Multiple sequence alignment - TraesCS4A01G222400

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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 TraesCS4A01G222400 chr4A 100.000 3449 0 0 1 3449 529625929 529629377 0.000000e+00 6370
1 TraesCS4A01G222400 chr4A 98.246 114 1 1 2465 2578 529628282 529628394 7.550000e-47 198
2 TraesCS4A01G222400 chr4A 98.246 114 1 1 2354 2466 529628393 529628506 7.550000e-47 198
3 TraesCS4A01G222400 chr4D 97.287 2470 46 8 1 2466 65940253 65937801 0.000000e+00 4170
4 TraesCS4A01G222400 chr4D 95.591 998 32 4 2464 3449 65937915 65936918 0.000000e+00 1589
5 TraesCS4A01G222400 chr4B 97.461 1812 45 1 656 2466 96641762 96639951 0.000000e+00 3090
6 TraesCS4A01G222400 chr4B 95.095 999 34 6 2464 3449 96640065 96639069 0.000000e+00 1559
7 TraesCS4A01G222400 chr4B 93.554 605 31 3 1 599 96642498 96641896 0.000000e+00 894


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 TraesCS4A01G222400 chr4A 529625929 529629377 3448 False 2255.333333 6370 98.830667 1 3449 3 chr4A.!!$F1 3448
1 TraesCS4A01G222400 chr4D 65936918 65940253 3335 True 2879.500000 4170 96.439000 1 3449 2 chr4D.!!$R1 3448
2 TraesCS4A01G222400 chr4B 96639069 96642498 3429 True 1847.666667 3090 95.370000 1 3449 3 chr4B.!!$R1 3448

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
348 352 1.004080 CACAGTGAGGCCTGGTCTG 60.004 63.158 12.00 17.77 36.75 3.51 F
349 353 2.046507 CAGTGAGGCCTGGTCTGC 60.047 66.667 12.00 0.00 0.00 4.26 F
386 400 2.178912 TTGTACCTGCCTTTTCCTCG 57.821 50.000 0.00 0.00 0.00 4.63 F
1499 1595 2.126071 CAGGTTCGGTCACGCGAT 60.126 61.111 15.93 0.00 40.69 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1595 1.000052 TGAACATCCTGTACGCGTTGA 60.000 47.619 20.78 10.11 0.00 3.18 R
1500 1596 1.390123 CTGAACATCCTGTACGCGTTG 59.610 52.381 20.78 11.47 0.00 4.10 R
2006 2102 1.672881 CCTCGAAATGTCCCATCTTGC 59.327 52.381 0.00 0.00 0.00 4.01 R
2526 2623 0.393537 GATTCTGCAGGACCACCCAG 60.394 60.000 15.13 0.00 37.41 4.45 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
205 209 2.282958 AGCGAGGAGTTGGACGGA 60.283 61.111 0.00 0.00 0.00 4.69
307 311 2.359602 CAGGAGTGGCACCAGCTG 60.360 66.667 15.27 6.78 41.70 4.24
339 343 2.864114 CCATGAAGGCACAGTGAGG 58.136 57.895 4.15 0.00 0.00 3.86
345 349 3.958860 GGCACAGTGAGGCCTGGT 61.959 66.667 12.00 0.00 46.74 4.00
346 350 2.359230 GCACAGTGAGGCCTGGTC 60.359 66.667 12.00 0.00 36.75 4.02
347 351 2.888447 GCACAGTGAGGCCTGGTCT 61.888 63.158 12.00 0.00 36.75 3.85
348 352 1.004080 CACAGTGAGGCCTGGTCTG 60.004 63.158 12.00 17.77 36.75 3.51
349 353 2.046507 CAGTGAGGCCTGGTCTGC 60.047 66.667 12.00 0.00 0.00 4.26
372 386 4.318546 CGCTCCGCCTGTATAATTTTGTAC 60.319 45.833 0.00 0.00 0.00 2.90
374 388 5.362105 TCCGCCTGTATAATTTTGTACCT 57.638 39.130 0.00 0.00 0.00 3.08
386 400 2.178912 TTGTACCTGCCTTTTCCTCG 57.821 50.000 0.00 0.00 0.00 4.63
403 417 4.584874 TCCTCGAGCCACATTTTGATTTA 58.415 39.130 6.99 0.00 0.00 1.40
404 418 5.192927 TCCTCGAGCCACATTTTGATTTAT 58.807 37.500 6.99 0.00 0.00 1.40
405 419 5.652014 TCCTCGAGCCACATTTTGATTTATT 59.348 36.000 6.99 0.00 0.00 1.40
467 481 3.085952 TCCTGCCGATTTCCTGATTTT 57.914 42.857 0.00 0.00 0.00 1.82
