(1) INPUT: RNA1 = 2GIS

# 95 2GIS_A CLEANED
# PDB: 2GIS_A.bpseq
1 G 93
2 G 92
3 C 91
4 U 90
5 U 89
6 A 88
7 U 87
8 C 86
9 A 0
10 A 0
11 G 0
12 A 0
13 G 0
14 A 0
15 G 40
16 G 39
17 U 38
18 G 0
19 G 0
20 A 0
21 G 31
22 G 30
23 G 29
24 A 0
25 C 0
26 U 0
27 G 0
28 G 0
29 C 23
30 C 22
31 C 21
32 G 0
33 A 0
34 U 0
35 G 0
36 A 0
37 A 0
38 A 17
39 C 16
40 C 15
41 C 0
42 G 60
43 G 59
44 C 58
45 A 0
46 A 0
47 C 56
48 C 55
49 A 54
50 G 0
51 A 0
52 A 0
53 A 0
54 U 49
55 G 48
56 G 47
57 U 0
58 G 44
59 C 43
60 C 42
61 A 0
62 A 0
63 U 0
64 U 0
65 C 0
66 C 0
67 U 0
68 G 0
69 C 82
70 A 81
71 G 80
72 C 79
73 G 78
74 G 0
75 A 0
76 A 0
77 A 0
78 C 73
79 G 72
80 U 71
81 U 70
82 G 69
83 A 0
84 A 0
85 A 0
86 G 8
87 A 7
88 U 6
89 G 5
90 A 4
91 G 3
92 C 2
93 C 1
94 A 0
95 A 0

(1) INPUT: RNA2 = 4B5R

# 95 4B5R_A CLEANED
# PDB: 4B5R_A.bpseq
1 G 93
2 G 92
3 C 91
4 U 90
5 U 89
6 A 88
7 U 87
8 C 86
9 A 0
10 A 0
11 G 0
12 A 0
13 G 0
14 A 0
15 G 40
16 G 39
17 G 38
18 G 0
19 G 0
20 A 0
21 G 31
22 C 30
23 G 29
24 A 0
25 C 0
26 U 0
27 G 0
28 G 0
29 C 23
30 G 22
31 C 21
32 G 0
33 A 0
34 A 0
35 G 0
36 A 0
37 A 0
38 C 17
39 C 16
40 C 15
41 C 0
42 G 60
43 G 59
44 C 58
45 A 0
46 A 0
47 C 56
48 C 55
49 A 54
50 G 0
51 A 0
52 A 0
53 A 0
54 U 49
55 G 48
56 G 47
57 U 0
58 G 44
59 C 43
60 C 42
61 A 0
62 A 0
63 U 0
64 U 0
65 C 0
66 C 0
67 U 0
68 G 0
69 C 82
70 A 81
71 G 80
72 C 79
73 G 78
74 G 0
75 A 0
76 A 0
77 A 0
78 C 73
79 G 72
80 U 71
81 U 70
82 G 69
83 A 0
84 A 0
85 A 0
86 G 8
87 A 7
88 U 6
89 G 5
90 A 4
91 G 3
92 C 2
93 C 1
94 G 0
95 A 0

(1) OUTPUT: RNA1 = 2GIS, RNA2 = 4B5R

CHSalign 1.0 report

--------------------------------------------------------------------------------
General information
--------------------------------------------------------------------------------

1. RNA
   # of nucleotides          95
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  2

2. RNA
   # of nucleotides          95
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  2

Runtime: 278ms

--------------------------------------------------------------------------------
1. RNA junction list
--------------------------------------------------------------------------------

Junction 1:
  Junction type: 4-way junction
  Helix 1: C(8)-G(86)
  Helix 2: G(15)-C(40)
  Helix 3: G(42)-C(60)
  Helix 4: C(69)-G(82)
  CHS 1: 2,3
  CHS 2: 1,4

--------------------------------------------------------------------------------
2. RNA junction list
--------------------------------------------------------------------------------

