Locus 7591

Sequence ID 3R_DroMel_CAF1
Location 20,349,435 – 20,349,560
Length 125
Max. P 0.991005
window12249 window12250 window12251

overview

Window 9

Location 20,349,435 – 20,349,530
Length 95
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.78
Mean single sequence MFE -26.15
Consensus MFE -12.59
Energy contribution -13.01
Covariance contribution 0.42
Combinations/Pair 1.32
Mean z-score -2.33
Structure conservation index 0.48
SVM decision value 1.09
SVM RNA-class probability 0.914182
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20349435 95 + 27905053
AUUUUUGGCCAAACACUUGCUG-------GCAGACUCAUGU----CCACAC--GCAUACAAGUGGAUGCCUAAGCCCAGUUGGACAAAAAAAUGUGCUGGCCAAACGA
...((((((((.(((...((((-------((((((....))----)..(((--........)))..))))..)))((....)).........)))..))))))))... ( -27.50)
>DroSec_CAF1 157986 95 + 1
AUUUUUGGCCAAACACUUGCUA-------GCAGACUCAUGU----CCACAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGA
...((((((((.(((.(((...-------.))).((..(((----(((.((--((((....))))..((....))...))))))))..))..)))..))))))))... ( -29.30)
>DroSim_CAF1 167152 95 + 1
AUUUUUGGCCAAACACUUGCCA-------GCAGACUCAUGU----CCACAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGA
...((((((((.((((((.(((-------((.(((....))----).....--((((....)))).............)))))....)))..)))..))))))))... ( -29.70)
>DroEre_CAF1 163805 95 + 1
AUUUUUGGCCAAACACUUGCUC-------GCAGACUCAUGU----UCAAAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGA
...((((((((.(((.(((...-------.))).((..(((----((((..--((((....))))..((....))....)))))))..))..)))..))))))))... ( -26.60)
>DroYak_CAF1 166519 73 + 1
AUUUUUGGCCAAACACUUGCUA-------GCAGACUCA----------------------------UGCCUAAGCGCAGUUGGACAAAAGAAUGUGCUGGCCAAACGA
...(((((((............-------(((......----------------------------)))...((((((.((........)).)))))))))))))... ( -20.20)
>DroAna_CAF1 164697 108 + 1
UUUUUUGGCUAAGCACUCUUAGACACAUAAAAGACGGAUUUACACUCACACUUACACACAACUGGCAGUAAUCGGCCAGUUAGAAAAAAGAAUGUGCUGUCCGAACGA
((((.((.(((((....)))))...)).))))..(((((...(((.....(((......(((((((........)))))))......)))...)))..)))))..... ( -23.60)
>consensus
AUUUUUGGCCAAACACUUGCUA_______GCAGACUCAUGU____CCACAC__GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGA
...((((((((.....((((.........))))....................(((((..........((...........)).........)))))))))))))... (-12.59 = -13.01 +   0.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,349,435 – 20,349,530
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 76.78
Mean single sequence MFE -32.33
Consensus MFE -17.91
Energy contribution -18.55
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.85
Structure conservation index 0.55
SVM decision value 2.24
SVM RNA-class probability 0.991005
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20349435 95 - 27905053
UCGUUUGGCCAGCACAUUUUUUUGUCCAACUGGGCUUAGGCAUCCACUUGUAUGC--GUGUGG----ACAUGAGUCUGC-------CAGCAAGUGUUUGGCCAAAAAU
...((((((((((((........((((....))))...(((((((((.((....)--).))))----)........)))-------).....))).)))))))))... ( -34.00)
>DroSec_CAF1 157986 95 - 1
UCGUUUGGCCAGCACAUUCUUUUGUCCAACUGGGCUUAGGCAUGCACUUGUGUGC--GUGUGG----ACAUGAGUCUGC-------UAGCAAGUGUUUGGCCAAAAAU
...((((((((((((...((...((((....))))..))((((((((....))))--))(..(----((....)))..)-------..))..))).)))))))))... ( -38.70)
>DroSim_CAF1 167152 95 - 1
UCGUUUGGCCAGCACAUUCUUUUGUCCAACUGGGCUUAGGCAUGCACUUGUGUGC--GUGUGG----ACAUGAGUCUGC-------UGGCAAGUGUUUGGCCAAAAAU
