Multiple sequence alignment - TraesCS3B01G182500

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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 TraesCS3B01G182500 chr3B 100.000 3518 0 0 1 3518 191191311 191187794 0.000000e+00 6497.0
1 TraesCS3B01G182500 chr3B 81.429 70 13 0 3411 3480 680336932 680337001 1.360000e-04 58.4
2 TraesCS3B01G182500 chr3A 93.858 2768 114 27 1 2748 149988367 149985636 0.000000e+00 4119.0
3 TraesCS3B01G182500 chr3D 95.091 2587 82 23 172 2746 135045977 135043424 0.000000e+00 4032.0
4 TraesCS3B01G182500 chr3D 75.930 457 93 11 3039 3480 5322925 5322471 5.910000e-53 219.0
5 TraesCS3B01G182500 chr3D 90.698 43 4 0 3438 3480 516959585 516959543 1.360000e-04 58.4
6 TraesCS3B01G182500 chr2A 76.510 596 104 18 2905 3480 701058378 701058957 3.430000e-75 292.0
7 TraesCS3B01G182500 chr2A 73.051 590 112 35 2911 3477 711520314 711520879 7.810000e-37 165.0
8 TraesCS3B01G182500 chr2A 77.436 195 28 8 2844 3029 5786237 5786424 6.210000e-18 102.0
9 TraesCS3B01G182500 chr7D 74.912 566 103 26 2928 3478 519404069 519403528 4.570000e-54 222.0
10 TraesCS3B01G182500 chr4B 73.057 579 127 20 2910 3480 460163762 460164319 1.000000e-40 178.0
11 TraesCS3B01G182500 chr7A 74.215 446 95 14 3049 3478 138385011 138384570 6.040000e-38 169.0
12 TraesCS3B01G182500 chr1A 75.445 281 55 9 2907 3186 291003565 291003832 1.330000e-24 124.0
13 TraesCS3B01G182500 chr1B 77.880 217 34 8 2902 3117 324012590 324012793 4.770000e-24 122.0
14 TraesCS3B01G182500 chr5B 77.519 129 23 5 3215 3340 408343539 408343414 4.870000e-09 73.1


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 TraesCS3B01G182500 chr3B 191187794 191191311 3517 True 6497 6497 100.000 1 3518 1 chr3B.!!$R1 3517
1 TraesCS3B01G182500 chr3A 149985636 149988367 2731 True 4119 4119 93.858 1 2748 1 chr3A.!!$R1 2747
2 TraesCS3B01G182500 chr3D 135043424 135045977 2553 True 4032 4032 95.091 172 2746 1 chr3D.!!$R2 2574
3 TraesCS3B01G182500 chr2A 701058378 701058957 579 False 292 292 76.510 2905 3480 1 chr2A.!!$F2 575
4 TraesCS3B01G182500 chr7D 519403528 519404069 541 True 222 222 74.912 2928 3478 1 chr7D.!!$R1 550

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
614 632 0.81401 CCCCAAATCTTCCTACGGCG 60.814 60.0 4.8 4.8 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 2606 1.066454 ACGGGCAAAAGTTACAAGCAC 59.934 47.619 0.0 0.0 0.0 4.4 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
150 158 7.272084 GCAGTTGCACTAAAATAGATGTCAAAG 59.728 37.037 0.00 0.00 41.59 2.77
151 159 8.506437 CAGTTGCACTAAAATAGATGTCAAAGA 58.494 33.333 0.00 0.00 0.00 2.52
210 226 2.446666 ACCAGCCAGCCATCCAATATAA 59.553 45.455 0.00 0.00 0.00 0.98
264 280 2.196749 GATGTCTTGCATGACGACGAT 58.803 47.619 23.17 13.60 39.64 3.73
265 281 2.078849 TGTCTTGCATGACGACGATT 57.921 45.000 23.17 0.00 39.64 3.34
266 282 1.992667 TGTCTTGCATGACGACGATTC 59.007 47.619 23.17 2.69 39.64 2.52
267 283 1.992667 GTCTTGCATGACGACGATTCA 59.007 47.619 16.02 0.00 0.00 2.57
268 284 1.992667 TCTTGCATGACGACGATTCAC 59.007 47.619 0.00 0.00 0.00 3.18
269 285 1.995484 CTTGCATGACGACGATTCACT 59.005 47.619 0.00 0.00 0.00 3.41
270 286 2.931512 TGCATGACGACGATTCACTA 57.068 45.000 0.00 0.00 0.00 2.74
381 397 0.982852 TCTCCACCCAATCCATCGCT 60.983 55.000 0.00 0.00 0.00 4.93
479 497 2.104331 CGCAGTAGCCGTCGGATT 59.896 61.111 17.49 4.56 37.52 3.01
480 498 1.357690 CGCAGTAGCCGTCGGATTA 59.642 57.895 17.49 3.45 37.52 1.75
485 503 1.887198 AGTAGCCGTCGGATTATGGAG 59.113 52.381 17.49 0.00 0.00 3.86
614 632 0.814010 CCCCAAATCTTCCTACGGCG 60.814 60.000 4.80 4.80 0.00 6.46
799 818 3.218398 CGATCGGGTTTATACGTACGTC 58.782 50.000 26.53 9.99 0.00 4.34
801 820 2.639065 TCGGGTTTATACGTACGTCCT 58.361 47.619 26.53 15.95 0.00 3.85
824 843 4.954933 GCATAAAGGTGGCGAGGA 57.045 55.556 0.00 0.00 0.00 3.71
991 1015 0.835941 AGTGGCTTGCTGGAGATAGG 59.164 55.000 0.00 0.00 0.00 2.57
999 1023 2.122989 TGGAGATAGGGGGCGGTC 60.123 66.667 0.00 0.00 0.00 4.79
1017 1041 2.044451 ATGGATTTTGGGCGGCGA 60.044 55.556 12.98 0.00 0.00 5.54
1503 1530 3.626924 GTCACCTCCCACAGCCGT 61.627 66.667 0.00 0.00 0.00 5.68
1725 1752 1.134670 GTCAAGGCGTGGAAGCTATCT 60.135 52.381 0.00 0.00 37.29 1.98
2010 2037 1.333636 ACATCTGGGAGAAGGAGGCG 61.334 60.000 0.00 0.00 0.00 5.52
