Multiple sequence alignment - TraesCS2D01G314100

Loading Multiple Alignment...

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 TraesCS2D01G314100 chr2D 100.000 3011 0 0 1 3011 403507012 403504002 0.000000e+00 5561.0
1 TraesCS2D01G314100 chr2D 83.410 217 20 12 2799 3005 501068764 501068974 1.430000e-43 187.0
2 TraesCS2D01G314100 chr2B 95.621 2535 83 14 7 2515 477609631 477607099 0.000000e+00 4041.0
3 TraesCS2D01G314100 chr2A 96.146 2491 67 9 1 2469 541845571 541843088 0.000000e+00 4041.0
4 TraesCS2D01G314100 chr6D 82.963 270 33 7 2745 3001 470662369 470662638 6.490000e-57 231.0
5 TraesCS2D01G314100 chr6D 84.524 168 22 3 2835 3001 69826375 69826539 2.400000e-36 163.0
6 TraesCS2D01G314100 chr6D 83.708 178 15 8 2838 3011 35017578 35017411 4.020000e-34 156.0
7 TraesCS2D01G314100 chr7B 88.439 173 16 2 2835 3003 609211887 609212059 3.930000e-49 206.0
8 TraesCS2D01G314100 chr3D 83.406 229 30 6 2514 2738 155944656 155944880 3.930000e-49 206.0
9 TraesCS2D01G314100 chr3D 80.786 229 31 5 2512 2739 166500931 166500715 1.860000e-37 167.0
10 TraesCS2D01G314100 chr5B 84.404 218 22 4 2806 3011 523451340 523451123 1.420000e-48 204.0
11 TraesCS2D01G314100 chr1D 80.471 297 28 14 2745 3011 454302442 454302146 1.830000e-47 200.0
12 TraesCS2D01G314100 chr1B 83.178 214 27 5 2807 3011 47399067 47398854 1.430000e-43 187.0
13 TraesCS2D01G314100 chr1B 82.258 186 28 3 2520 2703 644551120 644550938 4.020000e-34 156.0
14 TraesCS2D01G314100 chr1B 81.915 188 25 6 2520 2703 644332390 644332572 1.870000e-32 150.0
15 TraesCS2D01G314100 chr1B 74.812 266 35 23 2758 3000 444039467 444039211 1.150000e-14 91.6
16 TraesCS2D01G314100 chr6B 85.629 167 19 5 2834 2999 95498999 95499161 1.440000e-38 171.0
17 TraesCS2D01G314100 chr6B 83.784 185 24 5 2822 3005 95542674 95542853 1.440000e-38 171.0
18 TraesCS2D01G314100 chr3B 81.281 203 27 8 2514 2712 11014519 11014324 1.450000e-33 154.0
19 TraesCS2D01G314100 chr5A 80.000 225 21 5 2798 3005 396493741 396493958 8.700000e-31 145.0
20 TraesCS2D01G314100 chr7A 77.143 245 35 11 2514 2740 103397252 103397011 4.080000e-24 122.0


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 TraesCS2D01G314100 chr2D 403504002 403507012 3010 True 5561 5561 100.000 1 3011 1 chr2D.!!$R1 3010
1 TraesCS2D01G314100 chr2B 477607099 477609631 2532 True 4041 4041 95.621 7 2515 1 chr2B.!!$R1 2508
2 TraesCS2D01G314100 chr2A 541843088 541845571 2483 True 4041 4041 96.146 1 2469 1 chr2A.!!$R1 2468

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
97 98 3.527253 TGGAAAAGAAGGATGGCATAGGA 59.473 43.478 0.0 0.0 0.0 2.94 F
1071 1073 2.957402 TGGCAAGAACTCCAAGACAT 57.043 45.000 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1075 0.036765 TCGCCGGCTTGATAAGTTGT 60.037 50.0 26.68 0.0 0.0 3.32 R
2536 2564 0.036765 TTCCAACACGCGGCTAAGAT 60.037 50.0 12.47 0.0 0.0 2.40 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
97 98 3.527253 TGGAAAAGAAGGATGGCATAGGA 59.473 43.478 0.00 0.00 0.00 2.94
243 244 7.529158 TGAAATGTGCATAGTGTGAATAACAG 58.471 34.615 0.00 0.00 40.26 3.16
275 276 4.438200 GGTTCCACGCCTAACATTTATGTG 60.438 45.833 0.00 0.00 41.61 3.21
364 365 4.218200 TCCTTGCTGTATGACATTGTTTGG 59.782 41.667 0.00 0.00 0.00 3.28
381 382 9.128107 CATTGTTTGGTGTGCTTTACTTATAAG 57.872 33.333 11.05 11.05 0.00 1.73
403 404 4.346418 AGTGAACAGTCCTTTCATCTCTGT 59.654 41.667 0.00 0.00 40.40 3.41
404 405 4.450419 GTGAACAGTCCTTTCATCTCTGTG 59.550 45.833 0.00 0.00 38.97 3.66
623 624 6.744537 CAGCTGTTAGATAAGTTCAAACATGC 59.255 38.462 5.25 0.00 30.33 4.06
756 757 3.651803 AGCTTCTACGTGAGATATGGC 57.348 47.619 0.00 1.21 32.88 4.40
767 768 5.163405 ACGTGAGATATGGCAGTATCACTTT 60.163 40.000 20.72 10.27 35.93 2.66
902 904 6.448207 TCATTTGTTGTTGTCATGAAGTCA 57.552 33.333 0.00 0.00 0.00 3.41
1071 1073 2.957402 TGGCAAGAACTCCAAGACAT 57.043 45.000 0.00 0.00 0.00 3.06
1073 1075 2.106338 TGGCAAGAACTCCAAGACATCA 59.894 45.455 0.00 0.00 0.00 3.07
1075 1077 3.141398 GCAAGAACTCCAAGACATCACA 58.859 45.455 0.00 0.00 0.00 3.58
1358 1360 0.875059 GTGAAGGAGAAACCGGCAAG 59.125 55.000 0.00 0.00 44.74 4.01
1369 1371 2.386661 ACCGGCAAGTGAAGTATCAG 57.613 50.000 0.00 0.00 35.88 2.90
1800 1802 4.407621 ACGTTTCCTGATGGTGGTGATATA 59.592 41.667 0.00 0.00 34.23 0.86
1814 1816 6.263168 GGTGGTGATATAATGTTTTCTGGAGG 59.737 42.308 0.00 0.00 0.00 4.30
1821 1823 2.930826 TGTTTTCTGGAGGTCCTGAC 57.069 50.000 0.00 0.00 42.55 3.51
1842 1844 4.861210 ACATCCGATCATTACGAAGAGTC 58.139 43.478 0.00 0.00 0.00 3.36
1868 1870 2.289072 GCAGAGCTTACAGGACAAGTGA 60.289 50.000 0.00 0.00 0.00 3.41
2049 2070 1.912043 AGCACCTTACCATGAGAGCTT 59.088 47.619 0.00 0.00 0.00 3.74
2167 2189 6.375455 GGCCACTTCTTTTTCTCTGATGAATA 59.625 38.462 0.00 0.00 0.00 1.75
2323 2347 7.338196 TGGTCATTTCTGTTCAAAGTTAGTCAA 59.662 33.333 0.00 0.00 0.00 3.18
2410 2435 3.442996 GGGTGTTGTCCGATCTCAG 57.557 57.895 0.00 0.00 0.00 3.35
2486 2511 4.458989 TGCAAGCTAGTTTTCCCAGTAATG 59.541 41.667 0.00 0.00 0.00 1.90
2491 2519 7.439108 AGCTAGTTTTCCCAGTAATGAGTAT 57.561 36.000 0.00 0.00 0.00 2.12
