Locus 1364

Sequence ID	3R_DroMel_CAF1
Location	4,002,620 – 4,002,818
Length	198
Max. P	0.977841

overview

Window 4

Location	4,002,620 – 4,002,740
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.03
Mean single sequence MFE	-27.68
Consensus MFE	-27.10
Energy contribution	-27.35
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.98
SVM decision value	0.34
SVM RNA-class probability	0.697402
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4002620 120 + 27905053
AGUCACAAGACAAAAGUUAUUGCCAAAAUUUUCGGCAUGUUUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCUUGGGCUAUCAUAAAAAUUUCCGACUCACGA
.(((....)))((((((...((((.........)))).....))))))(((((....)))))....((((.((((..((((((((((((....))...))))))))))..))))..)))) ( -28.00)
>DroSec_CAF1 8212 120 + 1
AGUCACAAGACAAAAGUUAUUGCCAAAAUUUUCGGCAUGUUUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCAACUCACGA
........(((((((((...((((.........)))).....)))).((((((....))))))......)))))(((((((((((((((....))...))))))))...)))))...... ( -25.60)
>DroSim_CAF1 8783 120 + 1
AGUCACAAGACAAAAGUUAUUGCCAAAAUUUUCGGCAUGUUUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCGACUCACGA
.(((....)))((((((...((((.........)))).....))))))(((((....)))))....((((.((((..((((((((((((....))...))))))))))..))))..)))) ( -29.10)
>DroYak_CAF1 8142 120 + 1
AGUCACAAGACAAAAGUUAUUGCCAAAAUUUUCGGCAUGUUUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCUUGGGCUAUCAUAAAAAUUUCCGACUCACGA
.(((....)))((((((...((((.........)))).....))))))(((((....)))))....((((.((((..((((((((((((....))...))))))))))..))))..)))) ( -28.00)
>consensus
AGUCACAAGACAAAAGUUAUUGCCAAAAUUUUCGGCAUGUUUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCGACUCACGA
.(((....)))((((((...((((.........)))).....))))))(((((....)))))....((((.((((..((((((((((((....))...))))))))))..))))..)))) (-27.10 = -27.35 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	4,002,620 – 4,002,740
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.03
Mean single sequence MFE	-25.82
Consensus MFE	-24.91
Energy contribution	-24.72
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.96
SVM decision value	0.74
SVM RNA-class probability	0.837165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4002620 120 - 27905053
UCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAAACAUGCCGAAAAUUUUGGCAAUAACUUUUGUCUUGUGACU
(((..(((((....((((((((...((....))))))))))....)))).(((((.(((((((....)))))...........((((((.....))))))...)).))))).)..))).. ( -24.30)
>DroSec_CAF1 8212 120 - 1
UCGUGAGUUGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAAACAUGCCGAAAAUUUUGGCAAUAACUUUUGUCUUGUGACU
(((..((((((...((((((((...((....)))))))))))))))(((((......((((((....))))))..........((((((.....)))))).......))))))..))).. ( -28.50)
>DroSim_CAF1 8783 120 - 1
UCGUGAGUCGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAAACAUGCCGAAAAUUUUGGCAAUAACUUUUGUCUUGUGACU
(((..(((((....((((((((...((....))))))))))....)))).(((((.(((((((....)))))...........((((((.....))))))...)).))))).)..))).. ( -26.20)
>DroYak_CAF1 8142 120 - 1
UCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAAACAUGCCGAAAAUUUUGGCAAUAACUUUUGUCUUGUGACU
(((..(((((....((((((((...((....))))))))))....)))).(((((.(((((((....)))))...........((((((.....))))))...)).))))).)..))).. ( -24.30)
>consensus
UCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAAACAUGCCGAAAAUUUUGGCAAUAACUUUUGUCUUGUGACU
(((..(((((....((((((((...((....))))))))))....)))).(((((.(((((((....)))))...........((((((.....))))))...)).))))).)..))).. (-24.91 = -24.72 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	4,002,660 – 4,002,778
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-29.45
Consensus MFE	-28.42
Energy contribution	-28.92
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.96
SVM decision value	0.42
SVM RNA-class probability	0.727356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4002660 118 + 27905053
UUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCUUGGGCUAUCAUAAAAAUUUCCGACUCACGAGCAUGUGAGCUCUUAAGUGUG--UGUGCUGUUUUGGGCCA
..((((..(((((....((..((((((((..((((..((((((((((((....))...))))))))))..))))....((((......)))).))))))))--.))...))))))))).. ( -30.70)
>DroSec_CAF1 8252 118 + 1
UUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCAACUCACGAGCAUGUGAGCUCCUAAGUAUG--UGUUUUGUUUUGGGCCA
..(((..((((((....))))))(((.((((((.(((((((((((((((....))...))))))))...)))))..)).)))).)))))).((((((....--........))))))... ( -24.00)