...((((((((((((..((...(((((..(((....)))((((((((....))))--))))))----))).))(((...-------.)))..))).)))))))))... ( -39.10)
>DroEre_CAF1 163805 95 - 1
UCGUUUGGCCAGCACAUUCUUUUGUCCAACUGGGCUUAGGCAUGCACUUGUGUGC--GUUUGA----ACAUGAGUCUGC-------GAGCAAGUGUUUGGCCAAAAAU
...((((((((((((...((...((((....))))..))((.((((((..(((..--......----)))..)))..))-------).))..))).)))))))))... ( -35.20)
>DroYak_CAF1 166519 73 - 1
UCGUUUGGCCAGCACAUUCUUUUGUCCAACUGCGCUUAGGCA----------------------------UGAGUCUGC-------UAGCAAGUGUUUGGCCAAAAAU
...((((((((((((........((......))((((((((.----------------------------...))))).-------.)))..))).)))))))))... ( -22.90)
>DroAna_CAF1 164697 108 - 1
UCGUUCGGACAGCACAUUCUUUUUUCUAACUGGCCGAUUACUGCCAGUUGUGUGUAAGUGUGAGUGUAAAUCCGUCUUUUAUGUGUCUAAGAGUGCUUAGCCAAAAAA
.....((((....((((((.(((..(((((((((........)))))))).)...)))...))))))...)))).........((.(((((....))))).))..... ( -24.10)
>consensus
UCGUUUGGCCAGCACAUUCUUUUGUCCAACUGGGCUUAGGCAUGCACUUGUGUGC__GUGUGG____ACAUGAGUCUGC_______UAGCAAGUGUUUGGCCAAAAAU
...((((((((((((........((((....)))).(((((................................)))))..............)))).))))))))... (-17.91 = -18.55 +   0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,349,457 – 20,349,560
Length 103
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.20
Mean single sequence MFE -25.83
Consensus MFE -15.31
Energy contribution -17.37
Covariance contribution 2.06
Combinations/Pair 1.09
Mean z-score -2.05
Structure conservation index 0.59
SVM decision value 0.30
SVM RNA-class probability 0.677794
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20349457 103 + 27905053
-GCAGACUCAUGU----CCACAC--GCAUACAAGUGGAUGCCUAAGCCCAGUUGGACAAAAAAAUGUGCUGGCCAAACGAAAGACUUAGGCAACAAACUUGAAUUCGGUA
-...(((....))----).((.(--(.((.(((((...((((((((.(((((...(((......)))))))).....(....).))))))))....))))).)).)))). ( -28.20)
>DroSec_CAF1 158008 103 + 1
-GCAGACUCAUGU----CCACAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGAAAGACUUAGGUAACAAACUUGAAUUCGGUA
-(((.(.((.(((----(((.((--((((....))))..((....))...))))))))...)).).)))..(((...(....)..((((((.....))))))....))). ( -25.80)
>DroSim_CAF1 167174 103 + 1
-GCAGACUCAUGU----CCACAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGAAAGACUUAGGCAACAAACUUGAAUUCGGCA
-((.((.(((.((----......--((((....)))).((((((((.(((((...(((......)))))))).....(....).))))))))....)).)))..)).)). ( -28.90)
>DroEre_CAF1 163827 103 + 1
-GCAGACUCAUGU----UCAAAC--GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGAAAGACUUAGGCAACAAACUUGAAUUCGGCA
-((.((.....((----((((..--((((....)))).((((((((.(((((...(((......)))))))).....(....).))))))))......)))))))).)). ( -30.20)
>DroYak_CAF1 166541 81 + 1
-GCAGACUCA----------------------------UGCCUAAGCGCAGUUGGACAAAAGAAUGUGCUGGCCAAACGAAAGACUUAGGCAACAAACUUGAAUUCGGCA
-((.((.(((----------------------------((((((((....((..((((......))).)..))....(....).)))))))).......)))..)).)). ( -19.81)
>DroAna_CAF1 164725 107 + 1
AAAAGACGGAUUUACACUCACACUUACACACAACUGGCAGUAAUCGGCCAGUUAGAAAAAAGAAUGUGCUGUCCGAACGAAAGACUUAGGCAACAAACUUGAAUUCA---
..(((.(((((...(((.....(((......(((((((........)))))))......)))...)))..)))))..(....).))).(....).............--- ( -22.10)
>consensus
_GCAGACUCAUGU____CCACAC__GCACACAAGUGCAUGCCUAAGCCCAGUUGGACAAAAGAAUGUGCUGGCCAAACGAAAGACUUAGGCAACAAACUUGAAUUCGGCA
..............................(((((...((((((((.(((((...(((......)))))))).....(....).))))))))....)))))......... (-15.31 = -17.37 +   2.06)

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 12:49:39 2006