Locus 2268

Sequence ID	X_DroMel_CAF1
Location	6,147,056 – 6,147,237
Length	181
Max. P	0.997194

overview

Window 0

Location	6,147,056 – 6,147,165
Length	109
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	94.74
Mean single sequence MFE	-27.30
Consensus MFE	-25.85
Energy contribution	-25.63
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.52
Structure conservation index	0.95
SVM decision value	0.03
SVM RNA-class probability	0.549278
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147056 109 + 22224390
-----UGAUGAUGCUGCGACCGCAAUUAGCAGGCAGUGCUAAAAUUCUAACUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGC
-----................(((.((((((((((.((((......((((((..(((.((((((......))))))))))))))).....))))..)))....))))))).))) ( -27.60)
>DroEre_CAF1 2499 114 + 1
UGCUUUGAUGAUGCUGCGACCGCAAUUAGCAGGCAGUGCUAAAACUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGU
.((..(((((.(((((...((.(((((((..((.(((......)))))..))))))).((((((......)))))).......))....)))))....)))))..))....... ( -27.30)
>DroYak_CAF1 2525 114 + 1
UGCUUUGAUGAUGCUGCGACCGCAAUUAGCAGGCAGUGCUAAAAUUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCGAAAUGC
.((..(((((.(((((.........((((((.....))))))........((((((..((((((......))))))...))))))....)))))....)))))..))....... ( -27.00)
>consensus
UGCUUUGAUGAUGCUGCGACCGCAAUUAGCAGGCAGUGCUAAAAUUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGC
............(((((((...(((((((..((.(((......)))))..)))))))..))))).(((((((((......((((.....))))...)))))))))))....... (-25.85 = -25.63 +  -0.22)

alignment

secondary structure

dotplot

Window 1

Location	6,147,056 – 6,147,165
Length	109
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	94.74
Mean single sequence MFE	-30.07
Consensus MFE	-25.77
Energy contribution	-25.77
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.86
SVM decision value	0.91
SVM RNA-class probability	0.880108
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147056 109 - 22224390
GCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGUUAGAAUUUUAGCACUGCCUGCUAAUUGCGGUCGCAGCAUCAUCA-----
(((((.......)))))...((((((..((((((((((((((((......)))))).)))..))))......((((((.....))))))....))).))))))......----- ( -29.20)
>DroEre_CAF1 2499 114 - 1
ACAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAGUUUUAGCACUGCCUGCUAAUUGCGGUCGCAGCAUCAUCAAAGCA
.......(((....)))...((((((..(((....(((((((((......)))))).)))..((((((.((....)).))))))((.....))))).))))))........... ( -30.50)
>DroYak_CAF1 2525 114 - 1
GCAUUUCGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAAUUUUAGCACUGCCUGCUAAUUGCGGUCGCAGCAUCAUCAAAGCA
((.....(((....)))...((((((..(((....(((((((((......)))))).)))..((((((..........))))))((.....))))).))))))........)). ( -30.50)
>consensus
GCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAAUUUUAGCACUGCCUGCUAAUUGCGGUCGCAGCAUCAUCAAAGCA
.......(((....)))...((((((..(((......(((((((......)))))))(((((((.(((..............)))))))))).))).))))))........... (-25.77 = -25.77 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	6,147,091 – 6,147,205
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	94.74
Mean single sequence MFE	-34.93
Consensus MFE	-31.67
Energy contribution	-31.57
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-4.46
Structure conservation index	0.91
SVM decision value	1.54
SVM RNA-class probability	0.962176
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147091 114 + 22224390
AAAAUUCUAACUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGCACUUUGCCGUGAUUGGCACUCUGGCCAAUCGGAAUUUUUA
((((((((((((..(((.((((((......)))))))))))))(((((......((((((((.......)))))))))))))..(((((((......))))))))))))))).. ( -37.20)
>DroEre_CAF1 2539 114 + 1
AAAACUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGUACUUUGCCGUGAUUGACACUCUUGCCGAUAGGAAUUUUUA
.........(((..(((.((((((......))))))))).((((((((...(((((((((((.......))))))).)))).(((.....)))..)))))))))))........ ( -30.60)
>DroYak_CAF1 2565 114 + 1
AAAAUUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCGAAAUGCACUUUGCCGUGAUUGGCACACUGGCCAAUCGGAAUUUUUA
((((((((..((((((..((((((......))))))...))))))...((.(((((((((((.......))))))).)))).))(((((((......))))))))))))))).. ( -37.00)
>consensus
AAAAUUCUACCUAAUUGAUUUGCAAAAUGAUGCAAACAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGCACUUUGCCGUGAUUGGCACUCUGGCCAAUCGGAAUUUUUA
((((((((......(((.((((((......))))))))).((((((.....(((((((((((.......))))))).)))).(((.....)))....)))))).)))))))).. (-31.67 = -31.57 +  -0.11)

