Locus 1364

Sequence ID 2L_DroMel_CAF1
Location 3,617,761 – 3,617,888
Length 127
Max. P 0.986767
window2229 window2230 window2231

overview

Window 9

Location 3,617,761 – 3,617,857
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 82.21
Mean single sequence MFE -33.93
Consensus MFE -24.31
Energy contribution -25.00
Covariance contribution 0.69
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.72
SVM decision value 0.60
SVM RNA-class probability 0.795461
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3617761 96 - 22407834
GCUCGA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCCAUUGCGAUGCCGAUUGGCUCUGG-GCGAAACACU--CUCACACACUU
..(((.-..((((....((((((((((((......)).))))).)))))(((((...((....))..)))))))))-.)))......--........... ( -35.00)
>DroSec_CAF1 85504 96 - 1
GCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCAAUUUCGAUGCCGAUUGGCUCUGG-GCGAAACACU--CUCUCACACUU
((.(((-....((((((((((((((((((......)).)))))))))..((((.......)))).))))))).)))-))........--........... ( -35.00)
>DroSim_CAF1 90860 96 - 1
GCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCCAUUUCGAUGCCGAUUGGCUCUGG-GCGAAACACU--CUCUCACACUU
......-.....(((...(((((((((((......)).)))))))))(((((((..(((....))).)))).))))-))........--........... ( -33.50)
>DroEre_CAF1 86967 87 - 1
GCCCCACCACCAGCUGAUGGGAGUGGGCGUAGUAUCGACCCACUUCCCAGGCCAUUUCGAUGCCGAUUGGCUUUGG-------------CUCUCACACUU
...........(((..(((((((((((((......)).))))).)))))(((((..(((....))).))))))..)-------------))......... ( -32.40)
>DroYak_CAF1 90057 99 - 1
GCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUAUCGACCCACUUCCCAGGCCAUUGCGAUGCCGAUUGGCUCUGGGGCGAAUCACUCUCUCCCACACUU
((((((-....((((((((((((((((((......)).)))))))))..(((.........))).))))))).))))))..................... ( -37.00)
>DroAna_CAF1 92684 84 - 1
--------------UGUGGGGCGUGGGCGUUCUAUCGACCCACUUCCCAGGCCCUGGCACUGCCGAUUGGCUCUUG-G-AAAACACUCACUCUCACACUC
--------------(((((((.(((((((......)).)))))((((.(((((.((((...))))...))).)).)-)-)).........)))))))... ( -30.70)
>consensus
GCUCCA_CACCAGCUAAUGGGAGUGGGCGUUGUAUCGACCCACUUCCCAGGCCAUUGCGAUGCCGAUUGGCUCUGG_GCGAAACACU__CUCUCACACUU
..................(((((((((((......)).)))))))))(((((((...((....))..)))).)))......................... (-24.31 = -25.00 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,617,792 – 3,617,888
Length 96
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 84.64
Mean single sequence MFE -33.83
Consensus MFE -26.74
Energy contribution -27.14
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.62
Structure conservation index 0.79
SVM decision value 2.05
SVM RNA-class probability 0.986767
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3617792 96 + 22407834
UCGGCAUCGCAAUGGCCUGGGAAGUGGGUCGACACAACGCCCACUCCCAUUAGCUGGUG-UCGAGCCACUCCAACG-CUCAACUUCCCCA-------CCACCCAC
..(((.(((((..(((.(((((.(((((.((......))))))))))))...)))..))-.)))))).........-.............-------........ ( -31.80)
>DroSec_CAF1 85535 96 + 1
UCGGCAUCGAAAUUGCCUGGGAAGUGGGUCGACACAACGCCCACUCCCAUUAGCUGGUG-UGGAGCCACUCCAGCG-CUCAACUCCCCCA-------CCACCCAC
