Locus 4246

Sequence ID 3R_DroMel_CAF1
Location 11,383,856 – 11,384,055
Length 199
Max. P 0.999736
window6888 window6889 window6890 window6891 window6892

overview

Window 8

Location 11,383,856 – 11,383,976
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.83
Mean single sequence MFE -32.30
Consensus MFE -29.58
Energy contribution -29.66
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -2.34
Structure conservation index 0.92
SVM decision value 3.32
SVM RNA-class probability 0.999007
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383856 120 + 27905053
AGUUUUUACACUUUCCAGCAGCGUUUUUGGAGUUUCAGCGUUUCCUCAACGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUUUGGCCUUUGGCCAUA
............(((..(((.(((....((((((((((((((.....))))))...)))))).)).))).)))...)))...........(((((((.((......))))..)))))... ( -29.10)
>DroSec_CAF1 131583 120 + 1
AGUUUUUACACUUUCCAGCAGCGUUUUUGGAGUUUCGGCGUUUCCUCAUCGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUA
..............((((((.(((....((((((((((((.........))...)))))))).)).))).))).................((((((((....))))))))..)))..... ( -30.80)
>DroSim_CAF1 122684 120 + 1
AGUUUUUACACUUUCCAGCAGCGUUUUUGGAGUUUCGGCGUUUCCUCAACGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUA
..............((((((.(((....((((((((((((((.....))))...)))))))).)).))).))).................((((((((....))))))))..)))..... ( -33.30)
>DroEre_CAF1 119055 120 + 1
AGUUUUUACAGUUUCUAACAGCGUUUCUGGAGUUUCGGCGUUUCCUCAACGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUCUGGCCUCUGGCCAUA
.........(((((......(((((...((((((((((((((.....))))...)))))))).))...)))))...))))).........(((((((.((......)).).))))))... ( -33.50)
>DroYak_CAF1 121802 120 + 1
AGUUUGUACAGUUUCCAGCAGCGUUUUUGGAGUUUCGGCGUUUCCUCAACGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUA
....((..((((((...(((.(((....((((((((((((((.....))))...)))))))).)).))).)))...))))..........((((((((....))))))))..))..)).. ( -34.80)
>consensus
AGUUUUUACACUUUCCAGCAGCGUUUUUGGAGUUUCGGCGUUUCCUCAACGUUUCCGAAACUACUUACGAUGCCUUGAACUUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUA
..............(((...(((((...((((((((((((((.....))))...)))))))).))...))))).................((((((((....))))))))..)))..... (-29.58 = -29.66 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,383,856 – 11,383,976
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -35.64
Consensus MFE -33.00
Energy contribution -33.08
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.93
SVM decision value 3.97
SVM RNA-class probability 0.999736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383856 120 - 27905053
UAUGGCCAAAGGCCAAAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAACGCUGAAACUCCAAAAACGCUGCUGGAAAGUGUAAAAACU
..((((((..((((......)))).))))))(((.((((.((.....)).)))).....(((((((...((((.....))))))))))))))....(((((.......)))))....... ( -33.30)
>DroSec_CAF1 131583 120 - 1
UAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGAUGAGGAAACGCCGAAACUCCAAAAACGCUGCUGGAAAGUGUAAAAACU
..((((((..((((......)))).)))))).....((.((((...(((.............(((....)))...(....))))..)))).))...(((((.......)))))....... ( -34.20)
>DroSim_CAF1 122684 120 - 1
UAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAACGCCGAAACUCCAAAAACGCUGCUGGAAAGUGUAAAAACU
(((..((...((((((........)))))).))..)))...(((..((((.(((..(.((((((((...((((.....)))))))))))).)....))).)))).)))(((......))) ( -35.60)
>DroEre_CAF1 119055 120 - 1
UAUGGCCAGAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAACGCCGAAACUCCAGAAACGCUGUUAGAAACUGUAAAAACU
..(((((((.((((......)))))))))))........((((...((((.(((..(.((((((((...((((.....)))))))))))).)....))).))))...))))......... ( -37.50)
>DroYak_CAF1 121802 120 - 1
UAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAACGCCGAAACUCCAAAAACGCUGCUGGAAACUGUACAAACU
(((..((...((((((........)))))).))..))).((((...((((.(((..(.((((((((...((((.....)))))))))))).)....))).))))...))))......... ( -37.60)
>consensus
UAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAACGCCGAAACUCCAAAAACGCUGCUGGAAAGUGUAAAAACU
(((..((...((((((........)))))).))..)))...(((..((((.(((..(.((((((((...((((.....)))))))))))).)....))).)))).)))............ (-33.00 = -33.08 +   0.08)