499 513 4.691326 TCACAGGTATTGTTGTACCACA 57.309 40.909 5.94 0.00 45.35 4.17
502 516 5.297278 TCACAGGTATTGTTGTACCACAAAC 59.703 40.000 15.65 13.78 45.35 2.93
649 717 6.071165 AGGTGCTGAATTAATTCCTTTTCCTG 60.071 38.462 22.42 4.93 35.97 3.86
1499 1595 2.126071 CAGGTTCGGTCACGCGAT 60.126 61.111 15.93 0.00 40.69 4.58
1500 1596 2.158959 CAGGTTCGGTCACGCGATC 61.159 63.158 15.93 1.78 40.69 3.69
2006 2102 6.047870 TCTCAATTTTGGTCAATGGTTTGTG 58.952 36.000 0.00 0.00 34.32 3.33
2016 2112 2.299582 CAATGGTTTGTGCAAGATGGGA 59.700 45.455 0.00 0.00 0.00 4.37
2070 2166 4.246143 ACATGGAGATAAGGGACATGGAT 58.754 43.478 0.00 0.00 42.28 3.41
2352 2448 2.358737 AGGAAAGTTCGGGCAGCG 60.359 61.111 0.00 0.00 0.00 5.18
2456 2553 4.628766 CGAGAAGATCAATTGAGCAGACAA 59.371 41.667 24.50 0.00 31.88 3.18
2457 2554 5.121298 CGAGAAGATCAATTGAGCAGACAAA 59.879 40.000 24.50 0.00 33.44 2.83
2458 2555 6.183360 CGAGAAGATCAATTGAGCAGACAAAT 60.183 38.462 24.50 0.00 33.44 2.32
2459 2556 7.463961 AGAAGATCAATTGAGCAGACAAATT 57.536 32.000 24.50 8.92 33.44 1.82
2460 2557 7.313646 AGAAGATCAATTGAGCAGACAAATTG 58.686 34.615 24.50 0.00 33.44 2.32
2461 2558 6.829229 AGATCAATTGAGCAGACAAATTGA 57.171 33.333 24.50 11.25 34.90 2.57
2462 2559 7.223260 AGATCAATTGAGCAGACAAATTGAA 57.777 32.000 24.50 0.00 34.54 2.69
2463 2560 7.663827 AGATCAATTGAGCAGACAAATTGAAA 58.336 30.769 24.50 0.00 34.54 2.69
2464 2561 8.311836 AGATCAATTGAGCAGACAAATTGAAAT 58.688 29.630 24.50 0.00 34.54 2.17
2465 2562 8.842358 ATCAATTGAGCAGACAAATTGAAATT 57.158 26.923 14.54 0.00 34.54 1.82
2466 2563 9.932207 ATCAATTGAGCAGACAAATTGAAATTA 57.068 25.926 14.54 0.00 34.54 1.40
2467 2564 9.195411 TCAATTGAGCAGACAAATTGAAATTAC 57.805 29.630 3.38 0.00 31.53 1.89
2468 2565 7.801547 ATTGAGCAGACAAATTGAAATTACG 57.198 32.000 0.00 0.00 33.44 3.18
2469 2566 6.312399 TGAGCAGACAAATTGAAATTACGT 57.688 33.333 0.00 0.00 0.00 3.57
2470 2567 7.428282 TGAGCAGACAAATTGAAATTACGTA 57.572 32.000 0.00 0.00 0.00 3.57
2471 2568 8.039603 TGAGCAGACAAATTGAAATTACGTAT 57.960 30.769 0.00 0.00 0.00 3.06
2472 2569 7.962373 TGAGCAGACAAATTGAAATTACGTATG 59.038 33.333 0.00 7.81 31.59 2.39
2473 2570 7.250569 AGCAGACAAATTGAAATTACGTATGG 58.749 34.615 0.00 0.00 30.29 2.74
2474 2571 6.020678 GCAGACAAATTGAAATTACGTATGGC 60.021 38.462 0.00 0.00 30.29 4.40
2475 2572 7.250569 CAGACAAATTGAAATTACGTATGGCT 58.749 34.615 0.00 0.00 0.00 4.75
2476 2573 8.394877 CAGACAAATTGAAATTACGTATGGCTA 58.605 33.333 0.00 0.00 0.00 3.93
2477 2574 8.612619 AGACAAATTGAAATTACGTATGGCTAG 58.387 33.333 0.00 0.00 0.00 3.42
2478 2575 7.703328 ACAAATTGAAATTACGTATGGCTAGG 58.297 34.615 0.00 0.00 0.00 3.02
2479 2576 5.941948 ATTGAAATTACGTATGGCTAGGC 57.058 39.130 9.85 9.85 0.00 3.93
2480 2577 4.682778 TGAAATTACGTATGGCTAGGCT 57.317 40.909 18.18 5.72 0.00 4.58
2481 2578 4.377021 TGAAATTACGTATGGCTAGGCTG 58.623 43.478 18.18 7.29 0.00 4.85
2482 2579 4.141801 TGAAATTACGTATGGCTAGGCTGT 60.142 41.667 18.18 12.50 0.00 4.40
2483 2580 4.417426 AATTACGTATGGCTAGGCTGTT 57.583 40.909 18.18 5.12 0.00 3.16
2484 2581 5.540400 AATTACGTATGGCTAGGCTGTTA 57.460 39.130 18.18 4.15 0.00 2.41
