Analysis for 1JJ2.pdb Chain 2 1. Number of nucleotides in the molecule: --------------- 122 A. Ratio of nucleotide types: A: 23(18.8525%) C: 42(34.4262%) G: 39(31.9672%) U: 17(13.9344%) B. # Nucleotides that are stacked: 109 (89.3443%) C. # nt that are basepaired --- 94 (77.0492%) 1. # stacked: ----- 90 (95.7447%) 2. # unstacked: ---- 4 (4.2553%) D. # nt that are unpaired --- 28 (22.9508%) 1. # stacked: ----- 19 (67.8571%) 2. # unstacked: ---- 9 (32.1429%) 2. Number of base-base stacks: ------------ 96 A. Types of base-base stacks: 1. # Consecutive stacks: ----------- 72 (75%) 2. # Cross-strand stacks: ---------- 15 (15.625%) 3. # Not consecutive or X-strand: -- 9 (9.375%) B. Locations of base-base stacks: 1. BB: 76 (79.1667%) 2. NB: 8 (5.2083%) 3. BN: 5 (8.3333%) 4. NN: 7 (7.2917%) 3. Nucleotide stacking types total #/% |consecutive | cross strand | not consec | | | | or x-strand | TOTAL 96 | 72 (75.00%) | 15 (15.63%) | 9 ( 9.38%) | A vs _ 19/19.79% | 14/19.44% | 2/13.33% | 3/33.33% | A: 5/ 5.21% (26.32%) | 4/ 5.56% | 1/ 6.67% | 0/ 0.00% | C: 8/ 8.33% (42.11%) | 7/ 9.72% | 0/ 0.00% | 1/11.11% | G: 5/ 5.21% (26.32%) | 3/ 4.17% | 1/ 6.67% | 1/11.11% | U: 1/ 1.04% ( 5.26%) | 0/ 0.00% | 0/ 0.00% | 1/11.11% | C vs _ 25/26.04% | 22/30.56% | 1/ 6.67% | 2/22.22% | A: 3/ 3.13% (12.00%) | 2/ 2.78% | 0/ 0.00% | 1/11.11% | C: 14/14.58% (56.00%) | 13/18.06% | 0/ 0.00% | 1/11.11% | G: 4/ 4.17% (16.00%) | 3/ 4.17% | 1/ 6.67% | 0/ 0.00% | U: 4/ 4.17% (16.00%) | 4/ 5.56% | 0/ 0.00% | 0/ 0.00% | G vs _ 45/46.88% | 31/43.06% | 11/73.33% | 3/33.33% | A: 8/ 8.33% (17.78%) | 5/ 6.94% | 2/13.33% | 1/11.11% | C: 11/11.46% (24.44%) | 9/12.50% | 2/13.33% | 0/ 0.00% | G: 20/20.83% (44.44%) | 13/18.06% | 6/40.00% | 1/11.11% | U: 6/ 6.25% (13.33%) | 4/ 5.56% | 1/ 6.67% | 1/11.11% | U vs _ 7/ 7.29% | 5/ 6.94% | 1/ 6.67% | 1/11.11% | A: 1/ 1.04% (14.29%) | 1/ 1.39% | 0/ 0.00% | 0/ 0.00% | C: 3/ 3.13% (42.86%) | 3/ 4.17% | 0/ 0.00% | 0/ 0.00% | G: 2/ 2.08% (28.57%) | 0/ 0.00% | 1/ 6.67% | 1/11.11% | U: 1/ 1.04% (14.29%) | 1/ 1.39% | 0/ 0.00% | 0/ 0.00% | Start End Consec Nucs 32 33 2 34 35 2 36 37 2 41 42 2 62 63 2 88 89 2 4 6 3 7 9 3 19 21 3 49 51 3 52 54 3 70 72 3 91 93 3 100 102 3 114 116 3 66 69 4 79 82 4 83 86 4 109 112 4 14 18 5 44 48 5 73 77 5 26 31 6 56 61 6 94 99 6 103 108 6 ------------------------------------------------------------------------------------- Raw Data: CS NT1 NT2 2-->1 1-->2 1<-->2 vDist cDist theta type BP-1 BP-2 . 