2049 2076 2.280552 CGTCGGGTTCCTCAAGGGA 61.281 63.158 0.00 0.00 43.41 4.20
2349 2376 1.331138 GACGACGAAGATGACGAGGAT 59.669 52.381 0.00 0.00 34.70 3.24
2539 2579 0.811915 TCAGCGTTGACTAGGAGAGC 59.188 55.000 0.00 0.00 0.00 4.09
2545 2585 3.574445 GACTAGGAGAGCGCGCGA 61.574 66.667 37.18 9.88 0.00 5.87
2546 2586 3.515286 GACTAGGAGAGCGCGCGAG 62.515 68.421 37.18 22.30 0.00 5.03
2558 2598 4.079090 CGCGAGCAAGTACCTCTG 57.921 61.111 0.00 0.00 0.00 3.35
2560 2600 0.388649 CGCGAGCAAGTACCTCTGTT 60.389 55.000 0.00 0.00 0.00 3.16
2561 2601 1.797025 GCGAGCAAGTACCTCTGTTT 58.203 50.000 0.00 0.00 0.00 2.83
2562 2602 2.143925 GCGAGCAAGTACCTCTGTTTT 58.856 47.619 0.00 0.00 0.00 2.43
2563 2603 3.323243 GCGAGCAAGTACCTCTGTTTTA 58.677 45.455 0.00 0.00 0.00 1.52
2564 2604 3.368236 GCGAGCAAGTACCTCTGTTTTAG 59.632 47.826 0.00 0.00 0.00 1.85
2565 2605 3.368236 CGAGCAAGTACCTCTGTTTTAGC 59.632 47.826 0.00 0.00 0.00 3.09
2566 2606 3.326747 AGCAAGTACCTCTGTTTTAGCG 58.673 45.455 0.00 0.00 0.00 4.26
2567 2607 3.064931 GCAAGTACCTCTGTTTTAGCGT 58.935 45.455 0.00 0.00 0.00 5.07
2568 2608 3.120649 GCAAGTACCTCTGTTTTAGCGTG 60.121 47.826 0.00 0.00 0.00 5.34
2569 2609 2.685100 AGTACCTCTGTTTTAGCGTGC 58.315 47.619 0.00 0.00 0.00 5.34
2570 2610 2.299297 AGTACCTCTGTTTTAGCGTGCT 59.701 45.455 0.00 0.00 0.00 4.40
2571 2611 2.256117 ACCTCTGTTTTAGCGTGCTT 57.744 45.000 0.00 0.00 0.00 3.91
2572 2612 1.873591 ACCTCTGTTTTAGCGTGCTTG 59.126 47.619 0.00 0.00 0.00 4.01
2573 2613 1.873591 CCTCTGTTTTAGCGTGCTTGT 59.126 47.619 0.00 0.00 0.00 3.16
2574 2614 3.064207 CCTCTGTTTTAGCGTGCTTGTA 58.936 45.455 0.00 0.00 0.00 2.41
2575 2615 3.496884 CCTCTGTTTTAGCGTGCTTGTAA 59.503 43.478 0.00 0.00 0.00 2.41
2576 2616 4.455124 CTCTGTTTTAGCGTGCTTGTAAC 58.545 43.478 0.00 3.41 0.00 2.50
2577 2617 4.124238 TCTGTTTTAGCGTGCTTGTAACT 58.876 39.130 0.00 0.00 0.00 2.24
2578 2618 4.573201 TCTGTTTTAGCGTGCTTGTAACTT 59.427 37.500 0.00 0.00 0.00 2.66
2579 2619 5.065474 TCTGTTTTAGCGTGCTTGTAACTTT 59.935 36.000 0.00 0.00 0.00 2.66
2580 2620 5.642686 TGTTTTAGCGTGCTTGTAACTTTT 58.357 33.333 0.00 0.00 0.00 2.27
2581 2621 5.513495 TGTTTTAGCGTGCTTGTAACTTTTG 59.487 36.000 0.00 0.00 0.00 2.44
2582 2622 2.119671 AGCGTGCTTGTAACTTTTGC 57.880 45.000 0.00 0.00 0.00 3.68
2583 2623 1.128513 GCGTGCTTGTAACTTTTGCC 58.871 50.000 0.00 0.00 0.00 4.52
2584 2624 1.766069 CGTGCTTGTAACTTTTGCCC 58.234 50.000 0.00 0.00 0.00 5.36
2585 2625 1.766069 GTGCTTGTAACTTTTGCCCG 58.234 50.000 0.00 0.00 0.00 6.13
2586 2626 1.066454 GTGCTTGTAACTTTTGCCCGT 59.934 47.619 0.00 0.00 0.00 5.28
2587 2627 1.751924 TGCTTGTAACTTTTGCCCGTT 59.248 42.857 0.00 0.00 0.00 4.44
2588 2628 2.124122 GCTTGTAACTTTTGCCCGTTG 58.876 47.619 0.00 0.00 0.00 4.10
2676 2718 0.757188 ACCCACTATCTGCCTCTCCG 60.757 60.000 0.00 0.00 0.00 4.63
2684 2726 1.500474 TCTGCCTCTCCGATCCAAAT 58.500 50.000 0.00 0.00 0.00 2.32
2695 2737 6.591935 TCTCCGATCCAAATTTAGCATTACT 58.408 36.000 0.00 0.00 0.00 2.24
2699 2741 7.771361 TCCGATCCAAATTTAGCATTACTGTTA 59.229 33.333 0.00 0.00 0.00 2.41
2716 2758 2.167693 TGTTAACAGTATCCGGCTCAGG 59.832 50.000 3.59 0.00 0.00 3.86
2725 2767 1.073199 CCGGCTCAGGGTGTCTTTT 59.927 57.895 0.00 0.00 0.00 2.27
2749 2791 4.850859 TTTTCACACAGTATAATCGCGG 57.149 40.909 6.13 0.00 0.00 6.46
2750 2792 3.786516 TTCACACAGTATAATCGCGGA 57.213 42.857 6.13 0.00 0.00 5.54
2751 2793 3.786516 TCACACAGTATAATCGCGGAA 57.213 42.857 6.13 0.00 0.00 4.30
2752 2794 3.702330 TCACACAGTATAATCGCGGAAG 58.298 45.455 6.13 0.00 0.00 3.46
2765 2807 3.289128 CGGAAGCTCACACACTCAA 57.711 52.632 0.00 0.00 0.00 3.02
2766 2808 1.581934 CGGAAGCTCACACACTCAAA 58.418 50.000 0.00 0.00 0.00 2.69
2767 2809 1.939934 CGGAAGCTCACACACTCAAAA 59.060 47.619 0.00 0.00 0.00 2.44
2768 2810 2.354510 CGGAAGCTCACACACTCAAAAA 59.645 45.455 0.00 0.00 0.00 1.94
2788 2830 6.687081 AAAAACGTAGGTGAACATCTCAAA 57.313 33.333 0.00 0.00 35.22 2.69
2789 2831 6.877611 AAAACGTAGGTGAACATCTCAAAT 57.122 33.333 0.00 0.00 35.22 2.32
2790 2832 5.862924 AACGTAGGTGAACATCTCAAATG 57.137 39.130 0.00 0.00 35.22 2.32
2791 2833 4.894784 ACGTAGGTGAACATCTCAAATGT 58.105 39.130 0.00 0.00 35.22 2.71
2792 2834 4.690748 ACGTAGGTGAACATCTCAAATGTG 59.309 41.667 0.00 0.00 35.22 3.21
2793 2835 4.929211 CGTAGGTGAACATCTCAAATGTGA 59.071 41.667 0.00 0.00 35.22 3.58
