Analysis for 2AW4.pdb Chain 1 1. Number of nucleotides in the molecule: --------------- 118 A. Ratio of nucleotide types: A: 22(18.6441%) C: 36(30.5085%) G: 41(34.7458%) U: 18(15.2542%) B. # Nucleotides that are stacked: 103 (87.2881%) C. # nt that are basepaired --- 80 (67.7966%) 1. # stacked: ----- 76 (95%) 2. # unstacked: ---- 4 (5%) D. # nt that are unpaired --- 38 (32.2034%) 1. # stacked: ----- 27 (71.0526%) 2. # unstacked: ---- 11 (28.9474%) 2. Number of base-base stacks: ------------ 89 A. Types of base-base stacks: 1. # Consecutive stacks: ----------- 67 (75.2809%) 2. # Cross-strand stacks: ---------- 15 (16.8539%) 3. # Not consecutive or X-strand: -- 7 (7.8652%) B. Locations of base-base stacks: 1. BB: 61 (68.5393%) 2. NB: 9 (8.9888%) 3. BN: 8 (10.1124%) 4. NN: 11 (12.3596%) 3. Nucleotide stacking types total #/% |consecutive | cross strand | not consec | | | | or x-strand | TOTAL 89 | 67 (75.28%) | 15 (16.85%) | 7 ( 7.87%) | A vs _ 22/24.72% | 16/23.88% | 2/13.33% | 4/57.14% | A: 6/ 6.74% (27.27%) | 3/ 4.48% | 1/ 6.67% | 2/28.57% | C: 4/ 4.49% (18.18%) | 4/ 5.97% | 0/ 0.00% | 0/ 0.00% | G: 10/11.24% (45.45%) | 7/10.45% | 1/ 6.67% | 2/28.57% | U: 2/ 2.25% ( 9.09%) | 2/ 2.99% | 0/ 0.00% | 0/ 0.00% | C vs _ 21/23.60% | 19/28.36% | 1/ 6.67% | 1/14.29% | A: 3/ 3.37% (14.29%) | 2/ 2.99% | 0/ 0.00% | 1/14.29% | C: 10/11.24% (47.62%) | 10/14.93% | 0/ 0.00% | 0/ 0.00% | G: 5/ 5.62% (23.81%) | 4/ 5.97% | 1/ 6.67% | 0/ 0.00% | U: 3/ 3.37% (14.29%) | 3/ 4.48% | 0/ 0.00% | 0/ 0.00% | G vs _ 40/44.94% | 29/43.28% | 10/66.67% | 1/14.29% | A: 5/ 5.62% (12.50%) | 2/ 2.99% | 3/20.00% | 0/ 0.00% | C: 10/11.24% (25.00%) | 9/13.43% | 1/ 6.67% | 0/ 0.00% | G: 17/19.10% (42.50%) | 10/14.93% | 6/40.00% | 1/14.29% | U: 8/ 8.99% (20.00%) | 8/11.94% | 0/ 0.00% | 0/ 0.00% | U vs _ 6/ 6.74% | 3/ 4.48% | 2/13.33% | 1/14.29% | A: 1/ 1.12% (16.67%) | 0/ 0.00% | 0/ 0.00% | 1/14.29% | C: 1/ 1.12% (16.67%) | 1/ 1.49% | 0/ 0.00% | 0/ 0.00% | G: 4/ 4.49% (66.67%) | 2/ 2.99% | 2/13.33% | 0/ 0.00% | U: 0/ 0.00% ( 0.00%) | 0/ 0.00% | 0/ 0.00% | 0/ 0.00% | Start End Consec Nucs 37 38 2 42 43 2 50 51 2 64 65 2 67 68 2 69 70 2 71 72 2 81 82 2 90 91 2 92 93 2 94 95 2 3 5 3 6 8 3 9 11 3 20 22 3 32 34 3 53 55 3 78 80 3 96 98 3 109 111 3 16 19 4 104 107 4 45 49 5 73 77 5 83 87 5 99 103 5 26 31 6 57 63 7 ------------------------------------------------------------------------------------- Raw Data: CS NT1 NT2 2-->1 1-->2 1<-->2 vDist cDist theta type BP-1 BP-2 . 3 C 4 C 0.4294 0.1882 0.3088 3.2209 3.7941 7.1934 BB 117 G 116 G . 4 C 5 U 0.3765 0.1706 0.2735 3.0543 4.2046 12.5372 BB 116 G 115 A x 5 U 116 G 0.1429 0.4588 0.3008 3.2151 4.6061 10.3520 BB 115 A 4 C . 6 G 7 G 0.5500 0.3893 0.4696 3.4866 4.1704 5.9156 BB 114 C 113 C x 6 G 115 A 0.6630 0.3036 0.4833 3.4591 4.1262 12.2619 BB 114 C 5 U . 