2485 2582 5.540400 ATTACGTATGGCTAGGCTGTTAA 57.460 39.130 18.18 8.07 0.00 2.01
2486 2583 3.899052 ACGTATGGCTAGGCTGTTAAA 57.101 42.857 18.18 0.00 0.00 1.52
2487 2584 4.210724 ACGTATGGCTAGGCTGTTAAAA 57.789 40.909 18.18 0.00 0.00 1.52
2488 2585 3.937079 ACGTATGGCTAGGCTGTTAAAAC 59.063 43.478 18.18 4.40 0.00 2.43
2489 2586 4.189231 CGTATGGCTAGGCTGTTAAAACT 58.811 43.478 18.18 0.00 0.00 2.66
2490 2587 5.105228 ACGTATGGCTAGGCTGTTAAAACTA 60.105 40.000 18.18 0.00 0.00 2.24
2491 2588 5.989777 CGTATGGCTAGGCTGTTAAAACTAT 59.010 40.000 18.18 0.91 0.00 2.12
2492 2589 7.149973 CGTATGGCTAGGCTGTTAAAACTATA 58.850 38.462 18.18 0.00 0.00 1.31
2493 2590 7.654520 CGTATGGCTAGGCTGTTAAAACTATAA 59.345 37.037 18.18 0.00 0.00 0.98
2494 2591 9.503399 GTATGGCTAGGCTGTTAAAACTATAAT 57.497 33.333 18.18 0.00 0.00 1.28
2495 2592 8.622948 ATGGCTAGGCTGTTAAAACTATAATC 57.377 34.615 18.18 0.00 0.00 1.75
2496 2593 6.996282 TGGCTAGGCTGTTAAAACTATAATCC 59.004 38.462 18.18 0.00 0.00 3.01
2497 2594 6.996282 GGCTAGGCTGTTAAAACTATAATCCA 59.004 38.462 9.46 0.00 0.00 3.41
2498 2595 7.501225 GGCTAGGCTGTTAAAACTATAATCCAA 59.499 37.037 9.46 0.00 0.00 3.53
2499 2596 8.560374 GCTAGGCTGTTAAAACTATAATCCAAG 58.440 37.037 0.00 0.00 0.00 3.61
2500 2597 9.614792 CTAGGCTGTTAAAACTATAATCCAAGT 57.385 33.333 0.00 0.00 0.00 3.16
2501 2598 8.507524 AGGCTGTTAAAACTATAATCCAAGTC 57.492 34.615 0.00 0.00 0.00 3.01
2502 2599 7.556635 AGGCTGTTAAAACTATAATCCAAGTCC 59.443 37.037 0.00 0.00 0.00 3.85
2503 2600 7.338449 GGCTGTTAAAACTATAATCCAAGTCCA 59.662 37.037 0.00 0.00 0.00 4.02
2504 2601 8.736244 GCTGTTAAAACTATAATCCAAGTCCAA 58.264 33.333 0.00 0.00 0.00 3.53
2506 2603 9.238368 TGTTAAAACTATAATCCAAGTCCAAGG 57.762 33.333 0.00 0.00 0.00 3.61
2507 2604 9.457436 GTTAAAACTATAATCCAAGTCCAAGGA 57.543 33.333 0.00 0.00 38.50 3.36
2509 2606 8.950007 AAAACTATAATCCAAGTCCAAGGAAA 57.050 30.769 0.00 0.00 37.48 3.13
2510 2607 8.950007 AAACTATAATCCAAGTCCAAGGAAAA 57.050 30.769 0.00 0.00 37.48 2.29
2511 2608 7.939784 ACTATAATCCAAGTCCAAGGAAAAC 57.060 36.000 0.00 0.00 37.48 2.43
2512 2609 7.466804 ACTATAATCCAAGTCCAAGGAAAACA 58.533 34.615 0.00 0.00 37.48 2.83
2513 2610 6.840780 ATAATCCAAGTCCAAGGAAAACAG 57.159 37.500 0.00 0.00 37.48 3.16
2514 2611 3.662759 TCCAAGTCCAAGGAAAACAGT 57.337 42.857 0.00 0.00 0.00 3.55
2515 2612 3.551846 TCCAAGTCCAAGGAAAACAGTC 58.448 45.455 0.00 0.00 0.00 3.51
2516 2613 3.202151 TCCAAGTCCAAGGAAAACAGTCT 59.798 43.478 0.00 0.00 0.00 3.24
2517 2614 3.954258 CCAAGTCCAAGGAAAACAGTCTT 59.046 43.478 0.00 0.00 0.00 3.01
2518 2615 4.036852 CCAAGTCCAAGGAAAACAGTCTTC 59.963 45.833 0.00 0.00 0.00 2.87
2519 2616 4.503714 AGTCCAAGGAAAACAGTCTTCA 57.496 40.909 0.00 0.00 0.00 3.02
2520 2617 4.855340 AGTCCAAGGAAAACAGTCTTCAA 58.145 39.130 0.00 0.00 0.00 2.69
2521 2618 4.640647 AGTCCAAGGAAAACAGTCTTCAAC 59.359 41.667 0.00 0.00 0.00 3.18
2522 2619 4.640647 GTCCAAGGAAAACAGTCTTCAACT 59.359 41.667 0.00 0.00 39.44 3.16
2523 2620 5.125578 GTCCAAGGAAAACAGTCTTCAACTT 59.874 40.000 0.00 0.00 35.45 2.66
2524 2621 5.357032 TCCAAGGAAAACAGTCTTCAACTTC 59.643 40.000 0.00 0.00 35.45 3.01
2525 2622 5.125417 CCAAGGAAAACAGTCTTCAACTTCA 59.875 40.000 0.00 0.00 35.45 3.02
