Locus 3552

Sequence ID X_DroMel_CAF1
Location 9,526,968 – 9,527,125
Length 157
Max. P 0.594780
window5811 window5812 window5813

overview

Window 1

Location 9,526,968 – 9,527,088
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.28
Mean single sequence MFE -37.20
Consensus MFE -22.42
Energy contribution -21.82
Covariance contribution -0.61
Combinations/Pair 1.24
Mean z-score -1.68
Structure conservation index 0.60
SVM decision value -0.04
SVM RNA-class probability 0.511720
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9526968 120 + 22224390
UAAUCACCUGGUAUGGCGUUCAUGCCAUUGUUGCCAUUAUUCGAUAUUGACAUGGGCAUUGAGUUGACCAUACCCAUCUGAGUGCCCACCACCUGCUGCAUGCCGCCCUGGUUGGGUGAC
...((((((..(..((((..(((((((.(((((........))))).))...((((((((.((.((........)).)).)))))))).........))))).))))...)..)))))). ( -41.80)
>DroVir_CAF1 15981 114 + 1
GAAUUACCUGGUAUAGCAUUCAUGCCAUUAUUGCCAUUAUUUGAUAUGGACAUGGGCAUAGAAUUAACCAUGCCCAUUUGUGUAGUCAC------UUGUAUGCCACCCGUGUUAGGCGAU
........((((((.......))))))..((((((......((((((((..((((((((.(......).))))))))..(((....)))------...........)))))))))))))) ( -29.80)
>DroGri_CAF1 11150 114 + 1
GACUUACCUGGUAUGGUAUUCAUGCCAUUGUUGCCAUUAUUCGAUAUGGACAUGGGCAUUGAAUUGACCAUGCCCAUUUGUGUCGCAAC------CUGCAUGCCACCGGUGUUGGGCGAU
........(((((((.....)))))))..((((((......(((((..((..(((((((.(......).)))))))))..)))))((((------(((........))).)))))))))) ( -37.90)
>DroWil_CAF1 11369 114 + 1
CUCUUACCUGGUAUGGCGUUCAUUCCAUUAUUGCCAUUAUUCGAUAUGGACAUGGGCAUUGAGUUGACCAUGCCCAUUUGUGCGGCC---ACUUGCUGCAUGCCAGU---GUUGGGUGAU
...((((((..((((((......(((((.((((........))))))))).((((((((.(......).))))))))..(((((((.---....))))))))))).)---)..)))))). ( -40.70)
>DroMoj_CAF1 11729 112 + 1
--CUUACCUGGUAUGGAAUUCAUGCCGUUGUUGCCAUUAUUCGAUAUGGACAUGGGCAUUGAGUUGACCAUGCCCAUCUGUGUGGCCAC------CUGCAUGCCAGCCGUGUUGGGCGAU
--.(..(((..(((((....(((((....((.(((((....((..((((.(((((.((......)).))))).)))).)).))))).))------..)))))....)))))..)))..). ( -37.80)
>DroAna_CAF1 15749 120 + 1
CACUCACCUGGUAUGGCAUUCAUUCCGUUGUUGCCGUUAUUCGAUAUGGACAUGGGCAUCGAGUUGACCAUGCCCAUCUGUGUGCCCACCACCUGCUGCAUGCCGCCCUGGUUGGGACUC
..((((.(..(..((((((.((.(((((.((((........)))))))))..(((((((..((.((........)).))..)))))))........)).))))))..)..).)))).... ( -35.20)
>consensus
CACUUACCUGGUAUGGCAUUCAUGCCAUUGUUGCCAUUAUUCGAUAUGGACAUGGGCAUUGAGUUGACCAUGCCCAUCUGUGUGGCCAC______CUGCAUGCCACCCGUGUUGGGCGAU
......(((..(.((((((.((..((((.((((........))))))))..((((((((.(......).))))))))...................)).)))))).....)..))).... (-22.42 = -21.82 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,526,968 – 9,527,088
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.28
Mean single sequence MFE -35.12
Consensus MFE -20.82
Energy contribution -21.40
Covariance contribution 0.58
Combinations/Pair 1.15
Mean z-score -1.87
Structure conservation index 0.59
SVM decision value 0.09
SVM RNA-class probability 0.578214
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9526968 120 - 22224390
GUCACCCAACCAGGGCGGCAUGCAGCAGGUGGUGGGCACUCAGAUGGGUAUGGUCAACUCAAUGCCCAUGUCAAUAUCGAAUAAUGGCAACAAUGGCAUGAACGCCAUACCAGGUGAUUA
