Locus 4818

Sequence ID 3L_DroMel_CAF1
Location 13,512,662 – 13,512,851
Length 189
Max. P 0.758303
window7592 window7593 window7594

overview

Window 2

Location 13,512,662 – 13,512,782
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.88
Mean single sequence MFE -32.13
Consensus MFE -30.52
Energy contribution -30.58
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -0.83
Structure conservation index 0.95
SVM decision value 0.08
SVM RNA-class probability 0.574498
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13512662 120 + 23771897
GUGAAUUGCGUUUAAGGAACUCCGAUUGUUAAUAGGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCCG
((((((...(((...((....))((((.(....).))))))).(((.(((.(((((.......(((((....)))))........)))))...))).)))))))))((((.....)))). ( -33.16)
>DroVir_CAF1 10352 120 + 1
GUAAGUUACGCUUGAGGAACUCCGAUUGUUAAUAAGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCUG
..(((((.((.((((((.....(((((........)))))...(((........))).)))))).))))))).(((((..((((.((((...(((...)))....)))).)))).))))) ( -31.50)
>DroPse_CAF1 2 117 + 1
---AAUUACACUUAAGGAACUCCGAUUGUUAAUAGGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCCG
---............((....))((((.(....).))))((.((((.(((.(((((.......(((((....)))))........)))))...))).)))).))..((((.....)))). ( -32.56)
>DroGri_CAF1 5436 120 + 1
GUAAGUUGCGAUUAAGGAACUCCGAUUGUUAAUAAGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUAGCCUGAAUGGCCG
.......((.(((.(((......((((........))))((.((((.(((.(((((.......(((((....)))))........)))))...))).)))).))....))).))).)).. ( -29.96)
>DroMoj_CAF1 15 120 + 1
GUUGGUUACGCUUAAGGAACUCCGAUUGUUAAUAAGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCCG
((..(((((.((((...(((.......)))..)))))).)))..)).(((.(((((.......(((((....)))))........)))))...))).((((((((.....)))))))).. ( -33.06)
>DroPer_CAF1 2 117 + 1
---AAUUACACUUAAGGAACUCCGAUUGUUAAUAGGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCCG
---............((....))((((.(....).))))((.((((.(((.(((((.......(((((....)))))........)))))...))).)))).))..((((.....)))). ( -32.56)
>consensus
GU_AAUUACGCUUAAGGAACUCCGAUUGUUAAUAAGGUCGACUGGCAUCCUUUGGCCGCUUCAAUUGAACUUUCAGUCUUUUCAUGCCAAUCUGGAAGCCAUUCAUGGCCUGAAUGGCCG
...............((....))((((........))))((.((((.(((.(((((.......(((((....)))))........)))))...))).)))).))..((((.....)))). (-30.52 = -30.58 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,512,662 – 13,512,782
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.88
Mean single sequence MFE -30.69
Consensus MFE -30.09
Energy contribution -29.95
Covariance contribution -0.14
Combinations/Pair 1.03
Mean z-score -0.82
Structure conservation index 0.98
SVM decision value 0.49
SVM RNA-class probability 0.758303
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13512662 120 - 23771897
CGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCCUAUUAACAAUCGGAGUUCCUUAAACGCAAUUCAC
.((((.....)))).(((((.((.(((.(((((.........(((((....(((....)))(((.((...)).))))))))...........))))))))(((.....))))).))))). ( -30.65)
>DroVir_CAF1 10352 120 - 1
CAGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCUUAUUAACAAUCGGAGUUCCUCAAGCGUAACUUAC
.(((((((((.....)))))))))(((.(((((..((((...(((((....(((....)))(((.((...)).))))))))....))))...)))))))).................... ( -31.20)
>DroPse_CAF1 2 117 - 1
CGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCCUAUUAACAAUCGGAGUUCCUUAAGUGUAAUU---
.(((((((((.....)))))))))(((.(((((.........(((((....(((....)))(((.((...)).))))))))...........)))))))).................--- ( -29.95)
