Locus 8212

Sequence ID 3R_DroMel_CAF1
Location 22,041,096 – 22,041,241
Length 145
Max. P 0.666598
window13222 window13223

overview

Window 2

Location 22,041,096 – 22,041,209
Length 113
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 93.57
Mean single sequence MFE -23.97
Consensus MFE -18.40
Energy contribution -19.12
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -1.81
Structure conservation index 0.77
SVM decision value 0.28
SVM RNA-class probability 0.666598
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22041096 113 + 27905053
UUGGUUGUAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACCGUUUUCCACAGCCAACUGGCUG-UGUGGAAACUCUUAGUGUGUAAUUUUAUGACCAGUUUAUA
(((((..(((........((((((.....((.(((....))).))......(((((((((((((....)))))-)).))))))..)))))).......)))..)))))...... ( -30.06)
>DroSec_CAF1 39172 111 + 1
UUGGUUGCAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACCGUUUC---CAGCCAACUGGCUGAUGUGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUA
(((((((((.((..((((....)))))).))))).(((((....((((((......---(((((....)))))..(.(....).).......)))))).)))))))))...... ( -21.90)
>DroSim_CAF1 31689 111 + 1
UUGGUUGCAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACCGUUUC---CAGCCAACUGGCUGAUGGGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUA
(((((((((.((..((((....)))))).))))).(((((....((((((......---(((((....)))))..(((....))).......)))))).)))))))))...... ( -25.20)
>DroEre_CAF1 33426 110 + 1
UUGGUUGUAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACCGUUUC---UAGCCAACUGGCUG-UGAGGAAACUCUUAGUAUGUAAUUUCAUGACCAGUUUAUA
((((((........((((....))))..(((.((((((((((..............---(((((....)))))-.(((....)))..)))))).)))).)))))))))...... ( -23.10)
>DroYak_CAF1 41115 110 + 1
UUGGUUGUAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACAGUUUC---CAGCCAACUGGCGG-UGGGUAAACUCAUAGUAUGUAUUUUUCUGACCAGUUUAUA
((((((....(((((....))))).((((((((.......................---..(((....))).(-((((....)))))....))))))))...))))))...... ( -19.60)
>consensus
UUGGUUGUAAUUAAUGUUCAUUAACAAAAUGCAAUUCAUAUUCCAAUUACCGUUUC___CAGCCAACUGGCUG_UGGGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUA
(((((((((.((..((((....)))))).))))).(((((....((((((.........(((((....)))))..(((....))).......)))))).)))))))))...... (-18.40 = -19.12 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,041,136 – 22,041,241
Length 105
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 89.57
Mean single sequence MFE -25.52
Consensus MFE -17.88
Energy contribution -18.44
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.70
SVM decision value 0.03
SVM RNA-class probability 0.548583
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22041136 105 + 27905053
UUCCAAUUACCGUUUUCCACAGCCAACUGGCUG-UGUGGAAACUCUUAGUGUGUAAUUUUAUGACCAGUUUAUAUCGAACC--------AAGUCGGUUGUUACAAAACUGAUUU
...........(((((((((((((....)))))-)).))))))..(((((.((((((....((((..((((.....)))).--------..))))...))))))..)))))... ( -31.20)
>DroSec_CAF1 39212 103 + 1
UUCCAAUUACCGUUUC---CAGCCAACUGGCUGAUGUGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUAUCGAACC--------AAGUCGGUUGUUACAAAACUGAUUU
...........(((((---(((((....))).....)))))))..(((((.((((((....((((..((((.....)))).--------..))))...))))))..)))))... ( -23.00)
>DroSim_CAF1 31729 103 + 1
UUCCAAUUACCGUUUC---CAGCCAACUGGCUGAUGGGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUAUCGAACC--------AAGUCGGUUGUUACAAAACUGAUUU
................---(((((....)))))..(((....)))(((((.((((((....((((..((((.....)))).--------..))))...))))))..)))))... ( -24.40)
>DroEre_CAF1 33466 110 + 1
UUCCAAUUACCGUUUC---UAGCCAACUGGCUG-UGAGGAAACUCUUAGUAUGUAAUUUCAUGACCAGUUUAUAUCGAUCCAAGUCGGUAAGUCGGUUGUUACAAAACUGAUUU
................---.....(((((((((-.(((....))).)))((((......)))).))))))..(((((((....)))))))((((((((.......)))))))). ( -26.70)
>DroYak_CAF1 41155 103 + 1
UUCCAAUUACAGUUUC---CAGCCAACUGGCGG-UGGGUAAACUCAUAGUAUGUAUUUUUCUGACCAGUUUAUAUCGCAACA-------AAGUCGGUUGUUACAAAACUGAUUU
.........((((((.---(((((.(((.((((-(..(((((((..(((...........)))...))))))))))))....-------.))).))))).....)))))).... ( -22.30)
>consensus
UUCCAAUUACCGUUUC___CAGCCAACUGGCUG_UGGGGAAACUCUUAGUAUGUAAUUUUAUGACCAGUUUAUAUCGAACC________AAGUCGGUUGUUACAAAACUGAUUU
....((((((.........(((((....)))))..(((....))).......))))))...............................(((((((((.......))))))))) (-17.88 = -18.44 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:32 2006