2526 2623 5.819825 AGGAAAACAGTCTTCAACTTCAC 57.180 39.130 0.00 0.00 35.45 3.18
2527 2624 5.501156 AGGAAAACAGTCTTCAACTTCACT 58.499 37.500 0.00 0.00 35.45 3.41
2528 2625 5.355350 AGGAAAACAGTCTTCAACTTCACTG 59.645 40.000 0.00 0.00 41.77 3.66
2529 2626 5.449177 GGAAAACAGTCTTCAACTTCACTGG 60.449 44.000 3.18 0.00 40.57 4.00
2530 2627 3.199880 ACAGTCTTCAACTTCACTGGG 57.800 47.619 3.18 0.00 40.57 4.45
2531 2628 2.505819 ACAGTCTTCAACTTCACTGGGT 59.494 45.455 3.18 0.00 40.57 4.51
2532 2629 2.874701 CAGTCTTCAACTTCACTGGGTG 59.125 50.000 0.00 0.00 35.45 4.61
2533 2630 2.158755 AGTCTTCAACTTCACTGGGTGG 60.159 50.000 0.00 0.00 33.03 4.61
2534 2631 1.843851 TCTTCAACTTCACTGGGTGGT 59.156 47.619 0.00 0.00 33.87 4.16
2535 2632 2.158813 TCTTCAACTTCACTGGGTGGTC 60.159 50.000 0.00 0.00 33.87 4.02
2536 2633 0.472471 TCAACTTCACTGGGTGGTCC 59.528 55.000 0.00 0.00 33.87 4.46
2537 2634 0.474184 CAACTTCACTGGGTGGTCCT 59.526 55.000 0.00 0.00 33.87 3.85
2538 2635 0.474184 AACTTCACTGGGTGGTCCTG 59.526 55.000 0.00 0.00 39.98 3.86
2539 2636 1.302832 CTTCACTGGGTGGTCCTGC 60.303 63.158 0.00 0.00 37.94 4.85
2540 2637 2.055689 CTTCACTGGGTGGTCCTGCA 62.056 60.000 0.00 0.00 37.94 4.41
2541 2638 2.033141 CACTGGGTGGTCCTGCAG 59.967 66.667 6.78 6.78 37.94 4.41
2542 2639 2.122413 ACTGGGTGGTCCTGCAGA 60.122 61.111 17.39 0.00 37.94 4.26
2543 2640 1.770110 ACTGGGTGGTCCTGCAGAA 60.770 57.895 17.39 0.00 37.94 3.02
2544 2641 1.136329 ACTGGGTGGTCCTGCAGAAT 61.136 55.000 17.39 0.00 37.94 2.40
2545 2642 0.393537 CTGGGTGGTCCTGCAGAATC 60.394 60.000 17.39 0.00 36.20 2.52
2546 2643 1.450312 GGGTGGTCCTGCAGAATCG 60.450 63.158 17.39 0.00 0.00 3.34
2547 2644 1.596934 GGTGGTCCTGCAGAATCGA 59.403 57.895 17.39 0.00 0.00 3.59
2548 2645 0.460987 GGTGGTCCTGCAGAATCGAG 60.461 60.000 17.39 0.00 0.00 4.04
2549 2646 0.532573 GTGGTCCTGCAGAATCGAGA 59.467 55.000 17.39 0.00 0.00 4.04
2550 2647 1.066858 GTGGTCCTGCAGAATCGAGAA 60.067 52.381 17.39 0.00 0.00 2.87
2551 2648 1.205655 TGGTCCTGCAGAATCGAGAAG 59.794 52.381 17.39 0.00 0.00 2.85
2552 2649 1.478510 GGTCCTGCAGAATCGAGAAGA 59.521 52.381 17.39 0.00 0.00 2.87
2553 2650 2.102252 GGTCCTGCAGAATCGAGAAGAT 59.898 50.000 17.39 0.00 42.43 2.40
2554 2651 3.380142 GTCCTGCAGAATCGAGAAGATC 58.620 50.000 17.39 0.00 38.98 2.75
2555 2652 3.026694 TCCTGCAGAATCGAGAAGATCA 58.973 45.455 17.39 0.00 38.98 2.92
2556 2653 3.448660 TCCTGCAGAATCGAGAAGATCAA 59.551 43.478 17.39 0.00 38.98 2.57
2557 2654 4.100653 TCCTGCAGAATCGAGAAGATCAAT 59.899 41.667 17.39 0.00 38.98 2.57
2558 2655 4.815308 CCTGCAGAATCGAGAAGATCAATT 59.185 41.667 17.39 0.00 38.98 2.32
2559 2656 5.277393 CCTGCAGAATCGAGAAGATCAATTG 60.277 44.000 17.39 0.00 38.98 2.32
2560 2657 5.422145 TGCAGAATCGAGAAGATCAATTGA 58.578 37.500 11.26 11.26 38.98 2.57
2561 2658 5.522824 TGCAGAATCGAGAAGATCAATTGAG 59.477 40.000 14.54 0.00 38.98 3.02
2562 2659 5.558653 GCAGAATCGAGAAGATCAATTGAGC 60.559 44.000 15.87 15.87 38.98 4.26
2563 2660 5.522824 CAGAATCGAGAAGATCAATTGAGCA 59.477 40.000 24.50 4.10 38.98 4.26
2564 2661 5.754406 AGAATCGAGAAGATCAATTGAGCAG 59.246 40.000 24.50 10.68 38.98 4.24
2565 2662 4.725790 TCGAGAAGATCAATTGAGCAGA 57.274 40.909 24.50 12.58 31.88 4.26
