | 0.00 | 0.00 | 43.20 | 3.01 |
2348 | 2567 | 2.520458 | CAGGTGCCCCAACCAGAA | 59.480 | 61.111 | 0.00 | 0.00 | 43.20 | 3.02 |
2349 | 2568 | 4.284550 | GCAGGTGCCCCAACCAGA | 62.285 | 66.667 | 0.00 | 0.00 | 43.20 | 3.86 |
2359 | 2578 | 3.214696 | AGTCCAATATAAGGCAGGTGC | 57.785 | 47.619 | 0.00 | 0.00 | 41.14 | 5.01 |
2360 | 2579 | 6.207417 | CCAAATAGTCCAATATAAGGCAGGTG | 59.793 | 42.308 | 0.00 | 0.00 | 0.00 | 4.00 |
2361 | 2580 | 6.306987 | CCAAATAGTCCAATATAAGGCAGGT | 58.693 | 40.000 | 0.00 | 0.00 | 0.00 | 4.00 |
2362 | 2581 | 5.183904 | GCCAAATAGTCCAATATAAGGCAGG | 59.816 | 44.000 | 0.00 | 0.00 | 36.21 | 4.85 |
2363 | 2582 | 6.006449 | AGCCAAATAGTCCAATATAAGGCAG | 58.994 | 40.000 | 0.00 | 0.00 | 37.53 | 4.85 |
2364 | 2583 | 5.952387 | AGCCAAATAGTCCAATATAAGGCA | 58.048 | 37.500 | 0.00 | 0.00 | 37.53 | 4.75 |
2365 | 2584 | 7.665974 | AGTTAGCCAAATAGTCCAATATAAGGC | 59.334 | 37.037 | 0.00 | 0.00 | 36.33 | 4.35 |
2366 | 2585 | 9.574516 | AAGTTAGCCAAATAGTCCAATATAAGG | 57.425 | 33.333 | 0.00 | 0.00 | 0.00 | 2.69 |
2370 | 2589 | 9.474313 | TTTCAAGTTAGCCAAATAGTCCAATAT | 57.526 | 29.630 | 0.00 | 0.00 | 0.00 | 1.28 |
2371 | 2590 | 8.871629 | TTTCAAGTTAGCCAAATAGTCCAATA | 57.128 | 30.769 | 0.00 | 0.00 | 0.00 | 1.90 |
2372 | 2591 | 7.775053 | TTTCAAGTTAGCCAAATAGTCCAAT | 57.225 | 32.000 | 0.00 | 0.00 | 0.00 | 3.16 |
2373 | 2592 | 7.309744 | CCATTTCAAGTTAGCCAAATAGTCCAA | 60.310 | 37.037 | 0.00 | 0.00 | 0.00 | 3.53 |
2374 | 2593 | 6.152661 | CCATTTCAAGTTAGCCAAATAGTCCA | 59.847 | 38.462 | 0.00 | 0.00 | 0.00 | 4.02 |
2375 | 2594 | 6.152831 | ACCATTTCAAGTTAGCCAAATAGTCC | 59.847 | 38.462 | 0.00 | 0.00 | 0.00 | 3.85 |
2376 | 2595 | 7.158099 | ACCATTTCAAGTTAGCCAAATAGTC | 57.842 | 36.000 | 0.00 | 0.00 | 0.00 | 2.59 |
2377 | 2596 | 8.823220 | ATACCATTTCAAGTTAGCCAAATAGT | 57.177 | 30.769 | 0.00 | 0.00 | 0.00 | 2.12 |
2378 | 2597 | 9.520204 | CAATACCATTTCAAGTTAGCCAAATAG | 57.480 | 33.333 | 0.00 | 0.00 | 0.00 | 1.73 |
2379 | 2598 | 9.030452 | ACAATACCATTTCAAGTTAGCCAAATA | 57.970 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
2380 | 2599 | 7.906327 | ACAATACCATTTCAAGTTAGCCAAAT | 58.094 | 30.769 | 0.00 | 0.00 | 0.00 | 2.32 |
2381 | 2600 | 7.296628 | ACAATACCATTTCAAGTTAGCCAAA | 57.703 | 32.000 | 0.00 | 0.00 | 0.00 | 3.28 |
2382 | 2601 | 6.909550 | ACAATACCATTTCAAGTTAGCCAA | 57.090 | 33.333 | 0.00 | 0.00 | 0.00 | 4.52 |
2383 | 2602 | 6.909550 | AACAATACCATTTCAAGTTAGCCA | 57.090 | 33.333 | 0.00 | 0.00 | 0.00 | 4.75 |
2384 | 2603 | 8.601845 | AAAAACAATACCATTTCAAGTTAGCC | 57.398 | 30.769 | 0.00 | 0.00 | 0.00 | 3.93 |
2388 | 2607 | 9.830975 | AGCTTAAAAACAATACCATTTCAAGTT | 57.169 | 25.926 | 0.00 | 0.00 | 0.00 | 2.66 |
2389 | 2608 | 9.260002 | CAGCTTAAAAACAATACCATTTCAAGT | 57.740 | 29.630 | 0.00 | 0.00 | 0.00 | 3.16 |
2390 | 2609 | 9.474920 | TCAGCTTAAAAACAATACCATTTCAAG | 57.525 | 29.630 | 0.00 | 0.00 | 0.00 | 3.02 |
2391 | 2610 | 9.255304 | GTCAGCTTAAAAACAATACCATTTCAA | 57.745 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
2392 | 2611 | 8.417106 | TGTCAGCTTAAAAACAATACCATTTCA | 58.583 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
2393 | 2612 | 8.810652 | TGTCAGCTTAAAAACAATACCATTTC | 57.189 | 30.769 | 0.00 | 0.00 | 0.00 | 2.17 |
2394 | 2613 | 9.606631 | TTTGTCAGCTTAAAAACAATACCATTT | 57.393 | 25.926 | 0.00 | 0.00 | 32.16 | 2.32 |
2395 | 2614 | 9.777297 | ATTTGTCAGCTTAAAAACAATACCATT | 57.223 | 25.926 | 0.00 | 0.00 | 32.16 | 3.16 |
2396 | 2615 | 9.777297 | AATTTGTCAGCTTAAAAACAATACCAT | 57.223 | 25.926 | 0.00 | 0.00 | 32.16 | 3.55 |
2397 | 2616 | 9.255304 | GAATTTGTCAGCTTAAAAACAATACCA | 57.745 | 29.630 | 0.00 | 0.00 | 32.16 | 3.25 |
2398 | 2617 | 9.255304 | TGAATTTGTCAGCTTAAAAACAATACC | 57.745 | 29.630 | 0.00 | 0.00 | 32.16 | 2.73 |
2410 | 2629 | 9.060347 | CACCTACATATATGAATTTGTCAGCTT | 57.940 | 33.333 | 19.63 | 0.00 | 40.43 | 3.74 |
2411 | 2630 | 8.432013 | TCACCTACATATATGAATTTGTCAGCT | 58.568 | 33.333 | 19.63 | 0.00 | 40.43 | 4.24 |
2412 | 2631 | 8.607441 | TCACCTACATATATGAATTTGTCAGC | 57.393 | 34.615 | 19.63 | 0.00 | 40.43 | 4.26 |
2414 | 2633 | 9.725019 | GGATCACCTACATATATGAATTTGTCA | 57.275 | 33.333 | 19.63 | 0.00 | 41.67 | 3.58 |
2415 | 2634 | 9.950496 | AGGATCACCTACATATATGAATTTGTC | 57.050 | 33.333 | 19.63 | 8.42 | 45.83 | 3.18 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.