Multiple sequence alignment - TraesCS1D01G443500

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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 TraesCS1D01G443500 chr1D 100.000 2739 0 0 1 2739 487307374 487304636 0.000000e+00 5059
1 TraesCS1D01G443500 chr1D 98.934 2346 20 3 1 2346 30698305 30695965 0.000000e+00 4189
2 TraesCS1D01G443500 chr1D 93.333 405 20 7 2339 2739 208774293 208774694 2.350000e-165 592
3 TraesCS1D01G443500 chr1D 93.052 403 23 5 2339 2739 279302659 279303058 3.930000e-163 584
4 TraesCS1D01G443500 chr3D 99.147 2346 19 1 1 2346 465175691 465178035 0.000000e+00 4220
5 TraesCS1D01G443500 chr3D 97.656 2346 54 1 1 2346 516403664 516401320 0.000000e+00 4026
6 TraesCS1D01G443500 chr3D 97.264 402 10 1 2339 2739 170743125 170743526 0.000000e+00 680
7 TraesCS1D01G443500 chr3D 92.804 403 21 7 2339 2739 61498225 61498621 6.580000e-161 577
8 TraesCS1D01G443500 chr2B 97.659 2349 50 4 1 2346 431356 433702 0.000000e+00 4028
9 TraesCS1D01G443500 chr7A 96.078 2346 90 2 1 2346 303752226 303749883 0.000000e+00 3821
10 TraesCS1D01G443500 chr5A 95.319 2350 85 14 1 2346 168957345 168959673 0.000000e+00 3707
11 TraesCS1D01G443500 chr6A 95.183 2346 77 12 1 2346 276499067 276501376 0.000000e+00 3674
12 TraesCS1D01G443500 chr1B 94.260 2073 107 10 1 2072 40302773 40300712 0.000000e+00 3158
13 TraesCS1D01G443500 chr4B 93.584 2073 126 7 1 2072 272432847 272430781 0.000000e+00 3085
14 TraesCS1D01G443500 chr3A 97.170 1555 44 0 1 1555 706202316 706203870 0.000000e+00 2628
15 TraesCS1D01G443500 chr3A 92.822 404 24 4 2339 2739 120795568 120795167 5.080000e-162 580
16 TraesCS1D01G443500 chr1A 95.916 759 31 0 1588 2346 347417584 347416826 0.000000e+00 1230
17 TraesCS1D01G443500 chr1A 93.052 403 24 4 2339 2739 118226524 118226924 1.090000e-163 586
18 TraesCS1D01G443500 chr2D 97.030 404 9 3 2339 2739 438699403 438699806 0.000000e+00 676
19 TraesCS1D01G443500 chr2D 96.535 404 11 3 2339 2739 558987632 558987229 0.000000e+00 665
20 TraesCS1D01G443500 chr6B 92.593 405 24 5 2339 2739 55410088 55410490 6.580000e-161 577
21 TraesCS1D01G443500 chr6B 94.167 240 13 1 2107 2346 658921664 658921426 5.570000e-97 364


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 TraesCS1D01G443500 chr1D 487304636 487307374 2738 True 5059 5059 100.000 1 2739 1 chr1D.!!$R2 2738
1 TraesCS1D01G443500 chr1D 30695965 30698305 2340 True 4189 4189 98.934 1 2346 1 chr1D.!!$R1 2345
2 TraesCS1D01G443500 chr3D 465175691 465178035 2344 False 4220 4220 99.147 1 2346 1 chr3D.!!$F3 2345
3 TraesCS1D01G443500 chr3D 516401320 516403664 2344 True 4026 4026 97.656 1 2346 1 chr3D.!!$R1 2345
4 TraesCS1D01G443500 chr2B 431356 433702 2346 False 4028 4028 97.659 1 2346 1 chr2B.!!$F1 2345
5 TraesCS1D01G443500 chr7A 303749883 303752226 2343 True 3821 3821 96.078 1 2346 1 chr7A.!!$R1 2345
6 TraesCS1D01G443500 chr5A 168957345 168959673 2328 False 3707 3707 95.319 1 2346 1 chr5A.!!$F1 2345
7 TraesCS1D01G443500 chr6A 276499067 276501376 2309 False 3674 3674 95.183 1 2346 1 chr6A.!!$F1 2345
8 TraesCS1D01G443500 chr1B 40300712 40302773 2061 True 3158 3158 94.260 1 2072 1 chr1B.!!$R1 2071
9 TraesCS1D01G443500 chr4B 272430781 272432847 2066 True 3085 3085 93.584 1 2072 1 chr4B.!!$R1 2071
10 TraesCS1D01G443500 chr3A 706202316 706203870 1554 False 2628 2628 97.170 1 1555 1 chr3A.!!$F1 1554
11 TraesCS1D01G443500 chr1A 347416826 347417584 758 True 1230 1230 95.916 1588 2346 1 chr1A.!!$R1 758

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
