(1) INPUT: RNA1 = 2G9C(H1H3) # 68 2G9C_A CLEANED # PDB: 2G9C_A.bpseq 1 G 67 2 G 66 3 A 65 4 C 64 5 A 63 6 U 62 7 A 61 8 U 0 9 A 0 10 A 0 11 U 0 12 C 0 13 G 29 14 C 28 15 G 27 16 U 26 17 G 25 18 G 0 19 A 0 20 U 0 21 A 0 22 U 0 23 G 0 24 G 0 25 C 17 26 A 16 27 C 15 28 G 14 29 C 13 30 A 0 31 A 0 32 G 0 33 U 0 34 U 0 35 U 0 36 C 0 37 U 0 38 A 0 39 C 0 40 C 58 41 G 57 42 G 56 43 G 55 44 C 54 45 A 53 46 C 0 47 C 0 48 G 0 49 U 0 50 A 0 51 A 0 52 A 0 53 U 45 54 G 44 55 U 43 56 C 42 57 C 41 58 G 40 59 A 0 60 U 0 61 U 7 62 A 6 63 U 5 64 G 4 65 U 3 66 C 2 67 C 1 68 U 0 Number of junctions with CHS: 1 Junction: Helix 1: 7-61 Helix 2: 13-29 Helix 3: 40-58 CHS: 1,3 (1) INPUT: RNA2 = 2G9C(H1H2) # 68 2G9C_A CLEANED # PDB: 2G9C_A.bpseq 1 G 67 2 G 66 3 A 65 4 C 64 5 A 63 6 U 62 7 A 61 8 U 0 9 A 0 10 A 0 11 U 0 12 C 0 13 G 29 14 C 28 15 G 27 16 U 26 17 G 25 18 G 0 19 A 0 20 U 0 21 A 0 22 U 0 23 G 0 24 G 0 25 C 17 26 A 16 27 C 15 28 G 14 29 C 13 30 A 0 31 A 0 32 G 0 33 U 0 34 U 0 35 U 0 36 C 0 37 U 0 38 A 0 39 C 0 40 C 58 41 G 57 42 G 56 43 G 55 44 C 54 45 A 53 46 C 0 47 C 0 48 G 0 49 U 0 50 A 0 51 A 0 52 A 0 53 U 45 54 G 44 55 U 43 56 C 42 57 C 41 58 G 40 59 A 0 60 U 0 61 U 7 62 A 6 63 U 5 64 G 4 65 U 3 66 C 2 67 C 1 68 U 0 Number of junctions with CHS: 1 Junction: Helix 1: 7-61 Helix 2: 13-29 Helix 3: 40-58 CHS: 1,2 (1) OUTPUT: RNA1 = 2G9C(H1H3), RNA2 = 2G9C(H1H2) CHSalign 1.0 report -------------------------------------------------------------------------------- General information -------------------------------------------------------------------------------- 1. RNA # of nucleotides 68 # of junctions 1 # of junctions with CHS 1 # of CHS 1 2. RNA # of nucleotides 68 # of junctions 1 # of junctions with CHS 1 # of CHS 1 Runtime: 57ms -------------------------------------------------------------------------------- 1. RNA junction list -------------------------------------------------------------------------------- Junction 1: Junction type: 3-way junction Helix 1: A(7)-U(61) Helix 2: G(13)-C(29) Helix 3: C(40)-G(58) CHS 1: 1,3 -------------------------------------------------------------------------------- 2. RNA junction list -------------------------------------------------------------------------------- Junction 1: Junction type: 3-way junction Helix 1: A(7)-U(61) Helix 2: G(13)-C(29) Helix 3: C(40)-G(58) CHS 1: 1,2 -------------------------------------------------------------------------------- Alignment details -------------------------------------------------------------------------------- Alignment score: 36.69 Aligned junctions: None Aligned nucleotides: G(1) --- G(1) G(2) --- G(2) A(3) --- A(3) C(4) --- C(4) A(5) --- A(5) U(6) --- U(6) A(7) --- A(7) U(61) --- U(61) A(62) --- A(62) U(63) --- U(63) G(64) --- G(64) U(65) --- U(65) C(66) --- C(66) C(67) --- C(67) U(68) --- U(68) -------------------------------------------------------------------------------- 1. RNA -------------------------------------------------------------------------------- >RNA1 1 11 21 31 41 51 61 GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU (((((((.....(((((.......)))))..........((((((.......))))))..))))))). -------------------------------------------------------------------------------- 2. RNA -------------------------------------------------------------------------------- >RNA2 1 11 21 31 41 51 61 GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU (((((((.....(((((.......)))))..........((((((.......))))))