7 G 8 C 0.9882 0.4786 0.7334 3.4398 3.6494 11.8915 BB 113 C 112 G . 9 G 10 G 0.5286 0.2929 0.4107 3.0649 4.4338 5.2498 BB 111 U 110 C x 9 G 112 G 0.7250 0.5750 0.6500 3.3241 3.7824 8.7293 BB 111 U 8 C . 10 G 11 C 0.9647 0.5893 0.7770 3.3423 3.3921 9.9808 BN 110 C 0 . . 15 A 109 A 0.6111 0.4222 0.5167 3.5252 4.0118 6.5453 NN 0 . 0 . . 16 G 17 C 0.9000 0.3714 0.6357 3.2424 3.7980 2.6109 BB 68 C 67 G x 16 G 69 G 0.7464 0.4536 0.6000 3.2419 3.5883 2.8373 BN 68 C 0 . . 17 C 18 G 0.2607 0.1824 0.2215 3.0800 4.6948 5.4328 BB 67 G 65 U . 18 G 19 C 0.9471 0.4714 0.7092 3.3112 3.4316 8.6827 BB 65 U 64 G x 18 G 67 G 0.2000 0.5393 0.3696 3.1613 4.4814 8.4819 BB 65 U 17 C . 20 G 21 G 0.4393 0.5964 0.5179 2.9695 3.9494 12.1559 BB 63 C 62 C x 20 G 64 G 0.5250 0.7071 0.6161 3.2084 3.8459 5.4642 BB 63 C 19 C . 21 G 22 U 0.9765 0.4286 0.7025 3.3585 3.4943 3.0805 BB 62 C 61 G x 23 G 61 G 0.2429 0.5179 0.3804 3.2819 4.2318 7.7291 BB 60 C 22 U . 24 G 56 G 0.7071 0.9893 0.8482 3.2868 3.5616 12.3308 NB 0 . 28 C . 26 C 27 C 0.9059 0.7294 0.8176 3.5024 3.5315 3.8977 NN 0 . 0 . . 27 C 28 C 0.9824 0.9176 0.9500 3.7113 3.7392 13.6936 NB 0 . 56 G . 28 C 29 A 0.1852 0.3706 0.2779 2.9762 4.0941 14.0893 BB 56 G 55 U . 29 A 30 C 0.6778 0.6630 0.6704 3.3705 3.6690 2.3045 BB 55 U 54 G x 29 A 56 G 0.2000 0.4593 0.3296 3.1471 4.3873 4.2595 BB 55 U 28 C . 30 C 31 C 0.2647 0.3000 0.2824 2.9228 4.2740 13.5543 BB 54 G 51 G . 32 U 33 G 0.2071 0.3000 0.2536 2.8849 4.3045 15.3130 BB 50 A 49 C x 32 U 51 G 0.2357 0.4882 0.3620 3.2225 4.3018 3.0509 BB 50 A 31 C . 33 G 34 A 0.3741 0.4607 0.4174 3.1664 3.9772 10.6146 BB 49 C 48 U x 33 G 50 A 0.4296 0.3286 0.3791 3.1925 4.1532 14.8301 BB 49 C 32 U . 34 A 44 G 0.4286 0.3370 0.3828 3.5842 4.5115 13.0490 BN 48 U 0 . . 37 C 38 C 0.8529 0.5529 0.7029 3.5129 3.7504 12.0653 NN 0 . 0 . . 39 A 44 G 0.4286 0.4741 0.4513 3.3110 3.9937 4.1007 NN 0 . 0 . . 42 C 43 C 0.7647 0.7647 0.7647 3.5372 3.6723 11.7207 NN 0 . 0 . . 43 C 45 A 0.3296 0.3471 0.3383 3.5880 4.0708 5.7919 NN 0 . 0 . . 45 A 46 A 0.4259 0.4370 0.4315 3.3611 3.9460 3.8147 NN 0 . 0 . . 46 A 47 C 0.9706 0.7481 0.8594 3.3080 3.3435 6.9547 NN 0 . 0 . . 47 C 48 U 0.2824 0.1235 0.2029 3.3877 4.1688 13.2693 NB 0 . 34 A . 48 U 49 C 0.6118 0.3353 0.4735 3.1493 3.7770 11.1258 BB 34 A 33 G . 50 A 51 G 0.3786 0.3444 0.3615 3.3244 4.3961 3.9182 BB 32 U 31 C . 53 A 54 G 0.2357 0.5222 0.3790 2.9449 4.4043 24.4288 NB 0 . 30 C . 54 G 55 U 0.9471 0.5714 0.7592 3.3449 3.5857 0.8004 BB 30 C 29 A . 57 A 58 A 0.4852 0.6296 0.5574 3.6093 3.9819 9.7737 NN 0 . 0 . . 58 A 59 A 0.6370 0.4481 0.5426 3.4168 3.7140 19.9255 NN 0 . 0 . . 59 A 60 C 0.9647 0.4074 0.6861 3.3870 3.4270 12.5857 NB 0 . 23 G . 60 C 61 G 0.0821 0.3294 0.2058 2.8808 4.6035 11.3076 BB 23 G 22 U . 61 G 62 C 0.9706 0.5179 0.7442 3.2213 3.4035 1.1943 BB 22 U 21 G . 