2495 2523 7.923414 AGTTTTCCCAGTAATGAGTATGTTC 57.077 36.000 0.00 0.00 0.00 3.18
2498 2526 6.381498 TTCCCAGTAATGAGTATGTTCCAA 57.619 37.500 0.00 0.00 0.00 3.53
2515 2543 6.303054 TGTTCCAATTTGTCATCAGGTAAGA 58.697 36.000 0.00 0.00 0.00 2.10
2516 2544 6.430925 TGTTCCAATTTGTCATCAGGTAAGAG 59.569 38.462 0.00 0.00 0.00 2.85
2517 2545 4.943705 TCCAATTTGTCATCAGGTAAGAGC 59.056 41.667 0.00 0.00 0.00 4.09
2518 2546 4.701651 CCAATTTGTCATCAGGTAAGAGCA 59.298 41.667 0.00 0.00 0.00 4.26
2519 2547 5.359009 CCAATTTGTCATCAGGTAAGAGCAT 59.641 40.000 0.00 0.00 0.00 3.79
2520 2548 6.459298 CCAATTTGTCATCAGGTAAGAGCATC 60.459 42.308 0.00 0.00 0.00 3.91
2532 2560 3.997672 GAGCATCTCCAATAGGCGT 57.002 52.632 0.00 0.00 33.74 5.68
2533 2561 1.506493 GAGCATCTCCAATAGGCGTG 58.494 55.000 0.00 0.00 33.74 5.34
2534 2562 0.533755 AGCATCTCCAATAGGCGTGC 60.534 55.000 0.00 0.00 36.87 5.34
2535 2563 0.533755 GCATCTCCAATAGGCGTGCT 60.534 55.000 0.00 0.00 35.08 4.40
2536 2564 1.270305 GCATCTCCAATAGGCGTGCTA 60.270 52.381 0.00 0.00 35.08 3.49
2537 2565 2.613977 GCATCTCCAATAGGCGTGCTAT 60.614 50.000 0.00 0.00 35.08 2.97
2538 2566 3.257393 CATCTCCAATAGGCGTGCTATC 58.743 50.000 0.00 0.00 33.74 2.08
2539 2567 2.598565 TCTCCAATAGGCGTGCTATCT 58.401 47.619 0.00 0.00 33.74 1.98
2540 2568 2.965831 TCTCCAATAGGCGTGCTATCTT 59.034 45.455 0.00 0.00 33.74 2.40
2541 2569 4.149598 TCTCCAATAGGCGTGCTATCTTA 58.850 43.478 0.00 0.00 33.74 2.10
2542 2570 4.218635 TCTCCAATAGGCGTGCTATCTTAG 59.781 45.833 0.00 0.00 33.74 2.18
2543 2571 3.306088 TCCAATAGGCGTGCTATCTTAGC 60.306 47.826 0.00 0.00 42.94 3.09
2550 2578 4.732106 GCTATCTTAGCCGCGTGT 57.268 55.556 4.92 0.00 45.95 4.49
2551 2579 2.973420 GCTATCTTAGCCGCGTGTT 58.027 52.632 4.92 0.00 45.95 3.32
2552 2580 0.577269 GCTATCTTAGCCGCGTGTTG 59.423 55.000 4.92 0.00 45.95 3.33
2553 2581 1.209128 CTATCTTAGCCGCGTGTTGG 58.791 55.000 4.92 0.00 0.00 3.77
2554 2582 0.818938 TATCTTAGCCGCGTGTTGGA 59.181 50.000 4.92 0.00 0.00 3.53
2555 2583 0.036765 ATCTTAGCCGCGTGTTGGAA 60.037 50.000 4.92 0.00 0.00 3.53
2556 2584 0.249953 TCTTAGCCGCGTGTTGGAAA 60.250 50.000 4.92 0.00 0.00 3.13
2557 2585 0.589223 CTTAGCCGCGTGTTGGAAAA 59.411 50.000 4.92 0.00 0.00 2.29
2558 2586 1.002251 CTTAGCCGCGTGTTGGAAAAA 60.002 47.619 4.92 0.00 0.00 1.94
2595 2623 3.050275 GAGCTGAAACGGGCGCTT 61.050 61.111 7.64 0.00 31.96 4.68
2596 2624 3.028366 GAGCTGAAACGGGCGCTTC 62.028 63.158 7.64 3.40 31.96 3.86
2597 2625 3.353836 GCTGAAACGGGCGCTTCA 61.354 61.111 7.64 8.59 0.00 3.02
2598 2626 2.863153 CTGAAACGGGCGCTTCAG 59.137 61.111 18.90 18.90 40.43 3.02
2599 2627 3.314388 CTGAAACGGGCGCTTCAGC 62.314 63.158 20.00 0.00 40.10 4.26
2600 2628 3.353836 GAAACGGGCGCTTCAGCA 61.354 61.111 7.64 0.00 42.21 4.41
2601 2629 3.314388 GAAACGGGCGCTTCAGCAG 62.314 63.158 7.64 0.00 42.21 4.24
2610 2638 3.807538 CTTCAGCAGCCGCGCAAT 61.808 61.111 8.75 0.00 45.49 3.56
2611 2639 2.435762 TTCAGCAGCCGCGCAATA 60.436 55.556 8.75 0.00 45.49 1.90
2612 2640 1.980951 CTTCAGCAGCCGCGCAATAA 61.981 55.000 8.75 0.00 45.49 1.40
2613 2641 1.375853 TTCAGCAGCCGCGCAATAAT 61.376 50.000 8.75 0.00 45.49 1.28
2614 2642 1.369689 CAGCAGCCGCGCAATAATC 60.370 57.895 8.75 0.00 45.49 1.75
2615 2643 2.425773 GCAGCCGCGCAATAATCG 60.426 61.111 8.75 0.00 0.00 3.34
2633 2661 3.773630 CGCGCGCGGTATAATGGG 61.774 66.667 43.28 13.53 35.56 4.00
2634 2662 2.356553 GCGCGCGGTATAATGGGA 60.357 61.111 33.06 0.00 0.00 4.37
2635 2663 1.740296 GCGCGCGGTATAATGGGAT 60.740 57.895 33.06 0.00 0.00 3.85
2636 2664 1.693083 GCGCGCGGTATAATGGGATC 61.693 60.000 33.06 5.61 0.00 3.36
2637 2665 0.389296 CGCGCGGTATAATGGGATCA 60.389 55.000 24.84 0.00 0.00 2.92
2638 2666 1.359848 GCGCGGTATAATGGGATCAG 58.640 55.000 8.83 0.00 0.00 2.90
2639 2667 1.359848 CGCGGTATAATGGGATCAGC 58.640 55.000 0.00 0.00 0.00 4.26
2640 2668 1.359848 GCGGTATAATGGGATCAGCG 58.640 55.000 0.00 0.00 0.00 5.18
2641 2669 1.359848 CGGTATAATGGGATCAGCGC 58.640 55.000 0.00 0.00 0.00 5.92
2642 2670 1.359848 GGTATAATGGGATCAGCGCG 58.640 55.000 0.00 0.00 0.00 6.86
2643 2671 0.721718 GTATAATGGGATCAGCGCGC 59.278 55.000 26.66 26.66 0.00 6.86
2644 2672 0.735978 TATAATGGGATCAGCGCGCG 60.736 55.000 28.44 28.44 0.00 6.86
2649 2677 4.873129 GGATCAGCGCGCGGAGAA 62.873 66.667 34.98 16.40 0.00 2.87
2650 2678 2.885644 GATCAGCGCGCGGAGAAA 60.886 61.111 34.98 16.03 0.00 2.52
2651 2679 2.434185 ATCAGCGCGCGGAGAAAA 60.434 55.556 34.98 15.64 0.00 2.29
2652 2680 1.966493 GATCAGCGCGCGGAGAAAAA 61.966 55.000 34.98 14.89 0.00 1.94
2653 2681 1.369091 ATCAGCGCGCGGAGAAAAAT 61.369 50.000 34.98 17.59 0.00 1.82
2654 2682 0.738063 TCAGCGCGCGGAGAAAAATA 60.738 50.000 33.06 5.28 0.00 1.40
2655 2683 0.315382 CAGCGCGCGGAGAAAAATAG 60.315 55.000 33.06 0.00 0.00 1.73
2656 2684 1.651431 GCGCGCGGAGAAAAATAGC 60.651 57.895 33.06 5.75 0.00 2.97
2657 2685 1.713246 CGCGCGGAGAAAAATAGCA 59.287 52.632 24.84 0.00 0.00 3.49
2658 2686 0.304705 CGCGCGGAGAAAAATAGCAT 59.695 50.000 24.84 0.00 0.00 3.79
2659 2687 1.657538 CGCGCGGAGAAAAATAGCATC 60.658 52.381 24.84 0.00 0.00 3.91
2660 2688 1.330521 GCGCGGAGAAAAATAGCATCA 59.669 47.619 8.83 0.00 0.00 3.07
