Locus 392

Sequence ID 2R_DroMel_CAF1
Location 2,370,682 – 2,370,915
Length 233
Max. P 0.999812
window771 window772 window773

overview

Window 1

Location 2,370,682 – 2,370,795
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.72
Mean single sequence MFE -34.26
Consensus MFE -28.34
Energy contribution -28.38
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.54
Structure conservation index 0.83
SVM decision value 2.52
SVM RNA-class probability 0.994873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2370682 113 + 20766785
CAUGCAAAGG-------CGAAAUCACAAAAUACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAAUAUCCAUCUCGGGGAGUGUGUGUGUGCGAUUCCUUUGCCA
...(((((((-------...((((........(((((((((((..............)).)))).)))))(((((..((...(((.......)))...))..)))))))))))))))).. ( -34.04)
>DroSec_CAF1 20082 111 + 1
CAUGCAAAGG-------CGAAAUCACAAAACACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAAUAUCCAUCCCGUUGAGUGU--GUGUGCGAUUCCUUUGCCA
...(((((((-------...((((.((..(((((...((((((((....(((((.....)))))....)))))))).((((.........)))))))))--...)).))))))))))).. ( -33.80)
>DroSim_CAF1 20263 111 + 1
CAUGCAAAGG-------CGAAAUCACAAAACACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAAUAUCCAUCCCGGGGAGUGU--GUGUGCGAUUCCUUUGCCA
...(((((((-------...((((.((..(((((...((((((((....(((((.....)))))....))))))))......(((......))))))))--...)).))))))))))).. ( -35.60)
>DroEre_CAF1 19415 118 + 1
CAUGCAAAGGCGAAAGGCGAAAUCACAAAACACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAACAUCCAUCUCAGCGAGUGU--GUGUGCGAUUCCUUGGCCA
........(((..((((...((((.((..(((((...((((((((....(((((.....)))))....))))))))((.............)).)))))--...)).)))))))).))). ( -33.82)
>DroYak_CAF1 19543 111 + 1
CAUGCAAAGG-------CGAAAUCACAAAACACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAAUAUCCAUCUCAGCGAGUGU--GUGUGCGAUUCCUUUGCCA
...(((((((-------...((((.((..(((((...((((((((....(((((.....)))))....))))))))((.............)).)))))--...)).))))))))))).. ( -34.02)
>consensus
CAUGCAAAGG_______CGAAAUCACAAAACACUGAAACGUGCUUUUUGACAUUUUUGCAAUGUAUUUAGGCACGUGCAAUAUCCAUCUCGGCGAGUGU__GUGUGCGAUUCCUUUGCCA
...(((((((.......((....((((..((((....((((((((....(((((.....)))))....))))))))..........((.....))))))...))))))...))))))).. (-28.34 = -28.38 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,370,682 – 2,370,795
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -33.04
Consensus MFE -30.50
Energy contribution -30.14
Covariance contribution -0.36
Combinations/Pair 1.08
Mean z-score -2.45
Structure conservation index 0.92
SVM decision value 4.14
SVM RNA-class probability 0.999812
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2370682 113 - 20766785
UGGCAAAGGAAUCGCACACACACACUCCCCGAGAUGGAUAUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUAUUUUGUGAUUUCG-------CCUUUGCAUG
..((((((((((((((......(((((...))).))(((((((.((((((......(((((.....)))))......))))))..))))))).)))))))...-------)))))))... ( -33.60)
>DroSec_CAF1 20082 111 - 1
UGGCAAAGGAAUCGCACAC--ACACUCAACGGGAUGGAUAUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUGUUUUGUGAUUUCG-------CCUUUGCAUG
..((((((((((((((...--.((..(....)..))(((((((.((((((......(((((.....)))))......))))))..))))))).)))))))...-------)))))))... ( -33.10)
>DroSim_CAF1 20263 111 - 1
UGGCAAAGGAAUCGCACAC--ACACUCCCCGGGAUGGAUAUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUGUUUUGUGAUUUCG-------CCUUUGCAUG
..((((((((((((((...--.((..(....)..))(((((((.((((((......(((((.....)))))......))))))..))))))).)))))))...-------)))))))... ( -34.60)
>DroEre_CAF1 19415 118 - 1
UGGCCAAGGAAUCGCACAC--ACACUCGCUGAGAUGGAUGUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUGUUUUGUGAUUUCGCCUUUCGCCUUUGCAUG
.(((...(((((((((...--.....((((((((((....(((((.(((........))))))))...(((......)))))))))))))...))))))))))))....((....))... ( -30.30)
>DroYak_CAF1 19543 111 - 1
UGGCAAAGGAAUCGCACAC--ACACUCGCUGAGAUGGAUAUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUGUUUUGUGAUUUCG-------CCUUUGCAUG
..((((((((((((((...--.(((((...))).))(((((((.((((((......(((((.....)))))......))))))..))))))).)))))))...-------)))))))... ( -33.60)
>consensus
UGGCAAAGGAAUCGCACAC__ACACUCCCCGAGAUGGAUAUUGCACGUGCCUAAAUACAUUGCAAAAAUGUCAAAAAGCACGUUUCAGUGUUUUGUGAUUUCG_______CCUUUGCAUG
..((((((((((((((......(((((...))).))(((((((.((((((......(((((.....)))))......))))))..))))))).)))))))..........)))))))... (-30.50 = -30.14 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,370,795 – 2,370,915
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -28.25
Consensus MFE -23.30
Energy contribution -24.02
Covariance contribution 0.72
Combinations/Pair 1.07
Mean z-score -1.30
Structure conservation index 0.82
SVM decision value -0.04
SVM RNA-class probability 0.513108
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2370795 120 - 20766785
UGGGUUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUGCCGAUUCCGCUCGGCUUUCGCCUUUAAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
.(((..((((((((((((.(((......))))))))).)))))))))..........((((((((........(((....)))........(....)....))))))))........... ( -30.90)
>DroSec_CAF1 20193 120 - 1
AGGGUUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUGCUGAUUCCGCUCGGUUUUCGCCUUUUAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
((((..((((((((((((.(((......))))))))).)))))))))).........(((((..(......((((((..........))))))........)..)))))........... ( -29.64)
>DroSim_CAF1 20374 120 - 1
CGGGUUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUGCUGAUUCCGCUCGGCUUUCGCCUUUAAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
.(((..((((((((((((.(((......))))))))).)))))))))..........(((((..(........(((....)))........(....)....)..)))))........... ( -28.70)
>DroEre_CAF1 19533 120 - 1
GGGGCUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUCCUGAUUCCGCUCGGCUCCCGCCUUUAAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
((((..((((((((((((.(((......))))))))).))))))))))...((((((.....((((..((...(((....))).......))..)))).....))))))........... ( -28.50)
>DroYak_CAF1 19654 109 - 1
UGGGUUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUCCUGAUUCC-----------GCCUUUAAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
.(((..((((((((((((.(((......))))))))).)))))))))....((((((.....((((..(-----------(.........))..)))).....))))))........... ( -23.50)
>consensus
UGGGUUUCGAUUUUGUUGACAAUUCACUUUGCAGCGGUAAUUGACCCUAAUGCUGUUGCUGCUGAUUCCGCUCGGCUUUCGCCUUUAAAUCGAUAUCACUUUUGGCAGCUAAAUUCAAUU
.(((..((((((((((((.(((......))))))))).)))))))))..........((((((((........(((....)))........(....)....))))))))........... (-23.30 = -24.02 +   0.72)

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 09:37:25 2006