2807 2849 7.858052 CTCAAATGTGAGCGTCTTTTTATTT 57.142 32.000 0.00 0.00 44.74 1.40
2808 2850 8.285776 CTCAAATGTGAGCGTCTTTTTATTTT 57.714 30.769 0.00 0.00 44.74 1.82
2809 2851 8.641499 TCAAATGTGAGCGTCTTTTTATTTTT 57.359 26.923 0.00 0.00 0.00 1.94
2830 2872 5.643379 TTTTTCTCAAGTCAGCAACACTT 57.357 34.783 0.00 0.00 34.24 3.16
2831 2873 6.751514 TTTTTCTCAAGTCAGCAACACTTA 57.248 33.333 0.00 0.00 32.61 2.24
2832 2874 6.942532 TTTTCTCAAGTCAGCAACACTTAT 57.057 33.333 0.00 0.00 32.61 1.73
2833 2875 8.445275 TTTTTCTCAAGTCAGCAACACTTATA 57.555 30.769 0.00 0.00 32.61 0.98
2834 2876 8.445275 TTTTCTCAAGTCAGCAACACTTATAA 57.555 30.769 0.00 0.00 32.61 0.98
2835 2877 8.621532 TTTCTCAAGTCAGCAACACTTATAAT 57.378 30.769 0.00 0.00 32.61 1.28
2836 2878 9.719355 TTTCTCAAGTCAGCAACACTTATAATA 57.281 29.630 0.00 0.00 32.61 0.98
2837 2879 9.719355 TTCTCAAGTCAGCAACACTTATAATAA 57.281 29.630 0.00 0.00 32.61 1.40
2838 2880 9.890629 TCTCAAGTCAGCAACACTTATAATAAT 57.109 29.630 0.00 0.00 32.61 1.28
2840 2882 9.109393 TCAAGTCAGCAACACTTATAATAATCC 57.891 33.333 0.00 0.00 32.61 3.01
2841 2883 7.715265 AGTCAGCAACACTTATAATAATCCG 57.285 36.000 0.00 0.00 0.00 4.18
2842 2884 7.272978 AGTCAGCAACACTTATAATAATCCGT 58.727 34.615 0.00 0.00 0.00 4.69
2843 2885 7.769044 AGTCAGCAACACTTATAATAATCCGTT 59.231 33.333 0.00 0.00 0.00 4.44
2844 2886 9.037737 GTCAGCAACACTTATAATAATCCGTTA 57.962 33.333 0.00 0.00 0.00 3.18
2845 2887 9.602568 TCAGCAACACTTATAATAATCCGTTAA 57.397 29.630 0.00 0.00 0.00 2.01
2848 2890 9.991388 GCAACACTTATAATAATCCGTTAAACA 57.009 29.630 0.00 0.00 0.00 2.83
2856 2898 6.937436 AATAATCCGTTAAACATCCACCTC 57.063 37.500 0.00 0.00 0.00 3.85
2857 2899 4.569719 AATCCGTTAAACATCCACCTCT 57.430 40.909 0.00 0.00 0.00 3.69
2858 2900 5.687166 AATCCGTTAAACATCCACCTCTA 57.313 39.130 0.00 0.00 0.00 2.43
2859 2901 5.888982 ATCCGTTAAACATCCACCTCTAT 57.111 39.130 0.00 0.00 0.00 1.98
2860 2902 5.687166 TCCGTTAAACATCCACCTCTATT 57.313 39.130 0.00 0.00 0.00 1.73
2861 2903 6.057321 TCCGTTAAACATCCACCTCTATTT 57.943 37.500 0.00 0.00 0.00 1.40
2862 2904 6.478129 TCCGTTAAACATCCACCTCTATTTT 58.522 36.000 0.00 0.00 0.00 1.82
2863 2905 6.943718 TCCGTTAAACATCCACCTCTATTTTT 59.056 34.615 0.00 0.00 0.00 1.94
2884 2926 5.751243 TTTTCCTTAAGTCTGCAACACTC 57.249 39.130 0.97 0.00 0.00 3.51
2885 2927 4.415881 TTCCTTAAGTCTGCAACACTCA 57.584 40.909 0.97 0.00 0.00 3.41
2886 2928 4.415881 TCCTTAAGTCTGCAACACTCAA 57.584 40.909 0.97 0.00 0.00 3.02
2887 2929 4.776349 TCCTTAAGTCTGCAACACTCAAA 58.224 39.130 0.97 0.00 0.00 2.69
2888 2930 5.189928 TCCTTAAGTCTGCAACACTCAAAA 58.810 37.500 0.97 0.00 0.00 2.44
2889 2931 5.827797 TCCTTAAGTCTGCAACACTCAAAAT 59.172 36.000 0.97 0.00 0.00 1.82
2890 2932 5.916883 CCTTAAGTCTGCAACACTCAAAATG 59.083 40.000 0.97 0.00 0.00 2.32
2891 2933 6.238731 CCTTAAGTCTGCAACACTCAAAATGA 60.239 38.462 0.97 0.00 0.00 2.57
2892 2934 5.779529 AAGTCTGCAACACTCAAAATGAT 57.220 34.783 0.00 0.00 0.00 2.45
2893 2935 6.882610 AAGTCTGCAACACTCAAAATGATA 57.117 33.333 0.00 0.00 0.00 2.15
2894 2936 6.492007 AGTCTGCAACACTCAAAATGATAG 57.508 37.500 0.00 0.00 0.00 2.08
2895 2937 5.091431 GTCTGCAACACTCAAAATGATAGC 58.909 41.667 0.00 0.00 0.00 2.97
2896 2938 4.761227 TCTGCAACACTCAAAATGATAGCA 59.239 37.500 0.00 0.00 0.00 3.49
2897 2939 5.416639 TCTGCAACACTCAAAATGATAGCAT 59.583 36.000 0.00 0.00 35.92 3.79
2898 2940 6.598850 TCTGCAACACTCAAAATGATAGCATA 59.401 34.615 0.00 0.00 33.44 3.14
2899 2941 7.283807 TCTGCAACACTCAAAATGATAGCATAT 59.716 33.333 0.00 0.00 33.44 1.78
2900 2942 7.420002 TGCAACACTCAAAATGATAGCATATC 58.580 34.615 0.00 0.00 33.44 1.63
2901 2943 6.576313 GCAACACTCAAAATGATAGCATATCG 59.424 38.462 0.00 0.00 33.44 2.92
2902 2944 7.518848 GCAACACTCAAAATGATAGCATATCGA 60.519 37.037 0.00 0.00 33.44 3.59
2903 2945 7.649370 ACACTCAAAATGATAGCATATCGAG 57.351 36.000 10.30 10.30 33.44 4.04
2926 2968 8.070171 CGAGGAGTGAAAATATTAAAATGCGAT 58.930 33.333 0.00 0.00 0.00 4.58
3007 3051 6.762187 TCAAACATGAATTCAACTTGCACATT 59.238 30.769 13.09 0.00 0.00 2.71
3021 3065 5.356751 ACTTGCACATTTGTTCTAGTTGTCA 59.643 36.000 0.00 0.00 0.00 3.58
3033 3077 6.426937 TGTTCTAGTTGTCATCTTTAAGTGCC 59.573 38.462 0.00 0.00 0.00 5.01
3034 3078 5.488341 TCTAGTTGTCATCTTTAAGTGCCC 58.512 41.667 0.00 0.00 0.00 5.36