2661 2689 2.031682 GCGCGGAGAAAAATAGCATCAT 60.032 45.455 8.83 0.00 0.00 2.45
2662 2690 3.548587 CGCGGAGAAAAATAGCATCATG 58.451 45.455 0.00 0.00 0.00 3.07
2663 2691 3.303406 GCGGAGAAAAATAGCATCATGC 58.697 45.455 0.00 0.00 45.46 4.06
2664 2692 3.854784 GCGGAGAAAAATAGCATCATGCC 60.855 47.826 5.84 0.00 46.52 4.40
2665 2693 3.304928 CGGAGAAAAATAGCATCATGCCC 60.305 47.826 5.84 0.00 46.52 5.36
2666 2694 3.893813 GGAGAAAAATAGCATCATGCCCT 59.106 43.478 5.84 0.00 46.52 5.19
2667 2695 4.261909 GGAGAAAAATAGCATCATGCCCTG 60.262 45.833 5.84 0.00 46.52 4.45
2668 2696 3.069158 AGAAAAATAGCATCATGCCCTGC 59.931 43.478 5.84 6.63 46.52 4.85
2669 2697 2.376695 AAATAGCATCATGCCCTGCT 57.623 45.000 5.84 17.50 46.52 4.24
2670 2698 2.376695 AATAGCATCATGCCCTGCTT 57.623 45.000 18.26 7.61 46.22 3.91
2671 2699 3.513909 AATAGCATCATGCCCTGCTTA 57.486 42.857 18.26 0.00 46.22 3.09
2672 2700 3.733883 ATAGCATCATGCCCTGCTTAT 57.266 42.857 18.26 0.00 46.22 1.73
2673 2701 2.376695 AGCATCATGCCCTGCTTATT 57.623 45.000 5.84 0.00 46.22 1.40
2674 2702 2.674420 AGCATCATGCCCTGCTTATTT 58.326 42.857 5.84 0.00 46.22 1.40
2675 2703 2.626743 AGCATCATGCCCTGCTTATTTC 59.373 45.455 5.84 0.00 46.22 2.17
2676 2704 2.606308 GCATCATGCCCTGCTTATTTCG 60.606 50.000 0.00 0.00 37.42 3.46
2677 2705 1.024271 TCATGCCCTGCTTATTTCGC 58.976 50.000 0.00 0.00 0.00 4.70
2678 2706 0.317269 CATGCCCTGCTTATTTCGCG 60.317 55.000 0.00 0.00 0.00 5.87
2679 2707 2.024729 GCCCTGCTTATTTCGCGC 59.975 61.111 0.00 0.00 0.00 6.86
2680 2708 2.324477 CCCTGCTTATTTCGCGCG 59.676 61.111 26.76 26.76 0.00 6.86
2681 2709 2.461110 CCCTGCTTATTTCGCGCGT 61.461 57.895 30.98 13.76 0.00 6.01
2682 2710 1.012234 CCTGCTTATTTCGCGCGTC 60.012 57.895 30.98 11.26 0.00 5.19
2683 2711 1.692148 CCTGCTTATTTCGCGCGTCA 61.692 55.000 30.98 17.97 0.00 4.35
2684 2712 0.314578 CTGCTTATTTCGCGCGTCAG 60.315 55.000 30.98 18.82 0.00 3.51
2685 2713 1.648460 GCTTATTTCGCGCGTCAGC 60.648 57.895 30.98 23.94 40.74 4.26
2686 2714 1.999051 CTTATTTCGCGCGTCAGCT 59.001 52.632 30.98 13.38 42.32 4.24
2687 2715 0.043822 CTTATTTCGCGCGTCAGCTC 60.044 55.000 30.98 0.00 42.32 4.09
2688 2716 1.418342 TTATTTCGCGCGTCAGCTCC 61.418 55.000 30.98 0.00 42.32 4.70
2725 2753 4.389576 CGCGAGCAACCAACTGCC 62.390 66.667 0.00 0.00 43.73 4.85
2726 2754 4.389576 GCGAGCAACCAACTGCCG 62.390 66.667 0.00 0.00 43.73 5.69
2727 2755 4.389576 CGAGCAACCAACTGCCGC 62.390 66.667 0.00 0.00 43.73 6.53
2728 2756 4.043200 GAGCAACCAACTGCCGCC 62.043 66.667 0.00 0.00 43.73 6.13
2729 2757 4.892965 AGCAACCAACTGCCGCCA 62.893 61.111 0.00 0.00 43.73 5.69
2730 2758 3.910490 GCAACCAACTGCCGCCAA 61.910 61.111 0.00 0.00 36.25 4.52
2731 2759 2.027460 CAACCAACTGCCGCCAAC 59.973 61.111 0.00 0.00 0.00 3.77
2732 2760 3.223589 AACCAACTGCCGCCAACC 61.224 61.111 0.00 0.00 0.00 3.77
2733 2761 3.731766 AACCAACTGCCGCCAACCT 62.732 57.895 0.00 0.00 0.00 3.50
2734 2762 3.365265 CCAACTGCCGCCAACCTC 61.365 66.667 0.00 0.00 0.00 3.85
2735 2763 2.281761 CAACTGCCGCCAACCTCT 60.282 61.111 0.00 0.00 0.00 3.69
2736 2764 2.032681 AACTGCCGCCAACCTCTC 59.967 61.111 0.00 0.00 0.00 3.20
2737 2765 3.553095 AACTGCCGCCAACCTCTCC 62.553 63.158 0.00 0.00 0.00 3.71
2744 2772 3.470888 CCAACCTCTCCGGGCGAT 61.471 66.667 0.00 0.00 36.97 4.58
2745 2773 2.107141 CAACCTCTCCGGGCGATC 59.893 66.667 0.00 0.00 36.97 3.69
2746 2774 2.363795 AACCTCTCCGGGCGATCA 60.364 61.111 0.00 0.00 36.97 2.92
2747 2775 1.987855 AACCTCTCCGGGCGATCAA 60.988 57.895 0.00 0.00 36.97 2.57
2748 2776 2.107141 CCTCTCCGGGCGATCAAC 59.893 66.667 0.00 0.00 0.00 3.18
2749 2777 2.278857 CTCTCCGGGCGATCAACG 60.279 66.667 0.00 0.00 45.66 4.10
2758 2786 2.878991 CGATCAACGCGCGGAGAA 60.879 61.111 35.22 16.68 34.51 2.87
2759 2787 2.441378 CGATCAACGCGCGGAGAAA 61.441 57.895 35.22 14.74 34.51 2.52
2760 2788 1.785321 GATCAACGCGCGGAGAAAA 59.215 52.632 35.22 13.22 0.00 2.29
2761 2789 0.165079 GATCAACGCGCGGAGAAAAA 59.835 50.000 35.22 12.08 0.00 1.94
2762 2790 0.165944 ATCAACGCGCGGAGAAAAAG 59.834 50.000 35.22 13.56 0.00 2.27
2763 2791 1.440353 CAACGCGCGGAGAAAAAGG 60.440 57.895 35.22 8.04 0.00 3.11
2764 2792 3.249973 AACGCGCGGAGAAAAAGGC 62.250 57.895 35.22 0.00 0.00 4.35
2765 2793 3.722295 CGCGCGGAGAAAAAGGCA 61.722 61.111 24.84 0.00 0.00 4.75
2766 2794 2.877691 GCGCGGAGAAAAAGGCAT 59.122 55.556 8.83 0.00 0.00 4.40
2767 2795 1.226407 GCGCGGAGAAAAAGGCATC 60.226 57.895 8.83 0.00 0.00 3.91
2768 2796 1.922135 GCGCGGAGAAAAAGGCATCA 61.922 55.000 8.83 0.00 0.00 3.07
2769 2797 0.734889 CGCGGAGAAAAAGGCATCAT 59.265 50.000 0.00 0.00 0.00 2.45
2770 2798 1.532505 CGCGGAGAAAAAGGCATCATG 60.533 52.381 0.00 0.00 0.00 3.07
2771 2799 1.800286 GCGGAGAAAAAGGCATCATGC 60.800 52.381 0.00 0.00 44.08 4.06
2772 2800 1.532505 CGGAGAAAAAGGCATCATGCG 60.533 52.381 2.82 0.00 46.21 4.73
2773 2801 1.553308 GAGAAAAAGGCATCATGCGC 58.447 50.000 2.82 0.00 46.21 6.09
2774 2802 1.133790 GAGAAAAAGGCATCATGCGCT 59.866 47.619 9.73 0.00 46.21 5.92
2775 2803 1.135199 AGAAAAAGGCATCATGCGCTG 60.135 47.619 9.73 4.58 46.21 5.18
2776 2804 0.738412 AAAAAGGCATCATGCGCTGC 60.738 50.000 9.73 10.25 46.21 5.25