Junction 1:
  Junction type: 4-way junction
  Helix 1: C(8)-G(86)
  Helix 2: G(15)-C(40)
  Helix 3: G(42)-C(60)
  Helix 4: C(69)-G(82)
  CHS 1: 2,3
  CHS 2: 1,4

--------------------------------------------------------------------------------
Alignment details
--------------------------------------------------------------------------------

Alignment score: 252.61

Aligned junctions:
Junction 1 --- Junction 1

Aligned nucleotides:
G(1) --- G(1)
G(2) --- G(2)
C(3) --- C(3)
U(4) --- U(4)
U(5) --- U(5)
A(6) --- A(6)
U(7) --- U(7)
C(8) --- C(8)
A(9) --- A(9)
A(10) --- A(10)
G(11) --- G(11)
A(12) --- A(12)
G(13) --- G(13)
A(14) --- A(14)
G(15) --- G(15)
G(16) --- G(16)
U(17) --- G(17)
G(18) --- G(18)
G(19) --- G(19)
A(20) --- A(20)
G(21) --- G(21)
G(22) --- C(22)
G(23) --- G(23)
A(24) --- A(24)
C(25) --- C(25)
U(26) --- U(26)
G(27) --- G(27)
G(28) --- G(28)
C(29) --- C(29)
C(30) --- G(30)
C(31) --- C(31)
G(32) --- G(32)
A(33) --- A(33)
U(34) --- A(34)
G(35) --- G(35)
A(36) --- A(36)
A(37) --- A(37)
A(38) --- C(38)
C(39) --- C(39)
C(40) --- C(40)
C(41) --- C(41)
G(42) --- G(42)
G(43) --- G(43)
C(44) --- C(44)
A(45) --- A(45)
A(46) --- A(46)
C(47) --- C(47)
C(48) --- C(48)
A(49) --- A(49)
G(50) --- G(50)
A(51) --- A(51)
A(52) --- A(52)
A(53) --- A(53)
U(54) --- U(54)
G(55) --- G(55)
G(56) --- G(56)
U(57) --- U(57)
G(58) --- G(58)
C(59) --- C(59)
C(60) --- C(60)
A(61) --- A(61)
A(62) --- A(62)
U(63) --- U(63)
U(64) --- U(64)
C(65) --- C(65)
C(66) --- C(66)
U(67) --- U(67)
G(68) --- G(68)
C(69) --- C(69)
A(70) --- A(70)
G(71) --- G(71)
C(72) --- C(72)
G(73) --- G(73)
G(74) --- G(74)
A(75) --- A(75)
A(76) --- A(76)
A(77) --- A(77)
C(78) --- C(78)
G(79) --- G(79)
U(80) --- U(80)
U(81) --- U(81)
G(82) --- G(82)
A(83) --- A(83)
A(84) --- A(84)
A(85) --- A(85)
G(86) --- G(86)
A(87) --- A(87)
U(88) --- U(88)
G(89) --- G(89)
A(90) --- A(90)
G(91) --- G(91)
C(92) --- C(92)
C(93) --- C(93)
A(94) --- G(94)
A(95) --- A(95)

--------------------------------------------------------------------------------
1. RNA
--------------------------------------------------------------------------------

>RNA1
1         11        21        31        41        51        61        71
GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGU
((((((((......(((...(((.....)))......))).(((..(((....))).)))........(((((....)))

81        91
UGAAAGAUGAGCCAA
))...))))))))..

--------------------------------------------------------------------------------
2. RNA
--------------------------------------------------------------------------------

>RNA2
1         11        21        31        41        51        61        71
GGCUUAUCAAGAGAGGGGGAGCGACUGGCGCGAAGAACCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGU
((((((((......(((...(((.....)))......))).(((..(((....))).)))........(((((....)))

81        91
UGAAAGAUGAGCCGA
))...))))))))..


(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

(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

(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: 72ms

--------------------------------------------------------------------------------
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: C(11)-G(31)
  Helix 3: C(40)-G(58)
  CHS 1: 1,3

--------------------------------------------------------------------------------
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
(((((((...(((((((.......)))))))........((((((.......))))))..))))))).


