Locus 2309

Sequence ID X_DroMel_CAF1
Location 6,237,765 – 6,237,917
Length 152
Max. P 0.999578
window3740 window3741 window3742

overview

Window 0

Location 6,237,765 – 6,237,877
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.38
Mean single sequence MFE -24.69
Consensus MFE -18.47
Energy contribution -19.07
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.55
Structure conservation index 0.75
SVM decision value 1.44
SVM RNA-class probability 0.953730
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6237765 112 + 22224390
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCAAACGCCCACCCAC--------UAUCCACAUCCCAGCCACAAUCGGCCCACUAUUGGCAUCAACACGAUGCCACCGACACU
........(((......)))....(((((...(((.......)))........--------.............(((......))))))))..(((((((.....)))))))........ ( -27.50)
>DroSec_CAF1 10739 111 + 1
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCACCCGG-CACCCAC--------UAUCCACAUCCCGGCCACAAUCCACCCACUAUUGGCAUCAACACGAUGCCACCGACACU
........(((......))).....(((((.((.((.....((((-.......--------..........)))))).)).))))).......(((((((.....)))))))........ ( -27.33)
>DroSim_CAF1 13591 111 + 1
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCACCCGU-CACCCAC--------UAUCCACAUCCCAGCCACAAUCCACCCACUAUUGGCAUCAACACGAUGCCACCGACACU
........(((......)))....(((((...((((.....))))-...))))--------)...............................(((((((.....)))))))........ ( -25.20)
>DroEre_CAF1 5484 103 + 1
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCACCCAC----------------GAUCCACAUCUCAGCCAGCAUCC-CCCACUAUUGGCAUCAACACGAUGCCACCGACACU
........(((......)))....(((((.((((((.....))..----------------(((....))).......))))..-.)))))..(((((((.....)))))))........ ( -25.00)
>DroYak_CAF1 18503 118 + 1
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCACCCGC-CGCCUACUAUCCUUCUAUCCACAAGCCAGCCACAAUCC-CCCACUAUUGACAUCAACACGAUGCCACCGACACU
........(((......))).((..(((((..((((.....))))-.(....)..........)))))..))............-........((.((((.....)))).))........ ( -18.40)
>consensus
UUUAACAAGCAGAAUAAUGCAGCAAGUGGAAUGCGGACCACCCGC_CACCCAC________UAUCCACAUCCCAGCCACAAUCC_CCCACUAUUGGCAUCAACACGAUGCCACCGACACU
........(((......))).....((((.(((.(((..........................))).))).....))))..............(((((((.....)))))))........ (-18.47 = -19.07 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,237,765 – 6,237,877
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.38
Mean single sequence MFE -42.86
Consensus MFE -36.50
Energy contribution -38.06
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -3.24
Structure conservation index 0.85
SVM decision value 3.74
SVM RNA-class probability 0.999578
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6237765 112 - 22224390
AGUGUCGGUGGCAUCGUGUUGAUGCCAAUAGUGGGCCGAUUGUGGCUGGGAUGUGGAUA--------GUGGGUGGGCGUUUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
........(((((((.....))))))).(((..(((.((.((..((((((((((((((.--------..(.(....).)...))))))))))))...))..))....)).)))..))).. ( -44.20)
>DroSec_CAF1 10739 111 - 1
AGUGUCGGUGGCAUCGUGUUGAUGCCAAUAGUGGGUGGAUUGUGGCCGGGAUGUGGAUA--------GUGGGUG-CCGGGUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
........(((((((.....))))))).(((..((..((.((..((.((((((((((((--------.(.(...-.).).).)))))))))))....))..))....))..))..))).. ( -43.80)
>DroSim_CAF1 13591 111 - 1
AGUGUCGGUGGCAUCGUGUUGAUGCCAAUAGUGGGUGGAUUGUGGCUGGGAUGUGGAUA--------GUGGGUG-ACGGGUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
........(((((((.....))))))).(((..((..((.((..(((((((((((((((--------.(.(...-.).).).))))))))))))...))..))....))..))..))).. ( -48.00)
>DroEre_CAF1 5484 103 - 1
AGUGUCGGUGGCAUCGUGUUGAUGCCAAUAGUGGG-GGAUGCUGGCUGAGAUGUGGAUC----------------GUGGGUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
........(((((((.....)))))))..((..((-((((((.(((((..(((((((((----------------(....))))))))))..))...)))))))).)))..))....... ( -37.70)
>DroYak_CAF1 18503 118 - 1
AGUGUCGGUGGCAUCGUGUUGAUGUCAAUAGUGGG-GGAUUGUGGCUGGCUUGUGGAUAGAAGGAUAGUAGGCG-GCGGGUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
...((((((((((((.....)))))).(((((...-..))))).)))))).....(((((.((((((((..(((-((((((((........)))))))))))))))))))..)))))... ( -40.60)
>consensus
AGUGUCGGUGGCAUCGUGUUGAUGCCAAUAGUGGG_GGAUUGUGGCUGGGAUGUGGAUA________GUGGGUG_GCGGGUGGUCCGCAUUCCACUUGCUGCAUUAUUCUGCUUGUUAAA
........(((((((.....))))))).(((..((((((.((((((((((((((((((........................))))))))))))...))))))....))))))..))).. (-36.50 = -38.06 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,237,805 – 6,237,917
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.03
Mean single sequence MFE -21.15
Consensus MFE -19.10
Energy contribution -19.54
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.95
Structure conservation index 0.90
SVM decision value 1.94
SVM RNA-class probability 0.983403
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6237805 112 + 22224390
AACGCCCACCCAC--------UAUCCACAUCCCAGCCACAAUCGGCCCACUAUUGGCAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUUC
..((.........--------.............(((......))).......(((((((.....))))))).))...((((((.(((..((((.....))))))).))))))....... ( -23.90)
>DroSec_CAF1 10779 111 + 1
CCCGG-CACCCAC--------UAUCCACAUCCCGGCCACAAUCCACCCACUAUUGGCAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUUC
.((((-.......--------..........))))......(((.........(((((((.....))))))).......(((((.(((..((((.....))))))).))))))))..... ( -23.43)
>DroSim_CAF1 13631 111 + 1
CCCGU-CACCCAC--------UAUCCACAUCCCAGCCACAAUCCACCCACUAUUGGCAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUUC
.....-.......--------........(((..((((...............(((((((.....))))))).(((((..((......)).)))))..........))))..)))..... ( -22.30)
>DroEre_CAF1 5524 103 + 1
CCCAC----------------GAUCCACAUCUCAGCCAGCAUCC-CCCACUAUUGGCAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUUC
.....----------------........(((..(((((.....-........(((((((.....))))))).(((((..((......)).))))).........)))))..)))..... ( -21.40)
>DroYak_CAF1 18543 118 + 1
CCCGC-CGCCUACUAUCCUUCUAUCCACAAGCCAGCCACAAUCC-CCCACUAUUGACAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUCC
.....-.........(((((..........(((((.........-........((.((((.....)))).)).(((((..((......)).))))).........))))))))))..... ( -14.70)
>consensus
CCCGC_CACCCAC________UAUCCACAUCCCAGCCACAAUCC_CCCACUAUUGGCAUCAACACGAUGCCACCGACACUUGCCUGUUCAUUGUUGUUUAUAAAAUUGGCAAGGAAUUUC
.............................(((..((((...............(((((((.....))))))).(((((..((......)).)))))..........))))..)))..... (-19.10 = -19.54 +   0.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:13 2006