Locus 7651

Sequence ID	X_DroMel_CAF1
Location	19,064,321 – 19,064,451
Length	130
Max. P	0.996784

overview

Window 8

Location	19,064,321 – 19,064,434
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	95.68
Mean single sequence MFE	-39.68
Consensus MFE	-36.34
Energy contribution	-36.42
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.24
Structure conservation index	0.92
SVM decision value	0.44
SVM RNA-class probability	0.739259
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19064321 113 + 22224390
UUAGUGGCCCCCGCGGAUCUGCUUUUGUUUUGAUGCCCGCACCGUUGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCCCAGCUUCUGCUGCUCUACGAUGGGCUCU
.....(((((..(((....)))....((((..((((((((.......))))))))....))))..(((.((((..(((.((((....))))..))))))).)))..))))).. ( -38.00)
>DroSec_CAF1 16074 110 + 1
UUAGUGGCCCCCGCGGAUCUGCUUUUGUUUUGAUGCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCU
...((((...))))((.((.((....((((..((((((((.......))))))))....))))...)).)).))(((((..(..(((((....)))))..)---...))))). ( -41.00)
>DroSim_CAF1 18049 110 + 1
UUAGUGGCCCCCGCGGAUCUGCUUUUGUUUUGAUGCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCU
...((((...))))((.((.((....((((..((((((((.......))))))))....))))...)).)).))(((((..(..(((((....)))))..)---...))))). ( -41.00)
>DroEre_CAF1 16492 110 + 1
UUAGUGGCCCCCGCGGAUCUGCUUUUGUUUUGAUGCCCGCGCCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUGAGUCCCAGCUUCUGCUGCUCC---AUGGGCACU
..((((.((((.(((((((.((((..((((..((((((((.......))))))))....))))......)))).))((((.....)))).))))).)....---..))))))) ( -38.20)
>DroYak_CAF1 17511 110 + 1
UUAGUAGCCCCCGCGGAUUUGCUUUUGUUUUGAUGCCCGCGCCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCU
..((.(((((.....(((((((((..((((..((((((((.......))))))))..............)))).)))).)))))(((((....)))))...---..))))))) ( -40.19)
>consensus
UUAGUGGCCCCCGCGGAUCUGCUUUUGUUUUGAUGCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC___AUGGGCUCU
......((((....(((((.((((..((((..((((((((.......))))))))....))))......)))).))........(((((....)))))))).....))))... (-36.34 = -36.42 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	19,064,321 – 19,064,434
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	95.68
Mean single sequence MFE	-40.56
Consensus MFE	-34.82
Energy contribution	-35.46
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.46
Structure conservation index	0.86
SVM decision value	2.75
SVM RNA-class probability	0.996784
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19064321 113 - 22224390
AGAGCCCAUCGUAGAGCAGCAGAAGCUGGGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCAACGGUGCGGGCAUCAAAACAAAAGCAGAUCCGCGGGGGCCACUAA
.(.((((.(((..((...((.((.((((((......))))))))..............(((((((((....).))))))))..........))...))..))))))))..... ( -40.10)
>DroSec_CAF1 16074 110 - 1
AGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGCAUCAAAACAAAAGCAGAUCCGCGGGGGCCACUAA
.((((....---(..(((((....)))))..)...))))(((((..............(((((((((....).))))))))..........((......))..)))))..... ( -41.50)
>DroSim_CAF1 18049 110 - 1
AGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGCAUCAAAACAAAAGCAGAUCCGCGGGGGCCACUAA
.((((....---(..(((((....)))))..)...))))(((((..............(((((((((....).))))))))..........((......))..)))))..... ( -41.50)
>DroEre_CAF1 16492 110 - 1
AGUGCCCAU---GGAGCAGCAGAAGCUGGGACUCAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGCGCGGGCAUCAAAACAAAAGCAGAUCCGCGGGGGCCACUAA
(((((((.(---(((...((.((.((((((......))))))))..............(((((((((....).))))))))..........))...))))...))).)))).. ( -40.00)
>DroYak_CAF1 17511 110 - 1
AGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGCGCGGGCAUCAAAACAAAAGCAAAUCCGCGGGGGCUACUAA
(((((((.(---((((((((....)))))......(((((......))..........(((((((((....).)))))))).........)))...))))...))))).)).. ( -39.70)
>consensus
AGAGCCCAU___GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGCAUCAAAACAAAAGCAGAUCCGCGGGGGCCACUAA
.((((((.....)).(((((....)))))......))))(((((..............(((((((((....).))))))))..........((......))..)))))..... (-34.82 = -35.46 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	19,064,355 – 19,064,451
Length	96
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	91.77
Mean single sequence MFE	-34.98
Consensus MFE	-33.10
Energy contribution	-33.90
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.95
SVM decision value	1.63
SVM RNA-class probability	0.968907
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19064355 96 + 22224390
GCCCGCACCGUUGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCCCAGCUUCUGCUGCUCUACGAUGGGCUCUACGUGGAAG--UAUC----CCAA
((((((.......)))))).........((((((.(((((.(....((...((((....))))..))....).))))).))))))...--....----.... ( -34.90)
>DroSec_CAF1 16108 95 + 1
GCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCUACGUGGAAGUGUAUC----CCAA
((((((.......)))))).........((((((.(((((((......))(((((....)))))...---...))))).)))))).........----.... ( -37.20)
>DroSim_CAF1 18083 95 + 1
GCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCUACGUGGAAGUGUAUC----CCAA
((((((.......)))))).........((((((.(((((((......))(((((....)))))...---...))))).)))))).........----.... ( -37.20)
>DroEre_CAF1 16526 93 + 1
GCCCGCGCCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUGAGUCCCAGCUUCUGCUGCUCC---AUGGGCACUACGUGGAAG--UAUC----CCAA
((((((.......))))))....(((...(((....(((.((((((.....))))))..)))..(((---(((.......)))))).)--))..----.))) ( -32.30)
>DroYak_CAF1 17545 97 + 1
GCCCGCGCCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC---AUGGGCUCUACAUGGAAG--UAUACCCCCGAA
((((((.......)))))).............((.(((((((......))(((((....)))))...---...))))).)).(((..(--....)..))).. ( -33.30)
>consensus
GCCCGCACCGUCGGCGGGCAUAAUUGAAUUACGUUGAGCCGAGCUAAGUCGCAGCUUCUGCUGCUCC___AUGGGCUCUACGUGGAAG__UAUC____CCAA
((((((.......)))))).........((((((.(((((.(........(((((....))))).......).))))).))))))................. (-33.10 = -33.90 +   0.80)