2566 2663 4.428209 TCGAGAAGATCAATTGAGCAGAC 58.572 43.478 24.50 14.63 31.88 3.51
2567 2664 4.082026 TCGAGAAGATCAATTGAGCAGACA 60.082 41.667 24.50 1.71 31.88 3.41
2570 2667 6.183360 CGAGAAGATCAATTGAGCAGACAAAT 60.183 38.462 24.50 0.00 33.44 2.32
2605 2702 3.660865 TGATCCTGCATCGAGATGAATG 58.339 45.455 16.45 3.85 41.20 2.67
2625 2722 4.898829 TGTCAAACATCCAGTTCTTGTG 57.101 40.909 0.00 0.00 40.26 3.33
2658 2755 4.202409 GGAGGAAGGAAAGTAGGATCATGG 60.202 50.000 0.00 0.00 0.00 3.66
2680 2777 5.221601 TGGTATTGTTGACGGGTGTTACTAA 60.222 40.000 0.00 0.00 0.00 2.24
2752 2854 4.696479 ATGTAATCAGCCACCCTTAGAG 57.304 45.455 0.00 0.00 0.00 2.43
2907 3009 6.209192 TGAATATTATTTGGATGGCGCTGATT 59.791 34.615 7.64 0.00 0.00 2.57
3003 3105 2.995258 TCGTTTAACGCAGTGAATACCC 59.005 45.455 13.06 0.00 45.00 3.69
3010 3112 2.034305 ACGCAGTGAATACCCTATCGTC 59.966 50.000 0.00 0.00 42.51 4.20
3096 3198 5.826737 GTGTGATGATTTGATCAGGATCCTT 59.173 40.000 13.00 0.00 43.53 3.36
3135 3237 3.447742 CGCACACTGCAGTATAAGATCA 58.552 45.455 21.20 0.00 45.36 2.92
3227 3332 5.888691 TGTGAAGCGGCAGAAAAATAATA 57.111 34.783 1.45 0.00 0.00 0.98
3260 3365 6.751888 GGGAAACATCATGTAACAGCATTAAC 59.248 38.462 0.00 0.00 0.00 2.01
3262 3367 7.362920 GGAAACATCATGTAACAGCATTAACCT 60.363 37.037 0.00 0.00 0.00 3.50
3351 3457 5.011635 TGCCTACTCTGTAGATTTGTGTTGA 59.988 40.000 6.33 0.00 0.00 3.18
3360 3466 6.000840 TGTAGATTTGTGTTGAACAGGCATA 58.999 36.000 0.00 0.00 40.74 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 5.085275 TCCTCTCCATGGATATCTTCAGT 57.915 43.478 16.63 0.00 0.00 3.41
307 311 1.538047 TCATGGCTTTCTCCTTGCAC 58.462 50.000 0.00 0.00 32.92 4.57
355 369 4.887655 AGGCAGGTACAAAATTATACAGGC 59.112 41.667 0.00 0.00 0.00 4.85
372 386 1.746991 GGCTCGAGGAAAAGGCAGG 60.747 63.158 15.58 0.00 37.94 4.85
374 388 1.302511 GTGGCTCGAGGAAAAGGCA 60.303 57.895 15.58 3.11 44.76 4.75
417 431 7.881142 ACATACTCAAAAATCAAAATGTCGGA 58.119 30.769 0.00 0.00 0.00 4.55
467 481 8.855110 ACAACAATACCTGTGAATACAATGAAA 58.145 29.630 0.00 0.00 38.67 2.69
484 498 5.992729 ACATCGTTTGTGGTACAACAATAC 58.007 37.500 16.53 14.91 44.16 1.89
502 516 7.603297 ATGTTACAAAAAGAACGAAACATCG 57.397 32.000 0.00 0.00 32.23 3.84
567 581 6.142818 ACGAAAGATTCACAACAAATTGGA 57.857 33.333 0.00 0.00 40.42 3.53
649 717 5.148651 ACCCAACAGTCAGTGAGTATAAC 57.851 43.478 0.00 0.00 0.00 1.89
654 722 1.496060 TGACCCAACAGTCAGTGAGT 58.504 50.000 0.00 0.00 41.78 3.41
993 1089 2.440980 GCCCAGGTCATTGCTCCC 60.441 66.667 0.00 0.00 0.00 4.30
1499 1595 1.000052 TGAACATCCTGTACGCGTTGA 60.000 47.619 20.78 10.11 0.00 3.18
1500 1596 1.390123 CTGAACATCCTGTACGCGTTG 59.610 52.381 20.78 11.47 0.00 4.10
1524 1620 4.704103 AGCCCCGTCCTCTGCAGA 62.704 66.667 17.19 17.19 0.00 4.26
1642 1738 2.746277 GACGTTCGGGGCATGCTT 60.746 61.111 18.92 0.00 0.00 3.91
1901 1997 1.931007 ATCCAGCTTCCCTTCCTGGC 61.931 60.000 1.14 0.00 44.52 4.85
2006 2102 1.672881 CCTCGAAATGTCCCATCTTGC 59.327 52.381 0.00 0.00 0.00 4.01
2016 2112 2.401583 TATGTGCAGCCTCGAAATGT 57.598 45.000 0.00 0.00 0.00 2.71
2160 2256 7.377766 TGTGTAAGTAAAATCATCCTTCAGC 57.622 36.000 0.00 0.00 0.00 4.26
