Locus 6478

Sequence ID 3L_DroMel_CAF1
Location 17,248,362 – 17,248,586
Length 224
Max. P 0.993727
window10441 window10442 window10443

overview

Window 1

Location 17,248,362 – 17,248,466
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.16
Mean single sequence MFE -40.22
Consensus MFE -28.71
Energy contribution -28.95
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -1.89
Structure conservation index 0.71
SVM decision value 0.40
SVM RNA-class probability 0.720295
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17248362 104 - 23771897
CGCCAUCAAGUGGCAUCC-------UUCGCAUCCU---------GCAGCAUCCUAGGAUAGCGAACUUGGGCCGAGUGGCAGUAAGCUACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
.(((((....((((....-------((((((((((---------(........)))))).))))).....)))).)))))..((((((.((((((.....)))))).))))))....... ( -38.70)
>DroSec_CAF1 132148 104 - 1
CGCCAUCAAGUGGCAUCC-------UUCGCAUCCU---------GCAGCAACCGAGGAUGGCGAAGUCGGGCCGAGUUGCAGUAAGCUACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
.(((((...)))))...(-------((((((((((---------..........))))).))))))...(.(((((...((((...(.....).))))..))))).)............. ( -33.80)
>DroSim_CAF1 126969 104 - 1
CGCCAUCAAGUGGCAUCC-------UUCGCAUCCU---------GCAGCAACCGAGGAUGGCGAAGUCGGGCCGAGUGGCAGUAAGCUACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
.(((((....((((...(-------((((((((((---------..........))))).))))))....)))).)))))..((((((.((((((.....)))))).))))))....... ( -40.30)
>DroEre_CAF1 135392 111 - 1
CGCCAUCAAGUGGCACCCACCGCCAUCCGCAUCCU---------CGAGCUUCCGAGGAUGGCGAAGCCGGCCCGAGUGGCAGUAAGCUACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
((((.....(((((.......)))))....(((((---------((......)))))))))))((((..(((((((...((((...(.....).))))..))))))).))))........ ( -45.90)
>DroYak_CAF1 138979 120 - 1
CGCCAUCAAGUGGCAUCCACCUCCGUCCGCAUCUCCCAGGAAGACGAGCUCCCAAGGAAGGCGAAGUCAGGCCGAGUGGCAGUAAGCCACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
.(((((...)))))..........((((((...(((..((.((.....)).))..)))..))((..((((..((((((((.....))))))))..))))..))))))............. ( -42.40)
>consensus
CGCCAUCAAGUGGCAUCC_______UUCGCAUCCU_________GCAGCAACCGAGGAUGGCGAAGUCGGGCCGAGUGGCAGUAAGCUACUUGAGCUGAUCUCGGGCAGCUUAAACUUUU
.(((((...))))).(((..........(((((((...................))))).))((.(((((.(((((((((.....)))))))).)))))).))))).............. (-28.71 = -28.95 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,248,438 – 17,248,546
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.86
Mean single sequence MFE -23.95
Consensus MFE -21.72
Energy contribution -21.56
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.91
SVM decision value 2.42
SVM RNA-class probability 0.993727
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17248438 108 - 23771897
CCUGGAUGCUUGUCAUUGAAACAAAUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAUCCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCAUCC-------UUCGCAUCCU-----
...((((((.................((.(((.....)))..........................((((....).)))))(((((...)))))....-------...)))))).----- ( -22.00)
>DroSec_CAF1 132224 108 - 1
CCUGGAUGCUUGUCAUUGAAACAAGUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAGUCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCAUCC-------UUCGCAUCCU-----
...(((((((((.(.((((.....(((((........)))))............)))).).))).(((((....).)))).(((((...)))))....-------...)))))).----- ( -24.63)
>DroSim_CAF1 127045 108 - 1