77 79 2.558313 GTGCTTCGTGCTTGCCTC 59.442 61.111 5.0 0.0 43.37 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1821 4.69476 TCATCCATCAACATCCCTACAG 57.305 45.455 0.0 0.0 0.0 2.74 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
77 79 2.558313 GTGCTTCGTGCTTGCCTC 59.442 61.111 5.00 0.00 43.37 4.70
702 717 9.770097 TTAGTCATTCATTAAATAGAGGCTCAG 57.230 33.333 18.26 0.00 0.00 3.35
879 896 8.807948 TTGCTTAGATTAGCTCTAACCATTTT 57.192 30.769 0.00 0.00 40.72 1.82
880 897 8.807948 TGCTTAGATTAGCTCTAACCATTTTT 57.192 30.769 0.00 0.00 40.72 1.94
1316 1333 7.360113 TCCATACAAGCAGTGTCTATTATGA 57.640 36.000 0.00 0.00 41.98 2.15
1799 1821 9.241317 GTTCCTTGGTTAAGTTTTAGTTTAAGC 57.759 33.333 0.00 0.00 37.62 3.09
2157 2181 5.664294 AACCACCAACGTATATGAGTGTA 57.336 39.130 0.00 0.00 0.00 2.90
2346 2370 3.072915 TGCTATATGATGGGTCCTGTTGG 59.927 47.826 0.00 0.00 0.00 3.77
2347 2371 3.327757 GCTATATGATGGGTCCTGTTGGA 59.672 47.826 0.00 0.00 40.69 3.53
2348 2372 4.018960 GCTATATGATGGGTCCTGTTGGAT 60.019 45.833 0.00 0.00 45.29 3.41
2349 2373 5.515534 GCTATATGATGGGTCCTGTTGGATT 60.516 44.000 0.00 0.00 45.29 3.01
2350 2374 6.296432 GCTATATGATGGGTCCTGTTGGATTA 60.296 42.308 0.00 0.00 45.29 1.75
2351 2375 3.931907 TGATGGGTCCTGTTGGATTAG 57.068 47.619 0.00 0.00 45.29 1.73
2352 2376 2.509548 TGATGGGTCCTGTTGGATTAGG 59.490 50.000 0.00 0.00 45.29 2.69
2353 2377 2.352561 TGGGTCCTGTTGGATTAGGA 57.647 50.000 0.00 0.00 45.29 2.94
2359 2383 2.576191 TCCTGTTGGATTAGGACTTGGG 59.424 50.000 0.00 0.00 38.15 4.12
2360 2384 2.576191 CCTGTTGGATTAGGACTTGGGA 59.424 50.000 0.00 0.00 36.11 4.37
2361 2385 3.370953 CCTGTTGGATTAGGACTTGGGAG 60.371 52.174 0.00 0.00 36.11 4.30
2362 2386 2.576191 TGTTGGATTAGGACTTGGGAGG 59.424 50.000 0.00 0.00 0.00 4.30
2363 2387 1.893315 TGGATTAGGACTTGGGAGGG 58.107 55.000 0.00 0.00 0.00 4.30
2364 2388 1.141185 GGATTAGGACTTGGGAGGGG 58.859 60.000 0.00 0.00 0.00 4.79
2365 2389 1.141185 GATTAGGACTTGGGAGGGGG 58.859 60.000 0.00 0.00 0.00 5.40
2379 2403 4.074854 GGGGGAAAGAGGAGAGGG 57.925 66.667 0.00 0.00 0.00 4.30
2380 2404 1.396594 GGGGGAAAGAGGAGAGGGA 59.603 63.158 0.00 0.00 0.00 4.20
2381 2405 0.692756 GGGGGAAAGAGGAGAGGGAG 60.693 65.000 0.00 0.00 0.00 4.30
2382 2406 0.340208 GGGGAAAGAGGAGAGGGAGA 59.660 60.000 0.00 0.00 0.00 3.71
2383 2407 1.273896 GGGGAAAGAGGAGAGGGAGAA 60.274 57.143 0.00 0.00 0.00 2.87
2384 2408 2.115427 GGGAAAGAGGAGAGGGAGAAG 58.885 57.143 0.00 0.00 0.00 2.85
2385 2409 2.292587 GGGAAAGAGGAGAGGGAGAAGA 60.293 54.545 0.00 0.00 0.00 2.87
2386 2410 3.445987 GGAAAGAGGAGAGGGAGAAGAA 58.554 50.000 0.00 0.00 0.00 2.52
2387 2411 3.450817 GGAAAGAGGAGAGGGAGAAGAAG 59.549 52.174 0.00 0.00 0.00 2.85
2388 2412 2.846665 AGAGGAGAGGGAGAAGAAGG 57.153 55.000 0.00 0.00 0.00 3.46
2389 2413 2.293246 AGAGGAGAGGGAGAAGAAGGA 58.707 52.381 0.00 0.00 0.00 3.36
2390 2414 2.657459 AGAGGAGAGGGAGAAGAAGGAA 59.343 50.000 0.00 0.00 0.00 3.36
2391 2415 3.031013 GAGGAGAGGGAGAAGAAGGAAG 58.969 54.545 0.00 0.00 0.00 3.46
2392 2416 2.115427 GGAGAGGGAGAAGAAGGAAGG 58.885 57.143 0.00 0.00 0.00 3.46
2393 2417 2.115427 GAGAGGGAGAAGAAGGAAGGG 58.885 57.143 0.00 0.00 0.00 3.95
2394 2418 1.208706 GAGGGAGAAGAAGGAAGGGG 58.791 60.000 0.00 0.00 0.00 4.79
2395 2419 0.253394 AGGGAGAAGAAGGAAGGGGG 60.253 60.000 0.00 0.00 0.00 5.40
2415 2439 4.803908 GCCGCCCCCTTCTCCTTG 62.804 72.222 0.00 0.00 0.00 3.61
2416 2440 3.330720 CCGCCCCCTTCTCCTTGT 61.331 66.667 0.00 0.00 0.00 3.16
2417 2441 2.269241 CGCCCCCTTCTCCTTGTC 59.731 66.667 0.00 0.00 0.00 3.18
2418 2442 2.677848 GCCCCCTTCTCCTTGTCC 59.322 66.667 0.00 0.00 0.00 4.02
2419 2443 1.925972 GCCCCCTTCTCCTTGTCCT 60.926 63.158 0.00 0.00 0.00 3.85