2298 2394 2.047274 GCACTACGAAGGCCAGCA 60.047 61.111 5.01 0.00 0.00 4.41
2352 2448 2.884894 ACAGCCTAGCCATACGTAAC 57.115 50.000 0.00 0.00 0.00 2.50
2456 2553 6.017109 CAGCCTAGCCATACGTAATTTCAATT 60.017 38.462 0.00 0.00 0.00 2.32
2457 2554 5.470098 CAGCCTAGCCATACGTAATTTCAAT 59.530 40.000 0.00 0.00 0.00 2.57
2458 2555 4.814234 CAGCCTAGCCATACGTAATTTCAA 59.186 41.667 0.00 0.00 0.00 2.69
2459 2556 4.141801 ACAGCCTAGCCATACGTAATTTCA 60.142 41.667 0.00 0.00 0.00 2.69
2460 2557 4.377897 ACAGCCTAGCCATACGTAATTTC 58.622 43.478 0.00 0.00 0.00 2.17
2461 2558 4.417426 ACAGCCTAGCCATACGTAATTT 57.583 40.909 0.00 0.00 0.00 1.82
2462 2559 4.417426 AACAGCCTAGCCATACGTAATT 57.583 40.909 0.00 0.00 0.00 1.40
2463 2560 5.540400 TTAACAGCCTAGCCATACGTAAT 57.460 39.130 0.00 0.00 0.00 1.89
2464 2561 5.341872 TTTAACAGCCTAGCCATACGTAA 57.658 39.130 0.00 0.00 0.00 3.18
2465 2562 5.105228 AGTTTTAACAGCCTAGCCATACGTA 60.105 40.000 0.00 0.00 0.00 3.57
2466 2563 3.899052 TTTAACAGCCTAGCCATACGT 57.101 42.857 0.00 0.00 0.00 3.57
2467 2564 4.189231 AGTTTTAACAGCCTAGCCATACG 58.811 43.478 0.00 0.00 0.00 3.06
2468 2565 8.897872 TTATAGTTTTAACAGCCTAGCCATAC 57.102 34.615 0.00 0.00 0.00 2.39
2469 2566 9.720769 GATTATAGTTTTAACAGCCTAGCCATA 57.279 33.333 0.00 0.00 0.00 2.74
2470 2567 7.665974 GGATTATAGTTTTAACAGCCTAGCCAT 59.334 37.037 0.00 0.00 0.00 4.40
2471 2568 6.996282 GGATTATAGTTTTAACAGCCTAGCCA 59.004 38.462 0.00 0.00 0.00 4.75
2472 2569 6.996282 TGGATTATAGTTTTAACAGCCTAGCC 59.004 38.462 0.00 0.00 0.00 3.93
2473 2570 8.446599 TTGGATTATAGTTTTAACAGCCTAGC 57.553 34.615 0.00 0.00 0.00 3.42
2474 2571 9.614792 ACTTGGATTATAGTTTTAACAGCCTAG 57.385 33.333 0.00 0.00 0.00 3.02
2475 2572 9.609346 GACTTGGATTATAGTTTTAACAGCCTA 57.391 33.333 0.00 0.00 0.00 3.93
2476 2573 7.556635 GGACTTGGATTATAGTTTTAACAGCCT 59.443 37.037 0.00 0.00 0.00 4.58
2477 2574 7.338449 TGGACTTGGATTATAGTTTTAACAGCC 59.662 37.037 0.00 0.00 0.00 4.85
2478 2575 8.276252 TGGACTTGGATTATAGTTTTAACAGC 57.724 34.615 0.00 0.00 0.00 4.40
2480 2577 9.238368 CCTTGGACTTGGATTATAGTTTTAACA 57.762 33.333 0.00 0.00 0.00 2.41
2481 2578 9.457436 TCCTTGGACTTGGATTATAGTTTTAAC 57.543 33.333 0.00 0.00 0.00 2.01
2484 2581 8.950007 TTTCCTTGGACTTGGATTATAGTTTT 57.050 30.769 0.00 0.00 31.76 2.43
2485 2582 8.803235 GTTTTCCTTGGACTTGGATTATAGTTT 58.197 33.333 0.00 0.00 31.76 2.66
2486 2583 7.947890 TGTTTTCCTTGGACTTGGATTATAGTT 59.052 33.333 0.00 0.00 31.76 2.24
2487 2584 7.466804 TGTTTTCCTTGGACTTGGATTATAGT 58.533 34.615 0.00 0.00 31.76 2.12
2488 2585 7.611855 ACTGTTTTCCTTGGACTTGGATTATAG 59.388 37.037 0.00 0.00 31.76 1.31
2489 2586 7.466804 ACTGTTTTCCTTGGACTTGGATTATA 58.533 34.615 0.00 0.00 31.76 0.98
2490 2587 6.314917 ACTGTTTTCCTTGGACTTGGATTAT 58.685 36.000 0.00 0.00 31.76 1.28
2491 2588 5.701224 ACTGTTTTCCTTGGACTTGGATTA 58.299 37.500 0.00 0.00 31.76 1.75
2492 2589 4.546674 ACTGTTTTCCTTGGACTTGGATT 58.453 39.130 0.00 0.00 31.76 3.01
2493 2590 4.141158 AGACTGTTTTCCTTGGACTTGGAT 60.141 41.667 0.00 0.00 31.76 3.41
2494 2591 3.202151 AGACTGTTTTCCTTGGACTTGGA 59.798 43.478 0.00 0.00 0.00 3.53
2495 2592 3.555966 AGACTGTTTTCCTTGGACTTGG 58.444 45.455 0.00 0.00 0.00 3.61
