Locus 324

Sequence ID	2R_DroMel_CAF1
Location	2,127,939 – 2,128,081
Length	142
Max. P	0.999770

overview

Window 9

Location	2,127,939 – 2,128,041
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	98.82
Mean single sequence MFE	-20.68
Consensus MFE	-20.20
Energy contribution	-20.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.82
Structure conservation index	0.98
SVM decision value	4.03
SVM RNA-class probability	0.999767
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2127939 102 + 20766785
GCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACGAACAAUACCAAUUCGAACACUGCCAACAAUUC
........((((((.............((((......))))......(((.((((....)))).))).((((.........))))....))))))....... ( -20.80)
>DroSec_CAF1 106610 102 + 1
UCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACGAACAAUACCAAUUCGAACACUGCCAACAAUUC
........((((((.............((((......))))......(((.((((....)))).))).((((.........))))....))))))....... ( -20.80)
>DroSim_CAF1 110563 102 + 1
GCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACGAACAAUACCAAUUCGAACACUGCCAACAAUUC
........((((((.............((((......))))......(((.((((....)))).))).((((.........))))....))))))....... ( -20.80)
>DroEre_CAF1 105330 102 + 1
GCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACAAACAAUACCAAUUCGAACACUGCCAACAAUUC
........((((((.............((((......))))......(((.((((....)))).)))......................))))))....... ( -20.20)
>DroYak_CAF1 107666 102 + 1
GCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACGAACAAUACCAAUUUGAACACUGCCAACAAUUC
........((((((...((((......((((......))))......(((.((((....)))).)))..............))))....))))))....... ( -20.80)
>consensus
GCCACCACUGGCAGCCACAAACAAUAACAGUACGAACACUGCCACUCAGCCGCCGCCAUUGGCAGCUACGAACAAUACCAAUUCGAACACUGCCAACAAUUC
........((((((.............((((......))))......(((.((((....)))).)))......................))))))....... (-20.20 = -20.20 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	2,127,939 – 2,128,041
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	98.82
Mean single sequence MFE	-42.44
Consensus MFE	-41.54
Energy contribution	-41.62
Covariance contribution	0.08
Combinations/Pair	1.03
Mean z-score	-4.68
Structure conservation index	0.98
SVM decision value	3.53
SVM RNA-class probability	0.999342
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2127939 102 - 20766785
GAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGC
.....(((((((((...(((((.......)))))..)))))))))((((((.((..((((((((((....))))))))))....)).))))))......... ( -43.00)
>DroSec_CAF1 106610 102 - 1
GAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGA
.....(((((((((...(((((.......)))))..)))))))))((((((.((..((((((((((....))))))))))....)).))))))......... ( -43.00)
>DroSim_CAF1 110563 102 - 1
GAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGC
.....(((((((((...(((((.......)))))..)))))))))((((((.((..((((((((((....))))))))))....)).))))))......... ( -43.00)
>DroEre_CAF1 105330 102 - 1
GAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUUGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGC
.....(((((((((...(((((.......)))))..)))))))))((((((.((..((((((((((....))))))))))....)).))))))......... ( -40.90)
>DroYak_CAF1 107666 102 - 1
GAAUUGUUGGCAGUGUUCAAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGC
((((...((.((((......)))).))..))))...((..(((.(((((((.((..((((((((((....))))))))))....)).))))))).)))..)) ( -42.30)
>consensus
GAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUUAUUGUUUGUGGCUGCCAGUGGUGGC
.....(((((((((...(((((.......)))))..)))))))))((((((.((..((((((((((....))))))))))....)).))))))......... (-41.54 = -41.62 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	2,127,964 – 2,128,081
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	98.97
Mean single sequence MFE	-45.06
Consensus MFE	-44.90
Energy contribution	-44.98
Covariance contribution	0.08
Combinations/Pair	1.03
Mean z-score	-4.17
Structure conservation index	1.00
SVM decision value	4.04
SVM RNA-class probability	0.999770
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2127964 117 - 20766785
AUUAUUCGAGGCAUUAUGGUUGAUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.((((...((((((((..(((((.((((..(..((((((((...(((((.......)))))..))))))))..))))).))).))..)))))))))))).)))) ( -47.30)
>DroSec_CAF1 106635 117 - 1
AUUAUUCGAGGCAUUAUGGUUGUUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.(((((....((((((..(((((.((((..(..((((((((...(((((.......)))))..))))))))..))))).))).))..)))))).))))).)))) ( -46.50)
>DroSim_CAF1 110588 117 - 1
AUUAUUCGAGGCAUUAUGGUUGUUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.(((((....((((((..(((((.((((..(..((((((((...(((((.......)))))..))))))))..))))).))).))..)))))).))))).)))) ( -46.50)
>DroEre_CAF1 105355 117 - 1
AUUAUUCGAGGCAUUAUGGUUGUUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUUGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.(((((....((((((..(((((.((((..(..((((((((...(((((.......)))))..))))))))..))))).))).))..)))))).))))).)))) ( -44.40)
>DroYak_CAF1 107691 117 - 1
AUUAUUCGAGGCAUUAUGGUUGUUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCAAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.(((((....((((((..(((((.((((..(..((((((((...(.(((.......))).)..))))))))..))))).))).))..)))))).))))).)))) ( -40.60)
>consensus
AUUAUUCGAGGCAUUAUGGUUGUUACUGUUGCUGGCAGUCGAAUUGUUGGCAGUGUUCGAAUUGGUAUUGUUCGUAGCUGCCAAUGGCGGCGGCUGAGUGGCAGUGUUCGUACUGUU
.........((((.(((((....((((((..(((((.((((..(..((((((((...(((((.......)))))..))))))))..))))).))).))..)))))).))))).)))) (-44.90 = -44.98 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:34 2006