2777 2805 1.601419 AAAAGGCATCATGCGCTGCT 61.601 50.000 17.45 3.04 46.21 4.24
2778 2806 1.601419 AAAGGCATCATGCGCTGCTT 61.601 50.000 17.45 8.60 46.21 3.91
2779 2807 0.749091 AAGGCATCATGCGCTGCTTA 60.749 50.000 17.45 0.00 46.21 3.09
2780 2808 0.536687 AGGCATCATGCGCTGCTTAT 60.537 50.000 17.45 3.49 46.21 1.73
2781 2809 0.313043 GGCATCATGCGCTGCTTATT 59.687 50.000 17.45 0.00 46.21 1.40
2782 2810 1.269413 GGCATCATGCGCTGCTTATTT 60.269 47.619 17.45 0.00 46.21 1.40
2783 2811 2.049228 GCATCATGCGCTGCTTATTTC 58.951 47.619 9.73 0.00 35.49 2.17
2784 2812 2.304413 CATCATGCGCTGCTTATTTCG 58.696 47.619 9.73 0.00 0.00 3.46
2785 2813 1.368641 TCATGCGCTGCTTATTTCGT 58.631 45.000 9.73 0.00 0.00 3.85
2786 2814 1.062440 TCATGCGCTGCTTATTTCGTG 59.938 47.619 9.73 0.00 0.00 4.35
2787 2815 0.248215 ATGCGCTGCTTATTTCGTGC 60.248 50.000 9.73 0.00 0.00 5.34
2788 2816 1.929714 GCGCTGCTTATTTCGTGCG 60.930 57.895 0.00 0.00 45.12 5.34
2789 2817 1.419922 CGCTGCTTATTTCGTGCGT 59.580 52.632 0.00 0.00 38.81 5.24
2790 2818 0.584054 CGCTGCTTATTTCGTGCGTC 60.584 55.000 0.00 0.00 38.81 5.19
2791 2819 0.442310 GCTGCTTATTTCGTGCGTCA 59.558 50.000 0.00 0.00 0.00 4.35
2792 2820 1.527793 GCTGCTTATTTCGTGCGTCAG 60.528 52.381 0.00 0.00 0.00 3.51
2793 2821 0.442310 TGCTTATTTCGTGCGTCAGC 59.558 50.000 0.00 0.00 45.41 4.26
2794 2822 0.721718 GCTTATTTCGTGCGTCAGCT 59.278 50.000 0.00 0.00 45.42 4.24
2795 2823 1.267087 GCTTATTTCGTGCGTCAGCTC 60.267 52.381 0.00 0.00 45.42 4.09
2796 2824 1.324736 CTTATTTCGTGCGTCAGCTCC 59.675 52.381 0.00 0.00 45.42 4.70
2797 2825 0.459585 TATTTCGTGCGTCAGCTCCC 60.460 55.000 0.00 0.00 45.42 4.30
2798 2826 4.717629 TTCGTGCGTCAGCTCCCG 62.718 66.667 0.00 0.00 45.42 5.14
2824 2852 4.025401 CGACCAACTGCCGCCAAC 62.025 66.667 0.00 0.00 0.00 3.77
2825 2853 3.670377 GACCAACTGCCGCCAACC 61.670 66.667 0.00 0.00 0.00 3.77
2826 2854 4.204028 ACCAACTGCCGCCAACCT 62.204 61.111 0.00 0.00 0.00 3.50
2827 2855 3.365265 CCAACTGCCGCCAACCTC 61.365 66.667 0.00 0.00 0.00 3.85
2828 2856 2.281761 CAACTGCCGCCAACCTCT 60.282 61.111 0.00 0.00 0.00 3.69
2829 2857 2.032681 AACTGCCGCCAACCTCTC 59.967 61.111 0.00 0.00 0.00 3.20
2830 2858 3.553095 AACTGCCGCCAACCTCTCC 62.553 63.158 0.00 0.00 0.00 3.71
2861 2889 3.436055 CCCGGCGGCGAAATTCAA 61.436 61.111 34.49 0.00 0.00 2.69
2862 2890 2.770589 CCCGGCGGCGAAATTCAAT 61.771 57.895 34.49 0.00 0.00 2.57
2863 2891 1.298339 CCGGCGGCGAAATTCAATC 60.298 57.895 34.49 0.00 0.00 2.67
2864 2892 1.651132 CGGCGGCGAAATTCAATCG 60.651 57.895 29.19 0.00 42.99 3.34
2865 2893 1.719117 GGCGGCGAAATTCAATCGA 59.281 52.632 12.98 0.00 42.76 3.59
2866 2894 0.307760 GGCGGCGAAATTCAATCGAT 59.692 50.000 12.98 0.00 42.76 3.59
2867 2895 1.388888 GCGGCGAAATTCAATCGATG 58.611 50.000 12.98 0.00 42.76 3.84
2868 2896 1.921573 GCGGCGAAATTCAATCGATGG 60.922 52.381 12.98 0.00 42.76 3.51
2869 2897 1.597195 CGGCGAAATTCAATCGATGGA 59.403 47.619 0.00 0.00 42.76 3.41
2870 2898 2.031560 CGGCGAAATTCAATCGATGGAA 59.968 45.455 17.43 17.43 42.76 3.53
2871 2899 3.621794 GGCGAAATTCAATCGATGGAAG 58.378 45.455 19.62 8.04 42.76 3.46
2872 2900 3.548818 GGCGAAATTCAATCGATGGAAGG 60.549 47.826 19.62 10.33 42.76 3.46
2873 2901 3.621794 CGAAATTCAATCGATGGAAGGC 58.378 45.455 19.62 10.64 42.76 4.35
2874 2902 3.548818 CGAAATTCAATCGATGGAAGGCC 60.549 47.826 19.62 10.11 42.76 5.19
2875 2903 1.597742 ATTCAATCGATGGAAGGCCG 58.402 50.000 19.62 0.00 36.79 6.13
2876 2904 1.095228 TTCAATCGATGGAAGGCCGC 61.095 55.000 11.32 0.00 36.79 6.53
2877 2905 1.819208 CAATCGATGGAAGGCCGCA 60.819 57.895 0.00 0.00 36.79 5.69
2878 2906 1.819632 AATCGATGGAAGGCCGCAC 60.820 57.895 0.00 0.00 36.79 5.34
2879 2907 3.757248 ATCGATGGAAGGCCGCACC 62.757 63.158 0.00 2.68 36.79 5.01
2881 2909 4.467084 GATGGAAGGCCGCACCGA 62.467 66.667 0.00 0.00 46.52 4.69
2882 2910 4.778143 ATGGAAGGCCGCACCGAC 62.778 66.667 0.00 0.00 46.52 4.79
2884 2912 4.778143 GGAAGGCCGCACCGACAT 62.778 66.667 0.00 0.00 46.52 3.06
2885 2913 3.195698 GAAGGCCGCACCGACATC 61.196 66.667 0.00 0.00 46.52 3.06
2886 2914 4.778143 AAGGCCGCACCGACATCC 62.778 66.667 0.00 0.00 46.52 3.51
2904 2932 2.481890 CCCCCAACCCCTTTCTACA 58.518 57.895 0.00 0.00 0.00 2.74
2905 2933 0.039180 CCCCCAACCCCTTTCTACAC 59.961 60.000 0.00 0.00 0.00 2.90
2906 2934 0.039180 CCCCAACCCCTTTCTACACC 59.961 60.000 0.00 0.00 0.00 4.16
2907 2935 0.039180 CCCAACCCCTTTCTACACCC 59.961 60.000 0.00 0.00 0.00 4.61
2908 2936 0.322187 CCAACCCCTTTCTACACCCG 60.322 60.000 0.00 0.00 0.00 5.28
2909 2937 0.958876 CAACCCCTTTCTACACCCGC 60.959 60.000 0.00 0.00 0.00 6.13
2910 2938 2.125269 CCCCTTTCTACACCCGCG 60.125 66.667 0.00 0.00 0.00 6.46
2911 2939 2.652095 CCCCTTTCTACACCCGCGA 61.652 63.158 8.23 0.00 0.00 5.87
2912 2940 1.447314 CCCTTTCTACACCCGCGAC 60.447 63.158 8.23 0.00 0.00 5.19
2913 2941 1.447314 CCTTTCTACACCCGCGACC 60.447 63.158 8.23 0.00 0.00 4.79
2914 2942 1.447314 CTTTCTACACCCGCGACCC 60.447 63.158 8.23 0.00 0.00 4.46
2915 2943 2.847435 CTTTCTACACCCGCGACCCC 62.847 65.000 8.23 0.00 0.00 4.95
2916 2944 3.892104 TTCTACACCCGCGACCCCT 62.892 63.158 8.23 0.00 0.00 4.79