2420 2444 0.620700 GCCCCCTTCTCCTTGTCCTA 60.621 60.000 0.00 0.00 0.00 2.94
2421 2445 1.977202 GCCCCCTTCTCCTTGTCCTAT 60.977 57.143 0.00 0.00 0.00 2.57
2422 2446 2.493091 CCCCCTTCTCCTTGTCCTATT 58.507 52.381 0.00 0.00 0.00 1.73
2423 2447 2.439880 CCCCCTTCTCCTTGTCCTATTC 59.560 54.545 0.00 0.00 0.00 1.75
2424 2448 2.103263 CCCCTTCTCCTTGTCCTATTCG 59.897 54.545 0.00 0.00 0.00 3.34
2425 2449 2.103263 CCCTTCTCCTTGTCCTATTCGG 59.897 54.545 0.00 0.00 0.00 4.30
2426 2450 3.031736 CCTTCTCCTTGTCCTATTCGGA 58.968 50.000 0.00 0.00 40.30 4.55
2435 2459 1.537800 TCCTATTCGGACTAGGGGGA 58.462 55.000 18.20 0.77 36.69 4.81
2436 2460 1.428139 TCCTATTCGGACTAGGGGGAG 59.572 57.143 18.20 0.00 36.69 4.30
2437 2461 1.550409 CCTATTCGGACTAGGGGGAGG 60.550 61.905 12.38 0.00 33.45 4.30
2438 2462 0.485988 TATTCGGACTAGGGGGAGGG 59.514 60.000 0.00 0.00 0.00 4.30
2439 2463 2.327958 ATTCGGACTAGGGGGAGGGG 62.328 65.000 0.00 0.00 0.00 4.79
2464 2488 3.922640 CTCAGCCCTAGCCGCCTC 61.923 72.222 0.00 0.00 41.25 4.70
2465 2489 4.465446 TCAGCCCTAGCCGCCTCT 62.465 66.667 0.00 0.00 41.25 3.69
2466 2490 3.922640 CAGCCCTAGCCGCCTCTC 61.923 72.222 0.00 0.00 41.25 3.20
2469 2493 2.915137 CCCTAGCCGCCTCTCCTC 60.915 72.222 0.00 0.00 0.00 3.71
2470 2494 2.197324 CCTAGCCGCCTCTCCTCT 59.803 66.667 0.00 0.00 0.00 3.69
2471 2495 1.901464 CCTAGCCGCCTCTCCTCTC 60.901 68.421 0.00 0.00 0.00 3.20
2472 2496 1.150536 CTAGCCGCCTCTCCTCTCT 59.849 63.158 0.00 0.00 0.00 3.10
2473 2497 0.467290 CTAGCCGCCTCTCCTCTCTT 60.467 60.000 0.00 0.00 0.00 2.85
2474 2498 0.466555 TAGCCGCCTCTCCTCTCTTC 60.467 60.000 0.00 0.00 0.00 2.87
2475 2499 2.791868 GCCGCCTCTCCTCTCTTCC 61.792 68.421 0.00 0.00 0.00 3.46
2476 2500 1.380515 CCGCCTCTCCTCTCTTCCA 60.381 63.158 0.00 0.00 0.00 3.53
2477 2501 1.671901 CCGCCTCTCCTCTCTTCCAC 61.672 65.000 0.00 0.00 0.00 4.02
2478 2502 1.671901 CGCCTCTCCTCTCTTCCACC 61.672 65.000 0.00 0.00 0.00 4.61
2479 2503 0.325203 GCCTCTCCTCTCTTCCACCT 60.325 60.000 0.00 0.00 0.00 4.00
2480 2504 1.063567 GCCTCTCCTCTCTTCCACCTA 60.064 57.143 0.00 0.00 0.00 3.08
2481 2505 2.944129 CCTCTCCTCTCTTCCACCTAG 58.056 57.143 0.00 0.00 0.00 3.02
2482 2506 2.424234 CCTCTCCTCTCTTCCACCTAGG 60.424 59.091 7.41 7.41 39.47 3.02
2483 2507 1.063567 TCTCCTCTCTTCCACCTAGGC 60.064 57.143 9.30 0.00 37.29 3.93
2484 2508 0.032017 TCCTCTCTTCCACCTAGGCC 60.032 60.000 9.30 0.00 37.29 5.19
2485 2509 1.051556 CCTCTCTTCCACCTAGGCCC 61.052 65.000 9.30 0.00 37.29 5.80
2486 2510 0.325671 CTCTCTTCCACCTAGGCCCA 60.326 60.000 9.30 0.00 37.29 5.36
2487 2511 0.343372 TCTCTTCCACCTAGGCCCAT 59.657 55.000 9.30 0.00 37.29 4.00
2488 2512 1.216990 CTCTTCCACCTAGGCCCATT 58.783 55.000 9.30 0.00 37.29 3.16
2489 2513 2.022428 TCTCTTCCACCTAGGCCCATTA 60.022 50.000 9.30 0.00 37.29 1.90
2490 2514 2.982488 CTCTTCCACCTAGGCCCATTAT 59.018 50.000 9.30 0.00 37.29 1.28
2491 2515 2.711009 TCTTCCACCTAGGCCCATTATG 59.289 50.000 9.30 0.00 37.29 1.90
2492 2516 2.206322 TCCACCTAGGCCCATTATGT 57.794 50.000 9.30 0.00 37.29 2.29
2493 2517 2.498441 TCCACCTAGGCCCATTATGTT 58.502 47.619 9.30 0.00 37.29 2.71
2494 2518 2.174639 TCCACCTAGGCCCATTATGTTG 59.825 50.000 9.30 0.00 37.29 3.33
2495 2519 1.956477 CACCTAGGCCCATTATGTTGC 59.044 52.381 9.30 0.00 0.00 4.17
2496 2520 1.133482 ACCTAGGCCCATTATGTTGCC 60.133 52.381 9.30 13.10 44.35 4.52
2498 2522 3.128375 GGCCCATTATGTTGCCGG 58.872 61.111 0.00 0.00 33.59 6.13
2499 2523 2.498056 GGCCCATTATGTTGCCGGG 61.498 63.158 2.18 0.00 40.11 5.73
2500 2524 2.498056 GCCCATTATGTTGCCGGGG 61.498 63.158 2.18 0.00 37.38 5.73
