Locus 80

Sequence ID	2R_DroMel_CAF1
Location	1,334,010 – 1,334,170
Length	160
Max. P	0.974704

overview

Window 2

Location	1,334,010 – 1,334,130
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-30.26
Consensus MFE	-29.06
Energy contribution	-29.10
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.96
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1334010 120 + 20766785
CGUGGCUAGCUCGUUUGUUACGUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((((((......)))).(((((.(((....))).)).((((..((.....))...))))..)))....)))))....((((((.....))))))(((......))).......... ( -30.60)
>DroSec_CAF1 52540 120 + 1
CGUGGCUAGCUCAUUUGUUACGUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((((((......)))).(((((.(((....))).)).((((..((.....))...))))..)))....)))))....((((((.....))))))(((......))).......... ( -30.60)
>DroSim_CAF1 30695 120 + 1
CGUGGCUAGCUCGUUUGUUACCUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((((((......))))........((....))((((.((((..((.....))...))))...))))..)))))....((((((.....))))))(((......))).......... ( -30.10)
>DroEre_CAF1 34034 120 + 1
CGUGGCCAGCUCGUUUGUUACGUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGUCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((......(((..(((((.(((.(((....))).))).....)))))..)))...(((...)))....)))))....((((((.....))))))(((......))).......... ( -29.40)
>DroYak_CAF1 19887 120 + 1
CGUGGCUAGCUCGUUUGUUACGUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((((((......)))).(((((.(((....))).)).((((..((.....))...))))..)))....)))))....((((((.....))))))(((......))).......... ( -30.60)
>consensus
CGUGGCUAGCUCGUUUGUUACGUUACUCGCUUAUGCGUGUACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAG
.(((((((((......))))........((....))((((.((((..((.....))...))))...))))..)))))....((((((.....))))))(((......))).......... (-29.06 = -29.10 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	1,334,010 – 1,334,130
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-33.76
Consensus MFE	-33.48
Energy contribution	-33.52
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.99
SVM decision value	1.74
SVM RNA-class probability	0.974704
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1334010 120 - 20766785
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAACGUAACAAACGAGCUAGCCACG
..(((....)))..........((((((.....))))))....(((((((((((...((((.((((.....))))))))...)))))).(((..((..........))..))).))))). ( -35.20)
>DroSec_CAF1 52540 120 - 1
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAACGUAACAAAUGAGCUAGCCACG
..(((....)))..........((((((.....))))))....(((((((((((...((((.((((.....))))))))...)))))).(((..((..........))..))).))))). ( -33.70)
>DroSim_CAF1 30695 120 - 1
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAAGGUAACAAACGAGCUAGCCACG
..(((....)))..........((((((.....))))))....(((((((((((...((((.((((.....))))))))...)))))).(((..((..(....)..))..))).))))). ( -36.00)
>DroEre_CAF1 34034 120 - 1
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGACGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAACGUAACAAACGAGCUGGCCACG
..((......((((((((((((((((((.....)))))...((((((((...(((...)))..))))))))...)))(((((.(((....))).)).)))))))))..))))..)).... ( -28.70)
>DroYak_CAF1 19887 120 - 1
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAACGUAACAAACGAGCUAGCCACG
..(((....)))..........((((((.....))))))....(((((((((((...((((.((((.....))))))))...)))))).(((..((..........))..))).))))). ( -35.20)
>consensus
CUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGUACACGCAUAAGCGAGUAACGUAACAAACGAGCUAGCCACG
..(((....)))..........((((((.....))))))....(((((((((((...((((.((((.....))))))))...)))))).(((..((..........))..))).))))). (-33.48 = -33.52 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	1,334,050 – 1,334,170
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-23.60
Consensus MFE	-22.92
Energy contribution	-22.76
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.97
SVM decision value	1.40
SVM RNA-class probability	0.950361
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1334050 120 + 20766785
ACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGACAUUAUUAUCACACACACGAUAAACUAAGAGA
.((((..((.....))...))))..(((...(((.......((((((.....))))))(((......))).........))).))).......(((((........)))))......... ( -23.30)
>DroSec_CAF1 52580 120 + 1
ACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGCCAUUAUUAUCACACACACGAUAAACUAAGAGA
..(((.(((........))).....(((...(((.......((((((.....))))))(((......))).........))).))))))....(((((........)))))......... ( -23.40)
>DroSim_CAF1 30735 120 + 1
ACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGCCAUUAUUAUCACACACACGAUAAACUAAGAGA
..(((.(((........))).....(((...(((.......((((((.....))))))(((......))).........))).))))))....(((((........)))))......... ( -23.40)
>DroEre_CAF1 34074 120 + 1
ACGGCUCGUAAAUAACAACGUCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGACAUUAUUAUCACACACACGAUAAACUAAGAGA
....(((............(((((...(...(((.......((((((.....))))))(((......)))......)))...).)))))....(((((........))))).....))). ( -24.00)
>DroYak_CAF1 19927 120 + 1
ACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGUCAUUAUUAUCACACACACGAUAAACUAAGAGA
.((((..((.....))...))))..(((((.(((.......((((((.....))))))(((......))).........))).)).)))....(((((........)))))......... ( -23.90)
>consensus
ACGGCUCGUAAAUAACAACGCCGAAGACACAUGCCACUUUAUGUCAAUUAUUUUGACAGCUAACAAGAGCAAAUAUGCAGCAGGUCGACAUUAUUAUCACACACACGAUAAACUAAGAGA
.((((..((.....))...))))..(((...(((.......((((((.....))))))(((......))).........))).))).......(((((........)))))......... (-22.92 = -22.76 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	1,334,050 – 1,334,170
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-30.84
Consensus MFE	-29.10
Energy contribution	-29.42
Covariance contribution	0.32
Combinations/Pair	1.03
Mean z-score	-1.34
Structure conservation index	0.94
SVM decision value	0.32
SVM RNA-class probability	0.687524
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1334050 120 - 20766785
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGUCGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGU
.............((.((.((((((((((((((((((.(((..(......(((......)))((((((.....))))))....)..))).).....)))))))))))).))))).)))). ( -31.20)
>DroSec_CAF1 52580 120 - 1
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGGCGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGU
............(((((...((((((((..(((.(((((((..(......(((......)))((((((.....))))))....)..))).).))).)))..)))))))).)))))..... ( -30.10)
>DroSim_CAF1 30735 120 - 1
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGGCGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGU
............(((((...((((((((..(((.(((((((..(......(((......)))((((((.....))))))....)..))).).))).)))..)))))))).)))))..... ( -30.10)
>DroEre_CAF1 34074 120 - 1
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGUCGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGACGUUGUUAUUUACGAGCCGU
.............((.((.((((((((((((((((((.(((..(......(((......)))((((((.....))))))....)..))).).....)))))))))))).))))).)))). ( -31.80)
>DroYak_CAF1 19927 120 - 1
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGACGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGU
............(((((...((((((((..(((.(((((((..(......(((......)))((((((.....))))))....)..))).).))).)))..)))))))).)))))..... ( -31.00)
>consensus
UCUCUUAGUUUAUCGUGUGUGUGAUAAUAAUGGCGACCUGCUGCAUAUUUGCUCUUGUUAGCUGUCAAAAUAAUUGACAUAAAGUGGCAUGUGUCUUCGGCGUUGUUAUUUACGAGCCGU
............(((((...((((((((..(((.(((((((..(......(((......)))((((((.....))))))....)..))).).))).)))..)))))))).)))))..... (-29.10 = -29.42 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:10 2006