62 C 63 C 0.4529 0.4235 0.4382 3.0105 3.9789 14.2688 BB 21 G 20 G . 64 G 65 U 0.9941 0.7036 0.8488 3.3535 3.4522 5.5764 BB 19 C 18 G . 65 U 108 A 0.4074 0.7471 0.5772 3.3428 3.9427 23.4850 BN 18 G 0 . . 67 G 68 C 0.9471 0.3286 0.6378 3.3546 3.8460 1.8440 BB 17 C 16 G . 69 G 70 C 0.5882 0.3107 0.4495 3.3741 4.1375 14.9326 NB 0 . 106 G . 71 C 72 G 0.3321 0.3059 0.3190 3.3236 4.1177 8.5139 BB 105 G 104 A x 71 C 106 G 0.1786 0.3353 0.2569 3.5709 4.3492 7.5889 BB 105 G 70 C . 73 A 74 U 0.8647 0.4444 0.6546 3.3589 3.6340 9.2115 BB 103 U 102 G x 73 A 104 A 0.6815 0.4185 0.5500 3.2759 3.7893 5.3344 BB 103 U 72 G . 74 U 75 G 0.3571 0.5059 0.4315 3.1112 3.8090 7.1772 BB 102 G 101 A . 75 G 76 G 0.6464 0.5357 0.5911 3.5159 4.2362 12.5072 BB 101 A 100 G . 76 G 77 U 0.9235 0.5821 0.7528 3.4515 3.6255 8.4513 BN 100 G 0 . . 78 A 79 G 0.4964 0.3259 0.4112 3.5225 4.2750 6.8508 NB 0 . 97 C . 78 A 99 A 0.5519 0.5148 0.5333 3.2616 3.5708 5.8998 NN 0 . 0 . . 79 G 80 U 1.0000 0.5179 0.7589 3.4507 3.5093 6.3292 BB 97 C 96 G . 81 G 82 U 0.8882 0.5393 0.7138 3.3174 3.6021 7.9622 BB 95 U 94 A x 81 G 96 G 0.4857 0.5071 0.4964 3.3779 3.8787 11.8828 BB 95 U 80 U . 83 G 84 G 0.4464 0.4429 0.4446 3.1432 3.9486 3.5814 BB 93 C 92 C x 83 G 94 A 0.5815 0.4786 0.5300 3.2482 3.9426 15.7247 BB 93 C 82 U . 84 G 85 G 0.3179 0.2071 0.2625 3.0689 4.3739 4.4369 BB 92 C 91 C . 85 G 86 G 0.5500 0.1250 0.3375 3.3137 4.4266 6.5626 BB 91 C 90 C x 85 G 92 C 0.6647 0.2714 0.4681 3.3168 4.1954 5.0617 BB 91 C 84 G . 86 G 87 U 0.8000 0.3643 0.5821 3.3248 3.5403 3.3458 BN 90 C 0 . . 90 C 91 C 0.2706 0.0765 0.1735 3.4580 4.1368 8.6913 BB 86 G 85 G . 92 C 93 C 0.3941 0.1529 0.2735 3.0912 4.0473 3.4915 BB 84 G 83 G . 94 A 95 U 0.9647 0.5667 0.7657 3.2921 3.3582 6.8858 BB 82 U 81 G . 96 G 97 C 0.9765 0.4250 0.7007 3.4195 3.6101 4.7889 BB 80 U 79 G . 97 C 98 G 0.2357 0.1706 0.2032 3.5006 4.8202 7.9966 BN 79 G 0 . . 99 A 100 G 0.5143 0.6148 0.5646 3.1602 3.9094 3.9134 NB 0 . 76 G . 100 G 101 A 0.7630 0.4321 0.5976 3.3470 3.6446 7.9844 BB 76 G 75 G . 101 A 102 G 0.5679 0.3444 0.4562 3.5107 3.8932 14.1897 BB 75 G 74 U . 102 G 103 U 0.7941 0.3571 0.5756 3.1416 3.9144 11.9649 BB 74 U 73 A . 104 A 105 G 0.4750 0.1333 0.3042 3.5429 4.4036 7.8506 BB 72 G 71 C . 105 G 106 G 0.3179 0.3500 0.3339 3.3449 4.6320 6.8114 BB 71 C 70 C . 106 G 107 G 0.9357 0.6071 0.7714 3.5312 3.7212 9.8020 BN 70 C 0 . . 109 A 110 C 0.9471 0.6815 0.8143 3.3697 3.5089 11.2329 NB 0 . 10 G . 110 C 111 U 0.4588 0.2412 0.3500 3.2691 3.8518 2.5589 BB 10 G 9 G . 112 G 113 C 0.3647 0.3893 0.3770 3.0258 4.1231 12.1425 BB 8 C 7 G . 113 C 114 C 0.7941 0.4118 0.6029 3.4626 3.7438 5.3467 BB 7 G 6 G . 114 C 115 A 0.1704 0.2471 0.2087 3.0010 4.6334 13.1577 BB 6 G 5 U . 115 A 116 G 0.1179 0.3481 0.2330 3.0556 4.5215 10.5605 BB 5 U 4 C . 116 G 117 G 0.5000 0.2750 0.3875 2.9308 4.3368 7.9488 BB 4 C 3 C