alignment

secondary structure

dotplot

Window 3

Location	6,147,091 – 6,147,205
Length	114
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	94.74
Mean single sequence MFE	-37.23
Consensus MFE	-33.74
Energy contribution	-34.63
Covariance contribution	0.89
Combinations/Pair	1.05
Mean z-score	-5.02
Structure conservation index	0.91
SVM decision value	1.22
SVM RNA-class probability	0.931826
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147091 114 - 22224390
UAAAAAUUCCGAUUGGCCAGAGUGCCAAUCACGGCAAAGUGCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGUUAGAAUUUU
..(((((((.(((((((......)))))))(((((((.(((((((.......)))))))))))))).....(((((((((((((......)))))).)))..)))).))))))) ( -38.90)
>DroEre_CAF1 2539 114 - 1
UAAAAAUUCCUAUCGGCAAGAGUGUCAAUCACGGCAAAGUACAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAGUUUU
..(((((((.((((((((((.(((.....)))(((((.((.((((.......)))).))))))).))))))....(((((((((......)))))).)))...))))))))))) ( -31.20)
>DroYak_CAF1 2565 114 - 1
UAAAAAUUCCGAUUGGCCAGUGUGCCAAUCACGGCAAAGUGCAUUUCGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAAUUUU
..(((((((.(((((((......)))))))(((((((.(((((((.......)))))))))))))).((((....(((((((((......)))))).)))...))))))))))) ( -41.60)
>consensus
UAAAAAUUCCGAUUGGCCAGAGUGCCAAUCACGGCAAAGUGCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUGUUUGCAUCAUUUUGCAAAUCAAUUAGGUAGAAUUUU
..(((((((.(((((((......)))))))(((((((.(((((((.......)))))))))))))).((((....(((((((((......)))))).)))...))))))))))) (-33.74 = -34.63 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	6,147,127 – 6,147,237
Length	110
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-29.35
Consensus MFE	-22.96
Energy contribution	-22.97
Covariance contribution	0.01
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.78
SVM decision value	1.01
SVM RNA-class probability	0.899241
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147127 110 + 22224390
CAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGCACUUUGCCGUGAUUGGCACUCUGGCCAAUCGGAAUUUUUAAUAUUCAUACACUAAAAACGA--------UUAGUUUUGGG
.......(((((......((((((((.......))))))))))))).((((((((......))))))))((((.......)))).....((((((.(..--------...))))))). ( -29.20)
>DroEre_CAF1 2575 118 + 1
CAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGUACUUUGCCGUGAUUGACACUCUUGCCGAUAGGAAUUUUUAAUAUUCCUCCCCUAAAUACGAGAGAGAUCGCAGUUUUGUG
(((((..(((((......((((((((.......)))))))))))))((((((....((((((.....((((((.......))))))..........)))))).))))))..))))).. ( -28.96)
>DroYak_CAF1 2601 105 + 1
CAAAGUUGGCAAACAGCAAGUGCAUUAUUGCGAAAUGCACUUUGCCGUGAUUGGCACACUGGCCAAUCGGAAUUUUUAAUAU-------------ACGACAGAGAUAGCAGUUUUGCC
.......(((((((.(((((((((((.......))))))).)))).))(((((((......)))))))..............-------------..................))))) ( -29.90)
>consensus
CAAAGUUGGCAAACAGCAAGUGCAUUAUUGCUAAAUGCACUUUGCCGUGAUUGGCACUCUGGCCAAUCGGAAUUUUUAAUAUUC_U_C_CUAAA_ACGA_AGAGAU_GCAGUUUUGCG
((((..((....((.(((((((((((.......))))))).)))).))(((((((......)))))))........................................))..)))).. (-22.96 = -22.97 +   0.01)

alignment

secondary structure

dotplot

Window 5

Location	6,147,127 – 6,147,237
Length	110
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-32.24
Consensus MFE	-21.82
Energy contribution	-22.60
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-3.19
Structure conservation index	0.68
SVM decision value	2.81
SVM RNA-class probability	0.997194
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6147127 110 - 22224390
CCCAAAACUAA--------UCGUUUUUAGUGUAUGAAUAUUAAAAAUUCCGAUUGGCCAGAGUGCCAAUCACGGCAAAGUGCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUG
.......((((--------(((((((((((((....))))))))))...))))))).((((((..(((..(((((((.(((((((.......)))))))))))))))))...)))))) ( -34.30)
>DroEre_CAF1 2575 118 - 1
CACAAAACUGCGAUCUCUCUCGUAUUUAGGGGAGGAAUAUUAAAAAUUCCUAUCGGCAAGAGUGUCAAUCACGGCAAAGUACAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUG
........(((((......)))))..(((((.((((((.......))))))...((((((.(((.....)))(((((.((.((((.......)))).))))))).))))))..))))) ( -27.20)
>DroYak_CAF1 2601 105 - 1
GGCAAAACUGCUAUCUCUGUCGU-------------AUAUUAAAAAUUCCGAUUGGCCAGUGUGCCAAUCACGGCAAAGUGCAUUUCGCAAUAAUGCACUUGCUGUUUGCCAACUUUG
((((((...((......((((((-------------..............(((((((......)))))))))))))(((((((((.......)))))))))))..))))))....... ( -35.23)
>consensus
CACAAAACUGC_AUCUCU_UCGU_UUUAG_G_A_GAAUAUUAAAAAUUCCGAUUGGCCAGAGUGCCAAUCACGGCAAAGUGCAUUUAGCAAUAAUGCACUUGCUGUUUGCCAACUUUG
..((((............................................(((((((......)))))))(((((((.(((((((.......))))))))))))))........)))) (-21.82 = -22.60 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:13 2006