2501 2525 1.832167 CCCATTATGTTGCCGGGGG 60.832 63.158 2.18 0.00 32.88 5.40
2523 2547 4.344237 CGGTAACCTCCCGGTACT 57.656 61.111 0.00 0.00 44.73 2.73
2524 2548 2.110296 CGGTAACCTCCCGGTACTC 58.890 63.158 0.00 0.00 44.73 2.59
2525 2549 1.387295 CGGTAACCTCCCGGTACTCC 61.387 65.000 0.00 0.00 44.73 3.85
2537 2561 2.229675 GGTACTCCGGTAAAATCCCG 57.770 55.000 0.00 0.00 45.07 5.14
2546 2570 2.356695 CGGTAAAATCCCGATTTCACCC 59.643 50.000 14.34 8.80 43.21 4.61
2547 2571 2.356695 GGTAAAATCCCGATTTCACCCG 59.643 50.000 10.36 0.00 41.28 5.28
2548 2572 1.470051 AAAATCCCGATTTCACCCGG 58.530 50.000 3.25 0.00 39.88 5.73
2554 2578 3.226884 CGATTTCACCCGGAACACT 57.773 52.632 0.73 0.00 34.56 3.55
2555 2579 1.519408 CGATTTCACCCGGAACACTT 58.481 50.000 0.73 0.00 34.56 3.16
2556 2580 1.463444 CGATTTCACCCGGAACACTTC 59.537 52.381 0.73 0.00 34.56 3.01
2557 2581 1.810755 GATTTCACCCGGAACACTTCC 59.189 52.381 0.73 0.00 46.62 3.46
2568 2592 4.877323 GGAACACTTCCGATATCCAAAC 57.123 45.455 0.00 0.00 40.59 2.93
2569 2593 4.258543 GGAACACTTCCGATATCCAAACA 58.741 43.478 0.00 0.00 40.59 2.83
2570 2594 4.881850 GGAACACTTCCGATATCCAAACAT 59.118 41.667 0.00 0.00 40.59 2.71
2571 2595 6.053005 GGAACACTTCCGATATCCAAACATA 58.947 40.000 0.00 0.00 40.59 2.29
2572 2596 6.202954 GGAACACTTCCGATATCCAAACATAG 59.797 42.308 0.00 0.00 40.59 2.23
2573 2597 5.611374 ACACTTCCGATATCCAAACATAGG 58.389 41.667 0.00 0.00 0.00 2.57
2574 2598 4.452455 CACTTCCGATATCCAAACATAGGC 59.548 45.833 0.00 0.00 0.00 3.93
2575 2599 4.348168 ACTTCCGATATCCAAACATAGGCT 59.652 41.667 0.00 0.00 0.00 4.58
2576 2600 4.974645 TCCGATATCCAAACATAGGCTT 57.025 40.909 0.00 0.00 0.00 4.35
2577 2601 4.894784 TCCGATATCCAAACATAGGCTTC 58.105 43.478 0.00 0.00 0.00 3.86
2578 2602 4.003648 CCGATATCCAAACATAGGCTTCC 58.996 47.826 0.00 0.00 0.00 3.46
2579 2603 4.504864 CCGATATCCAAACATAGGCTTCCA 60.505 45.833 0.00 0.00 0.00 3.53
2580 2604 5.063204 CGATATCCAAACATAGGCTTCCAA 58.937 41.667 0.00 0.00 0.00 3.53
2581 2605 5.707298 CGATATCCAAACATAGGCTTCCAAT 59.293 40.000 0.00 0.00 0.00 3.16
2582 2606 6.878923 CGATATCCAAACATAGGCTTCCAATA 59.121 38.462 0.00 0.00 0.00 1.90
2583 2607 7.554118 CGATATCCAAACATAGGCTTCCAATAT 59.446 37.037 0.00 0.00 0.00 1.28
2584 2608 9.905713 GATATCCAAACATAGGCTTCCAATATA 57.094 33.333 0.00 0.00 0.00 0.86
2586 2610 8.814038 ATCCAAACATAGGCTTCCAATATATC 57.186 34.615 0.00 0.00 0.00 1.63
2587 2611 7.754624 TCCAAACATAGGCTTCCAATATATCA 58.245 34.615 0.00 0.00 0.00 2.15
2588 2612 8.224025 TCCAAACATAGGCTTCCAATATATCAA 58.776 33.333 0.00 0.00 0.00 2.57
2589 2613 9.028284 CCAAACATAGGCTTCCAATATATCAAT 57.972 33.333 0.00 0.00 0.00 2.57
2608 2632 9.784531 ATATCAATCTTTATGTCTCGACCATTT 57.215 29.630 0.00 0.00 0.00 2.32
2609 2633 7.539712 TCAATCTTTATGTCTCGACCATTTC 57.460 36.000 0.00 0.00 0.00 2.17
2629 2653 0.378962 GAGACTCCTCGTCATGTCCG 59.621 60.000 0.00 0.00 45.32 4.79
2630 2654 0.322636 AGACTCCTCGTCATGTCCGT 60.323 55.000 7.27 0.00 45.32 4.69
2631 2655 0.179161 GACTCCTCGTCATGTCCGTG 60.179 60.000 7.27 5.40 42.37 4.94
2632 2656 0.608308 ACTCCTCGTCATGTCCGTGA 60.608 55.000 9.87 6.71 0.00 4.35
2633 2657 0.741326 CTCCTCGTCATGTCCGTGAT 59.259 55.000 9.87 0.00 0.00 3.06
2634 2658 0.738975 TCCTCGTCATGTCCGTGATC 59.261 55.000 9.87 0.00 0.00 2.92
2635 2659 0.455815 CCTCGTCATGTCCGTGATCA 59.544 55.000 0.00 0.00 0.00 2.92
2636 2660 1.550065 CTCGTCATGTCCGTGATCAC 58.450 55.000 16.21 16.21 0.00 3.06
2637 2661 0.885196 TCGTCATGTCCGTGATCACA 59.115 50.000 24.93 6.43 0.00 3.58
2638 2662 1.476488 TCGTCATGTCCGTGATCACAT 59.524 47.619 24.93 8.58 33.29 3.21
2639 2663 1.854743 CGTCATGTCCGTGATCACATC 59.145 52.381 24.93 14.22 30.48 3.06
