Locus 372

Sequence ID	X_DroMel_CAF1
Location	1,125,486 – 1,125,678
Length	192
Max. P	0.999721

overview

Window 8

Location	1,125,486 – 1,125,577
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	97.36
Mean single sequence MFE	-19.68
Consensus MFE	-17.90
Energy contribution	-18.50
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-3.07
Structure conservation index	0.91
SVM decision value	3.95
SVM RNA-class probability	0.999721
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1125486 91 + 22224390
AUAUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGUUCGUCUAUUCUUGGAGCAUCC
..(((((((......(((((......))))).((((((((((((((...........))))))))...))))))........))))))).. ( -21.50)
>DroSec_CAF1 22213 91 + 1
GCAUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGUUCGUCUAUUCUUGGAGCAUCC
..(((((((......(((((......))))).((((((((((((((...........))))))))...))))))........))))))).. ( -21.60)
>DroSim_CAF1 23563 91 + 1
GCAUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGUUCGUCUAUUCUUGGAGCAUCC
..(((((((......(((((......))))).((((((((((((((...........))))))))...))))))........))))))).. ( -21.60)
>DroEre_CAF1 23377 91 + 1
GCCUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGUUCGUCUAUUCUUGGCGCAUCC
(((............(((((......))))).((((((((((((((...........))))))))...))))))........)))...... ( -18.30)
>DroYak_CAF1 22955 91 + 1
GCCUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGCUCGUCUAUUCUUGGCGCAUCC
(((............(((((......))))).((((..((((((((...........)))))))).))))............)))...... ( -15.40)
>consensus
GCAUGCUCUUUUAAUUGUUAUAUAAUUAACAUGCGAACUGUUAUUAUAGUUUAUUAUUAAUAACAAUUGUUCGUCUAUUCUUGGAGCAUCC
...((((((......(((((......))))).((((((((((((((...........))))))))...))))))........))))))... (-17.90 = -18.50 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	1,125,486 – 1,125,577
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	97.36
Mean single sequence MFE	-18.10
Consensus MFE	-16.04
Energy contribution	-16.28
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.81
Structure conservation index	0.89
SVM decision value	3.31
SVM RNA-class probability	0.998970
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1125486 91 - 22224390
GGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAUAU
..((((((........(.(((((...((((((((...........)))))))))))))).(((((......))))).......)))))).. ( -19.30)
>DroSec_CAF1 22213 91 - 1
GGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAUGC
(.((((((........(.(((((...((((((((...........)))))))))))))).(((((......))))).......)))))).) ( -19.70)
>DroSim_CAF1 23563 91 - 1
GGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAUGC
(.((((((........(.(((((...((((((((...........)))))))))))))).(((((......))))).......)))))).) ( -19.70)
>DroEre_CAF1 23377 91 - 1
GGAUGCGCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAGGC
......(((.......(.(((((...((((((((...........)))))))))))))).(((((......)))))............))) ( -15.50)
>DroYak_CAF1 22955 91 - 1
GGAUGCGCCAAGAAUAGACGAGCAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAGGC
......(((............(((((((((((((...........))))))))))).)).(((((......)))))............))) ( -16.30)
>consensus
GGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAUUAAAAGAGCAUGC
...(((((........(.(((((...((((((((...........)))))))))))))).(((((......))))).......)))))... (-16.04 = -16.28 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	1,125,499 – 1,125,617
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	96.41
Mean single sequence MFE	-16.88
Consensus MFE	-14.84
Energy contribution	-15.08
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.40
Structure conservation index	0.88
SVM decision value	0.50
SVM RNA-class probability	0.760361