4 G 5 G 0.6464 0.3000 0.4732 3.2913 4.3042 6.2785 BB 119 C 118 C x 4 G 120 A 0.4963 0.1643 0.3303 3.0867 4.3456 5.4953 BN 119 C 0 . . 5 G 6 C 0.9353 0.5000 0.7176 3.6004 3.7926 6.6678 BB 118 C 117 G . 7 G 8 G 0.4821 0.2857 0.3839 2.9523 4.3874 6.0781 BB 116 C 115 C x 7 G 117 G 0.5821 0.4000 0.4911 3.2179 3.8381 3.5734 BB 116 C 6 C . 8 G 9 C 0.9765 0.6179 0.7972 3.3860 3.5334 8.5312 BB 115 C 114 G . 13 A 114 G 0.5286 0.7852 0.6569 3.3037 3.7133 2.4783 NB 0 . 9 C . 14 G 15 C 0.5765 0.3536 0.4650 3.2989 3.8849 4.5832 BB 67 C 66 G x 14 G 68 G 0.3321 0.5464 0.4393 3.3249 3.9705 6.1933 BB 67 C 11 A . 15 C 16 G 0.3607 0.3588 0.3598 3.4496 4.2736 5.8231 BB 66 G 64 C . 16 G 17 G 0.4714 0.3607 0.4161 3.5923 4.2997 6.4133 BB 64 C 63 C . 17 G 18 U 0.5706 0.3357 0.4532 3.4790 4.1404 8.1643 BB 63 C 62 A . 19 G 20 G 0.4607 0.4143 0.4375 3.1234 4.2640 4.9730 BB 61 C 60 C x 19 G 62 A 0.6000 0.4321 0.5161 3.1448 4.0343 3.6262 BB 61 C 18 U . 20 G 21 G 0.6929 0.3429 0.5179 3.7197 4.2521 12.8044 BB 60 C 59 C x 20 G 61 C 0.2882 0.2036 0.2459 3.2029 4.5680 9.8587 BB 60 C 19 G . 22 G 55 U 0.9000 0.4143 0.6571 3.5221 3.6100 18.0304 BB 26 C 27 C . 26 C 27 C 0.5941 0.3706 0.4824 3.2601 4.0057 6.8447 BB 22 G 55 U . 27 C 28 U 0.4588 0.2882 0.3735 3.4927 3.8237 6.6592 BB 55 U 54 A . 28 U 29 C 0.6176 0.3176 0.4676 3.3822 3.8141 9.6802 BB 54 A 53 G . 29 C 30 C 0.4353 0.2529 0.3441 3.6285 4.1998 4.5758 BB 53 G 50 G . 30 C 31 C 0.3941 0.5235 0.4588 3.4745 4.5240 19.5976 BB 50 G 49 G . 32 G 33 U 0.6706 0.4429 0.5567 3.4249 3.8202 17.8444 BB 48 C 47 A x 32 G 49 G 0.6929 0.4107 0.5518 3.2608 3.9159 3.2643 BB 48 C 31 C . 33 U 43 G 0.2714 0.2000 0.2357 3.0848 4.3607 10.6197 BB 47 A 37 C . 34 A 35 C 0.9412 0.4630 0.7021 3.4905 3.5311 11.0720 NN 0 . 0 . . 36 C 37 C 0.8235 0.3882 0.6059 3.5728 3.7758 16.2015 NB 0 . 43 G x 38 A 43 G 0.4107 0.6037 0.5072 3.4564 4.2123 3.6868 BB 45 A 37 C . 41 C 42 C 0.5235 0.7706 0.6471 3.5963 4.0080 24.3492 NN 0 . 0 . . 42 C 44 A 0.5370 0.5353 0.5362 3.7269 3.9628 21.3307 NB 0 . 38 A . 