(3) INPUT: RNA1 = 2GDI

# 80 2GDI_X CLEANED
# PDB: 2GDI_X.bpseq
1 G 80
2 G 79
3 A 78
4 C 77
5 U 76
6 C 42
7 G 41
8 G 40
9 G 39
10 G 0
11 U 0
12 G 29
13 C 28
14 C 27
15 C 0
16 U 26
17 U 25
18 C 24
19 U 0
20 G 0
21 C 0
22 G 0
23 U 0
24 G 18
25 A 17
26 A 16
27 G 14
28 G 13
29 C 12
30 U 0
31 G 0
32 A 0
33 G 0
34 A 0
35 A 0
36 A 0
37 U 0
38 A 0
39 C 9
40 C 8
41 C 7
42 G 6
43 U 0
44 A 0
45 U 0
46 C 0
47 A 0
48 C 73
49 C 72
50 U 71
51 G 0
52 A 0
53 U 0
54 C 67
55 U 66
56 G 65
57 G 64
58 A 0
59 U 0
60 A 0
61 A 0
62 U 0
63 G 0
64 C 57
65 C 56
66 A 55
67 G 54
68 C 0
69 G 0
70 U 0
71 A 50
72 G 49
73 G 48
74 G 0
75 A 0
76 A 5
77 G 4
78 U 3
79 U 2
80 C 1

(3) INPUT: RNA2 = 3D2G

# 77 3D2G_A CLEANED
# PDB: 3D2G_A.bpseq
1 G 0
2 G 0
3 G 77
4 A 76
5 C 75
6 C 0
7 A 39
8 G 38
9 G 37
10 G 36
11 G 0
12 U 0
13 G 26
14 C 25
15 U 24
16 U 23
17 G 22
18 U 0
19 U 0
20 C 0
21 A 0
22 C 17
23 A 16
24 G 15
25 G 14
26 C 13
27 U 0
28 G 0
29 A 0
30 G 0
31 A 0
32 A 0
33 A 0
34 G 0
35 U 0
36 C 10
37 C 9
38 C 8
39 U 7
40 U 0
41 U 0
42 G 0
43 A 0
44 A 0
45 C 70
46 C 69
47 U 68
48 G 0
49 A 0
50 A 0
51 C 64
52 A 63
53 G 62
54 G 61
55 G 0
56 U 0
57 A 0
58 A 0
59 U 0
60 G 0
61 C 54
62 C 53
63 U 52
64 G 51
65 C 0
66 G 0
67 C 0
68 A 47
69 G 46
70 G 45
71 G 0
72 A 0
73 G 0
74 U 0
75 G 5
76 U 4
77 C 3

(3) OUTPUT: RNA1 = 2GDI, RNA2 = 3D2G

CHSalign 1.0 report

--------------------------------------------------------------------------------
General information
--------------------------------------------------------------------------------

1. RNA
   # of nucleotides          80
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  1

2. RNA
   # of nucleotides          77
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  1

Runtime: 77ms

--------------------------------------------------------------------------------
1. RNA junction list
--------------------------------------------------------------------------------

Junction 1:
  Junction type: 3-way junction
  Helix 1: U(5)-A(76)
  Helix 2: C(6)-G(42)
  Helix 3: C(48)-G(73)
  CHS 1: 1,2

--------------------------------------------------------------------------------
2. RNA junction list
--------------------------------------------------------------------------------

Junction 1:
  Junction type: 3-way junction
  Helix 1: C(5)-G(75)
  Helix 2: A(7)-U(39)
  Helix 3: C(45)-G(70)
  CHS 1: 1,2

--------------------------------------------------------------------------------
Alignment details
--------------------------------------------------------------------------------