3035 3079 4.098914 AGTTGTCATCTTTAAGTGCCCA 57.901 40.909 0.00 0.00 0.00 5.36
3036 3080 4.469657 AGTTGTCATCTTTAAGTGCCCAA 58.530 39.130 0.00 0.00 0.00 4.12
3037 3081 4.520492 AGTTGTCATCTTTAAGTGCCCAAG 59.480 41.667 0.00 0.00 0.00 3.61
3038 3082 3.420893 TGTCATCTTTAAGTGCCCAAGG 58.579 45.455 0.00 0.00 0.00 3.61
3051 3095 1.593265 CCAAGGCCACAAATGCTCC 59.407 57.895 5.01 0.00 0.00 4.70
3054 3098 1.276989 CAAGGCCACAAATGCTCCATT 59.723 47.619 5.01 0.00 35.39 3.16
3062 3106 5.521372 GCCACAAATGCTCCATTAAATCTTC 59.479 40.000 0.00 0.00 32.43 2.87
3066 3110 8.469200 CACAAATGCTCCATTAAATCTTCCTTA 58.531 33.333 0.00 0.00 32.43 2.69
3068 3112 9.305925 CAAATGCTCCATTAAATCTTCCTTAAC 57.694 33.333 0.00 0.00 32.43 2.01
3071 3115 6.828785 TGCTCCATTAAATCTTCCTTAACCTC 59.171 38.462 0.00 0.00 0.00 3.85
3105 3149 3.855858 TCGATGTCGAATTTGTGGATGA 58.144 40.909 2.12 0.00 46.30 2.92
3118 3162 5.604758 TTGTGGATGAATTTGGACAAACA 57.395 34.783 0.00 0.00 32.51 2.83
3120 3164 4.403752 TGTGGATGAATTTGGACAAACACA 59.596 37.500 10.61 10.61 35.80 3.72
3121 3165 4.744631 GTGGATGAATTTGGACAAACACAC 59.255 41.667 0.00 0.98 32.51 3.82
3129 3173 4.543590 TTGGACAAACACACCAAATGTT 57.456 36.364 0.00 0.00 40.64 2.71
3138 3182 4.985845 CCAAATGTTGGCGGGTTC 57.014 55.556 0.00 0.00 45.17 3.62
3140 3184 1.540267 CCAAATGTTGGCGGGTTCTA 58.460 50.000 0.00 0.00 45.17 2.10
3145 3189 5.336849 CCAAATGTTGGCGGGTTCTAATTTA 60.337 40.000 0.00 0.00 45.17 1.40
3146 3190 5.986501 AATGTTGGCGGGTTCTAATTTAA 57.013 34.783 0.00 0.00 0.00 1.52
3149 3193 6.158023 TGTTGGCGGGTTCTAATTTAAAAA 57.842 33.333 0.00 0.00 0.00 1.94
3155 3199 6.311935 GGCGGGTTCTAATTTAAAAATTGGAC 59.688 38.462 12.17 8.63 42.88 4.02
3157 3201 7.385478 GCGGGTTCTAATTTAAAAATTGGACAA 59.615 33.333 12.17 0.00 42.88 3.18
3166 3210 9.671279 AATTTAAAAATTGGACAAGATCATCCC 57.329 29.630 7.90 0.00 37.24 3.85
3184 3228 4.021102 TCCCTGTTCTCAAATTCCAGAC 57.979 45.455 0.00 0.00 0.00 3.51
3188 3232 4.263243 CCTGTTCTCAAATTCCAGACCTCT 60.263 45.833 0.00 0.00 0.00 3.69
3206 3259 1.002430 TCTGTCAGCATCTTCACCCAC 59.998 52.381 0.00 0.00 0.00 4.61
3249 3303 3.760151 CACAACATGTCATCACCTTCCAT 59.240 43.478 0.00 0.00 0.00 3.41
3251 3305 5.591472 CACAACATGTCATCACCTTCCATAT 59.409 40.000 0.00 0.00 0.00 1.78
3257 3311 4.474651 TGTCATCACCTTCCATATGGTCTT 59.525 41.667 21.28 2.14 33.75 3.01
3276 3331 3.945285 TCTTCGGATCCCATTTTTAGCAC 59.055 43.478 6.06 0.00 0.00 4.40
3279 3334 2.422127 CGGATCCCATTTTTAGCACGTT 59.578 45.455 6.06 0.00 0.00 3.99
3297 3352 3.672867 ACGTTCACAAACAACTGCAAAAG 59.327 39.130 0.00 0.00 34.93 2.27
3298 3353 3.481789 CGTTCACAAACAACTGCAAAAGC 60.482 43.478 0.00 0.00 34.93 3.51
3301 3356 0.929615 CAAACAACTGCAAAAGCGGG 59.070 50.000 1.03 0.00 0.00 6.13
3302 3357 0.809636 AAACAACTGCAAAAGCGGGC 60.810 50.000 1.03 0.00 0.00 6.13
3304 3359 1.067916 CAACTGCAAAAGCGGGCTT 59.932 52.632 0.00 0.00 37.98 4.35
3305 3360 1.067916 AACTGCAAAAGCGGGCTTG 59.932 52.632 6.69 0.00 36.26 4.01
3306 3361 1.675720 AACTGCAAAAGCGGGCTTGT 61.676 50.000 6.69 0.00 36.26 3.16
3309 3364 0.821711 TGCAAAAGCGGGCTTGTAGT 60.822 50.000 6.69 0.00 36.26 2.73
3313 3368 2.381725 AAAGCGGGCTTGTAGTACTC 57.618 50.000 6.69 0.00 36.26 2.59
3320 3375 3.618997 CGGGCTTGTAGTACTCCAAATGT 60.619 47.826 0.00 0.00 0.00 2.71
3340 3395 6.821616 ATGTCCTCTTCACATCCTTTCTAT 57.178 37.500 0.00 0.00 27.49 1.98
3347 3402 6.882656 TCTTCACATCCTTTCTATCTCCTTG 58.117 40.000 0.00 0.00 0.00 3.61
3349 3404 6.227298 TCACATCCTTTCTATCTCCTTGTC 57.773 41.667 0.00 0.00 0.00 3.18
3352 3407 6.538021 CACATCCTTTCTATCTCCTTGTCTTG 59.462 42.308 0.00 0.00 0.00 3.02
3353 3408 6.441924 ACATCCTTTCTATCTCCTTGTCTTGA 59.558 38.462 0.00 0.00 0.00 3.02
3359 3418 6.114187 TCTATCTCCTTGTCTTGAGCAAAA 57.886 37.500 0.00 0.00 0.00 2.44
3363 3422 4.758674 TCTCCTTGTCTTGAGCAAAATGAG 59.241 41.667 0.00 0.00 0.00 2.90
3364 3423 3.254166 TCCTTGTCTTGAGCAAAATGAGC 59.746 43.478 0.00 0.00 0.00 4.26
3379 3438 6.144563 GCAAAATGAGCTCTTTTCTAACCAAC 59.855 38.462 23.36 7.55 0.00 3.77
3381 3440 8.567948 CAAAATGAGCTCTTTTCTAACCAACTA 58.432 33.333 23.36 0.00 0.00 2.24
3387 3446 5.701290 GCTCTTTTCTAACCAACTAGCTCAA 59.299 40.000 0.00 0.00 0.00 3.02
3393 3452 6.605471 TCTAACCAACTAGCTCAAAGATGA 57.395 37.500 0.00 0.00 0.00 2.92
3428 3491 1.502039 ACCCACGGAGGATAGATACCA 59.498 52.381 0.00 0.00 41.22 3.25
