Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL
12 bulge: 5 nts; [1x0]; linked by [#174, #175]
.9.G.86.+.9.U.87.+.9.G.88.+.9.C.95.+.9.C.96. [GUGCC]
1 nts bulge .9.U.87. [U]; .9.G.86.-->.9.G.88. [GUG]
0 nts bulge ; .9.C.95.-->.9.C.96. [CC]
so far so good 93 nts=2 .9.A.51.+.9.A.52. [AA]
94 nts=1 .9.A.65. [A]
I know that 1FFK is not the only file where right bulges exist, so I think that's a common bug.****************************************************************************
List of 2 hairpin loop(s)
1 nts=4 GCGA closed by pair {9.C89+9.G94 [CG], #8}
9.C89+9.G90+9.C91+9.G92+9.A93+9.G94 [CGCGAG]
2 nts=5 AUCCC closed by pair {9.C37+9.G43 [CG], #-1}
9.C37+9.A38+9.U39+9.C40+9.C41+9.C42+9.G43 [CAUCCCG]
****************************************************************************
List of 3 bulge(s)
1 bulge: 5 nts; [0x1]; linked by [#2, #3]
9.C15+9.G16+9.C64+9.A65+9.G66 [CGCAG]
0 nts bulge ; 9.C15-->9.G16 [CG]
1 nts bulge 9.A65 [A]; 9.C64-->9.G66 [CAG]
2 bulge: 6 nts; [0x2]; linked by [#4, #5]
9.C29+9.C30+9.G50+9.A51+9.A52+9.G53 [CCGAAG]
0 nts bulge ; 9.C29-->9.C30 [CC]
2 nts bulge 9.A51+9.A52 [AA]; 9.G50-->9.G53 [GAAG]
3 bulge: 5 nts; [1x0]; linked by [#7, #8]
9.G86+9.U87+9.G88+9.C95+9.C96 [GUGCC]
1 nts bulge 9.U87 [U]; 9.G86-->9.G88 [GUG]
0 nts bulge ; 9.C95-->9.C96 [CC]
****************************************************************************
List of 3 internal loop(s)
1 asymmetric internal loop: 14 nts; [6x4]; linked by [#3, #4]
9.G21+9.G22+9.U23+9.U24+9.G25+9.C26+9.C27+9.U28+9.A54+9.U55+9.A56+9.A57+9.G58+9.C59 [GGUUGCCUAUAAGC]
6 nts iloop 9.G22+9.U23+9.U24+9.G25+9.C26+9.C27 [GUUGCC]; 9.G21-->9.U28 [GGUUGCCU]
4 nts iloop 9.U55+9.A56+9.A57+9.G58 [UAAG]; 9.A54-->9.C59 [AUAAGC]
2 symmetric internal loop: 10 nts; [3x3]; linked by [#5, #-1]
9.U33+9.A34+9.C35+9.C36+9.C37+9.G43+9.A44+9.A45+9.C46+9.A47 [UACCCGAACA]
3 nts iloop 9.A34+9.C35+9.C36 [ACC]; 9.U33-->9.C37 [UACCC]
3 nts iloop 9.A44+9.A45+9.C46 [AAC]; 9.G43-->9.A47 [GAACA]
3 asymmetric internal loop: 13 nts; [5x4]; linked by [#6, #7]
9.G75+9.G76+9.A77+9.G78+9.U79+9.A80+9.C81+9.G101+9.G102+9.A103+9.A104+9.A105+9.C106 [GGAGUACGGAAAC]
5 nts iloop 9.G76+9.A77+9.G78+9.U79+9.A80 [GAGUA]; 9.G75-->9.C81 [GGAGUAC]
4 nts iloop 9.G102+9.A103+9.A104+9.A105 [GAAA]; 9.G101-->9.C106 [GGAAAC]
****************************************************************************
List of 1 junction(s)
1 3-way junctions: 16 nts; [4x3x3]; linked by [#1, #2, #6]
9.C9+9.C10+9.A11+9.C12+9.A13+9.G14+9.C67+9.G68+9.U69+9.U70+9.C71+9.G110+9.U111+9.U112+9.C113+9.G114 [CCACAGCGUUCGUUCG]
4 nts junction 9.C10+9.A11+9.C12+9.A13 [CACA]; 9.C9-->9.G14 [CCACAG]
3 nts junction 9.G68+9.U69+9.U70 [GUU]; 9.C67-->9.C71 [CGUUC]
3 nts junction 9.U111+9.U112+9.C113 [UUC]; 9.G110-->9.G114 [GUUCG]
****************************************************************************
List of 2 non-loop single-stranded segment(s)
1 nts=3 9.U1-->9.A3 [UUA]
2 nts=3 9.A120-->9.C122 [ACC]
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.