Alignment score: 191.06

Aligned junctions:
Junction 1 --- Junction 1

Aligned nucleotides:
G(2) --- G(1)
A(3) --- G(2)
U(5) --- G(3)
C(6) --- A(7)
G(7) --- G(8)
G(10) --- G(9)
U(11) --- G(10)
G(12) --- G(11)
C(13) --- U(12)
C(14) --- G(13)
C(15) --- C(14)
U(16) --- U(15)
U(17) --- U(16)
C(18) --- G(17)
G(24) --- C(22)
A(25) --- A(23)
A(26) --- G(24)
G(27) --- G(25)
C(29) --- C(26)
U(30) --- G(28)
G(31) --- A(29)
A(32) --- G(30)
G(33) --- A(31)
A(34) --- A(32)
A(35) --- A(33)
A(36) --- G(34)
U(37) --- U(35)
A(38) --- C(36)
C(39) --- C(37)
C(41) --- C(38)
G(42) --- U(39)
U(43) --- U(40)
A(44) --- A(43)
A(47) --- A(44)
C(48) --- C(45)
C(49) --- C(46)
U(50) --- U(47)
G(51) --- G(48)
A(52) --- A(49)
U(53) --- A(50)
C(54) --- C(51)
U(55) --- A(52)
G(56) --- G(53)
G(57) --- G(54)
A(58) --- G(55)
U(59) --- U(56)
A(60) --- A(57)
A(61) --- A(58)
U(62) --- U(59)
G(63) --- G(60)
C(64) --- C(61)
C(65) --- C(62)
A(66) --- U(63)
G(67) --- G(64)
C(68) --- C(65)
G(69) --- G(66)
U(70) --- C(67)
A(71) --- A(68)
G(72) --- G(69)
G(73) --- G(70)
G(74) --- G(71)
A(75) --- A(72)
A(76) --- G(75)
U(78) --- U(76)
U(79) --- C(77)

--------------------------------------------------------------------------------
1. RNA
--------------------------------------------------------------------------------

>RNA1
1         11        21        31        41        51        61        71
GGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUUC
(((((((((..(((.(((.....)))))).........)))).....(((...((((......))))...)))..)))))

--------------------------------------------------------------------------------
2. RNA
--------------------------------------------------------------------------------

>RNA2
1         11        21        31        41        51        61        71
GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC
..(((.((((..(((((....))))).........)))).....(((...((((......))))...)))....)))


(4) INPUT: RNA1 = 2GIS

# 95 2GIS_A CLEANED
# PDB: 2GIS_A.bpseq
1 G 93
2 G 92
3 C 91
4 U 90
5 U 89
6 A 88
7 U 87
8 C 86
9 A 0
10 A 0
11 G 0
12 A 0
13 G 0
14 A 0
15 G 40
16 G 39
17 U 38
18 G 0
19 G 0
20 A 0
21 G 31
22 G 30
23 G 29
24 A 0
25 C 0
26 U 0
27 G 0
28 G 0
29 C 23
30 C 22
31 C 21
32 G 0
33 A 0
34 U 0
35 G 0
36 A 0
37 A 0
38 A 17
39 C 16
40 C 15
41 C 0
42 G 60
43 G 59
44 C 58
45 A 0
46 A 0
47 C 56
48 C 55
49 A 54
50 G 0
51 A 0
52 A 0
53 A 0
54 U 49
55 G 48
56 G 47
57 U 0
58 G 44
59 C 43
60 C 42
61 A 0
62 A 0
63 U 0
64 U 0
65 C 0
66 C 0
67 U 0
68 G 0
69 C 82
70 A 81
71 G 80
72 C 79
73 G 78
74 G 0
75 A 0
76 A 0
77 A 0
78 C 73
79 G 72
80 U 71
81 U 70
82 G 69
83 A 0
84 A 0
85 A 0
86 G 8
87 A 7
88 U 6
89 G 5
90 A 4
91 G 3
92 C 2
93 C 1
94 A 0
95 A 0

(4) INPUT: RNA2 = 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

(4) OUTPUT: RNA1 = 2GIS, RNA2 = 2G9C

CHSalign 1.0 report

--------------------------------------------------------------------------------
General information
--------------------------------------------------------------------------------

1. RNA
   # of nucleotides          95
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  2

2. RNA
   # of nucleotides          68
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  1

Runtime: 62ms

--------------------------------------------------------------------------------
1. RNA junction list
--------------------------------------------------------------------------------