3436 3499 5.960811 ACGGAGGATAGATACCATCAATCAT 59.039 40.000 0.00 0.00 0.00 2.45
3452 3515 9.631257 CCATCAATCATATAATAGCCCATGTTA 57.369 33.333 0.00 0.00 0.00 2.41
3481 3544 5.097742 TGTCCATTGACAGTATAGTTGGG 57.902 43.478 0.00 0.00 46.40 4.12
3482 3545 4.534500 TGTCCATTGACAGTATAGTTGGGT 59.466 41.667 0.00 0.00 46.40 4.51
3483 3546 5.013704 TGTCCATTGACAGTATAGTTGGGTT 59.986 40.000 0.00 0.00 46.40 4.11
3484 3547 5.354234 GTCCATTGACAGTATAGTTGGGTTG 59.646 44.000 0.00 0.00 41.37 3.77
3485 3548 4.096382 CCATTGACAGTATAGTTGGGTTGC 59.904 45.833 0.00 0.00 0.00 4.17
3486 3549 4.634012 TTGACAGTATAGTTGGGTTGCT 57.366 40.909 0.00 0.00 0.00 3.91
3487 3550 4.634012 TGACAGTATAGTTGGGTTGCTT 57.366 40.909 0.00 0.00 0.00 3.91
3488 3551 4.575885 TGACAGTATAGTTGGGTTGCTTC 58.424 43.478 0.00 0.00 0.00 3.86
3489 3552 4.041075 TGACAGTATAGTTGGGTTGCTTCA 59.959 41.667 0.00 0.00 0.00 3.02
3490 3553 4.980573 ACAGTATAGTTGGGTTGCTTCAA 58.019 39.130 0.00 0.00 0.00 2.69
3491 3554 5.003804 ACAGTATAGTTGGGTTGCTTCAAG 58.996 41.667 0.00 0.00 0.00 3.02
3492 3555 5.221843 ACAGTATAGTTGGGTTGCTTCAAGA 60.222 40.000 0.00 0.00 0.00 3.02
3493 3556 5.705441 CAGTATAGTTGGGTTGCTTCAAGAA 59.295 40.000 0.00 0.00 0.00 2.52
3494 3557 6.375455 CAGTATAGTTGGGTTGCTTCAAGAAT 59.625 38.462 0.00 0.00 0.00 2.40
3495 3558 7.552687 CAGTATAGTTGGGTTGCTTCAAGAATA 59.447 37.037 0.00 0.00 0.00 1.75
3496 3559 8.107095 AGTATAGTTGGGTTGCTTCAAGAATAA 58.893 33.333 0.00 0.00 0.00 1.40
3497 3560 7.961326 ATAGTTGGGTTGCTTCAAGAATAAT 57.039 32.000 0.00 0.00 0.00 1.28
3498 3561 6.029346 AGTTGGGTTGCTTCAAGAATAATG 57.971 37.500 0.00 0.00 0.00 1.90
3499 3562 5.774690 AGTTGGGTTGCTTCAAGAATAATGA 59.225 36.000 0.00 0.00 0.00 2.57
3500 3563 6.438425 AGTTGGGTTGCTTCAAGAATAATGAT 59.562 34.615 0.00 0.00 0.00 2.45
3501 3564 6.211587 TGGGTTGCTTCAAGAATAATGATG 57.788 37.500 0.00 0.00 0.00 3.07
3502 3565 5.951148 TGGGTTGCTTCAAGAATAATGATGA 59.049 36.000 0.00 0.00 0.00 2.92
3503 3566 6.095860 TGGGTTGCTTCAAGAATAATGATGAG 59.904 38.462 0.00 0.00 0.00 2.90
3504 3567 6.096001 GGGTTGCTTCAAGAATAATGATGAGT 59.904 38.462 0.00 0.00 0.00 3.41
3505 3568 7.363268 GGGTTGCTTCAAGAATAATGATGAGTT 60.363 37.037 0.00 0.00 0.00 3.01
3506 3569 8.031277 GGTTGCTTCAAGAATAATGATGAGTTT 58.969 33.333 0.00 0.00 0.00 2.66
3507 3570 8.857216 GTTGCTTCAAGAATAATGATGAGTTTG 58.143 33.333 0.00 0.00 0.00 2.93
3508 3571 8.114331 TGCTTCAAGAATAATGATGAGTTTGT 57.886 30.769 0.00 0.00 0.00 2.83
3509 3572 8.579006 TGCTTCAAGAATAATGATGAGTTTGTT 58.421 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 32 4.393062 CACTCCTCTTGTACAATCGCAAAT 59.607 41.667 9.13 0.00 0.00 2.32
155 163 7.519032 TTTATTTTACTACTGCACTGCCTTT 57.481 32.000 0.00 0.00 0.00 3.11
157 165 7.703058 ATTTTATTTTACTACTGCACTGCCT 57.297 32.000 0.00 0.00 0.00 4.75
158 166 8.455682 TGTATTTTATTTTACTACTGCACTGCC 58.544 33.333 0.00 0.00 0.00 4.85
264 280 1.153369 GCTCAGCGCCCATAGTGAA 60.153 57.895 2.29 0.00 0.00 3.18
265 281 2.501128 GCTCAGCGCCCATAGTGA 59.499 61.111 2.29 0.00 0.00 3.41
505 523 3.181503 CCATCAAGGCTTGAACTCGAATG 60.182 47.826 31.57 22.19 43.95 2.67
799 818 1.873591 GCCACCTTTATGCGTATCAGG 59.126 52.381 9.37 9.37 0.00 3.86
801 820 1.577468 CGCCACCTTTATGCGTATCA 58.423 50.000 0.00 0.00 43.12 2.15
824 843 2.434185 CACCACCGCTACGCACAT 60.434 61.111 0.00 0.00 0.00 3.21
991 1015 1.675720 CCAAAATCCATGACCGCCCC 61.676 60.000 0.00 0.00 0.00 5.80
999 1023 1.943116 TTCGCCGCCCAAAATCCATG 61.943 55.000 0.00 0.00 0.00 3.66
1666 1693 2.363975 TGTAAAGGAGGCCCGCGAT 61.364 57.895 8.23 0.00 37.58 4.58
1680 1707 4.325304 TCGTGCGACGCGGTGTAA 62.325 61.111 16.14 0.00 42.21 2.41
1764 1791 1.141657 ACGAGCATGGCATTGATAGGT 59.858 47.619 0.00 0.00 0.00 3.08
1794 1821 1.737735 CGTGAAGATGCAGCCGTCA 60.738 57.895 0.00 0.00 0.00 4.35
2349 2376 1.674651 CTCCTCCTCACCGTCGTCA 60.675 63.158 0.00 0.00 0.00 4.35
2530 2570 4.973360 GCTCGCGCGCTCTCCTAG 62.973 72.222 30.48 16.73 0.00 3.02
2539 2579 3.248171 GAGGTACTTGCTCGCGCG 61.248 66.667 26.76 26.76 41.55 6.86
2545 2585 3.244112 ACGCTAAAACAGAGGTACTTGCT 60.244 43.478 0.00 0.00 41.55 3.91
2546 2586 3.064931 ACGCTAAAACAGAGGTACTTGC 58.935 45.455 0.00 0.00 41.55 4.01
2547 2587 3.120649 GCACGCTAAAACAGAGGTACTTG 60.121 47.826 0.00 0.00 41.55 3.16