..((((.......))))(((((.(((((.((......))))))))))))...(((((.(-((....))).))))).-.............-------........ ( -38.40)
>DroSim_CAF1 90891 96 + 1
UCGGCAUCGAAAUGGCCUGGGAAGUGGGUCGACACAACGCCCACUCCCAUUAGCUGGUG-UGGAGCCACUCCAACG-CUCAACUCCCCCA-------CCACCCAC
..(((.........)))(((((.(((((.((......)))))))))))).....(((((-.((((...........-.....))))..))-------)))..... ( -30.89)
>DroEre_CAF1 86988 82 + 1
UCGGCAUCGAAAUGGCCUGGGAAGUGGGUCGAUACUACGCCCACUCCCAUCAGCUGGUGGUGGGGCCACUCCAACG-----------------------CCCUAC
..(((.......((((((((((.(((((.((......)))))))))))..((.(....).)))))))).......)-----------------------)).... ( -32.94)
>DroYak_CAF1 90091 104 + 1
UCGGCAUCGCAAUGGCCUGGGAAGUGGGUCGAUACAACGCCCACUCCCAUUAGCUGGUG-UGGAGCCACUCCAACUACUCUACUCCCCCCCUCCCAGCCACCCAC
..(((........(((.(((((.(((((.((......))))))))))))...)))((.(-(((((............)))))).))..........)))...... ( -35.10)
>consensus
UCGGCAUCGAAAUGGCCUGGGAAGUGGGUCGACACAACGCCCACUCCCAUUAGCUGGUG_UGGAGCCACUCCAACG_CUCAACUCCCCCA_______CCACCCAC
..(((.(((...((((.(((((.(((((.((......))))))))))))...))))....))).)))...................................... (-26.74 = -27.14 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,617,792 – 3,617,888
Length 96
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 84.64
Mean single sequence MFE -42.80
Consensus MFE -30.03
Energy contribution -30.87
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.70
SVM decision value 1.30
SVM RNA-class probability 0.939107
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3617792 96 - 22407834
GUGGGUGG-------UGGGGAAGUUGAG-CGUUGGAGUGGCUCGA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCCAUUGCGAUGCCGA
....(..(-------(((((..((((((-(.........))))))-).))......((((((((((((......)).))))).)))))..))))..)........ ( -39.00)
>DroSec_CAF1 85535 96 - 1
GUGGGUGG-------UGGGGGAGUUGAG-CGCUGGAGUGGCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCAAUUUCGAUGCCGA
.(((.(((-------((..(((((((..-(....)..))))))).-))))).))).((((((((((((......)).))))).)))))((((.......)))).. ( -45.00)
>DroSim_CAF1 90891 96 - 1
GUGGGUGG-------UGGGGGAGUUGAG-CGUUGGAGUGGCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCCAUUUCGAUGCCGA
.(((.(((-------((..(((((((..-(....)..))))))).-))))).))).((((((((((((......)).))))).)))))(((.........))).. ( -42.90)
>DroEre_CAF1 86988 82 - 1
GUAGGG-----------------------CGUUGGAGUGGCCCCACCACCAGCUGAUGGGAGUGGGCGUAGUAUCGACCCACUUCCCAGGCCAUUUCGAUGCCGA
....((-----------------------(((((((((((((.((.(....).)).((((((((((((......)).))))).)))))))))))))))))))).. ( -44.50)
>DroYak_CAF1 90091 104 - 1
GUGGGUGGCUGGGAGGGGGGGAGUAGAGUAGUUGGAGUGGCUCCA-CACCAGCUAAUGGGAGUGGGCGUUGUAUCGACCCACUUCCCAGGCCAUUGCGAUGCCGA
(..(.(((((..................(((((((.(((....))-).))))))).((((((((((((......)).))))).)))))))))))..)........ ( -42.60)
>consensus
GUGGGUGG_______UGGGGGAGUUGAG_CGUUGGAGUGGCUCCA_CACCAGCUAAUGGGAGUGGGCGUUGUGUCGACCCACUUCCCAGGCCAUUUCGAUGCCGA
.............................(((((((((((((..............((((((((((((......)).))))).)))))))))))))))))).... (-30.03 = -30.87 +   0.84)

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 10:00:43 2006