2917 2945 3.834799 CTACACCCGCGACCCCTC 61.835 72.222 8.23 0.00 0.00 4.30
2943 2971 2.359850 CCGCTGCTGCAAACCCTA 60.360 61.111 16.29 0.00 39.64 3.53
2944 2972 2.401766 CCGCTGCTGCAAACCCTAG 61.402 63.158 16.29 0.00 39.64 3.02
2945 2973 2.880648 GCTGCTGCAAACCCTAGC 59.119 61.111 11.11 0.00 39.41 3.42
2946 2974 3.044059 GCTGCTGCAAACCCTAGCG 62.044 63.158 11.11 0.00 40.24 4.26
2947 2975 3.044059 CTGCTGCAAACCCTAGCGC 62.044 63.158 3.02 0.00 40.24 5.92
2948 2976 4.166011 GCTGCAAACCCTAGCGCG 62.166 66.667 0.00 0.00 0.00 6.86
2949 2977 3.499737 CTGCAAACCCTAGCGCGG 61.500 66.667 8.83 0.00 0.00 6.46
2956 2984 4.530857 CCCTAGCGCGGGGTTGAG 62.531 72.222 26.28 1.61 40.75 3.02
2958 2986 4.148825 CTAGCGCGGGGTTGAGCT 62.149 66.667 10.18 0.00 46.90 4.09
2959 2987 3.665675 CTAGCGCGGGGTTGAGCTT 62.666 63.158 10.18 0.00 42.62 3.74
2960 2988 3.248446 TAGCGCGGGGTTGAGCTTT 62.248 57.895 10.18 0.00 42.62 3.51
2961 2989 1.890625 TAGCGCGGGGTTGAGCTTTA 61.891 55.000 10.18 0.00 42.62 1.85
2962 2990 2.750888 GCGCGGGGTTGAGCTTTAG 61.751 63.158 8.83 0.00 0.00 1.85
2963 2991 2.750888 CGCGGGGTTGAGCTTTAGC 61.751 63.158 0.00 0.00 42.49 3.09
2973 3001 4.223964 GCTTTAGCTTCGCCGCCG 62.224 66.667 0.00 0.00 38.21 6.46
2974 3002 3.564027 CTTTAGCTTCGCCGCCGG 61.564 66.667 0.00 0.00 34.56 6.13
2975 3003 4.382320 TTTAGCTTCGCCGCCGGT 62.382 61.111 4.45 0.00 34.56 5.28
2989 3017 4.101448 CGGTGCCCCTCCTCCAAG 62.101 72.222 0.00 0.00 0.00 3.61
2990 3018 4.432741 GGTGCCCCTCCTCCAAGC 62.433 72.222 0.00 0.00 0.00 4.01
2991 3019 3.650950 GTGCCCCTCCTCCAAGCA 61.651 66.667 0.00 0.00 0.00 3.91
2992 3020 3.650950 TGCCCCTCCTCCAAGCAC 61.651 66.667 0.00 0.00 0.00 4.40
2993 3021 4.432741 GCCCCTCCTCCAAGCACC 62.433 72.222 0.00 0.00 0.00 5.01
2994 3022 4.101448 CCCCTCCTCCAAGCACCG 62.101 72.222 0.00 0.00 0.00 4.94
2995 3023 4.101448 CCCTCCTCCAAGCACCGG 62.101 72.222 0.00 0.00 0.00 5.28
2996 3024 3.322466 CCTCCTCCAAGCACCGGT 61.322 66.667 0.00 0.00 0.00 5.28
2997 3025 2.266055 CTCCTCCAAGCACCGGTC 59.734 66.667 2.59 0.00 0.00 4.79
2998 3026 2.203788 TCCTCCAAGCACCGGTCT 60.204 61.111 2.59 1.72 0.00 3.85
2999 3027 2.232298 CTCCTCCAAGCACCGGTCTC 62.232 65.000 2.59 0.00 0.00 3.36
3000 3028 2.125912 CTCCAAGCACCGGTCTCG 60.126 66.667 2.59 0.00 0.00 4.04
3001 3029 4.373116 TCCAAGCACCGGTCTCGC 62.373 66.667 2.59 5.49 34.56 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.468333 TTTTACTAAGGGTTGTGGTTTTCC 57.532 37.500 0.00 0.00 41.14 3.13
18 19 6.605594 TGTATTGCAGGGGATTTTTACTAAGG 59.394 38.462 0.00 0.00 0.00 2.69
97 98 9.308000 TCTATTTGACAATGAGGGTAAAATGTT 57.692 29.630 0.00 0.00 32.74 2.71
243 244 3.470645 AGGCGTGGAACCTAATATCAC 57.529 47.619 0.00 0.00 35.10 3.06
275 276 6.371825 AGTGCCAGCTAACAACTTCTTAATAC 59.628 38.462 0.00 0.00 0.00 1.89
364 365 8.084590 ACTGTTCACTTATAAGTAAAGCACAC 57.915 34.615 17.62 7.61 37.08 3.82
381 382 4.450419 CACAGAGATGAAAGGACTGTTCAC 59.550 45.833 0.00 0.00 39.33 3.18
403 404 5.724328 CAAAAGCATGTCCTAGAGAGTACA 58.276 41.667 0.00 0.00 0.00 2.90
404 405 4.568760 GCAAAAGCATGTCCTAGAGAGTAC 59.431 45.833 0.00 0.00 0.00 2.73
623 624 5.888161 ACTTTTATTAGTGAGGAAGCATGGG 59.112 40.000 0.00 0.00 0.00 4.00
756 757 9.778993 CATCACCTTCAAAATAAAGTGATACTG 57.221 33.333 3.36 0.00 30.45 2.74
767 768 7.894708 TCAAATTGCTCATCACCTTCAAAATA 58.105 30.769 0.00 0.00 0.00 1.40
824 825 9.988815 CTGTATACAGAAAGATGGCTACTTTAT 57.011 33.333 25.83 4.50 46.59 1.40
1006 1008 5.885912 GGGATCTAGAATAGTGGCACAAAAA 59.114 40.000 21.41 2.28 44.16 1.94
1071 1073 1.448985 GCCGGCTTGATAAGTTGTGA 58.551 50.000 22.15 0.00 0.00 3.58
1073 1075 0.036765 TCGCCGGCTTGATAAGTTGT 60.037 50.000 26.68 0.00 0.00 3.32
1075 1077 0.249398 AGTCGCCGGCTTGATAAGTT 59.751 50.000 26.68 0.00 0.00 2.66
1358 1360 2.160417 GCCACTGCAACTGATACTTCAC 59.840 50.000 0.00 0.00 37.47 3.18
1413 1415 2.969238 CGGCAGATAGGGCAAGCG 60.969 66.667 0.00 0.00 0.00 4.68
1800 1802 3.138283 TGTCAGGACCTCCAGAAAACATT 59.862 43.478 0.00 0.00 38.89 2.71
1814 1816 3.004419 TCGTAATGATCGGATGTCAGGAC 59.996 47.826 0.00 0.00 0.00 3.85
1821 1823 3.908978 CGACTCTTCGTAATGATCGGATG 59.091 47.826 0.00 0.00 40.61 3.51
1842 1844 0.109272 TCCTGTAAGCTCTGCGAACG 60.109 55.000 0.00 0.00 0.00 3.95
1868 1870 1.345415 CATTTTGCCTTGGTCTTGCCT 59.655 47.619 0.00 0.00 38.35 4.75
2167 2189 0.898320 ATTCACAGGTCTAGCAGCGT 59.102 50.000 0.00 0.00 0.00 5.07
2323 2347 7.931578 TCGGAAACATATAACAAAATGGTCT 57.068 32.000 0.00 0.00 0.00 3.85
2410 2435 1.279840 GAACCGCAACTCAGCACAC 59.720 57.895 0.00 0.00 0.00 3.82
2486 2511 6.375455 ACCTGATGACAAATTGGAACATACTC 59.625 38.462 0.00 0.00 39.30 2.59
2491 2519 6.303054 TCTTACCTGATGACAAATTGGAACA 58.697 36.000 0.00 0.00 0.00 3.18
2495 2523 4.701651 TGCTCTTACCTGATGACAAATTGG 59.298 41.667 0.00 0.00 0.00 3.16
2498 2526 5.999044 AGATGCTCTTACCTGATGACAAAT 58.001 37.500 0.00 0.00 0.00 2.32
2515 2543 0.533755 GCACGCCTATTGGAGATGCT 60.534 55.000 3.63 0.00 37.28 3.79
2516 2544 0.533755 AGCACGCCTATTGGAGATGC 60.534 55.000 3.63 9.55 38.93 3.91
2517 2545 2.820059 TAGCACGCCTATTGGAGATG 57.180 50.000 3.63 0.29 36.60 2.90