2548 2588 3.064931 GCACGCTAAAACAGAGGTACTT 58.935 45.455 0.00 0.00 41.55 2.24
2550 2590 2.685100 AGCACGCTAAAACAGAGGTAC 58.315 47.619 0.00 0.00 0.00 3.34
2551 2591 3.064207 CAAGCACGCTAAAACAGAGGTA 58.936 45.455 0.00 0.00 0.00 3.08
2552 2592 1.873591 CAAGCACGCTAAAACAGAGGT 59.126 47.619 0.00 0.00 0.00 3.85
2553 2593 1.873591 ACAAGCACGCTAAAACAGAGG 59.126 47.619 0.00 0.00 0.00 3.69
2554 2594 4.211374 AGTTACAAGCACGCTAAAACAGAG 59.789 41.667 11.37 0.00 0.00 3.35
2555 2595 4.124238 AGTTACAAGCACGCTAAAACAGA 58.876 39.130 11.37 0.00 0.00 3.41
2557 2597 4.886247 AAGTTACAAGCACGCTAAAACA 57.114 36.364 11.37 0.00 0.00 2.83
2558 2598 5.553766 GCAAAAGTTACAAGCACGCTAAAAC 60.554 40.000 0.00 0.00 0.00 2.43
2560 2600 4.039032 GCAAAAGTTACAAGCACGCTAAA 58.961 39.130 0.00 0.00 0.00 1.85
2561 2601 3.549221 GGCAAAAGTTACAAGCACGCTAA 60.549 43.478 0.00 0.00 0.00 3.09
2562 2602 2.031508 GGCAAAAGTTACAAGCACGCTA 60.032 45.455 0.00 0.00 0.00 4.26
2563 2603 1.269051 GGCAAAAGTTACAAGCACGCT 60.269 47.619 0.00 0.00 0.00 5.07
2564 2604 1.128513 GGCAAAAGTTACAAGCACGC 58.871 50.000 0.00 0.00 0.00 5.34
2565 2605 1.766069 GGGCAAAAGTTACAAGCACG 58.234 50.000 0.00 0.00 0.00 5.34
2566 2606 1.066454 ACGGGCAAAAGTTACAAGCAC 59.934 47.619 0.00 0.00 0.00 4.40
2567 2607 1.394618 ACGGGCAAAAGTTACAAGCA 58.605 45.000 0.00 0.00 0.00 3.91
2568 2608 2.124122 CAACGGGCAAAAGTTACAAGC 58.876 47.619 0.00 0.00 0.00 4.01
2569 2609 2.124122 GCAACGGGCAAAAGTTACAAG 58.876 47.619 0.00 0.00 43.97 3.16
2570 2610 2.211353 GCAACGGGCAAAAGTTACAA 57.789 45.000 0.00 0.00 43.97 2.41
2571 2611 3.949031 GCAACGGGCAAAAGTTACA 57.051 47.368 0.00 0.00 43.97 2.41
2585 2625 2.032636 ACCGCTAAACTAACGTTGCAAC 60.033 45.455 19.89 19.89 32.65 4.17
2586 2626 2.211806 ACCGCTAAACTAACGTTGCAA 58.788 42.857 11.99 0.00 32.65 4.08
2587 2627 1.868469 ACCGCTAAACTAACGTTGCA 58.132 45.000 11.99 0.00 32.65 4.08
2588 2628 2.955607 AACCGCTAAACTAACGTTGC 57.044 45.000 11.99 3.29 32.65 4.17
2593 2633 8.498358 ACAATACTGTTAAACCGCTAAACTAAC 58.502 33.333 0.00 0.00 28.57 2.34
2649 2691 2.501723 GGCAGATAGTGGGTGAAGAAGA 59.498 50.000 0.00 0.00 0.00 2.87
2666 2708 2.338577 AATTTGGATCGGAGAGGCAG 57.661 50.000 0.00 0.00 43.63 4.85
2667 2709 2.806945 AAATTTGGATCGGAGAGGCA 57.193 45.000 0.00 0.00 43.63 4.75
2668 2710 2.550180 GCTAAATTTGGATCGGAGAGGC 59.450 50.000 5.63 0.00 43.63 4.70
2695 2737 2.167693 CCTGAGCCGGATACTGTTAACA 59.832 50.000 5.05 8.28 0.00 2.41
2699 2741 0.617820 ACCCTGAGCCGGATACTGTT 60.618 55.000 5.05 0.00 0.00 3.16
2704 2746 0.325296 AAGACACCCTGAGCCGGATA 60.325 55.000 5.05 0.00 0.00 2.59
2706 2748 1.415672 AAAAGACACCCTGAGCCGGA 61.416 55.000 5.05 0.00 0.00 5.14
2708 2750 3.021451 AAAAAGACACCCTGAGCCG 57.979 52.632 0.00 0.00 0.00 5.52
2732 2774 2.218759 GCTTCCGCGATTATACTGTGTG 59.781 50.000 8.23 0.00 0.00 3.82
2735 2777 2.361119 TGAGCTTCCGCGATTATACTGT 59.639 45.455 8.23 0.00 42.32 3.55
2741 2783 0.245266 TGTGTGAGCTTCCGCGATTA 59.755 50.000 8.23 0.00 42.32 1.75
2765 2807 6.687081 TTTGAGATGTTCACCTACGTTTTT 57.313 33.333 0.00 0.00 34.94 1.94
2766 2808 6.262273 ACATTTGAGATGTTCACCTACGTTTT 59.738 34.615 0.00 0.00 34.94 2.43
2767 2809 5.763204 ACATTTGAGATGTTCACCTACGTTT 59.237 36.000 0.00 0.00 34.94 3.60
2768 2810 5.179368 CACATTTGAGATGTTCACCTACGTT 59.821 40.000 0.00 0.00 34.94 3.99
2769 2811 4.690748 CACATTTGAGATGTTCACCTACGT 59.309 41.667 0.00 0.00 34.94 3.57
2770 2812 4.929211 TCACATTTGAGATGTTCACCTACG 59.071 41.667 0.00 0.00 34.94 3.51
2784 2826 8.641499 AAAAATAAAAAGACGCTCACATTTGA 57.359 26.923 0.00 0.00 0.00 2.69
2808 2850 5.643379 AAGTGTTGCTGACTTGAGAAAAA 57.357 34.783 0.00 0.00 32.30 1.94
2809 2851 6.942532 ATAAGTGTTGCTGACTTGAGAAAA 57.057 33.333 0.00 0.00 35.30 2.29
2810 2852 8.621532 ATTATAAGTGTTGCTGACTTGAGAAA 57.378 30.769 0.00 0.00 35.30 2.52
2811 2853 9.719355 TTATTATAAGTGTTGCTGACTTGAGAA 57.281 29.630 0.00 0.00 35.30 2.87
2812 2854 9.890629 ATTATTATAAGTGTTGCTGACTTGAGA 57.109 29.630 0.00 0.00 35.30 3.27
2814 2856 9.109393 GGATTATTATAAGTGTTGCTGACTTGA 57.891 33.333 0.00 0.00 35.30 3.02
2815 2857 8.064222 CGGATTATTATAAGTGTTGCTGACTTG 58.936 37.037 0.00 0.00 35.30 3.16
2816 2858 7.769044 ACGGATTATTATAAGTGTTGCTGACTT 59.231 33.333 0.00 0.00 37.43 3.01
2817 2859 7.272978 ACGGATTATTATAAGTGTTGCTGACT 58.727 34.615 0.00 0.00 0.00 3.41
