Locus 1887

Sequence ID 2R_DroMel_CAF1
Location 7,110,768 – 7,110,902
Length 134
Max. P 0.899602
window3123 window3124

overview

Window 3

Location 7,110,768 – 7,110,862
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.92
Mean single sequence MFE -16.04
Consensus MFE -7.06
Energy contribution -7.66
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.44
SVM decision value 1.01
SVM RNA-class probability 0.899602
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7110768 94 - 20766785
ACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACAUCCUGACUCAUCUUCGUAAUUACG-----------------UUU--A-------CCUAACAACCUUUGAAAUACAUU
.((((((((((.((((((((....))))))))((((.........)))).........))))))).(-----------------((.--.-------...))).....)))......... ( -13.10)
>DroSec_CAF1 138721 103 - 1
AUAAUAAUUACUAGAUUUCGUAUCGGAAAUCUUCAGUAAAACUUGCUGAUUCAUCUUCGUAAUUACA-----------------GCUGUAUCUCAAUACUAACAACCUUUGAAAUACAUU
....(((((((.(((((((......)))))))((((((.....)))))).........)))))))..-----------------..(((((.((((............)))).))))).. ( -20.80)
>DroSim_CAF1 138742 94 - 1
AUAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACUUGCUGAUUCAUCUUCGUAAUUACA-----------------GCUGUAUCUCAAUACUAACAACCUUUG---------
....(((((((.((((((((....))))))))((((((.....)))))).........)))))))..-----------------...((((....))))............--------- ( -16.60)
>DroEre_CAF1 143898 120 - 1
ACAAUAAUUACUAGUUUUCUUAUCGGAAAUCUUCAGCAAAAAAUACCGACUCAUCUUGGCAAUUACAUUUGGAAGCACAUCGUGGCUGUAUCUCAACACUAACAACAUUUGAAAUACAUG
.......((((..((((((.....))))))((((...........((((......))))(((......)))))))......)))).(((((.((((............)))).))))).. ( -11.60)
>DroYak_CAF1 148061 108 - 1
ACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAUAACAUCCCAACUCAUCUUCGCA------------AGCACAUCGUAGCUGUAUCUCAACACUAACAGCAGUUGAAACAUAUU
........((((((((((((....))))))))..))))........(((((......(...------------.).........(((((............))))))))))......... ( -18.10)
>consensus
ACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACAUCCUGACUCAUCUUCGUAAUUACA_________________GCUGUAUCUCAACACUAACAACCUUUGAAAUACAUU
.......((((((((((((......)))))))..)))))................................................................................. ( -7.06 =  -7.66 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,110,795 – 7,110,902
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.98
Mean single sequence MFE -19.60
Consensus MFE -7.56
Energy contribution -9.72
Covariance contribution 2.16
Combinations/Pair 1.05
Mean z-score -2.28
Structure conservation index 0.39
SVM decision value 0.82
SVM RNA-class probability 0.858423
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7110795 107 - 20766785
UCAAGUGCAUUACAACAACGGAAAACUCUUUUCCAUGGAUACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACAUCCUGACUCAUCUUCGUAAUUACG-------------
....(((.(((((......(((((.....)))))..((((.......(((((((((((((....))))))))..)))))...))))............)))))))).------------- ( -20.90)
>DroSec_CAF1 138757 107 - 1
UCAAGUGCAUUACAACAACGGAAAACUCUUUUCCGUGGAUAUAAUAAUUACUAGAUUUCGUAUCGGAAAUCUUCAGUAAAACUUGCUGAUUCAUCUUCGUAAUUACA-------------
....(((.(((((....(((((((.....)))))))((((............(((((((......)))))))((((((.....))))))...))))..)))))))).------------- ( -25.00)
>DroSim_CAF1 138769 107 - 1
UCAAGUGCAUUACAACAGCGGAAAACUCUUUUCCAUGGAUAUAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACUUGCUGAUUCAUCUUCGUAAUUACA-------------
....(((.(((((......(((((.....)))))(((((.............((((((((....))))))))((((((.....)))))))))))....)))))))).------------- ( -22.70)
>DroEre_CAF1 143938 119 - 1
UCAAGUGCAUUUCAACUUCGAAAAACUC-UAGCAACAGAUACAAUAAUUACUAGUUUUCUUAUCGGAAAUCUUCAGCAAAAAAUACCGACUCAUCUUGGCAAUUACAUUUGGAAGCACAU
....((((.((((((.(((((......(-(((..................))))........)))))..................((((......)))).........)))))))))).. ( -15.51)
>DroYak_CAF1 148101 107 - 1
UCAAGUGCAUUACAACUUAGAAAAUCCC-AACCAACAGAUACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAUAACAUCCCAACUCAUCUUCGCA------------AGCACAU
....((((...............(((..-........)))........((((((((((((....))))))))..)))).......................------------.)))).. ( -13.90)
>consensus
UCAAGUGCAUUACAACAACGGAAAACUCUUUUCCAUGGAUACAAUAAUUACUAGAUUUCUUAUCGGAAAUCUUCAGUAAAACAUCCUGACUCAUCUUCGUAAUUACA_____________
.....(((...........(((((.....))))).............((((((((((((......)))))))..)))))...................)))................... ( -7.56 =  -9.72 +   2.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:33 2006