alignment

secondary structure

dotplot

Window 1

Location	19,064,355 – 19,064,451
Length	96
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	91.77
Mean single sequence MFE	-35.02
Consensus MFE	-29.55
Energy contribution	-29.99
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.84
SVM decision value	0.77
SVM RNA-class probability	0.846662
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19064355 96 - 22224390
UUGG----GAUA--CUUCCACGUAGAGCCCAUCGUAGAGCAGCAGAAGCUGGGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCAACGGUGCGGGC
...(----((..--..)))((((.(((((....((.(((((((....))))...))).))..))))).))))...........(((((((....).)))))) ( -32.90)
>DroSec_CAF1 16108 95 - 1
UUGG----GAUACACUUCCACGUAGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGC
...(----((......)))((((.(((((...---(..(((((....)))))..).......))))).))))...........(((((((....).)))))) ( -36.60)
>DroSim_CAF1 18083 95 - 1
UUGG----GAUACACUUCCACGUAGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGC
...(----((......)))((((.(((((...---(..(((((....)))))..).......))))).))))...........(((((((....).)))))) ( -36.60)
>DroEre_CAF1 16526 93 - 1
UUGG----GAUA--CUUCCACGUAGUGCCCAU---GGAGCAGCAGAAGCUGGGACUCAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGCGCGGGC
.(((----(.((--((.......)))))))).---.((((....((.((((.....)))))).))))................(((((((....).)))))) ( -31.60)
>DroYak_CAF1 17545 97 - 1
UUCGGGGGUAUA--CUUCCAUGUAGAGCCCAU---GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGCGCGGGC
...(((((....--)))))((((.(((((...---(..(((((....)))))..).......))))).))))...........(((((((....).)))))) ( -37.40)
>consensus
UUGG____GAUA__CUUCCACGUAGAGCCCAU___GGAGCAGCAGAAGCUGCGACUUAGCUCGGCUCAACGUAAUUCAAUUAUGCCCGCCGACGGUGCGGGC
...................((((.(((((.........(((((....)))))..........))))).))))...........(((((((....).)))))) (-29.55 = -29.99 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:21 2006