2818 2860 7.478520 ACGGATTATTATAAGTGTTGCTGAC 57.521 36.000 0.00 0.00 0.00 3.51
2819 2861 9.602568 TTAACGGATTATTATAAGTGTTGCTGA 57.397 29.630 8.51 0.00 0.00 4.26
2822 2864 9.991388 TGTTTAACGGATTATTATAAGTGTTGC 57.009 29.630 8.51 0.00 0.00 4.17
2830 2872 9.715121 GAGGTGGATGTTTAACGGATTATTATA 57.285 33.333 0.00 0.00 0.00 0.98
2831 2873 8.437575 AGAGGTGGATGTTTAACGGATTATTAT 58.562 33.333 0.00 0.00 0.00 1.28
2832 2874 7.798071 AGAGGTGGATGTTTAACGGATTATTA 58.202 34.615 0.00 0.00 0.00 0.98
2833 2875 6.659824 AGAGGTGGATGTTTAACGGATTATT 58.340 36.000 0.00 0.00 0.00 1.40
2834 2876 6.248569 AGAGGTGGATGTTTAACGGATTAT 57.751 37.500 0.00 0.00 0.00 1.28
2835 2877 5.687166 AGAGGTGGATGTTTAACGGATTA 57.313 39.130 0.00 0.00 0.00 1.75
2836 2878 4.569719 AGAGGTGGATGTTTAACGGATT 57.430 40.909 0.00 0.00 0.00 3.01
2837 2879 5.888982 ATAGAGGTGGATGTTTAACGGAT 57.111 39.130 0.00 0.00 0.00 4.18
2838 2880 5.687166 AATAGAGGTGGATGTTTAACGGA 57.313 39.130 0.00 0.00 0.00 4.69
2839 2881 6.753107 AAAATAGAGGTGGATGTTTAACGG 57.247 37.500 0.00 0.00 0.00 4.44
2861 2903 5.650266 TGAGTGTTGCAGACTTAAGGAAAAA 59.350 36.000 7.53 0.00 0.00 1.94
2862 2904 5.189928 TGAGTGTTGCAGACTTAAGGAAAA 58.810 37.500 7.53 0.00 0.00 2.29
2863 2905 4.776349 TGAGTGTTGCAGACTTAAGGAAA 58.224 39.130 7.53 0.00 0.00 3.13
2864 2906 4.415881 TGAGTGTTGCAGACTTAAGGAA 57.584 40.909 7.53 0.00 0.00 3.36
2865 2907 4.415881 TTGAGTGTTGCAGACTTAAGGA 57.584 40.909 7.53 0.00 0.00 3.36
2866 2908 5.499139 TTTTGAGTGTTGCAGACTTAAGG 57.501 39.130 7.53 0.00 0.00 2.69
2867 2909 6.728200 TCATTTTGAGTGTTGCAGACTTAAG 58.272 36.000 0.00 0.00 0.00 1.85
2868 2910 6.691754 TCATTTTGAGTGTTGCAGACTTAA 57.308 33.333 2.27 2.24 0.00 1.85
2869 2911 6.882610 ATCATTTTGAGTGTTGCAGACTTA 57.117 33.333 2.27 0.00 0.00 2.24
2870 2912 5.779529 ATCATTTTGAGTGTTGCAGACTT 57.220 34.783 2.27 0.00 0.00 3.01
2871 2913 5.106396 GCTATCATTTTGAGTGTTGCAGACT 60.106 40.000 0.25 0.25 0.00 3.24
2872 2914 5.091431 GCTATCATTTTGAGTGTTGCAGAC 58.909 41.667 0.00 0.00 0.00 3.51
2873 2915 4.761227 TGCTATCATTTTGAGTGTTGCAGA 59.239 37.500 0.00 0.00 0.00 4.26
2874 2916 5.050644 TGCTATCATTTTGAGTGTTGCAG 57.949 39.130 0.00 0.00 0.00 4.41
2875 2917 5.648178 ATGCTATCATTTTGAGTGTTGCA 57.352 34.783 0.00 0.00 0.00 4.08
2876 2918 6.576313 CGATATGCTATCATTTTGAGTGTTGC 59.424 38.462 0.00 0.00 34.22 4.17
2877 2919 7.854534 TCGATATGCTATCATTTTGAGTGTTG 58.145 34.615 0.00 0.00 34.22 3.33
2878 2920 7.172190 CCTCGATATGCTATCATTTTGAGTGTT 59.828 37.037 11.17 0.00 38.99 3.32
2879 2921 6.648310 CCTCGATATGCTATCATTTTGAGTGT 59.352 38.462 11.17 0.00 38.99 3.55
2880 2922 6.870439 TCCTCGATATGCTATCATTTTGAGTG 59.130 38.462 11.17 5.57 38.99 3.51
2881 2923 6.997655 TCCTCGATATGCTATCATTTTGAGT 58.002 36.000 11.17 0.00 38.99 3.41
2882 2924 7.063191 CACTCCTCGATATGCTATCATTTTGAG 59.937 40.741 7.09 7.09 39.69 3.02
2883 2925 6.870439 CACTCCTCGATATGCTATCATTTTGA 59.130 38.462 0.00 0.00 34.22 2.69
2884 2926 6.870439 TCACTCCTCGATATGCTATCATTTTG 59.130 38.462 0.00 0.00 34.22 2.44
2885 2927 6.997655 TCACTCCTCGATATGCTATCATTTT 58.002 36.000 0.00 0.00 34.22 1.82
2886 2928 6.596309 TCACTCCTCGATATGCTATCATTT 57.404 37.500 0.00 0.00 34.22 2.32
2887 2929 6.596309 TTCACTCCTCGATATGCTATCATT 57.404 37.500 0.00 0.00 34.22 2.57
2888 2930 6.596309 TTTCACTCCTCGATATGCTATCAT 57.404 37.500 0.00 0.00 36.73 2.45
2889 2931 6.405278 TTTTCACTCCTCGATATGCTATCA 57.595 37.500 0.00 0.00 0.00 2.15
2890 2932 9.593134 AATATTTTCACTCCTCGATATGCTATC 57.407 33.333 0.00 0.00 0.00 2.08
2893 2935 9.778741 TTTAATATTTTCACTCCTCGATATGCT 57.221 29.630 0.00 0.00 0.00 3.79
2898 2940 8.070171 CGCATTTTAATATTTTCACTCCTCGAT 58.930 33.333 0.00 0.00 0.00 3.59
2899 2941 7.279090 TCGCATTTTAATATTTTCACTCCTCGA 59.721 33.333 0.00 0.00 0.00 4.04
2900 2942 7.406553 TCGCATTTTAATATTTTCACTCCTCG 58.593 34.615 0.00 0.00 0.00 4.63
2981 3024 6.104665 TGTGCAAGTTGAATTCATGTTTGAA 58.895 32.000 21.58 13.76 45.57 2.69
2984 3027 7.066043 ACAAATGTGCAAGTTGAATTCATGTTT 59.934 29.630 9.40 1.59 0.00 2.83
2986 3029 6.050432 ACAAATGTGCAAGTTGAATTCATGT 58.950 32.000 9.40 3.11 0.00 3.21
2987 3030 6.533819 ACAAATGTGCAAGTTGAATTCATG 57.466 33.333 9.40 6.07 0.00 3.07
3000 3044 5.764686 AGATGACAACTAGAACAAATGTGCA 59.235 36.000 0.00 0.00 0.00 4.57
3007 3051 7.041372 GGCACTTAAAGATGACAACTAGAACAA 60.041 37.037 0.00 0.00 0.00 2.83