2518 2546 3.169099 AGATAGCACGCCTATTGGAGAT 58.831 45.455 3.63 0.00 36.88 2.75
2519 2547 2.598565 AGATAGCACGCCTATTGGAGA 58.401 47.619 3.63 0.00 36.88 3.71
2520 2548 3.393089 AAGATAGCACGCCTATTGGAG 57.607 47.619 0.00 0.00 36.88 3.86
2521 2549 4.521130 CTAAGATAGCACGCCTATTGGA 57.479 45.455 0.00 0.00 36.88 3.53
2534 2562 1.202371 TCCAACACGCGGCTAAGATAG 60.202 52.381 12.47 0.00 0.00 2.08
2535 2563 0.818938 TCCAACACGCGGCTAAGATA 59.181 50.000 12.47 0.00 0.00 1.98
2536 2564 0.036765 TTCCAACACGCGGCTAAGAT 60.037 50.000 12.47 0.00 0.00 2.40
2537 2565 0.249953 TTTCCAACACGCGGCTAAGA 60.250 50.000 12.47 0.00 0.00 2.10
2538 2566 0.589223 TTTTCCAACACGCGGCTAAG 59.411 50.000 12.47 0.00 0.00 2.18
2539 2567 1.022735 TTTTTCCAACACGCGGCTAA 58.977 45.000 12.47 0.00 0.00 3.09
2540 2568 2.704108 TTTTTCCAACACGCGGCTA 58.296 47.368 12.47 0.00 0.00 3.93
2541 2569 3.515611 TTTTTCCAACACGCGGCT 58.484 50.000 12.47 0.00 0.00 5.52
2566 2594 4.681643 CAGCTCCGCGCGCAAAAA 62.682 61.111 32.61 11.70 45.59 1.94
2578 2606 3.028366 GAAGCGCCCGTTTCAGCTC 62.028 63.158 2.29 0.00 39.25 4.09
2579 2607 3.050275 GAAGCGCCCGTTTCAGCT 61.050 61.111 2.29 0.00 42.35 4.24
2580 2608 3.353836 TGAAGCGCCCGTTTCAGC 61.354 61.111 14.42 0.00 39.70 4.26
2582 2610 3.353836 GCTGAAGCGCCCGTTTCA 61.354 61.111 16.79 16.79 41.70 2.69
2583 2611 3.314388 CTGCTGAAGCGCCCGTTTC 62.314 63.158 2.29 9.80 45.83 2.78
2584 2612 3.357079 CTGCTGAAGCGCCCGTTT 61.357 61.111 2.29 0.00 45.83 3.60
2593 2621 1.980951 TTATTGCGCGGCTGCTGAAG 61.981 55.000 17.03 6.33 39.65 3.02
2594 2622 1.375853 ATTATTGCGCGGCTGCTGAA 61.376 50.000 17.03 8.26 39.65 3.02
2595 2623 1.775039 GATTATTGCGCGGCTGCTGA 61.775 55.000 17.03 1.00 39.65 4.26
2596 2624 1.369689 GATTATTGCGCGGCTGCTG 60.370 57.895 17.03 10.42 39.65 4.41
2597 2625 2.885676 CGATTATTGCGCGGCTGCT 61.886 57.895 17.03 0.00 39.65 4.24
2598 2626 2.425773 CGATTATTGCGCGGCTGC 60.426 61.111 8.83 7.70 37.91 5.25
2599 2627 2.425773 GCGATTATTGCGCGGCTG 60.426 61.111 8.83 0.00 45.27 4.85
2615 2643 4.424430 CCATTATACCGCGCGCGC 62.424 66.667 45.06 42.65 38.24 6.86
2616 2644 3.773630 CCCATTATACCGCGCGCG 61.774 66.667 43.73 43.73 39.44 6.86
2617 2645 1.693083 GATCCCATTATACCGCGCGC 61.693 60.000 27.36 23.91 0.00 6.86
2618 2646 0.389296 TGATCCCATTATACCGCGCG 60.389 55.000 25.67 25.67 0.00 6.86
2619 2647 1.359848 CTGATCCCATTATACCGCGC 58.640 55.000 0.00 0.00 0.00 6.86
2620 2648 1.359848 GCTGATCCCATTATACCGCG 58.640 55.000 0.00 0.00 0.00 6.46
2621 2649 1.359848 CGCTGATCCCATTATACCGC 58.640 55.000 0.00 0.00 0.00 5.68
2622 2650 1.359848 GCGCTGATCCCATTATACCG 58.640 55.000 0.00 0.00 0.00 4.02
2623 2651 1.359848 CGCGCTGATCCCATTATACC 58.640 55.000 5.56 0.00 0.00 2.73
2624 2652 0.721718 GCGCGCTGATCCCATTATAC 59.278 55.000 26.67 0.00 0.00 1.47
2625 2653 0.735978 CGCGCGCTGATCCCATTATA 60.736 55.000 30.48 0.00 0.00 0.98
2626 2654 2.029288 CGCGCGCTGATCCCATTAT 61.029 57.895 30.48 0.00 0.00 1.28
2627 2655 2.661537 CGCGCGCTGATCCCATTA 60.662 61.111 30.48 0.00 0.00 1.90
2632 2660 4.873129 TTCTCCGCGCGCTGATCC 62.873 66.667 30.48 0.00 0.00 3.36
2633 2661 1.966493 TTTTTCTCCGCGCGCTGATC 61.966 55.000 30.48 0.00 0.00 2.92
2634 2662 1.369091 ATTTTTCTCCGCGCGCTGAT 61.369 50.000 30.48 8.99 0.00 2.90
2635 2663 0.738063 TATTTTTCTCCGCGCGCTGA 60.738 50.000 30.48 26.95 0.00 4.26
2636 2664 0.315382 CTATTTTTCTCCGCGCGCTG 60.315 55.000 30.48 23.89 0.00 5.18
2637 2665 2.006772 CTATTTTTCTCCGCGCGCT 58.993 52.632 30.48 9.42 0.00 5.92
2638 2666 1.651431 GCTATTTTTCTCCGCGCGC 60.651 57.895 27.36 23.91 0.00 6.86
2639 2667 0.304705 ATGCTATTTTTCTCCGCGCG 59.695 50.000 25.67 25.67 0.00 6.86
2640 2668 1.330521 TGATGCTATTTTTCTCCGCGC 59.669 47.619 0.00 0.00 0.00 6.86
2641 2669 3.548587 CATGATGCTATTTTTCTCCGCG 58.451 45.455 0.00 0.00 0.00 6.46
2642 2670 3.303406 GCATGATGCTATTTTTCTCCGC 58.697 45.455 10.72 0.00 40.96 5.54
2643 2671 3.304928 GGGCATGATGCTATTTTTCTCCG 60.305 47.826 17.84 0.00 44.28 4.63
2644 2672 3.893813 AGGGCATGATGCTATTTTTCTCC 59.106 43.478 17.84 6.42 44.28 3.71
2645 2673 4.795308 GCAGGGCATGATGCTATTTTTCTC 60.795 45.833 17.84 0.00 44.28 2.87
2646 2674 3.069158 GCAGGGCATGATGCTATTTTTCT 59.931 43.478 17.84 1.59 44.28 2.52
2647 2675 3.387397 GCAGGGCATGATGCTATTTTTC 58.613 45.455 17.84 0.00 44.28 2.29
2648 2676 3.464111 GCAGGGCATGATGCTATTTTT 57.536 42.857 17.84 0.00 44.28 1.94
2655 2683 2.606308 CGAAATAAGCAGGGCATGATGC 60.606 50.000 9.33 9.33 44.08 3.91
2656 2684 2.606308 GCGAAATAAGCAGGGCATGATG 60.606 50.000 1.99 0.00 34.19 3.07
2657 2685 1.610522 GCGAAATAAGCAGGGCATGAT 59.389 47.619 1.99 0.00 34.19 2.45
2658 2686 1.024271 GCGAAATAAGCAGGGCATGA 58.976 50.000 1.99 0.00 34.19 3.07
2659 2687 0.317269 CGCGAAATAAGCAGGGCATG 60.317 55.000 0.00 0.00 34.19 4.06
2660 2688 2.024918 CGCGAAATAAGCAGGGCAT 58.975 52.632 0.00 0.00 34.19 4.40
2661 2689 2.760159 GCGCGAAATAAGCAGGGCA 61.760 57.895 12.10 0.00 41.34 5.36
2662 2690 2.024729 GCGCGAAATAAGCAGGGC 59.975 61.111 12.10 0.00 35.54 5.19
2663 2691 2.324477 CGCGCGAAATAAGCAGGG 59.676 61.111 28.94 0.00 34.19 4.45