alignment

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secondary structure

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Window 0

Location 11,383,896 – 11,384,016
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.20
Mean single sequence MFE -34.54
Consensus MFE -29.98
Energy contribution -30.98
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.87
SVM decision value 2.38
SVM RNA-class probability 0.993169
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383896 120 - 27905053
UUUUAUUUUUUUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAAAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAA
........(((((((((((((((....(((.((..((((((((..((...(((((..........))))).))..)))))..)))..)).))).)))))))).((....))..))))))) ( -31.30)
>DroSec_CAF1 131623 116 - 1
CCUU--UU--UUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGAUGAGGAAA
((((--..--.....((((((((....(((.((..((((((((..((...((((((........)))))).))..)))))..)))..)).))).))))))))(((....))).))))... ( -39.30)
>DroSim_CAF1 122724 118 - 1
UCUU--UUUUUUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAA
((((--(........((((((((....(((.((..((((((((..((...((((((........)))))).))..)))))..)))..)).))).)))))))).((....))..))))).. ( -36.20)
>DroEre_CAF1 119095 109 - 1
UUU-------U---UUGCAG-CUUCUUUGAGGCAAUGAUUUAUGGCCAGAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAA
.((-------(---(..(((-(...((((((((.....(((.(((((((.((((......))))))))))).)))((((.((.....)).)))).....))))))))...))))..)))) ( -33.80)
>DroYak_CAF1 121842 113 - 1
UUU-------UUUUUUGCUGCCUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAA
.((-------((((((((((((((....)))))..((((((((..((...((((((........)))))).))..)))))..))).)))).............((....))..))))))) ( -32.10)
>consensus
UUUU__UU__UUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAAGUUCAAGGCAUCGUAAGUAGUUUCGGAAACGUUGAGGAAA
................(((((((....(((.((..((((((((..((...((((((........)))))).))..)))))..)))..)).))).)))))))..((....))......... (-29.98 = -30.98 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,383,936 – 11,384,055
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.26
Mean single sequence MFE -28.07
Consensus MFE -21.31
Energy contribution -20.83
Covariance contribution -0.48
Combinations/Pair 1.14
Mean z-score -2.00
Structure conservation index 0.76
SVM decision value 0.78
SVM RNA-class probability 0.847621
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383936 119 + 27905053
UUCAUUUCCCGGCCAGGACCUUUUUUGGCCUUUGGCCAUAAAUCAUUGCCUCAAAGAAAGCAGCCAAAAAAAAAAUAAAAAGAGAAAUACGAGA-AAAAGAGGUAAAUAAAAAGGUAGAG
....(((.(((((((((.((......))))..)))))........(((((((..........................................-....))))))).......)).))). ( -21.75)
>DroSec_CAF1 131663 115 + 1
UUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUAAAUCAUUGCCUCAAAGAAAGCAGCCAAAAA--AA--AAGGAGAGAAAUCCGAGA-AAAAGGGGUAAAUAAAAAGGUAGAG
......((((((((((((....))))))))((((((......((.(((...))).)).....))))))..--..--..(((......)))....-....))))................. ( -27.50)
>DroSim_CAF1 122764 117 + 1
UUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUAAAUCAUUGCCUCAAAGAAAGCAGCCAAAAAAAAA--AAGAAGAGAAAUCCGAGG-AAAAGGGGUAAAUAAAAAGGUAGAG