CCUGGAUGCUUGUCAUUGAAACAAAUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAGCCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCAUCC-------UUCGCAUCCU-----
...((((((.................((.(((.....)))..........................((((....).)))))(((((...)))))....-------...)))))).----- ( -22.00)
>DroEre_CAF1 135468 115 - 1
CCCGGAUGCAUGUCAUUGAAACAAAUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAGCCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCACCCACCGCCAUCCGCAUCCU-----
...((((((......((((......((((........))))..................((....(((((....).)))).))..))))(((((.......)))))..)))))).----- ( -24.10)
>DroYak_CAF1 139059 120 - 1
CCUGGAUGCCUGUCAUUGAAACAAAUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAGCCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCAUCCACCUCCGUCCGCAUCUCCCAGG
(((((.(((.((.((((......))))))))).((.((((.........................(((((....).)))).(((((...)))))..............)))).))))))) ( -27.00)
>consensus
CCUGGAUGCUUGUCAUUGAAACAAAUGCAGCACGAAAUGCACCCAAAACCCCAAUCAAAGCCAAAUUACCUAACGAGUAGCGCCAUCAAGUGGCAUCC_______UUCGCAUCCU_____
...((((((.................((.(((.....)))..........................((((....).)))))(((((...)))))..............))))))...... (-21.72 = -21.56 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,248,466 – 17,248,586
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -34.28
Consensus MFE -32.94
Energy contribution -32.86
Covariance contribution -0.08
Combinations/Pair 1.08
Mean z-score -1.19
Structure conservation index 0.96
SVM decision value 0.54
SVM RNA-class probability 0.776170
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17248466 120 + 23771897
CUACUCGUUAGGUAAUUUGGAUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCAUUUGUUUCAAUGACAAGCAUCCAGGAAAAUCAAAGCUGUGGACUCUGCAAAGUUUCUUGGCUGAU
......((((((.(((((...(((((((....((((((((((...((((...((....))....))))...)))))))))).)))))))..((..(...)..))))))).)))))).... ( -29.50)
>DroSec_CAF1 132252 120 + 1
CUACUCGUUAGGUAAUUUGACUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCACUUGUUUCAAUGACAAGCAUCCAGGAAAAUCAAAGUUGUGGACUCUGCAAAGUUCCUUGGCUGAU
......((((((.(((((((((((((((....((((((((((.....(((...)))(((((.....))))))))))))))).))))))))))(..(...)..).))))).)))))).... ( -34.70)
>DroSim_CAF1 127073 120 + 1
CUACUCGUUAGGUAAUUUGGCUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCAUUUGUUUCAAUGACAAGCAUCCAGGAAAAUCAAAGUUGUGGACUCUGCAAAGUUCCUUGGCUGAU
......((((((.(((((.(((((((((....((((((((((...((((...((....))....))))...)))))))))).)))))))))((..(...)..))))))).)))))).... ( -33.60)
>DroEre_CAF1 135503 120 + 1
CUACUCGUUAGGUAAUUUGGCUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCAUUUGUUUCAAUGACAUGCAUCCGGGAAAAUCAAAGUUGUGGACUCUGCGAAGUUCCUCGGCUGAU
....((((..(((....(((((((((((....((((((((((((.((((...((....))....)))).)))))))))))).)))))))))))...)))..))))(((......)))... ( -37.60)
>DroYak_CAF1 139099 120 + 1
CUACUCGUUAGGUAAUUUGGCUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCAUUUGUUUCAAUGACAGGCAUCCAGGAAAAUCAAAGUUGUGGACUCUGCAAAGUUCCUUGGCUGGG
...((.((((((.(((((.(((((((((....((((((((((...((((...((....))....))))...)))))))))).)))))))))((..(...)..))))))).)))))).)). ( -36.00)
>consensus
CUACUCGUUAGGUAAUUUGGCUUUGAUUGGGGUUUUGGGUGCAUUUCGUGCUGCAUUUGUUUCAAUGACAAGCAUCCAGGAAAAUCAAAGUUGUGGACUCUGCAAAGUUCCUUGGCUGAU
......((((((.(((((((((((((((....((((((((((...((((...((....))....))))...)))))))))).))))))))))(..(...)..).))))).)))))).... (-32.94 = -32.86 +  -0.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:34 2006