2640 2664 2.205074 GTCATGTCCGTGATCACATCC 58.795 52.381 24.93 11.86 30.48 3.51
2641 2665 1.202405 TCATGTCCGTGATCACATCCG 60.202 52.381 24.93 11.26 30.48 4.18
2642 2666 0.104855 ATGTCCGTGATCACATCCGG 59.895 55.000 24.93 19.53 41.44 5.14
2643 2667 1.227263 GTCCGTGATCACATCCGGG 60.227 63.158 24.93 16.92 40.88 5.73
2644 2668 1.380650 TCCGTGATCACATCCGGGA 60.381 57.895 24.93 18.83 40.88 5.14
2645 2669 1.227263 CCGTGATCACATCCGGGAC 60.227 63.158 24.93 0.00 38.56 4.46
2646 2670 1.676678 CCGTGATCACATCCGGGACT 61.677 60.000 24.93 0.00 38.56 3.85
2647 2671 0.249073 CGTGATCACATCCGGGACTC 60.249 60.000 24.93 0.00 0.00 3.36
2648 2672 0.105039 GTGATCACATCCGGGACTCC 59.895 60.000 21.07 0.00 0.00 3.85
2660 2684 1.641577 GGGACTCCGAACAATCTTCG 58.358 55.000 0.00 0.00 41.21 3.79
2670 2694 5.524511 CGAACAATCTTCGGTACATCAAA 57.475 39.130 0.00 0.00 38.19 2.69
2671 2695 5.922546 CGAACAATCTTCGGTACATCAAAA 58.077 37.500 0.00 0.00 38.19 2.44
2672 2696 5.788531 CGAACAATCTTCGGTACATCAAAAC 59.211 40.000 0.00 0.00 38.19 2.43
2673 2697 6.565060 CGAACAATCTTCGGTACATCAAAACA 60.565 38.462 0.00 0.00 38.19 2.83
2674 2698 6.817765 ACAATCTTCGGTACATCAAAACAT 57.182 33.333 0.00 0.00 0.00 2.71
2675 2699 7.915293 ACAATCTTCGGTACATCAAAACATA 57.085 32.000 0.00 0.00 0.00 2.29
2676 2700 8.506168 ACAATCTTCGGTACATCAAAACATAT 57.494 30.769 0.00 0.00 0.00 1.78
2677 2701 9.607988 ACAATCTTCGGTACATCAAAACATATA 57.392 29.630 0.00 0.00 0.00 0.86
2681 2705 9.661563 TCTTCGGTACATCAAAACATATAAACT 57.338 29.630 0.00 0.00 0.00 2.66
2682 2706 9.916397 CTTCGGTACATCAAAACATATAAACTC 57.084 33.333 0.00 0.00 0.00 3.01
2683 2707 9.438228 TTCGGTACATCAAAACATATAAACTCA 57.562 29.630 0.00 0.00 0.00 3.41
2684 2708 9.607988 TCGGTACATCAAAACATATAAACTCAT 57.392 29.630 0.00 0.00 0.00 2.90
2705 2729 9.181805 ACTCATAATATAACTGTCATCGAAACG 57.818 33.333 0.00 0.00 0.00 3.60
2706 2730 9.181805 CTCATAATATAACTGTCATCGAAACGT 57.818 33.333 0.00 0.00 0.00 3.99
2707 2731 9.524106 TCATAATATAACTGTCATCGAAACGTT 57.476 29.630 0.00 0.00 0.00 3.99
2711 2735 4.385244 AACTGTCATCGAAACGTTAAGC 57.615 40.909 0.00 0.00 0.00 3.09
2721 2745 3.484547 CGTTAAGCGTGCGGACCC 61.485 66.667 0.00 0.00 35.54 4.46
2722 2746 2.047560 GTTAAGCGTGCGGACCCT 60.048 61.111 0.00 0.00 0.00 4.34
2723 2747 1.216178 GTTAAGCGTGCGGACCCTA 59.784 57.895 0.00 0.00 0.00 3.53
2724 2748 1.080435 GTTAAGCGTGCGGACCCTAC 61.080 60.000 0.00 0.00 0.00 3.18
2725 2749 2.546645 TTAAGCGTGCGGACCCTACG 62.547 60.000 0.00 10.04 40.52 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
702 717 0.457681 ACCTGCGCACAAACAAACAC 60.458 50.000 5.66 0.00 0.00 3.32
879 896 3.498774 AGAGCAGAAAAGAAGGCTGAA 57.501 42.857 0.00 0.00 36.59 3.02
880 897 3.498774 AAGAGCAGAAAAGAAGGCTGA 57.501 42.857 0.00 0.00 36.59 4.26
1316 1333 9.591792 GTACCTACTTAGTTGACGGATTAAAAT 57.408 33.333 0.00 0.00 0.00 1.82
1799 1821 4.694760 TCATCCATCAACATCCCTACAG 57.305 45.455 0.00 0.00 0.00 2.74
2157 2181 7.324354 ACAACACATAAAACCGACTTTTACT 57.676 32.000 0.00 0.00 37.19 2.24
2346 2370 1.141185 CCCCCTCCCAAGTCCTAATC 58.859 60.000 0.00 0.00 0.00 1.75
2347 2371 3.359669 CCCCCTCCCAAGTCCTAAT 57.640 57.895 0.00 0.00 0.00 1.73
2348 2372 4.933607 CCCCCTCCCAAGTCCTAA 57.066 61.111 0.00 0.00 0.00 2.69
2362 2386 0.692756 CTCCCTCTCCTCTTTCCCCC 60.693 65.000 0.00 0.00 0.00 5.40
2363 2387 0.340208 TCTCCCTCTCCTCTTTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
2364 2388 2.115427 CTTCTCCCTCTCCTCTTTCCC 58.885 57.143 0.00 0.00 0.00 3.97
2365 2389 3.108847 TCTTCTCCCTCTCCTCTTTCC 57.891 52.381 0.00 0.00 0.00 3.13