2496 2593 4.640201 TGAAGACTGTTTTCCTTGGACTTG 59.360 41.667 8.40 0.00 0.00 3.16
2497 2594 4.855340 TGAAGACTGTTTTCCTTGGACTT 58.145 39.130 8.40 0.00 0.00 3.01
2498 2595 4.503714 TGAAGACTGTTTTCCTTGGACT 57.496 40.909 8.40 0.00 0.00 3.85
2499 2596 4.640647 AGTTGAAGACTGTTTTCCTTGGAC 59.359 41.667 8.40 1.29 37.17 4.02
2500 2597 4.855340 AGTTGAAGACTGTTTTCCTTGGA 58.145 39.130 8.40 0.00 37.17 3.53
2501 2598 5.125417 TGAAGTTGAAGACTGTTTTCCTTGG 59.875 40.000 8.40 0.00 39.00 3.61
2502 2599 6.030228 GTGAAGTTGAAGACTGTTTTCCTTG 58.970 40.000 8.40 0.00 39.00 3.61
2503 2600 5.946377 AGTGAAGTTGAAGACTGTTTTCCTT 59.054 36.000 8.40 5.67 39.00 3.36
2504 2601 5.355350 CAGTGAAGTTGAAGACTGTTTTCCT 59.645 40.000 8.40 0.00 39.00 3.36
2505 2602 5.449177 CCAGTGAAGTTGAAGACTGTTTTCC 60.449 44.000 8.40 0.00 39.00 3.13
2506 2603 5.449177 CCCAGTGAAGTTGAAGACTGTTTTC 60.449 44.000 4.26 4.26 39.00 2.29
2507 2604 4.399303 CCCAGTGAAGTTGAAGACTGTTTT 59.601 41.667 0.00 0.00 39.00 2.43
2508 2605 3.947834 CCCAGTGAAGTTGAAGACTGTTT 59.052 43.478 0.00 0.00 39.00 2.83
2509 2606 3.054361 ACCCAGTGAAGTTGAAGACTGTT 60.054 43.478 0.00 0.00 39.00 3.16
2510 2607 2.505819 ACCCAGTGAAGTTGAAGACTGT 59.494 45.455 0.00 0.00 39.00 3.55
2511 2608 2.874701 CACCCAGTGAAGTTGAAGACTG 59.125 50.000 0.00 0.00 39.00 3.51
2512 2609 2.158755 CCACCCAGTGAAGTTGAAGACT 60.159 50.000 0.00 0.00 41.47 3.24
2513 2610 2.222027 CCACCCAGTGAAGTTGAAGAC 58.778 52.381 0.00 0.00 35.23 3.01
2514 2611 1.843851 ACCACCCAGTGAAGTTGAAGA 59.156 47.619 0.00 0.00 35.23 2.87
2515 2612 2.222027 GACCACCCAGTGAAGTTGAAG 58.778 52.381 0.00 0.00 35.23 3.02
2516 2613 1.133915 GGACCACCCAGTGAAGTTGAA 60.134 52.381 0.00 0.00 35.23 2.69
2517 2614 0.472471 GGACCACCCAGTGAAGTTGA 59.528 55.000 0.00 0.00 35.23 3.18
2518 2615 0.474184 AGGACCACCCAGTGAAGTTG 59.526 55.000 0.00 0.00 35.23 3.16
2519 2616 0.474184 CAGGACCACCCAGTGAAGTT 59.526 55.000 0.00 0.00 35.23 2.66
2520 2617 2.056906 GCAGGACCACCCAGTGAAGT 62.057 60.000 0.00 0.00 35.23 3.01
2521 2618 1.302832 GCAGGACCACCCAGTGAAG 60.303 63.158 0.00 0.00 35.23 3.02
2522 2619 2.055689 CTGCAGGACCACCCAGTGAA 62.056 60.000 5.57 0.00 35.23 3.18
2523 2620 2.447572 TGCAGGACCACCCAGTGA 60.448 61.111 0.00 0.00 35.23 3.41
2524 2621 2.033141 CTGCAGGACCACCCAGTG 59.967 66.667 5.57 0.00 37.41 3.66
2525 2622 1.136329 ATTCTGCAGGACCACCCAGT 61.136 55.000 15.13 0.00 37.41 4.00
2526 2623 0.393537 GATTCTGCAGGACCACCCAG 60.394 60.000 15.13 0.00 37.41 4.45
2527 2624 1.685224 GATTCTGCAGGACCACCCA 59.315 57.895 15.13 0.00 37.41 4.51
2528 2625 1.450312 CGATTCTGCAGGACCACCC 60.450 63.158 15.13 0.00 36.73 4.61
2529 2626 0.460987 CTCGATTCTGCAGGACCACC 60.461 60.000 15.13 0.00 0.00 4.61
2530 2627 0.532573 TCTCGATTCTGCAGGACCAC 59.467 55.000 15.13 0.00 0.00 4.16
2531 2628 1.205655 CTTCTCGATTCTGCAGGACCA 59.794 52.381 15.13 0.00 0.00 4.02
2532 2629 1.478510 TCTTCTCGATTCTGCAGGACC 59.521 52.381 15.13 0.00 0.00 4.46
2533 2630 2.949451 TCTTCTCGATTCTGCAGGAC 57.051 50.000 15.13 4.82 0.00 3.85
2534 2631 3.026694 TGATCTTCTCGATTCTGCAGGA 58.973 45.455 15.13 5.14 30.84 3.86
2535 2632 3.449528 TGATCTTCTCGATTCTGCAGG 57.550 47.619 15.13 0.00 30.84 4.85