>DroGri_CAF1 5436 120 - 1
CGGCCAUUCAGGCUAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCUUAUUAACAAUCGGAGUUCCUUAAUCGCAACUUAC
.(((((((((.....)))))))))(((.(((((..((((...(((((....(((....)))(((.((...)).))))))))....))))...)))))))).................... ( -31.20)
>DroMoj_CAF1 15 120 - 1
CGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCUUAUUAACAAUCGGAGUUCCUUAAGCGUAACCAAC
.(((((((((.....)))))))))(((.(((((..((((...(((((....(((....)))(((.((...)).))))))))....))))...)))))))).................... ( -31.20)
>DroPer_CAF1 2 117 - 1
CGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCCUAUUAACAAUCGGAGUUCCUUAAGUGUAAUU---
.(((((((((.....)))))))))(((.(((((.........(((((....(((....)))(((.((...)).))))))))...........)))))))).................--- ( -29.95)
>consensus
CGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAAAAGACUGAAAGUUCAAUUGAAGCGGCCAAAGGAUGCCAGUCGACCCUAUUAACAAUCGGAGUUCCUUAAGCGUAACU_AC
.(((((((((.....)))))))))(((.(((((.........(((((....(((....)))(((.((...)).))))))))...........)))))))).................... (-30.09 = -29.95 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,512,742 – 13,512,851
Length 109
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.35
Mean single sequence MFE -28.45
Consensus MFE -19.81
Energy contribution -20.17
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.55
Structure conservation index 0.70
SVM decision value 0.43
SVM RNA-class probability 0.732313
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13512742 109 - 23771897
UUUGUCUAACGAGUUAUAUUUCA-U--UCU---UGGCAGGAUUUGUUUCAUUCGAUAAUCCCGCCAGCGCUCAAGCGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
....((....)).......((((-(--..(---((((.(((((....((....)).))))).)))))(((....)))((((.((((((((....))))))...)).))))))))) ( -31.20)
>DroVir_CAF1 10432 107 - 1
-AUUGCUAAC--AUUCAAUUUUGAA--AAU---UUGUAGGUUUUGUUUCAUUUGAUAACCCCACCAGCGCUCAAGCAGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
-..((((...--.((((....))))--(((---(((..((..(((((......)))))..))....((......))(((((((((.....)))))))))..)))))))))).... ( -26.30)
>DroGri_CAF1 5516 109 - 1
-UUGGCUAACGAAUCGAAUUAUGGU--AUU---UUAUAGGUUUUGUUUCAUUUGAUAACCCCACCAGCGCUCAAGCGGCCAUUCAGGCUAUGAAUGGCUUCCAGAUUGGCAUGAA
-.................(((((..--...---.....((..(((((......)))))..)).(((((((....)))((((((((.....)))))))).......))))))))). ( -25.60)
>DroMoj_CAF1 95 109 - 1
-AUUUCUAAU--AUUCAACUUUGUACAAUU---UUGUAGGUUUUGUUUCAUUUGAUAAUCCCACCAGCGCUCAAGCGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
-.........--.((((......((((...---.))))((..(((((......)))))..)).(((((((....)))((((((((.....)))))))).......))))..)))) ( -25.00)
>DroAna_CAF1 95 108 - 1
-CUGUCAGAUUAAU---AUUGCC-C--UCUUUGUUGCAGGUUUUGUUUCAUUUGAUAAUCCCGCCAGCGCUCAAGCGGCCAUUCAAGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
-.((((((((.(((---(..(((-.--.(......)..)))..))))..)))))))).....((((((((....)))((((((((.....)))))))).......)))))..... ( -32.60)
>DroPer_CAF1 79 107 - 1
UUUGCCUAAUCAA----AUGACU-C--UCUUU-AUGUAGGUUUCGUGUCCUUCGAUAAUCCAGCCAGCGCUCAAGCGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
...(((((.....----((((..-.--...))-)).)))))((((((((..((..............(((....)))((((((((.....)))))))).....))..)))))))) ( -30.00)
>consensus
_UUGUCUAAC_AAUU_AAUUUCG_A__ACU___UUGUAGGUUUUGUUUCAUUUGAUAAUCCCACCAGCGCUCAAGCGGCCAUUCAGGCCAUGAAUGGCUUCCAGAUUGGCAUGAA
......................................((..(((((......)))))..)).(((((((....))(((((((((.....)))))))))....).))))...... (-19.81 = -20.17 +   0.36)

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 11:34:16 2006