2366 2390 3.450817 CCTTCTTCTCCCTCTCCTCTTTC 59.549 52.174 0.00 0.00 0.00 2.62
2367 2391 3.078305 TCCTTCTTCTCCCTCTCCTCTTT 59.922 47.826 0.00 0.00 0.00 2.52
2368 2392 2.657459 TCCTTCTTCTCCCTCTCCTCTT 59.343 50.000 0.00 0.00 0.00 2.85
2369 2393 2.293246 TCCTTCTTCTCCCTCTCCTCT 58.707 52.381 0.00 0.00 0.00 3.69
2370 2394 2.838637 TCCTTCTTCTCCCTCTCCTC 57.161 55.000 0.00 0.00 0.00 3.71
2371 2395 2.292851 CCTTCCTTCTTCTCCCTCTCCT 60.293 54.545 0.00 0.00 0.00 3.69
2372 2396 2.115427 CCTTCCTTCTTCTCCCTCTCC 58.885 57.143 0.00 0.00 0.00 3.71
2373 2397 2.115427 CCCTTCCTTCTTCTCCCTCTC 58.885 57.143 0.00 0.00 0.00 3.20
2374 2398 1.274126 CCCCTTCCTTCTTCTCCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
2375 2399 1.208706 CCCCTTCCTTCTTCTCCCTC 58.791 60.000 0.00 0.00 0.00 4.30
2376 2400 0.253394 CCCCCTTCCTTCTTCTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
2377 2401 2.312323 CCCCCTTCCTTCTTCTCCC 58.688 63.158 0.00 0.00 0.00 4.30
2398 2422 4.803908 CAAGGAGAAGGGGGCGGC 62.804 72.222 0.00 0.00 0.00 6.53
2399 2423 3.330720 ACAAGGAGAAGGGGGCGG 61.331 66.667 0.00 0.00 0.00 6.13
2400 2424 2.269241 GACAAGGAGAAGGGGGCG 59.731 66.667 0.00 0.00 0.00 6.13
2401 2425 0.620700 TAGGACAAGGAGAAGGGGGC 60.621 60.000 0.00 0.00 0.00 5.80
2402 2426 2.198334 ATAGGACAAGGAGAAGGGGG 57.802 55.000 0.00 0.00 0.00 5.40
2403 2427 2.103263 CGAATAGGACAAGGAGAAGGGG 59.897 54.545 0.00 0.00 0.00 4.79
2404 2428 2.103263 CCGAATAGGACAAGGAGAAGGG 59.897 54.545 0.00 0.00 45.00 3.95
2405 2429 3.031736 TCCGAATAGGACAAGGAGAAGG 58.968 50.000 0.00 0.00 45.98 3.46
2417 2441 1.550409 CCTCCCCCTAGTCCGAATAGG 60.550 61.905 13.97 13.97 39.71 2.57
2418 2442 1.550409 CCCTCCCCCTAGTCCGAATAG 60.550 61.905 0.00 0.00 0.00 1.73
2419 2443 0.485988 CCCTCCCCCTAGTCCGAATA 59.514 60.000 0.00 0.00 0.00 1.75
2420 2444 1.236282 CCCTCCCCCTAGTCCGAAT 59.764 63.158 0.00 0.00 0.00 3.34
2421 2445 2.694305 CCCTCCCCCTAGTCCGAA 59.306 66.667 0.00 0.00 0.00 4.30
2422 2446 3.436028 CCCCTCCCCCTAGTCCGA 61.436 72.222 0.00 0.00 0.00 4.55
2449 2473 3.922640 GAGAGGCGGCTAGGGCTG 61.923 72.222 13.24 0.00 43.66 4.85
2452 2476 2.915137 GAGGAGAGGCGGCTAGGG 60.915 72.222 13.24 0.00 0.00 3.53
2453 2477 1.901464 GAGAGGAGAGGCGGCTAGG 60.901 68.421 13.24 0.00 0.00 3.02
2454 2478 0.467290 AAGAGAGGAGAGGCGGCTAG 60.467 60.000 13.24 0.00 0.00 3.42
2455 2479 0.466555 GAAGAGAGGAGAGGCGGCTA 60.467 60.000 13.24 0.00 0.00 3.93
2456 2480 1.756561 GAAGAGAGGAGAGGCGGCT 60.757 63.158 13.09 13.09 0.00 5.52
2457 2481 2.791868 GGAAGAGAGGAGAGGCGGC 61.792 68.421 0.00 0.00 0.00 6.53
2458 2482 1.380515 TGGAAGAGAGGAGAGGCGG 60.381 63.158 0.00 0.00 0.00 6.13
2459 2483 1.671901 GGTGGAAGAGAGGAGAGGCG 61.672 65.000 0.00 0.00 0.00 5.52
2460 2484 0.325203 AGGTGGAAGAGAGGAGAGGC 60.325 60.000 0.00 0.00 0.00 4.70
2461 2485 2.424234 CCTAGGTGGAAGAGAGGAGAGG 60.424 59.091 0.00 0.00 38.35 3.69
2462 2486 2.944129 CCTAGGTGGAAGAGAGGAGAG 58.056 57.143 0.00 0.00 38.35 3.20
2463 2487 1.063567 GCCTAGGTGGAAGAGAGGAGA 60.064 57.143 11.31 0.00 38.35 3.71
2464 2488 1.408969 GCCTAGGTGGAAGAGAGGAG 58.591 60.000 11.31 0.00 38.35 3.69
2465 2489 0.032017 GGCCTAGGTGGAAGAGAGGA 60.032 60.000 11.31 0.00 38.35 3.71
2466 2490 1.051556 GGGCCTAGGTGGAAGAGAGG 61.052 65.000 11.31 0.00 38.35 3.69
2467 2491 0.325671 TGGGCCTAGGTGGAAGAGAG 60.326 60.000 11.31 0.00 38.35 3.20
2468 2492 0.343372 ATGGGCCTAGGTGGAAGAGA 59.657 55.000 11.31 0.00 38.35 3.10
2469 2493 1.216990 AATGGGCCTAGGTGGAAGAG 58.783 55.000 11.31 0.00 38.35 2.85
2470 2494 2.579624 TAATGGGCCTAGGTGGAAGA 57.420 50.000 11.31 0.00 38.35 2.87
2471 2495 2.443255 ACATAATGGGCCTAGGTGGAAG 59.557 50.000 11.31 0.00 38.35 3.46