2664 2692 1.012234 GACGCGCGAAATAAGCAGG 60.012 57.895 39.36 2.23 34.19 4.85
2665 2693 0.314578 CTGACGCGCGAAATAAGCAG 60.315 55.000 39.36 23.66 34.19 4.24
2666 2694 1.707451 CTGACGCGCGAAATAAGCA 59.293 52.632 39.36 19.11 34.19 3.91
2667 2695 1.648460 GCTGACGCGCGAAATAAGC 60.648 57.895 39.36 28.90 0.00 3.09
2668 2696 0.043822 GAGCTGACGCGCGAAATAAG 60.044 55.000 39.36 24.03 42.32 1.73
2669 2697 1.418342 GGAGCTGACGCGCGAAATAA 61.418 55.000 39.36 15.16 42.32 1.40
2670 2698 1.876714 GGAGCTGACGCGCGAAATA 60.877 57.895 39.36 17.58 42.32 1.40
2671 2699 3.188786 GGAGCTGACGCGCGAAAT 61.189 61.111 39.36 15.50 42.32 2.17
2706 2734 4.724697 CAGTTGGTTGCTCGCGCG 62.725 66.667 26.76 26.76 39.65 6.86
2708 2736 4.389576 GGCAGTTGGTTGCTCGCG 62.390 66.667 0.00 0.00 43.57 5.87
2709 2737 4.389576 CGGCAGTTGGTTGCTCGC 62.390 66.667 0.00 0.00 43.57 5.03
2710 2738 4.389576 GCGGCAGTTGGTTGCTCG 62.390 66.667 0.00 1.99 43.57 5.03
2711 2739 4.043200 GGCGGCAGTTGGTTGCTC 62.043 66.667 3.07 0.00 43.57 4.26
2712 2740 4.892965 TGGCGGCAGTTGGTTGCT 62.893 61.111 7.97 0.00 43.57 3.91
2713 2741 3.910490 TTGGCGGCAGTTGGTTGC 61.910 61.111 12.87 0.00 43.34 4.17
2714 2742 2.027460 GTTGGCGGCAGTTGGTTG 59.973 61.111 12.87 0.00 0.00 3.77
2715 2743 3.223589 GGTTGGCGGCAGTTGGTT 61.224 61.111 12.87 0.00 0.00 3.67
2716 2744 4.204028 AGGTTGGCGGCAGTTGGT 62.204 61.111 12.87 0.00 0.00 3.67
2717 2745 3.365265 GAGGTTGGCGGCAGTTGG 61.365 66.667 12.87 0.00 0.00 3.77
2718 2746 2.281761 AGAGGTTGGCGGCAGTTG 60.282 61.111 12.87 0.00 0.00 3.16
2719 2747 2.032681 GAGAGGTTGGCGGCAGTT 59.967 61.111 12.87 1.21 0.00 3.16
2720 2748 4.021925 GGAGAGGTTGGCGGCAGT 62.022 66.667 12.87 0.25 0.00 4.40
2727 2755 3.447025 GATCGCCCGGAGAGGTTGG 62.447 68.421 0.73 0.00 38.74 3.77
2728 2756 2.107141 GATCGCCCGGAGAGGTTG 59.893 66.667 0.73 0.00 38.74 3.77
2729 2757 1.987855 TTGATCGCCCGGAGAGGTT 60.988 57.895 0.73 0.00 38.74 3.50
2730 2758 2.363795 TTGATCGCCCGGAGAGGT 60.364 61.111 0.73 0.00 38.74 3.85
2731 2759 2.107141 GTTGATCGCCCGGAGAGG 59.893 66.667 0.73 0.00 40.63 3.69
2732 2760 2.278857 CGTTGATCGCCCGGAGAG 60.279 66.667 0.73 0.00 0.00 3.20
2741 2769 1.951181 TTTTCTCCGCGCGTTGATCG 61.951 55.000 29.95 12.39 43.12 3.69
2742 2770 0.165079 TTTTTCTCCGCGCGTTGATC 59.835 50.000 29.95 0.00 0.00 2.92
2743 2771 0.165944 CTTTTTCTCCGCGCGTTGAT 59.834 50.000 29.95 0.00 0.00 2.57
2744 2772 1.567537 CTTTTTCTCCGCGCGTTGA 59.432 52.632 29.95 22.26 0.00 3.18
2745 2773 1.440353 CCTTTTTCTCCGCGCGTTG 60.440 57.895 29.95 20.24 0.00 4.10
2746 2774 2.943653 CCTTTTTCTCCGCGCGTT 59.056 55.556 29.95 0.00 0.00 4.84
2747 2775 3.723348 GCCTTTTTCTCCGCGCGT 61.723 61.111 29.95 0.00 0.00 6.01
2748 2776 2.903079 GATGCCTTTTTCTCCGCGCG 62.903 60.000 25.67 25.67 0.00 6.86
2749 2777 1.226407 GATGCCTTTTTCTCCGCGC 60.226 57.895 0.00 0.00 0.00 6.86
2750 2778 0.734889 ATGATGCCTTTTTCTCCGCG 59.265 50.000 0.00 0.00 0.00 6.46
2751 2779 1.800286 GCATGATGCCTTTTTCTCCGC 60.800 52.381 6.04 0.00 37.42 5.54
2752 2780 1.532505 CGCATGATGCCTTTTTCTCCG 60.533 52.381 12.40 0.00 41.12 4.63
2753 2781 1.800286 GCGCATGATGCCTTTTTCTCC 60.800 52.381 12.40 0.00 41.12 3.71
2754 2782 1.133790 AGCGCATGATGCCTTTTTCTC 59.866 47.619 12.40 0.00 41.12 2.87
2755 2783 1.135199 CAGCGCATGATGCCTTTTTCT 60.135 47.619 12.40 0.00 41.12 2.52
2756 2784 1.274596 CAGCGCATGATGCCTTTTTC 58.725 50.000 12.40 0.00 41.12 2.29
2757 2785 3.429043 CAGCGCATGATGCCTTTTT 57.571 47.368 12.40 0.00 41.12 1.94
2764 2792 2.286595 ACGAAATAAGCAGCGCATGATG 60.287 45.455 11.47 0.00 33.68 3.07
2765 2793 1.942657 ACGAAATAAGCAGCGCATGAT 59.057 42.857 11.47 0.01 0.00 2.45
2766 2794 1.062440 CACGAAATAAGCAGCGCATGA 59.938 47.619 11.47 0.00 0.00 3.07
2767 2795 1.459756 CACGAAATAAGCAGCGCATG 58.540 50.000 11.47 6.31 0.00 4.06
2768 2796 0.248215 GCACGAAATAAGCAGCGCAT 60.248 50.000 11.47 0.00 0.00 4.73
2769 2797 1.134487 GCACGAAATAAGCAGCGCA 59.866 52.632 11.47 0.00 0.00 6.09
2770 2798 1.929714 CGCACGAAATAAGCAGCGC 60.930 57.895 0.00 0.00 38.68 5.92
2771 2799 4.252242 CGCACGAAATAAGCAGCG 57.748 55.556 0.00 0.00 39.17 5.18
2772 2800 0.442310 TGACGCACGAAATAAGCAGC 59.558 50.000 0.00 0.00 0.00 5.25
2773 2801 1.527793 GCTGACGCACGAAATAAGCAG 60.528 52.381 0.00 0.00 35.78 4.24
2774 2802 0.442310 GCTGACGCACGAAATAAGCA 59.558 50.000 0.00 0.00 35.78 3.91
2775 2803 0.721718 AGCTGACGCACGAAATAAGC 59.278 50.000 0.00 0.00 39.10 3.09
2776 2804 1.324736 GGAGCTGACGCACGAAATAAG 59.675 52.381 0.00 0.00 39.10 1.73
2777 2805 1.355971 GGAGCTGACGCACGAAATAA 58.644 50.000 0.00 0.00 39.10 1.40
2778 2806 0.459585 GGGAGCTGACGCACGAAATA 60.460 55.000 0.00 0.00 39.10 1.40
2779 2807 1.741770 GGGAGCTGACGCACGAAAT 60.742 57.895 0.00 0.00 39.10 2.17
2780 2808 2.357034 GGGAGCTGACGCACGAAA 60.357 61.111 0.00 0.00 39.10 3.46
2781 2809 4.717629 CGGGAGCTGACGCACGAA 62.718 66.667 0.00 0.00 39.10 3.85
2808 2836 3.670377 GGTTGGCGGCAGTTGGTC 61.670 66.667 12.87 0.14 0.00 4.02
2809 2837 4.204028 AGGTTGGCGGCAGTTGGT 62.204 61.111 12.87 0.00 0.00 3.67
2810 2838 3.365265 GAGGTTGGCGGCAGTTGG 61.365 66.667 12.87 0.00 0.00 3.77
2811 2839 2.281761 AGAGGTTGGCGGCAGTTG 60.282 61.111 12.87 0.00 0.00 3.16
