Locus 4465

Sequence ID 3R_DroMel_CAF1
Location 11,813,442 – 11,813,679
Length 237
Max. P 0.997951
window7298 window7299 window7300 window7301 window7302

overview

Window 8

Location 11,813,442 – 11,813,562
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.75
Mean single sequence MFE -31.00
Consensus MFE -28.52
Energy contribution -28.64
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.87
Structure conservation index 0.92
SVM decision value 2.49
SVM RNA-class probability 0.994589
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11813442 120 + 27905053
CACAUAUUAUAGUCAAGCGAAUUGUCGUAGUUAACCGACAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACACAGCCAUCCGACUCCCCUGACAC
...........((((.((.((((((((........)))))))))).....((((....((..(((....(((((((...))))))).......)))...))....)))).....)))).. ( -30.40)
>DroSec_CAF1 17831 120 + 1
CACAUAUAAUAGUCAAGCGAAUUGUCGUAGUUAACCGACAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACACAGCCAUCCGACUCCCCUGACAC
...........((((.((.((((((((........)))))))))).....((((....((..(((....(((((((...))))))).......)))...))....)))).....)))).. ( -30.40)
>DroSim_CAF1 18209 120 + 1
CACAUAUAAUAGUCAAGCGAAUUGUCGUAGUUAACCGACAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACACAGCCAUCCGACUCCCCUGACAC
...........((((.((.((((((((........)))))))))).....((((....((..(((....(((((((...))))))).......)))...))....)))).....)))).. ( -30.40)
>DroEre_CAF1 18129 119 + 1
CACAUCUUAUAGUCAAGCGAAUUGUGG-CGUUAACCGGCAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACAAUGCCAUCCGACUCCCCUGACAC
...........((((.(.((.((((((-((((....(((....)))................(((....(((((((...))))))).......))))))))))..))).)).).)))).. ( -32.80)
>DroYak_CAF1 18132 120 + 1
CACAUAUUAUUGUCAAGCGAAUUGUCGUAGUUAAGCGUCAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACACUGCCAUCCAACUCCCCUGACAC
..........(((((.((.(((((.(((......))).))))))).....((((....((.((((....(((((((...)))))))((.....))))))))....)))).....))))). ( -31.00)
>consensus
CACAUAUUAUAGUCAAGCGAAUUGUCGUAGUUAACCGACAAUUGCCUUUUGUUGUUCAGCCAGUGAUUUUCCAGGGAAACCCUGGAUGCAUCCCACACAGCCAUCCGACUCCCCUGACAC
...........((((.((.((((((((........)))))))))).....((((....((..(((....(((((((...))))))).......)))...))....)))).....)))).. (-28.52 = -28.64 +   0.12)

alignment

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secondary structure

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Window 9

Location 11,813,442 – 11,813,562
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.75
Mean single sequence MFE -39.60
Consensus MFE -34.32
Energy contribution -34.92
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.87
SVM decision value 2.13
SVM RNA-class probability 0.988656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11813442 120 - 27905053
GUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGUCGGUUAACUACGACAAUUCGCUUGACUAUAAUAUGUG
..((((((.((((.(..((((((.((((......(((((((...)))))))...))))))))))..).))........(((((((........))))))))).))))))........... ( -39.00)
>DroSec_CAF1 17831 120 - 1
GUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGUCGGUUAACUACGACAAUUCGCUUGACUAUUAUAUGUG
..((((((.((((.(..((((((.((((......(((((((...)))))))...))))))))))..).))........(((((((........))))))))).))))))........... ( -39.00)
>DroSim_CAF1 18209 120 - 1
GUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGUCGGUUAACUACGACAAUUCGCUUGACUAUUAUAUGUG
..((((((.((((.(..((((((.((((......(((((((...)))))))...))))))))))..).))........(((((((........))))))))).))))))........... ( -39.00)
>DroEre_CAF1 18129 119 - 1
GUGUCAGGGGAGUCGGAUGGCAUUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGCCGGUUAACG-CCACAAUUCGCUUGACUAUAAGAUGUG
..((((((.(((((....)))((((((((((...(((((((...)))))))..)))((((((...................)))))).....-))))))))).))))))........... ( -41.01)
>DroYak_CAF1 18132 120 - 1
GUGUCAGGGGAGUUGGAUGGCAGUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGACGCUUAACUACGACAAUUCGCUUGACAAUAAUAUGUG
.(((((((.((((((..(((.(((((.((.(((.(((((((...)))))))...(((.....)))..........))).)).)))))...)))...)))))).))))))).......... ( -40.00)
>consensus
GUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGGGUUUCCCUGGAAAAUCACUGGCUGAACAACAAAAGGCAAUUGUCGGUUAACUACGACAAUUCGCUUGACUAUAAUAUGUG
..((((((.((((.(..((((...((((......(((((((...)))))))...))))..))))..).))........(((((((........))))))))).))))))........... (-34.32 = -34.92 +   0.60)