2472 2496 2.498441 ACATAATGGGCCTAGGTGGAA 58.502 47.619 11.31 0.00 38.35 3.53
2473 2497 2.174639 CAACATAATGGGCCTAGGTGGA 59.825 50.000 11.31 0.00 38.35 4.02
2474 2498 2.586425 CAACATAATGGGCCTAGGTGG 58.414 52.381 11.31 0.00 39.35 4.61
2475 2499 1.956477 GCAACATAATGGGCCTAGGTG 59.044 52.381 11.31 0.84 0.00 4.00
2476 2500 1.133482 GGCAACATAATGGGCCTAGGT 60.133 52.381 11.31 0.00 38.42 3.08
2477 2501 1.620822 GGCAACATAATGGGCCTAGG 58.379 55.000 3.67 3.67 38.42 3.02
2478 2502 1.238439 CGGCAACATAATGGGCCTAG 58.762 55.000 4.53 0.00 39.03 3.02
2479 2503 0.179004 CCGGCAACATAATGGGCCTA 60.179 55.000 4.53 0.00 39.03 3.93
2480 2504 1.455587 CCGGCAACATAATGGGCCT 60.456 57.895 4.53 0.00 39.03 5.19
2481 2505 2.498056 CCCGGCAACATAATGGGCC 61.498 63.158 0.00 0.00 38.20 5.80
2482 2506 2.498056 CCCCGGCAACATAATGGGC 61.498 63.158 0.00 0.00 38.60 5.36
2483 2507 1.832167 CCCCCGGCAACATAATGGG 60.832 63.158 0.00 0.00 39.69 4.00
2484 2508 3.854856 CCCCCGGCAACATAATGG 58.145 61.111 0.00 0.00 0.00 3.16
2527 2551 2.356695 CCGGGTGAAATCGGGATTTTAC 59.643 50.000 16.38 16.38 42.81 2.01
2528 2552 2.239150 TCCGGGTGAAATCGGGATTTTA 59.761 45.455 0.00 1.72 45.69 1.52
2529 2553 1.004979 TCCGGGTGAAATCGGGATTTT 59.995 47.619 0.00 0.00 45.69 1.82
2530 2554 0.621609 TCCGGGTGAAATCGGGATTT 59.378 50.000 0.00 6.36 45.69 2.17
2531 2555 0.621609 TTCCGGGTGAAATCGGGATT 59.378 50.000 0.00 0.00 45.69 3.01
2532 2556 0.107361 GTTCCGGGTGAAATCGGGAT 60.107 55.000 0.00 0.00 45.69 3.85
2533 2557 1.297364 GTTCCGGGTGAAATCGGGA 59.703 57.895 0.00 0.00 45.69 5.14
2534 2558 1.003112 TGTTCCGGGTGAAATCGGG 60.003 57.895 0.00 0.00 45.69 5.14
2535 2559 0.321298 AGTGTTCCGGGTGAAATCGG 60.321 55.000 0.00 0.00 46.89 4.18
2536 2560 1.463444 GAAGTGTTCCGGGTGAAATCG 59.537 52.381 0.00 0.00 33.94 3.34
2537 2561 1.810755 GGAAGTGTTCCGGGTGAAATC 59.189 52.381 0.00 0.00 40.59 2.17
2538 2562 1.905637 GGAAGTGTTCCGGGTGAAAT 58.094 50.000 0.00 0.00 40.59 2.17
2539 2563 3.407443 GGAAGTGTTCCGGGTGAAA 57.593 52.632 0.00 0.00 40.59 2.69
2547 2571 4.258543 TGTTTGGATATCGGAAGTGTTCC 58.741 43.478 0.00 0.00 46.62 3.62
2548 2572 6.202954 CCTATGTTTGGATATCGGAAGTGTTC 59.797 42.308 0.00 0.00 0.00 3.18
2549 2573 6.055588 CCTATGTTTGGATATCGGAAGTGTT 58.944 40.000 0.00 0.00 0.00 3.32
2550 2574 5.611374 CCTATGTTTGGATATCGGAAGTGT 58.389 41.667 0.00 0.00 0.00 3.55
2551 2575 4.452455 GCCTATGTTTGGATATCGGAAGTG 59.548 45.833 0.00 0.00 0.00 3.16
2552 2576 4.348168 AGCCTATGTTTGGATATCGGAAGT 59.652 41.667 0.00 0.00 0.00 3.01
2553 2577 4.899502 AGCCTATGTTTGGATATCGGAAG 58.100 43.478 0.00 0.00 0.00 3.46
2554 2578 4.974645 AGCCTATGTTTGGATATCGGAA 57.025 40.909 0.00 0.00 0.00 4.30
2555 2579 4.262894 GGAAGCCTATGTTTGGATATCGGA 60.263 45.833 0.00 0.00 0.00 4.55
2556 2580 4.003648 GGAAGCCTATGTTTGGATATCGG 58.996 47.826 0.00 0.00 0.00 4.18
2557 2581 4.641396 TGGAAGCCTATGTTTGGATATCG 58.359 43.478 0.00 0.00 0.00 2.92
2558 2582 8.814038 ATATTGGAAGCCTATGTTTGGATATC 57.186 34.615 0.00 0.00 0.00 1.63
2560 2584 9.905713 GATATATTGGAAGCCTATGTTTGGATA 57.094 33.333 0.00 0.00 0.00 2.59
2561 2585 8.393259 TGATATATTGGAAGCCTATGTTTGGAT 58.607 33.333 0.00 0.00 0.00 3.41
2562 2586 7.754624 TGATATATTGGAAGCCTATGTTTGGA 58.245 34.615 0.00 0.00 0.00 3.53
2563 2587 8.408043 TTGATATATTGGAAGCCTATGTTTGG 57.592 34.615 0.00 0.00 0.00 3.28
2582 2606 9.784531 AAATGGTCGAGACATAAAGATTGATAT 57.215 29.630 5.55 0.00 0.00 1.63
2583 2607 9.261180 GAAATGGTCGAGACATAAAGATTGATA 57.739 33.333 5.55 0.00 0.00 2.15
2584 2608 8.147642 GAAATGGTCGAGACATAAAGATTGAT 57.852 34.615 5.55 0.00 0.00 2.57