..))))))). (2) INPUT: RNA1 = 2G9C # 68 2G9C_A CLEANED # PDB: 2G9C_A.bpseq 1 G 67 2 G 66 3 A 65 4 C 64 5 A 63 6 U 62 7 A 61 8 U 0 9 A 0 10 A 0 11 U 0 12 C 0 13 G 29 14 C 28 15 G 27 16 U 26 17 G 25 18 G 0 19 A 0 20 U 0 21 A 0 22 U 0 23 G 0 24 G 0 25 C 17 26 A 16 27 C 15 28 G 14 29 C 13 30 A 0 31 A 0 32 G 0 33 U 0 34 U 0 35 U 0 36 C 0 37 U 0 38 A 0 39 C 0 40 C 58 41 G 57 42 G 56 43 G 55 44 C 54 45 A 53 46 C 0 47 C 0 48 G 0 49 U 0 50 A 0 51 A 0 52 A 0 53 U 45 54 G 44 55 U 43 56 C 42 57 C 41 58 G 40 59 A 0 60 U 0 61 U 7 62 A 6 63 U 5 64 G 4 65 U 3 66 C 2 67 C 1 68 U 0 Number of junctions with CHS: 1 Junction: Helix 1: 7-61 Helix 2: 13-29 Helix 3: 40-58 CHS: 1,2 (2) INPUT: RNA2 = 3RKF # 68 3RKF_A CLEANED # PDB: 3RKF_A.bpseq 1 G 67 2 G 66 3 C 65 4 C 64 5 A 63 6 U 62 7 A 61 8 U 0 9 A 0 10 A 0 11 C 31 12 U 30 13 G 29 14 C 28 15 G 27 16 U 26 17 G 25 18 G 0 19 A 0 20 U 0 21 A 0 22 U 0 23 A 0 24 G 0 25 C 17 26 A 16 27 C 15 28 G 14 29 C 13 30 A 12 31 G 11 32 G 0 33 U 0 34 U 0 35 U 0 36 C 0 37 U 0 38 A 0 39 C 0 40 C 58 41 G 57 42 G 56 43 G 55 44 C 54 45 A 53 46 C 0 47 U 0 48 G 0 49 U 0 50 A 0 51 A 0 52 A 0 53 U 45 54 G 44 55 U 43 56 C 42 57 C 41 58 G 40 59 A 0 60 C 0 61 U 7 62 A 6 63 U 5 64 G 4 65 G 3 66 U 2 67 C 1 68 G 0 Number of junctions with CHS: 1 Junction: Helix 1: 7-61 Helix 2: 11-31 Helix 3: 40-58 CHS: 1,2 (2) OUTPUT: RNA1 = 2G9C, RNA2 = 3RKF CHSalign 1.0 report -------------------------------------------------------------------------------- General information -------------------------------------------------------------------------------- 1. RNA # of nucleotides 68 # of junctions 1 # of junctions with CHS 1 # of CHS 1 2. RNA # of nucleotides 68 # of junctions 1 # of junctions with CHS 1 # of CHS 1 Runtime: 73ms -------------------------------------------------------------------------------- 1. RNA junction list -------------------------------------------------------------------------------- Junction 1: Junction type: 3-way junction Helix 1: A(7)-U(61) Helix 2: G(13)-C(29) Helix 3: C(40)-G(58) CHS 1: 1,2 -------------------------------------------------------------------------------- 2. RNA junction list -------------------------------------------------------------------------------- Junction 1: Junction type: 3-way junction Helix 1: A(7)-U(61) Helix 2: C(11)-G(31) Helix 3: C(40)-G(58) CHS 1: 1,2 -------------------------------------------------------------------------------- Alignment details -------------------------------------------------------------------------------- Alignment score: 179.68 Aligned junctions: Junction 1 --- Junction 1 Aligned nucleotides: G(1) --- G(1) G(2) --- G(2) A(3) --- C(3) C(4) --- C(4) A(5) --- A(5) U(6) --- U(6) A(7) --- A(7) U(8) --- U(8) A(9) --- A(9) A(10) --- A(10) G(13) --- C(11) C(14) --- U(12) G(15) --- G(13) U(16) --- C(14) G(17) --- G(15) G(18) --- G(18) A(19) --- A(19) U(20) --- U(20) A(21) --- A(21) U(22) --- U(22) G(23) --- A(23) G(24) --- G(24) C(25) --- C(27) A(26) --- G(28) C(27) --- C(29) G(28) --- A(30) C(29) --- G(31) G(32) --- G(32) U(33) --- U(33) U(34) --- U(34) U(35) --- U(35) C(36) --- C(36) U(37) --- U(37) A(38) --- A(38) C(39) --- C(39) C(40) --- C(40) G(41) --- G(41) G(42) --- G(42) G(43) --- G(43) C(44) --- C(44) A(45) --- A(45) C(46) --- C(46) C(47) --- U(47) G(48) --- G(48) U(49) --- U(49) A(50) --- A(50) A(51) --- A(51) A(52) --- A(52) U(53) --- U(53) G(54) --- G(54) U(55) --- U(55) C(56) --- C(56) C(57) --- C(57) G(58) --- G(58) A(59) --- A(59) U(60) --- C(60) U(61) --- U(61) A(62) --- A(62) U(63) --- U(63) G(64) --- G(64) U(65) --- G(65) C(66) --- U(66) C(67) --- C(67) U(68) --- G(68) -------------------------------------------------------------------------------- 1. RNA -------------------------------------------------------------------------------- >RNA1 1 11 21 31 41 51 61 GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU (((((((.....(((((.......)))))..........((((((.......))))))..))))))). -------------------------------------------------------------------------------- 2. RNA -------------------------------------------------------------------------------- >RNA2 1 11 21 31 41 51 61 GGCCAUAUAACUGCGUGGAUAUAGCACGCAGGUUUCUACCGGGCACUGUAAAUGUCCGACUAUGGUCG (((((((...(((((((.......)))))))........((((((.......))))))..))))))).