43 G 47 A 0.4370 0.1500 0.2935 3.2105 4.6659 11.4156 BB 37 C 33 U . 44 A 45 A 0.7000 0.4333 0.5667 3.3682 3.7320 12.6152 BB 38 A 39 U . 45 A 46 C 0.9588 0.5556 0.7572 3.3176 3.3617 14.8387 BN 39 U 0 . . 46 C 47 A 0.2630 0.3235 0.2932 3.3923 4.4161 16.0176 NB 0 . 33 U . 47 A 48 C 0.9118 0.5444 0.7281 3.4974 3.5411 11.5560 BB 33 U 32 G . 49 G 50 G 0.5143 0.3250 0.4196 3.5222 4.0927 5.9190 BB 31 C 30 C . 50 G 51 A 0.5000 0.5679 0.5339 3.4534 3.8042 14.0195 BN 30 C 0 . . 52 A 53 G 0.4679 0.4519 0.4599 3.4111 4.2810 2.8505 NB 0 . 29 C . 53 G 54 A 0.5444 0.3643 0.4544 3.5347 4.2630 3.9305 BB 29 C 28 U . 56 A 57 A 0.4000 0.4407 0.4204 3.5688 4.3194 6.1159 NN 0 . 0 . . 57 A 58 G 0.3500 0.3630 0.3565 3.4966 4.5988 15.8345 NN 0 . 0 . . 58 G 59 C 0.9471 0.3107 0.6289 3.4518 3.6864 11.2811 NB 0 . 21 G . 59 C 60 C 0.3294 0.3824 0.3559 3.1678 3.9504 11.5326 BB 21 G 20 G . 60 C 61 C 0.3235 0.3824 0.3529 3.0252 4.1282 14.9397 BB 20 G 19 G . 62 A 63 C 0.9294 0.4444 0.6869 3.6007 3.8570 6.0773 BB 18 U 17 G . 64 C 113 C 0.7118 0.4588 0.5853 3.5251 3.8736 7.6637 BN 16 G 0 . . 65 A 113 C 0.4353 0.4704 0.4528 3.0669 3.7793 6.7546 NN 0 . 0 . . 66 G 67 C 0.9706 0.4429 0.7067 3.5985 3.9297 6.3316 BB 15 C 14 G . 67 C 68 G 0.0179 0.3235 0.1707 3.0937 4.7047 19.9392 BB 14 G 11 A . 68 G 69 U 1.0000 0.4143 0.7071 3.4033 3.5368 10.5757 BB 11 A 112 U . 70 U 71 C 0.7647 0.2824 0.5235 3.5679 3.7954 13.8615 BB 111 U 110 G . 71 C 72 C 0.4412 0.3059 0.3735 3.4907 4.3346 11.3273 BB 110 G 109 G x 72 C 110 G 0.0786 0.2824 0.1805 3.3612 4.5283 6.1147 BB 109 G 71 C . 73 G 74 G 0.8821 0.6036 0.7429 3.3766 3.7444 11.6431 BB 108 C 107 C x 73 G 109 G 0.6393 0.4929 0.5661 3.2264 3.9403 1.7039 BB 108 C 72 C . 74 G 75 G 0.3000 0.3714 0.3357 3.0712 4.3212 11.4078 BB 107 C 106 C . 75 G 76 G 0.7107 0.3179 0.5143 3.4740 3.9066 13.5273 BB 106 C 105 A . 76 G 77 A 0.4778 0.4000 0.4389 3.4749 3.8022 15.2590 BB 105 A 104 A . 77 A 79 U 0.3647 0.6111 0.4879 3.1735 3.9160 4.5792 BB 104 A 103 A . 78 G 102 G 0.8929 0.6929 0.7929 3.6184 3.9192 11.6804 NB 0 . 80 A . 79 U 80 A 0.1812 0.1529 0.1671 3.2943 4.9569 13.9681 BB 103 A 102 G . 80 A 81 C 0.9412 0.4188 0.6800 3.6245 3.7749 5.5578 BB 102 G 101 G x 80 A 103 A 0.5741 0.5375 0.5558 3.4578 3.7527 9.4009 BB 102 G 79 U . 