2585 2609 7.539712 GAAATGGTCGAGACATAAAGATTGA 57.460 36.000 5.55 0.00 0.00 2.57
2613 2637 0.608308 TCACGGACATGACGAGGAGT 60.608 55.000 18.41 0.00 34.93 3.85
2614 2638 0.741326 ATCACGGACATGACGAGGAG 59.259 55.000 18.41 7.68 34.93 3.69
2615 2639 0.738975 GATCACGGACATGACGAGGA 59.261 55.000 18.41 14.97 34.93 3.71
2616 2640 0.455815 TGATCACGGACATGACGAGG 59.544 55.000 18.41 11.22 34.93 4.63
2617 2641 1.135402 TGTGATCACGGACATGACGAG 60.135 52.381 20.54 12.05 34.93 4.18
2618 2642 0.885196 TGTGATCACGGACATGACGA 59.115 50.000 20.54 0.00 34.93 4.20
2619 2643 1.854743 GATGTGATCACGGACATGACG 59.145 52.381 20.54 6.35 32.85 4.35
2620 2644 2.205074 GGATGTGATCACGGACATGAC 58.795 52.381 20.54 0.00 32.85 3.06
2621 2645 1.202405 CGGATGTGATCACGGACATGA 60.202 52.381 20.54 1.72 32.85 3.07
2622 2646 1.211743 CGGATGTGATCACGGACATG 58.788 55.000 20.54 4.98 32.85 3.21
2623 2647 0.104855 CCGGATGTGATCACGGACAT 59.895 55.000 20.54 8.71 42.14 3.06
2624 2648 1.515487 CCGGATGTGATCACGGACA 59.485 57.895 20.54 3.72 42.14 4.02
2625 2649 1.227263 CCCGGATGTGATCACGGAC 60.227 63.158 20.64 13.99 42.14 4.79
2626 2650 1.380650 TCCCGGATGTGATCACGGA 60.381 57.895 20.64 17.06 42.14 4.69
2627 2651 1.227263 GTCCCGGATGTGATCACGG 60.227 63.158 20.54 17.03 40.49 4.94
2628 2652 0.249073 GAGTCCCGGATGTGATCACG 60.249 60.000 20.54 8.81 0.00 4.35
2629 2653 0.105039 GGAGTCCCGGATGTGATCAC 59.895 60.000 19.27 19.27 0.00 3.06
2630 2654 2.516448 GGAGTCCCGGATGTGATCA 58.484 57.895 0.73 0.00 0.00 2.92
2641 2665 1.641577 CGAAGATTGTTCGGAGTCCC 58.358 55.000 7.99 0.00 38.19 4.46
2648 2672 5.524511 TTTGATGTACCGAAGATTGTTCG 57.475 39.130 8.84 8.84 41.21 3.95
2649 2673 6.664515 TGTTTTGATGTACCGAAGATTGTTC 58.335 36.000 0.00 0.00 0.00 3.18
2650 2674 6.627395 TGTTTTGATGTACCGAAGATTGTT 57.373 33.333 0.00 0.00 0.00 2.83
2651 2675 6.817765 ATGTTTTGATGTACCGAAGATTGT 57.182 33.333 0.00 0.00 0.00 2.71
2655 2679 9.661563 AGTTTATATGTTTTGATGTACCGAAGA 57.338 29.630 0.00 0.00 0.00 2.87
2656 2680 9.916397 GAGTTTATATGTTTTGATGTACCGAAG 57.084 33.333 0.00 0.00 0.00 3.79
2657 2681 9.438228 TGAGTTTATATGTTTTGATGTACCGAA 57.562 29.630 0.00 0.00 0.00 4.30
2658 2682 9.607988 ATGAGTTTATATGTTTTGATGTACCGA 57.392 29.630 0.00 0.00 0.00 4.69
2679 2703 9.181805 CGTTTCGATGACAGTTATATTATGAGT 57.818 33.333 0.00 0.00 0.00 3.41
2680 2704 9.181805 ACGTTTCGATGACAGTTATATTATGAG 57.818 33.333 0.00 0.00 0.00 2.90
2681 2705 9.524106 AACGTTTCGATGACAGTTATATTATGA 57.476 29.630 0.00 0.00 0.00 2.15
2685 2709 8.325997 GCTTAACGTTTCGATGACAGTTATATT 58.674 33.333 5.91 0.00 0.00 1.28
2686 2710 7.305820 CGCTTAACGTTTCGATGACAGTTATAT 60.306 37.037 5.91 0.00 36.87 0.86
2687 2711 6.021232 CGCTTAACGTTTCGATGACAGTTATA 60.021 38.462 5.91 0.00 36.87 0.98
2688 2712 5.220154 CGCTTAACGTTTCGATGACAGTTAT 60.220 40.000 5.91 0.00 36.87 1.89
2689 2713 4.088923 CGCTTAACGTTTCGATGACAGTTA 59.911 41.667 5.91 0.23 36.87 2.24
2690 2714 3.121126 CGCTTAACGTTTCGATGACAGTT 60.121 43.478 5.91 1.13 36.87 3.16
2691 2715 2.407361 CGCTTAACGTTTCGATGACAGT 59.593 45.455 5.91 0.00 36.87 3.55
2692 2716 3.008456 CGCTTAACGTTTCGATGACAG 57.992 47.619 5.91 0.00 36.87 3.51
2704 2728 2.546645 TAGGGTCCGCACGCTTAACG 62.547 60.000 0.00 0.00 43.11 3.18
2705 2729 1.080435 GTAGGGTCCGCACGCTTAAC 61.080 60.000 0.00 0.00 43.11 2.01
2706 2730 1.216178 GTAGGGTCCGCACGCTTAA 59.784 57.895 0.00 0.00 43.11 1.85
2707 2731 2.887360 GTAGGGTCCGCACGCTTA 59.113 61.111 0.00 0.00 43.11 3.09
2708 2732 4.430765 CGTAGGGTCCGCACGCTT 62.431 66.667 0.00 0.00 43.11 4.68


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

AutoCloner maintained by Alex Coulton.