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1125499 118 - 22224390
UUGCCAAAAAAAAAGCACUGAAACGAAAUCAAAAACCGUCGGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
.(((.........((((((((..((...........)))))).))))............((((...((((((((...........)))))))))))))))(((((......))))).. ( -17.40)
>DroSec_CAF1 22226 116 - 1
UUGCCAAAA--AAAGCACUGAAACGAAAUCAAAAACCGUCGGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
.(((.....--..((((((((..((...........)))))).))))............((((...((((((((...........)))))))))))))))(((((......))))).. ( -17.40)
>DroSim_CAF1 23576 117 - 1
UUGCCAAAAA-AAAACACUGAAACGAAAUCAAAAACCGUCGGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
.(((......-.........................((((.....(.....)....))))...(((((((((((...........))))))))))).)))(((((......))))).. ( -14.40)
>DroEre_CAF1 23390 115 - 1
UUGCCAAA---AAAGCACUGAAUCGAAAUCAAAAACCGUCGGAUGCGCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
.(((....---...(((((((..((...........)))))).))).............((((...((((((((...........)))))))))))))))(((((......))))).. ( -17.30)
>DroYak_CAF1 22968 115 - 1
UUGCCAAA---AAAGCAAUGAAACGAAAUGAAAAACCGUCGGAUGCGCCAAGAAUAGACGAGCAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
((((....---...))))..................((((.....(.....)....)))).(((((((((((((...........))))))))))).)).(((((......))))).. ( -17.90)
>consensus
UUGCCAAAA__AAAGCACUGAAACGAAAUCAAAAACCGUCGGAUGCUCCAAGAAUAGACGAACAAUUGUUAUUAAUAAUAAACUAUAAUAACAGUUCGCAUGUUAAUUAUAUAACAAU
.(((..........(((((((..((...........)))))).))).............((((...((((((((...........)))))))))))))))(((((......))))).. (-14.84 = -15.08 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	1,125,577 – 1,125,678
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.41
Mean single sequence MFE	-18.05
Consensus MFE	-15.95
Energy contribution	-15.75
Covariance contribution	-0.20
Combinations/Pair	1.10
Mean z-score	-2.04
Structure conservation index	0.88
SVM decision value	1.72
SVM RNA-class probability	0.973788
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1125577 101 - 22224390
UCGGUGUUACGCUUUUUGAUCCAUUAAAUCAGACGGCAAACGCAGCACACAGC-----------AAAAUA--------UAUUGCCAAAAAAAAAGCACUGAAACGAAAUCAAAAACCGUC
((((((((..(((.((((((.......)))))).)))..............((-----------((....--------..)))).........))))))))................... ( -19.40)
>DroSec_CAF1 22304 99 - 1
UCGGUGUUAUGCUUUUUGAUCCAUUAAAUCAGACGGCAAACGCAGCACACAAC-----------GAAAUA--------UAUUGCCAAAA--AAAGCACUGAAACGAAAUCAAAAACCGUC
((((((((.((((.((((((.......)))))).))))...((((........-----------......--------..)))).....--..))))))))................... ( -18.09)
>DroSim_CAF1 23654 100 - 1
UCGGUGUUACGCUUUUUGAUCCAUUAAAUCAGACGGCAAACGCAGCACACAAC-----------GAAAUA--------UAUUGCCAAAAA-AAAACACUGAAACGAAAUCAAAAACCGUC
((((((((..(((.((((((.......)))))).)))....((((........-----------......--------..))))......-..))))))))................... ( -17.39)
>DroEre_CAF1 23468 100 - 1
UCGGUGUUACGCUUUUUGAUCCAUAAAAUCAGACGGCAAACGCAACACACAAA-----------AAAAUA------UAUAUUGCCAAA---AAAGCACUGAAUCGAAAUCAAAAACCGUC
((((((((..(((.((((((.......)))))).)))....((((........-----------......------....))))....---..))))))))................... ( -17.57)
>DroYak_CAF1 23046 117 - 1
UCGGUGUUACGCUUUUUGAUCCAUAAAAUCAGACGGCAAACGCAACACACACAACAACAACAACAAAAUAUAUAUGUAUAUUGCCAAA---AAAGCAAUGAAACGAAAUGAAAAACCGUC
((((((((..(((.((((((.......)))))).))).)))))...................................((((((....---...))))))...))).............. ( -17.80)
>consensus
UCGGUGUUACGCUUUUUGAUCCAUUAAAUCAGACGGCAAACGCAGCACACAAC___________AAAAUA________UAUUGCCAAAA__AAAGCACUGAAACGAAAUCAAAAACCGUC
((((((((..(((.((((((.......)))))).)))....((((...................................)))).........))))))))................... (-15.95 = -15.75 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:51 2006