alignment

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secondary structure

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Window 0

Location 11,813,522 – 11,813,639
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 96.58
Mean single sequence MFE -45.38
Consensus MFE -45.02
Energy contribution -45.02
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.99
SVM decision value 2.97
SVM RNA-class probability 0.997951
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11813522 117 - 27905053
UAUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUGGAGAUGCACGUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((..(((..((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).)))...))))........... ( -47.40)
>DroSec_CAF1 17911 117 - 1
UAUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCCAUGGAGAUGCACGUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((..(((..((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).)))...))))........... ( -47.40)
>DroSim_CAF1 18289 117 - 1
UGUUGUCGCGGUUUCCUUCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCCAUGGAGAUGCACGUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((..(((..((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).)))...))))........... ( -45.20)
>DroEre_CAF1 18208 117 - 1
UGUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUUGCUAUGGAGAUGCACGUGUCAGGGGAGUCGGAUGGCAUUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((.......((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).......))))........... ( -43.04)
>DroYak_CAF1 18212 117 - 1
UGUUGUCGCGGUUUCCUUCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUAGAGAUGCACGUGUCAGGGGAGUUGGAUGGCAGUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((.......((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).......))))........... ( -43.84)
>consensus
UGUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUGGAGAUGCACGUGUCAGGGGAGUCGGAUGGCUGUGUGGGAUGCAUCCAGG
...((((((((......))))))))((((..(((..((((.((((.((((((..((((((((......))))))))..)).)))).)))).)))).)))...))))........... (-45.02 = -45.02 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,813,562 – 11,813,679
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 91.82
Mean single sequence MFE -24.32
Consensus MFE -21.94
Energy contribution -22.14
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.90
SVM decision value 1.44
SVM RNA-class probability 0.954369
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11813562 117 + 27905053
GUGCAUCUCCAUAGCGAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGGAGGAAACCGCGACAAUAAACACCGCAAAAACAAAAAAACCAAAACCAAAACCAAACC
((((((.((......)).))))))((((......)))).......(((((((((.(((((......)))))........)))).)))))............................ ( -24.70)
>DroSec_CAF1 17951 110 + 1
GUGCAUCUCCAUGGCGAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGGAGGAAACCGCGACAAUAAACACCGCAAAAACAAAA-------AACCAAAACCAAGCC
((((((.((......)).))))))..((.......(((..(((..(((((((((.(((((......)))))........)))).)))))...)))-------..))).......)). ( -25.04)
>DroSim_CAF1 18329 110 + 1
GUGCAUCUCCAUGGCGAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGAAGGAAACCGCGACAACAAACACCGCAAAAACAAAA-------AACCAAAACCAAGCC
((((((.((......)).))))))..((.......(((..(((..(((((((((.((((..(....)))))........)))).)))))...)))-------..))).......)). ( -23.04)
>DroEre_CAF1 18248 115 + 1
GUGCAUCUCCAUAGCAAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGGAGGAAACCGCGACAACAAACACCGCAAAAACCCA--AACCAAAACCAAAACCAAACC
(((.(((......((.....))..((((......))))))).))).(((((((...((((.(....).(......).....))))....)))))--))................... ( -24.20)
>DroYak_CAF1 18252 110 + 1
GUGCAUCUCUAUAGCGAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGAAGGAAACCGCGACAACAAACACCGCAAAAACCC-------AAAACCAAAACCAAACC
((((((.((......)).))))))((((......)))).......((((((((.((.....)).....(((...........)))....))))-------))))............. ( -24.60)
>consensus
GUGCAUCUCCAUAGCGAAAUGCAUCCGCAAACAAGUGGGAUUUACUUUUGGGUGCCGCGGAGGAAACCGCGACAACAAACACCGCAAAAACAAAA_____AAAACCAAAACCAAACC
((((((.((......)).))))))((((......)))).......(((((((((.((((..(....)))))........)))).)))))............................ (-21.94 = -22.14 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,813,562 – 11,813,679
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 91.82
Mean single sequence MFE -33.97
Consensus MFE -33.64
Energy contribution -33.64
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 0.99
SVM decision value 1.94
SVM RNA-class probability 0.983398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11813562 117 - 27905053
GGUUUGGUUUUGGUUUUGGUUUUUUUGUUUUUGCGGUGUUUAUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUGGAGAUGCAC
((((((.((((((...........((((....)))).......((((((((......)))))))).)))))).))))))((.(......).)).((((((((......)))))))). ( -36.30)
>DroSec_CAF1 17951 110 - 1
GGCUUGGUUUUGGUU-------UUUUGUUUUUGCGGUGUUUAUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCCAUGGAGAUGCAC
.((.......(((..-------.((((((((((.(((((.......(((((......))))))))))))))))))))..))).......))...((((((((......)))))))). ( -33.85)
>DroSim_CAF1 18329 110 - 1
GGCUUGGUUUUGGUU-------UUUUGUUUUUGCGGUGUUUGUUGUCGCGGUUUCCUUCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCCAUGGAGAUGCAC
.((.......(((..-------.((((((((((.(((((.......(((((......))))))))))))))))))))..))).......))...((((((((......)))))))). ( -31.65)
>DroEre_CAF1 18248 115 - 1
GGUUUGGUUUUGGUUUUGGUU--UGGGUUUUUGCGGUGUUUGUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUUGCUAUGGAGAUGCAC
.........((.((.......--((((..(((((....((((.((((((((......))))))))..)))).))))).)))).......)).))((((((((......)))))))). ( -33.44)
>DroYak_CAF1 18252 110 - 1
GGUUUGGUUUUGGUUUU-------GGGUUUUUGCGGUGUUUGUUGUCGCGGUUUCCUUCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUAGAGAUGCAC
(((..((.((((.((((-------((((....(((.....))).(((((((......))))))))))))))).)))).)).)))..........((((((((......)))))))). ( -34.60)
>consensus
GGUUUGGUUUUGGUUUU_____UUUUGUUUUUGCGGUGUUUGUUGUCGCGGUUUCCUCCGCGGCACCCAAAAGUAAAUCCCACUUGUUUGCGGAUGCAUUUCGCUAUGGAGAUGCAC
((((((.((((((.............((....)).........((((((((......)))))))).)))))).))))))((.(......).)).((((((((......)))))))). (-33.64 = -33.64 +   0.00)

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 11:30:02 2006