Junction 1:
  Junction type: 4-way junction
  Helix 1: C(8)-G(86)
  Helix 2: G(15)-C(40)
  Helix 3: G(42)-C(60)
  Helix 4: C(69)-G(82)
  CHS 1: 2,3
  CHS 2: 1,4

--------------------------------------------------------------------------------
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: 1,3

--------------------------------------------------------------------------------
Alignment details
--------------------------------------------------------------------------------

Alignment score: 20.40

Aligned junctions:
None

Aligned nucleotides:
G(1) --- G(1)
G(2) --- G(2)
C(3) --- A(3)
U(5) --- C(4)
A(6) --- A(5)
U(7) --- U(6)
C(8) --- A(7)
G(86) --- U(61)
U(88) --- A(62)
G(89) --- U(63)
A(90) --- G(64)
G(91) --- U(65)
C(93) --- C(66)
A(94) --- C(67)
A(95) --- U(68)

--------------------------------------------------------------------------------
1. RNA
--------------------------------------------------------------------------------

>RNA1
1         11        21        31        41        51        61        71
GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGU
((((((((......(((...(((.....)))......))).(((..(((....))).)))........(((((....)))

81        91
UGAAAGAUGAGCCAA
))...))))))))..

--------------------------------------------------------------------------------
2. RNA
--------------------------------------------------------------------------------

>RNA2
1         11        21        31        41        51        61
GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU
(((((((.....(((((.......)))))..........((((((.......))))))..))))))).


(5) 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

(5) INPUT: RNA2 = 2GDI

# 80 2GDI_X CLEANED
# PDB: 2GDI_X.bpseq
1 G 80
2 G 79
3 A 78
4 C 77
5 U 76
6 C 42
7 G 41
8 G 40
9 G 39
10 G 0
11 U 0
12 G 29
13 C 28
14 C 27
15 C 0
16 U 26
17 U 25
18 C 24
19 U 0
20 G 0
21 C 0
22 G 0
23 U 0
24 G 18
25 A 17
26 A 16
27 G 14
28 G 13
29 C 12
30 U 0
31 G 0
32 A 0
33 G 0
34 A 0
35 A 0
36 A 0
37 U 0
38 A 0
39 C 9
40 C 8
41 C 7
42 G 6
43 U 0
44 A 0
45 U 0
46 C 0
47 A 0
48 C 73
49 C 72
50 U 71
51 G 0
52 A 0
53 U 0
54 C 67
55 U 66
56 G 65
57 G 64
58 A 0
59 U 0
60 A 0
61 A 0
62 U 0
63 G 0
64 C 57
65 C 56
66 A 55
67 G 54
68 C 0
69 G 0
70 U 0
71 A 50
72 G 49
73 G 48
74 G 0
75 A 0
76 A 5
77 G 4
78 U 3
79 U 2
80 C 1

(5) OUTPUT: RNA1 = 2G9C, RNA2 = 2GDI

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          80
   # of junctions            1
   # of junctions with CHS   1
   # of CHS                  1

Runtime: 59ms

--------------------------------------------------------------------------------
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: U(5)-A(76)
  Helix 2: C(6)-G(42)
  Helix 3: C(48)-G(73)
  CHS 1: 1,2

--------------------------------------------------------------------------------
Alignment details
--------------------------------------------------------------------------------

Alignment score: 13.65

Aligned junctions:
None

Aligned nucleotides:
G(2) --- G(1)
C(4) --- G(2)
A(5) --- A(3)
U(6) --- C(4)
A(7) --- U(5)
A(62) --- A(76)
U(63) --- G(77)
G(64) --- U(78)
U(65) --- U(79)
C(67) --- C(80)

--------------------------------------------------------------------------------
1. RNA
--------------------------------------------------------------------------------

>RNA1
1         11        21        31        41        51        61
GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU
(((((((.....(((((.......)))))..........((((((.......))))))..))))))).

--------------------------------------------------------------------------------
2. RNA
--------------------------------------------------------------------------------

>RNA2
1         11        21        31        41        51        61        71
GGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUUC
(((((((((..(((.(((.....)))))).........)))).....(((...((((......))))...)))..)))))