>DroSim_CAF1 8823 118 + 1
UUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCGACUCACGAGCAUGUGAGCUCUUAAGUGUG--UGUGUUGUUUUGGGCCA
..((((..(((((....((..((((((((..((((..((((((((((((....))...))))))))))..))))....((((......)))).))))))))--.))...))))))))).. ( -31.80)
>DroYak_CAF1 8182 120 + 1
UUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCUUGGGCUAUCAUAAAAAUUUCCGACUCACGAGCAUGUGAGCUCUUAAGUGUGUGUGUGUUGUUUUGGGCCA
..((((..(((((........((((((((..((((..((((((((((((....))...))))))))))..))))....((((......)))).))))))))........))))))))).. ( -31.29)
>consensus
UUGCUUUUGAAAUUUAAAUUUCACAUUUGUUGUCGUUGGUUUUUAUGGCCUGGGCUAUCAUAAAAAUUUCCGACUCACGAGCAUGUGAGCUCUUAAGUGUG__UGUGUUGUUUUGGGCCA
..((((..(((((........((((((((..((((..((((((((((((....))...))))))))))..))))....((((......)))).))))))))........))))))))).. (-28.42 = -28.92 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	4,002,660 – 4,002,778
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-23.25
Consensus MFE	-22.16
Energy contribution	-21.98
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.59
Structure conservation index	0.95
SVM decision value	1.80
SVM RNA-class probability	0.977841
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4002660 118 - 27905053
UGGCCCAAAACAGCACA--CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAA
............((...--.........((((......))))((..((((....((((((((...((....))))))))))....)))).)).....((((((....))))))...)).. ( -22.40)
>DroSec_CAF1 8252 118 - 1
UGGCCCAAAACAAAACA--CAUACUUAGGAGCUCACAUGCUCGUGAGUUGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAA
...............((--(((..(((.((((......)))).)))(((((...((((((((...((....)))))))))))))))........)))))..................... ( -25.50)
>DroSim_CAF1 8823 118 - 1
UGGCCCAAAACAACACA--CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAA
..((.....(((.....--.........((((......))))((..((((....((((((((...((....))))))))))....)))).))...)))(((((....)))))....)).. ( -23.50)
>DroYak_CAF1 8182 120 - 1
UGGCCCAAAACAACACACACACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAA
..((.....(((................((((......))))((..((((....((((((((...((....))))))))))....)))).))...)))(((((....)))))....)).. ( -21.60)
>consensus
UGGCCCAAAACAACACA__CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAAACCAACGACAACAAAUGUGAAAUUUAAAUUUCAAAAGCAA
..((.....(((................((((......))))((..((((....((((((((...((....))))))))))....)))).))...)))(((((....)))))....)).. (-22.16 = -21.98 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	4,002,700 – 4,002,818
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.68
Mean single sequence MFE	-28.85
Consensus MFE	-26.56
Energy contribution	-27.13
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.92
SVM decision value	0.98
SVM RNA-class probability	0.893236
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4002700 118 - 27905053
UAGUUUUUUGGCUUAAACGCAGAGGCCAAUGCAGUUUUAAUGGCCCAAAACAGCACA--CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAA
...((((.((((((....((.(.(((((.((......)).))))))...........--..((((((.((((......)))).))))).)...............))..)))))).)))) ( -27.40)
>DroSec_CAF1 8292 118 - 1
UAGUUUUUUGGCUUAAACGAUGAGGCCAAUGCAGUUUUAAUGGCCCAAAACAAAACA--CAUACUUAGGAGCUCACAUGCUCGUGAGUUGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAA
..((...(((((((........))))))).)).......((((((............--...(((((.((((......)))).))))).((..(((.....)))..))..)))))).... ( -32.10)
>DroSim_CAF1 8863 118 - 1
UAGUUUUUUGGCUUAAACGCUGAGGCCAAUGCAGUUUUAAUGGCCCAAAACAACACA--CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAGGCCAUAAAA
..((...(((((((........))))))).)).......((((((............--...(((((.((((......)))).))))).((..(((.....)))..))..)))))).... ( -30.40)
>DroYak_CAF1 8222 120 - 1
UAGUUUUUUGGCUUAAACGCAGAACCCAAUGCAGUUUUAAUGGCCCAAAACAACACACACACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAA
..(((((..((((.(((((((........))).))))....)))).)))))..........((((((.((((......)))).))))).).....(((((((...((....))))))))) ( -25.50)
>consensus
UAGUUUUUUGGCUUAAACGCAGAGGCCAAUGCAGUUUUAAUGGCCCAAAACAACACA__CACACUUAAGAGCUCACAUGCUCGUGAGUCGGAAAUUUUUAUGAUAGCCCAAGCCAUAAAA
..((...(((((((........))))))).)).......((((((.................(((((.((((......)))).))))).((..(((.....)))..))..)))))).... (-26.56 = -27.13 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:11 2006