81 C 82 U 0.8235 0.3000 0.5618 3.5697 3.9637 9.3713 BB 101 G 100 G x 82 U 101 G 0.0821 0.2588 0.1705 3.2940 4.5235 17.6152 BB 100 G 81 C . 83 G 84 G 0.4821 0.2679 0.3750 3.1200 4.3184 6.3343 BB 99 U 98 C x 83 G 100 G 0.3250 0.3929 0.3589 3.4132 3.8437 10.2938 BB 99 U 82 U . 84 G 85 A 0.4889 0.4429 0.4659 3.2100 4.1310 6.7567 BB 98 C 97 U x 84 G 99 U 0.1353 0.1964 0.1659 3.0927 4.7300 9.9280 BB 98 C 83 G . 85 A 86 G 0.3964 0.4222 0.4093 3.7469 4.3476 13.6098 BB 97 U 96 C . 88 G 89 C 0.7412 0.3107 0.5259 3.5312 3.9930 8.2570 BB 95 C 94 G x 88 G 96 C 0.0294 0.2750 0.1522 2.7598 4.4856 11.8393 BB 95 C 86 G x 90 G 94 G 0.5321 0.3214 0.4268 3.2109 4.0975 3.3669 BB 93 A 89 C . 91 C 92 G 0.5821 0.5412 0.5617 3.6494 3.8721 12.8686 NN 0 . 0 . . 92 G 93 A 0.9519 0.7536 0.8527 3.3229 3.4230 9.2743 NB 0 . 90 G . 94 G 95 C 0.8647 0.4179 0.6413 3.6255 3.8126 9.3624 BB 89 C 88 G . 95 C 96 C 0.2941 0.1588 0.2265 3.6279 4.1258 6.4985 BB 88 G 86 G . 96 C 97 U 0.4529 0.3706 0.4118 3.3648 4.1550 9.8126 BB 86 G 85 A . 97 U 98 C 0.2471 0.3882 0.3176 3.3224 4.1641 12.2896 BB 85 A 84 G . 98 C 99 U 0.4412 0.2471 0.3441 3.3626 3.9625 13.8883 BB 84 G 83 G . 100 G 101 G 0.3214 0.1857 0.2536 3.2865 4.5453 8.7982 BB 82 U 81 C . 101 G 102 G 0.5786 0.4679 0.5232 3.4884 4.1403 2.4790 BB 81 C 80 A . 103 A 104 A 0.5926 0.5185 0.5556 3.3843 3.8390 2.1155 BB 79 U 77 A . 104 A 105 A 0.4333 0.4074 0.4204 3.7517 4.3477 5.7287 BB 77 A 76 G . 105 A 106 C 0.6824 0.2556 0.4690 3.7024 4.0817 16.2424 BB 76 G 75 G . 106 C 107 C 0.2882 0.3765 0.3324 3.5170 4.4726 16.0723 BB 75 G 74 G . 107 C 108 C 0.3294 0.5235 0.4265 3.3644 3.8649 16.1234 BB 74 G 73 G . 109 G 110 G 0.3357 0.3929 0.3643 3.1314 4.2406 8.3100 BB 72 C 71 C . 110 G 111 U 0.9353 0.2857 0.6105 3.4374 3.7423 2.9248 BB 71 C 70 U . 111 U 112 U 0.9588 0.2824 0.6206 3.7024 3.8044 23.2404 BB 70 U 69 U . 114 G 115 C 0.9706 0.6179 0.7942 3.3602 3.5928 8.9200 BB 9 C 8 G . 115 C 116 C 0.4294 0.4647 0.4471 3.3087 3.8149 9.7280 BB 8 G 7 G . 117 G 118 C 0.9706 0.5857 0.7782 3.5460 3.8118 4.3868 BB 6 C 5 G . 118 C 119 C 0.2471 0.1471 0.1971 3.4042 4.0571 10.0964 BB 5 G 4 G . 119 C 120 A 0.3259 0.1824 0.2541 3.3833 4.1886 5.6417 BN 4 G 0 . . 120 A 121 C 0.9471 0.4815 0.7143 3.6582 3.6996 11.7511 NN 0 . 0 .