Locus 657

Sequence ID 3L_DroMel_CAF1
Location 1,955,758 – 1,955,872
Length 114
Max. P 0.785691
window1002 window1003

overview

Window 2

Location 1,955,758 – 1,955,872
Length 114
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 77.54
Mean single sequence MFE -34.19
Consensus MFE -20.18
Energy contribution -20.35
Covariance contribution 0.17
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.59
SVM decision value 0.57
SVM RNA-class probability 0.785691
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1955758 114 + 23771897
GCUCAGA-GAAUCAUUUUCAGGCCCCACU-UUCCCCAGAAACUUUCAGACAUUCGCCCACUUCCUGAAGGCUUCCGUGGGCACUGGCGUCCUGGCCAUGCCCAGUGCCUUCGCACA
((...((-((.....))))((((......-.......(((.(((((((...............))))))).)))..((((((.((((......))))))))))..))))..))... ( -32.76)
>DroPse_CAF1 7101 106 + 1
GGUUAGCCAAAACAUUAUC---------U-UUCCUUAGGAACUGGCAGACUUUUGCCCAUUUCCUGAAGGCCUCUGUGGGCACUGGGGUCCUGGCCAUGCCCAGUGCCUUUUCCCA
((....))....(((....---------.-..(((((((((..(((((....)))))...)))))).))).....)))(((((((((((....))....)))))))))........ ( -34.90)
>DroSec_CAF1 7072 113 + 1
ACUUAUG-GAAUUAUUUUCCGGC-CCACU-UUCCCCAGAAACUUCCAGACAUUCACCCACUUCCUGAAGGCUUCCGUGGGCACUGGCGUCCUGGCCAUGCCCAGUGCCUUCGCACA
.....((-(((....((((.((.-.....-....)).)))).)))))..................((((((...(.((((((.((((......))))))))))).))))))..... ( -32.50)
>DroEre_CAF1 6856 114 + 1
GCCCAAG-GAAUCAUUUUCUGGC-CUGUUCUCCCCCAGCAACUUUCAGACCUUUGCCCACUUCCUGAAGGCCUCCGUGGGCACUGGAGUCCUGGCCAUGCCCAGUGCCUUCGCACA
(((..((-((.......(((((.-..(((((.....)).)))..)))))((..(((((((..((....)).....)))))))..))..)))))))........((((....)))). ( -33.20)
>DroAna_CAF1 5619 114 + 1
AUUUACG-ACAUAUUAUUCUCGU-UUAUUUGGCCCUAGAAACUGGCAGACCUUUGCCCAUUUCCUCAAGGCGUCGGUGGGCACGGGGGUCCUGGCCAUGCCCAGCGCCUUCGCCCA
.....((-((..........((.-.....))(((...((((..(((((....)))))..)))).....))))))).(((((..((((((.((((......)))).))))))))))) ( -36.90)
>DroPer_CAF1 7804 106 + 1
GGUUAGCCAAAACAUUAUC---------U-UUCCUUAGGAACUGGCAGACUUUUGCCCAUUUCCUGAAGGCCUCUGUGGGCACUGGGGUCCUGGCCAUGCCCAGUGCCUUUUCCCA
((....))....(((....---------.-..(((((((((..(((((....)))))...)))))).))).....)))(((((((((((....))....)))))))))........ ( -34.90)
>consensus
GCUUAGG_AAAUCAUUUUC_GGC_C_A_U_UUCCCCAGAAACUGGCAGACAUUUGCCCACUUCCUGAAGGCCUCCGUGGGCACUGGGGUCCUGGCCAUGCCCAGUGCCUUCGCACA
.................................................................((((((.....((((((.(((........)))))))))..))))))..... (-20.18 = -20.35 +   0.17)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 1,955,758 – 1,955,872
Length 114
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 77.54
Mean single sequence MFE -38.89
Consensus MFE -22.61
Energy contribution -22.28
Covariance contribution -0.33
Combinations/Pair 1.26
Mean z-score -1.55
Structure conservation index 0.58
SVM decision value 0.12
SVM RNA-class probability 0.593067
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1955758 114 - 23771897
UGUGCGAAGGCACUGGGCAUGGCCAGGACGCCAGUGCCCACGGAAGCCUUCAGGAAGUGGGCGAAUGUCUGAAAGUUUCUGGGGAA-AGUGGGGCCUGAAAAUGAUUC-UCUGAGC
.((((....)))).((((((...((((.(.(((.(.(((.(((((((.((((((..(....).....)))))).))))))))))..-).))).)))))...))).)))-....... ( -41.30)
>DroPse_CAF1 7101 106 - 1
UGGGAAAAGGCACUGGGCAUGGCCAGGACCCCAGUGCCCACAGAGGCCUUCAGGAAAUGGGCAAAAGUCUGCCAGUUCCUAAGGAA-A---------GAUAAUGUUUUGGCUAACC
..((..((((((.(((((((((........))).))))))......((((.(((((...((((......))))..)))))))))..-.---------.....))))))..)).... ( -34.30)
>DroSec_CAF1 7072 113 - 1
UGUGCGAAGGCACUGGGCAUGGCCAGGACGCCAGUGCCCACGGAAGCCUUCAGGAAGUGGGUGAAUGUCUGGAAGUUUCUGGGGAA-AGUGG-GCCGGAAAAUAAUUC-CAUAAGU
.....((((((.(((((((((((......)))).)))))).)...)))))).....(((((......(((((.(.((((....)))-).)..-.))))).......))-))).... ( -41.32)
>DroEre_CAF1 6856 114 - 1
UGUGCGAAGGCACUGGGCAUGGCCAGGACUCCAGUGCCCACGGAGGCCUUCAGGAAGUGGGCAAAGGUCUGAAAGUUGCUGGGGGAGAACAG-GCCAGAAAAUGAUUC-CUUGGGC
.((((....)))).......(.((((((.((...(((((((.....((....))..)))))))..((((((....((.(....).))..)))-))).......)).))-).))).) ( -39.20)
>DroAna_CAF1 5619 114 - 1
UGGGCGAAGGCGCUGGGCAUGGCCAGGACCCCCGUGCCCACCGACGCCUUGAGGAAAUGGGCAAAGGUCUGCCAGUUUCUAGGGCCAAAUAA-ACGAGAAUAAUAUGU-CGUAAAU
..(((.((((((((((((((((.........)))))))))..).))))))..((((((.((((......)))).))))))...)))......-((((.(......).)-))).... ( -42.90)
>DroPer_CAF1 7804 106 - 1
UGGGAAAAGGCACUGGGCAUGGCCAGGACCCCAGUGCCCACAGAGGCCUUCAGGAAAUGGGCAAAAGUCUGCCAGUUCCUAAGGAA-A---------GAUAAUGUUUUGGCUAACC
..((..((((((.(((((((((........))).))))))......((((.(((((...((((......))))..)))))))))..-.---------.....))))))..)).... ( -34.30)
>consensus
UGGGCGAAGGCACUGGGCAUGGCCAGGACCCCAGUGCCCACGGAGGCCUUCAGGAAAUGGGCAAAAGUCUGCAAGUUUCUAGGGAA_A_U_G_GCC_GAAAAUGAUUC_CCUAAGC
........(((((((((............)))))))))........((((.(((((.(((((....)))))....)))))))))................................ (-22.61 = -22.28 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:47 2006