2812 2840 2.032681 GAGAGGTTGGCGGCAGTT 59.967 61.111 12.87 1.21 0.00 3.16
2813 2841 4.021925 GGAGAGGTTGGCGGCAGT 62.022 66.667 12.87 0.25 0.00 4.40
2844 2872 2.662091 GATTGAATTTCGCCGCCGGG 62.662 60.000 4.77 0.00 34.56 5.73
2845 2873 1.298339 GATTGAATTTCGCCGCCGG 60.298 57.895 0.00 0.00 34.56 6.13
2846 2874 1.651132 CGATTGAATTTCGCCGCCG 60.651 57.895 0.00 0.00 0.00 6.46
2847 2875 0.307760 ATCGATTGAATTTCGCCGCC 59.692 50.000 0.00 0.00 36.56 6.13
2848 2876 1.388888 CATCGATTGAATTTCGCCGC 58.611 50.000 0.00 0.00 36.56 6.53
2849 2877 1.597195 TCCATCGATTGAATTTCGCCG 59.403 47.619 0.00 0.00 36.56 6.46
2850 2878 3.548818 CCTTCCATCGATTGAATTTCGCC 60.549 47.826 11.91 0.00 36.56 5.54
2851 2879 3.621794 CCTTCCATCGATTGAATTTCGC 58.378 45.455 11.91 0.00 36.56 4.70
2852 2880 3.548818 GGCCTTCCATCGATTGAATTTCG 60.549 47.826 11.91 1.61 37.94 3.46
2853 2881 3.548818 CGGCCTTCCATCGATTGAATTTC 60.549 47.826 11.91 5.10 0.00 2.17
2854 2882 2.358898 CGGCCTTCCATCGATTGAATTT 59.641 45.455 11.91 0.00 0.00 1.82
2855 2883 1.949525 CGGCCTTCCATCGATTGAATT 59.050 47.619 11.91 0.00 0.00 2.17
2856 2884 1.597742 CGGCCTTCCATCGATTGAAT 58.402 50.000 11.91 0.00 0.00 2.57
2857 2885 1.095228 GCGGCCTTCCATCGATTGAA 61.095 55.000 11.10 11.10 0.00 2.69
2858 2886 1.523711 GCGGCCTTCCATCGATTGA 60.524 57.895 0.00 0.00 0.00 2.57
2859 2887 1.819208 TGCGGCCTTCCATCGATTG 60.819 57.895 0.00 0.00 0.00 2.67
2860 2888 1.819632 GTGCGGCCTTCCATCGATT 60.820 57.895 0.00 0.00 0.00 3.34
2861 2889 2.203070 GTGCGGCCTTCCATCGAT 60.203 61.111 0.00 0.00 0.00 3.59
2862 2890 4.467084 GGTGCGGCCTTCCATCGA 62.467 66.667 0.00 0.00 0.00 3.59
2864 2892 4.467084 TCGGTGCGGCCTTCCATC 62.467 66.667 0.00 0.00 34.25 3.51
2865 2893 4.778143 GTCGGTGCGGCCTTCCAT 62.778 66.667 0.00 0.00 34.25 3.41
2867 2895 4.778143 ATGTCGGTGCGGCCTTCC 62.778 66.667 0.00 0.00 34.25 3.46
2868 2896 3.195698 GATGTCGGTGCGGCCTTC 61.196 66.667 0.00 0.00 34.25 3.46
2869 2897 4.778143 GGATGTCGGTGCGGCCTT 62.778 66.667 0.00 0.00 34.25 4.35
2886 2914 0.039180 GTGTAGAAAGGGGTTGGGGG 59.961 60.000 0.00 0.00 0.00 5.40
2887 2915 0.039180 GGTGTAGAAAGGGGTTGGGG 59.961 60.000 0.00 0.00 0.00 4.96
2888 2916 0.039180 GGGTGTAGAAAGGGGTTGGG 59.961 60.000 0.00 0.00 0.00 4.12
2889 2917 0.322187 CGGGTGTAGAAAGGGGTTGG 60.322 60.000 0.00 0.00 0.00 3.77
2890 2918 0.958876 GCGGGTGTAGAAAGGGGTTG 60.959 60.000 0.00 0.00 0.00 3.77
2891 2919 1.377612 GCGGGTGTAGAAAGGGGTT 59.622 57.895 0.00 0.00 0.00 4.11
2892 2920 2.951101 CGCGGGTGTAGAAAGGGGT 61.951 63.158 0.00 0.00 0.00 4.95
2893 2921 2.125269 CGCGGGTGTAGAAAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
2894 2922 1.447314 GTCGCGGGTGTAGAAAGGG 60.447 63.158 6.13 0.00 0.00 3.95
2895 2923 1.447314 GGTCGCGGGTGTAGAAAGG 60.447 63.158 6.13 0.00 0.00 3.11
2896 2924 1.447314 GGGTCGCGGGTGTAGAAAG 60.447 63.158 6.13 0.00 0.00 2.62
2897 2925 2.658422 GGGTCGCGGGTGTAGAAA 59.342 61.111 6.13 0.00 0.00 2.52
2898 2926 3.384532 GGGGTCGCGGGTGTAGAA 61.385 66.667 6.13 0.00 0.00 2.10
2899 2927 4.371417 AGGGGTCGCGGGTGTAGA 62.371 66.667 6.13 0.00 0.00 2.59
2900 2928 3.834799 GAGGGGTCGCGGGTGTAG 61.835 72.222 6.13 0.00 0.00 2.74
2926 2954 2.359850 TAGGGTTTGCAGCAGCGG 60.360 61.111 0.00 0.00 46.23 5.52
2927 2955 3.044059 GCTAGGGTTTGCAGCAGCG 62.044 63.158 0.00 0.00 46.23 5.18
2928 2956 2.880648 GCTAGGGTTTGCAGCAGC 59.119 61.111 0.00 0.00 42.57 5.25
2929 2957 3.044059 GCGCTAGGGTTTGCAGCAG 62.044 63.158 8.77 0.00 34.94 4.24
2930 2958 3.055719 GCGCTAGGGTTTGCAGCA 61.056 61.111 8.77 0.00 34.94 4.41
2931 2959 4.166011 CGCGCTAGGGTTTGCAGC 62.166 66.667 5.56 0.00 0.00 5.25
2932 2960 3.499737 CCGCGCTAGGGTTTGCAG 61.500 66.667 5.56 0.00 0.00 4.41
2941 2969 3.665675 AAGCTCAACCCCGCGCTAG 62.666 63.158 5.56 0.00 31.48 3.42
2942 2970 1.890625 TAAAGCTCAACCCCGCGCTA 61.891 55.000 5.56 0.00 31.48 4.26
2943 2971 3.248446 TAAAGCTCAACCCCGCGCT 62.248 57.895 5.56 0.00 0.00 5.92
2944 2972 2.744709 TAAAGCTCAACCCCGCGC 60.745 61.111 0.00 0.00 0.00 6.86
2945 2973 2.750888 GCTAAAGCTCAACCCCGCG 61.751 63.158 0.00 0.00 38.21 6.46
2946 2974 3.188011 GCTAAAGCTCAACCCCGC 58.812 61.111 0.00 0.00 38.21 6.13
2974 3002 3.650950 TGCTTGGAGGAGGGGCAC 61.651 66.667 0.00 0.00 0.00 5.01
2975 3003 3.650950 GTGCTTGGAGGAGGGGCA 61.651 66.667 0.00 0.00 0.00 5.36
2976 3004 4.432741 GGTGCTTGGAGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
2977 3005 4.101448 CGGTGCTTGGAGGAGGGG 62.101 72.222 0.00 0.00 0.00 4.79
2978 3006 4.101448 CCGGTGCTTGGAGGAGGG 62.101 72.222 0.00 0.00 0.00 4.30
2979 3007 3.316573 GACCGGTGCTTGGAGGAGG 62.317 68.421 14.63 0.00 0.00 4.30
2980 3008 2.232298 GAGACCGGTGCTTGGAGGAG 62.232 65.000 14.63 0.00 0.00 3.69
2981 3009 2.203788 AGACCGGTGCTTGGAGGA 60.204 61.111 14.63 0.00 0.00 3.71
2982 3010 2.266055 GAGACCGGTGCTTGGAGG 59.734 66.667 14.63 0.00 0.00 4.30
2983 3011 2.125912 CGAGACCGGTGCTTGGAG 60.126 66.667 14.63 0.00 0.00 3.86
2984 3012 4.373116 GCGAGACCGGTGCTTGGA 62.373 66.667 14.63 0.00 36.06 3.53


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

AutoCloner maintained by Alex Coulton.