2536 2633 5.522824 TCAATTGATCTTCTCGATTCTGCAG 59.477 40.000 7.63 7.63 36.05 4.41
2537 2634 5.422145 TCAATTGATCTTCTCGATTCTGCA 58.578 37.500 3.38 0.00 36.05 4.41
2538 2635 5.558653 GCTCAATTGATCTTCTCGATTCTGC 60.559 44.000 8.96 0.00 36.05 4.26
2539 2636 5.522824 TGCTCAATTGATCTTCTCGATTCTG 59.477 40.000 8.96 0.00 36.05 3.02
2540 2637 5.668471 TGCTCAATTGATCTTCTCGATTCT 58.332 37.500 8.96 0.00 36.05 2.40
2541 2638 5.752472 TCTGCTCAATTGATCTTCTCGATTC 59.248 40.000 8.96 0.00 36.05 2.52
2542 2639 5.523188 GTCTGCTCAATTGATCTTCTCGATT 59.477 40.000 8.96 0.00 38.32 3.34
2543 2640 5.049167 GTCTGCTCAATTGATCTTCTCGAT 58.951 41.667 8.96 0.00 34.25 3.59
2544 2641 4.082026 TGTCTGCTCAATTGATCTTCTCGA 60.082 41.667 8.96 0.00 0.00 4.04
2545 2642 4.179298 TGTCTGCTCAATTGATCTTCTCG 58.821 43.478 8.96 0.00 0.00 4.04
2546 2643 6.492007 TTTGTCTGCTCAATTGATCTTCTC 57.508 37.500 8.96 0.00 0.00 2.87
2547 2644 7.176165 TCAATTTGTCTGCTCAATTGATCTTCT 59.824 33.333 8.96 0.00 0.00 2.85
2548 2645 7.310664 TCAATTTGTCTGCTCAATTGATCTTC 58.689 34.615 8.96 0.00 0.00 2.87
2549 2646 7.223260 TCAATTTGTCTGCTCAATTGATCTT 57.777 32.000 8.96 0.00 0.00 2.40
2550 2647 6.829229 TCAATTTGTCTGCTCAATTGATCT 57.171 33.333 8.96 0.00 0.00 2.75
2551 2648 7.878477 TTTCAATTTGTCTGCTCAATTGATC 57.122 32.000 8.96 5.36 31.81 2.92
2552 2649 8.842358 AATTTCAATTTGTCTGCTCAATTGAT 57.158 26.923 8.96 0.00 31.81 2.57
2553 2650 8.552865 CAAATTTCAATTTGTCTGCTCAATTGA 58.447 29.630 14.43 8.12 46.27 2.57
2554 2651 8.708075 CAAATTTCAATTTGTCTGCTCAATTG 57.292 30.769 14.43 0.00 46.27 2.32
2595 2692 4.633126 ACTGGATGTTTGACATTCATCTCG 59.367 41.667 15.24 10.95 42.79 4.04
2605 2702 3.550842 GCCACAAGAACTGGATGTTTGAC 60.551 47.826 0.00 0.00 39.30 3.18
2625 2722 3.366052 TTCCTTCCTCCAGTTTATGCC 57.634 47.619 0.00 0.00 0.00 4.40
2658 2755 6.815142 AGATTAGTAACACCCGTCAACAATAC 59.185 38.462 0.00 0.00 0.00 1.89
2680 2777 7.795534 ATCTCCAAGAGCTGATGTATAAGAT 57.204 36.000 0.00 0.00 0.00 2.40
2718 2815 5.276270 GCTGATTACATACTGCAACATTGG 58.724 41.667 0.00 0.00 0.00 3.16
2752 2854 7.306983 GCTGTATAATTTCAAATGATGCTTGGC 60.307 37.037 0.00 0.00 0.00 4.52
2840 2942 2.553904 CCAGGCAAAGATCACTTCCTGT 60.554 50.000 17.23 0.00 42.05 4.00
2907 3009 9.639563 TGGAATGCTAATAATCACTTGGATTTA 57.360 29.630 0.00 0.00 43.76 1.40
2983 3085 2.997986 AGGGTATTCACTGCGTTAAACG 59.002 45.455 0.00 0.00 45.88 3.60
3003 3105 3.692791 TGAACTCCATGACGACGATAG 57.307 47.619 0.00 0.00 46.19 2.08
3010 3112 5.173673 CACACAAAATTTGAACTCCATGACG 59.826 40.000 13.19 0.00 0.00 4.35
3096 3198 1.089112 CGCATCATGTCTGGAGCAAA 58.911 50.000 0.00 0.00 0.00 3.68
3234 3339 3.088532 TGCTGTTACATGATGTTTCCCC 58.911 45.455 2.29 0.00 0.00 4.81
3260 3365 6.096705 TGGCATACATATTTTCCTCAAACAGG 59.903 38.462 0.00 0.00 45.15 4.00
3262 3367 7.473735 TTGGCATACATATTTTCCTCAAACA 57.526 32.000 0.00 0.00 0.00 2.83
3269 3374 9.598517 TTTCTTTCATTGGCATACATATTTTCC 57.401 29.630 0.00 0.00 0.00 3.13
3360 3466 6.040842 TCAAAATCTTAAGAAAAGGCAGCAGT 59.959 34.615 9.71 0.00 0.00 4.40
3395 3501 8.997323 TGCAAAAATAATTTGGTGATGGTTTAG 58.003 29.630 3.41 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.