3033 3077 1.186917 TGGAGCATTTGTGGCCTTGG 61.187 55.000 3.32 0.00 0.00 3.61
3034 3078 0.899720 ATGGAGCATTTGTGGCCTTG 59.100 50.000 3.32 0.00 0.00 3.61
3035 3079 1.648116 AATGGAGCATTTGTGGCCTT 58.352 45.000 3.32 0.00 28.76 4.35
3036 3080 2.530460 TAATGGAGCATTTGTGGCCT 57.470 45.000 3.32 0.00 35.54 5.19
3037 3081 3.608316 TTTAATGGAGCATTTGTGGCC 57.392 42.857 0.00 0.00 35.54 5.36
3038 3082 5.014808 AGATTTAATGGAGCATTTGTGGC 57.985 39.130 0.00 0.00 35.54 5.01
3044 3088 7.841222 AGGTTAAGGAAGATTTAATGGAGCATT 59.159 33.333 0.00 0.00 37.80 3.56
3051 3095 8.844244 CATGAGGAGGTTAAGGAAGATTTAATG 58.156 37.037 0.00 0.00 0.00 1.90
3054 3098 7.749377 TCATGAGGAGGTTAAGGAAGATTTA 57.251 36.000 0.00 0.00 0.00 1.40
3062 3106 3.054802 AGCAACTCATGAGGAGGTTAAGG 60.055 47.826 26.08 6.15 42.28 2.69
3066 3110 1.066573 CGAGCAACTCATGAGGAGGTT 60.067 52.381 26.08 12.77 42.28 3.50
3071 3115 2.200067 GACATCGAGCAACTCATGAGG 58.800 52.381 26.08 10.87 0.00 3.86
3100 3144 4.202202 TGGTGTGTTTGTCCAAATTCATCC 60.202 41.667 0.00 4.68 32.36 3.51
3129 3173 6.014499 TCCAATTTTTAAATTAGAACCCGCCA 60.014 34.615 0.47 0.00 36.52 5.69
3131 3175 6.869388 TGTCCAATTTTTAAATTAGAACCCGC 59.131 34.615 0.47 0.00 36.52 6.13
3140 3184 9.671279 GGGATGATCTTGTCCAATTTTTAAATT 57.329 29.630 12.37 0.00 39.07 1.82
3145 3189 5.781818 ACAGGGATGATCTTGTCCAATTTTT 59.218 36.000 12.37 0.00 36.19 1.94
3146 3190 5.336102 ACAGGGATGATCTTGTCCAATTTT 58.664 37.500 12.37 0.00 36.19 1.82
3149 3193 4.229123 AGAACAGGGATGATCTTGTCCAAT 59.771 41.667 12.37 1.15 36.19 3.16
3155 3199 6.183360 GGAATTTGAGAACAGGGATGATCTTG 60.183 42.308 0.00 0.00 0.00 3.02
3157 3201 5.044624 TGGAATTTGAGAACAGGGATGATCT 60.045 40.000 0.00 0.00 0.00 2.75
3166 3210 4.694509 CAGAGGTCTGGAATTTGAGAACAG 59.305 45.833 0.00 0.00 40.20 3.16
3184 3228 1.406614 GGGTGAAGATGCTGACAGAGG 60.407 57.143 6.65 0.00 0.00 3.69
3188 3232 0.320683 CGTGGGTGAAGATGCTGACA 60.321 55.000 0.00 0.00 0.00 3.58
3245 3299 2.257207 GGGATCCGAAGACCATATGGA 58.743 52.381 28.77 3.97 38.94 3.41
3249 3303 4.788925 AAAATGGGATCCGAAGACCATA 57.211 40.909 5.45 0.00 42.60 2.74
3251 3305 3.449746 AAAAATGGGATCCGAAGACCA 57.550 42.857 5.45 0.00 37.41 4.02
3257 3311 2.285083 CGTGCTAAAAATGGGATCCGA 58.715 47.619 5.45 1.07 0.00 4.55
3276 3331 3.481789 GCTTTTGCAGTTGTTTGTGAACG 60.482 43.478 0.00 0.00 46.58 3.95
3297 3352 0.248289 TTGGAGTACTACAAGCCCGC 59.752 55.000 16.89 0.00 0.00 6.13
3298 3353 2.754946 TTTGGAGTACTACAAGCCCG 57.245 50.000 19.71 0.00 34.43 6.13
3301 3356 4.833390 AGGACATTTGGAGTACTACAAGC 58.167 43.478 19.71 11.01 34.43 4.01
3302 3357 6.287589 AGAGGACATTTGGAGTACTACAAG 57.712 41.667 19.71 12.35 34.43 3.16
3304 3359 5.778241 TGAAGAGGACATTTGGAGTACTACA 59.222 40.000 2.78 2.78 27.99 2.74
3305 3360 6.100668 GTGAAGAGGACATTTGGAGTACTAC 58.899 44.000 0.00 0.00 27.99 2.73
3306 3361 5.778241 TGTGAAGAGGACATTTGGAGTACTA 59.222 40.000 0.00 0.00 27.99 1.82
3309 3364 5.338381 GGATGTGAAGAGGACATTTGGAGTA 60.338 44.000 0.00 0.00 34.10 2.59
3313 3368 3.960571 AGGATGTGAAGAGGACATTTGG 58.039 45.455 0.00 0.00 34.10 3.28
3320 3375 5.600484 GGAGATAGAAAGGATGTGAAGAGGA 59.400 44.000 0.00 0.00 0.00 3.71
3340 3395 4.717877 TCATTTTGCTCAAGACAAGGAGA 58.282 39.130 0.00 0.00 32.87 3.71
3353 3408 5.536161 TGGTTAGAAAAGAGCTCATTTTGCT 59.464 36.000 17.31 14.60 44.24 3.91
3359 3418 5.877564 GCTAGTTGGTTAGAAAAGAGCTCAT 59.122 40.000 17.77 0.00 0.00 2.90
3363 3422 5.238583 TGAGCTAGTTGGTTAGAAAAGAGC 58.761 41.667 0.00 0.00 0.00 4.09
3364 3423 7.657761 TCTTTGAGCTAGTTGGTTAGAAAAGAG 59.342 37.037 0.00 0.00 30.82 2.85
3387 3446 5.435291 GGTGACCTTCATCAAGATCATCTT 58.565 41.667 0.00 0.00 34.41 2.40
3408 3467 1.502039 TGGTATCTATCCTCCGTGGGT 59.498 52.381 0.00 0.00 36.20 4.51
3461 3524 5.496556 CAACCCAACTATACTGTCAATGGA 58.503 41.667 0.00 0.00 0.00 3.41
3480 3543 7.093322 ACTCATCATTATTCTTGAAGCAACC 57.907 36.000 0.00 0.00 0.00 3.77
3481 3544 8.857216 CAAACTCATCATTATTCTTGAAGCAAC 58.143 33.333 0.00 0.00 0.00 4.17
3482 3545 8.579006 ACAAACTCATCATTATTCTTGAAGCAA 58.421 29.630 0.00 0.00 0.00 3.91
3483 3546 8.114331 ACAAACTCATCATTATTCTTGAAGCA 57.886 30.769 0.00 0.00 0.00 3.91
3484 3547 8.976986 AACAAACTCATCATTATTCTTGAAGC 57.023 30.769 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.