......((((((((((((....))))))))((((((......((.(((...))).)).....))))))......--.....((....)).....-....))))................. ( -25.10)
>DroEre_CAF1 119135 109 + 1
UUCAUUUCCCGGCCAGGACCUUUUCUGGCCUCUGGCCAUAAAUCAUUGCCUCAAAGAAG-CUGCAA---A-------AAAAGAGAAAUCCGAGGCAAAAGGGGUAAAUAAGGAGGUGGGG
(((((((((.(((((((.((......)).).))))))........(((((((...(...-...)..---.-------....((....)).))))))).............))))))))). ( -35.10)
>DroYak_CAF1 121882 112 + 1
UUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUAAAUCAUUGCCUCAAAGAAGGCAGCAAAAAA-------AAAAGAGAAAUCCGAGG-AAACGGGGUAAAUAAAAAGGUAGAG
......(((((.((.(((..((((((((((...))))........((((((......)))))).......-------...)))))).)))..))-...)))))................. ( -30.90)
>consensus
UUCAUUUCCCGGCCAGGACCUUUUCUGGCCUUUGGCCAUAAAUCAUUGCCUCAAAGAAAGCAGCCAAAAA__AA__AAAAAGAGAAAUCCGAGG_AAAAGGGGUAAAUAAAAAGGUAGAG
....(((.(((((((((.((......))))..)))))........(((((((...............................................))))))).......)).))). (-21.31 = -20.83 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,383,936 – 11,384,055
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.26
Mean single sequence MFE -30.98
Consensus MFE -24.14
Energy contribution -23.94
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -2.79
Structure conservation index 0.78
SVM decision value 2.15
SVM RNA-class probability 0.989086
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383936 119 - 27905053
CUCUACCUUUUUAUUUACCUCUUUU-UCUCGUAUUUCUCUUUUUAUUUUUUUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAAAAAAGGUCCUGGCCGGGAAAUGAA
.........................-.....((((((((...................((((((....)))))).........(((((..((((......)))).))))))))))))).. ( -25.70)
>DroSec_CAF1 131663 115 - 1
CUCUACCUUUUUAUUUACCCCUUUU-UCUCGGAUUUCUCUCCUU--UU--UUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAA
.........(((((((.(((.....-....(((......)))..--..--..((((((((((((....)))))..........)))))))((((((........)))))))))))))))) ( -30.80)
>DroSim_CAF1 122764 117 - 1
CUCUACCUUUUUAUUUACCCCUUUU-CCUCGGAUUUCUCUUCUU--UUUUUUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAA
.........(((((((.(((.....-..................--......((((((((((((....)))))..........)))))))((((((........)))))))))))))))) ( -29.10)
>DroEre_CAF1 119135 109 - 1
CCCCACCUCCUUAUUUACCCCUUUUGCCUCGGAUUUCUCUUUU-------U---UUGCAG-CUUCUUUGAGGCAAUGAUUUAUGGCCAGAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAA
..........((((((.(((...((((((((((...(((....-------.---..).))-....))))))))))........((((((.((((......))))))))))))))))))). ( -37.20)
>DroYak_CAF1 121882 112 - 1
CUCUACCUUUUUAUUUACCCCGUUU-CCUCGGAUUUCUCUUUU-------UUUUUUGCUGCCUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAA
....................(((((-((.(((......(((((-------((..((..((((((....))))))..))....(((((...))))))))))))......)))))))))).. ( -32.10)
>consensus
CUCUACCUUUUUAUUUACCCCUUUU_CCUCGGAUUUCUCUUUUU__UU__UUUUUGGCUGCUUUCUUUGAGGCAAUGAUUUAUGGCCAAAGGCCAGAAAAGGUCCUGGCCGGGAAAUGAA
..........((((((.(((.......................................(((((....)))))..........(((((..((((......)))).)))))))))))))). (-24.14 = -23.94 +  -0.20)

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 11:23:24 2006