((((((.......((((.(((((....((((...((((......(((((((.(......).)))))))))))..))))......((....))...)))))..))))......)))))).. ( -38.02)
>DroVir_CAF1 15981 114 - 1
AUCGCCUAACACGGGUGGCAUACAA------GUGACUACACAAAUGGGCAUGGUUAAUUCUAUGCCCAUGUCCAUAUCAAAUAAUGGCAAUAAUGGCAUGAAUGCUAUACCAGGUAAUUC
...((((.....(((((((((....------(((.(((.....((((((((((......))))))))))(.((((........))))).....))))))..))))))).))))))..... ( -33.40)
>DroGri_CAF1 11150 114 - 1
AUCGCCCAACACCGGUGGCAUGCAG------GUUGCGACACAAAUGGGCAUGGUCAAUUCAAUGCCCAUGUCCAUAUCGAAUAAUGGCAACAAUGGCAUGAAUACCAUACCAGGUAAGUC
.(((((.......)))))(((((..------(((((((((....(((((((((.....)).)))))))))))(((........))))))))....)))))..((((......)))).... ( -35.90)
>DroWil_CAF1 11369 114 - 1
AUCACCCAAC---ACUGGCAUGCAGCAAGU---GGCCGCACAAAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGAAUAAUGGCAAUAAUGGAAUGAACGCCAUACCAGGUAAGAG
...(((...(---(((.((.....)).)))---)((((.....((((((((((.((......)).)))))))))).........)))).....(((.(((.....))).))))))..... ( -31.64)
>DroMoj_CAF1 11729 112 - 1
AUCGCCCAACACGGCUGGCAUGCAG------GUGGCCACACAGAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGAAUAAUGGCAACAACGGCAUGAAUUCCAUACCAGGUAAG--
((((((......)))((((((((..------((.((((.....((((((((((.((......)).)))))))))).........)))).))....)))))....))).....)))...-- ( -34.44)
>DroAna_CAF1 15749 120 - 1
GAGUCCCAACCAGGGCGGCAUGCAGCAGGUGGUGGGCACACAGAUGGGCAUGGUCAACUCGAUGCCCAUGUCCAUAUCGAAUAACGGCAACAACGGAAUGAAUGCCAUACCAGGUGAGUG
..((((......))))..(((.((.(.((((...((((..((.((((((((((.((......)).))))))))))..........(....).......))..)))).)))).).)).))) ( -37.30)
>consensus
AUCGCCCAACACGGGUGGCAUGCAG______GUGGCCACACAAAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGAAUAAUGGCAACAAUGGCAUGAAUGCCAUACCAGGUAAGUC
...(((..........(.(((..........(((....)))..((((((((((.((......)).))))))))))........))).)......((.(((.....))).)).)))..... (-20.82 = -21.40 +   0.58)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,527,008 – 9,527,125
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.97
Mean single sequence MFE -38.12
Consensus MFE -22.16
Energy contribution -22.85
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -1.76
Structure conservation index 0.58
SVM decision value 0.12
SVM RNA-class probability 0.594780
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9527008 117 - 22224390
GCAUGCAGCAGCUGGGCA---GCAAGUCGCCCAACCUGCAGUCACCCAACCAGGGCGGCAUGCAGCAGGUGGUGGGCACUCAGAUGGGUAUGGUCAACUCAAUGCCCAUGUCAAUAUCGA
((.((((((((.(((((.---.......)))))..)))).(((.(((.....))).))).)))))).((((...((((......(((((((.(......).)))))))))))..)))).. ( -44.30)
>DroGri_CAF1 11190 111 - 1
GCAUGAAUCAACUUGGCA---GCAAGUCACCCAAUUUACAAUCGCCCAACACCGGUGGCAUGCAG------GUUGCGACACAAAUGGGCAUGGUCAAUUCAAUGCCCAUGUCCAUAUCGA
...(((..(((((((.((---....((((((......................)))))).)))))------))))........((((((((((.((......)).)))))))))).))). ( -31.05)
>DroWil_CAF1 11409 114 - 1
GAAUGCAACAAUUGGGCAGUAGCAAGUCACCGAAUCUACAAUCACCCAAC---ACUGGCAUGCAGCAAGU---GGCCGCACAAAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGA
((.(((.....(((((..((((....((...))..)))).....)))))(---(((.((.....)).)))---)...)))...((((((((((.((......)).)))))))))).)).. ( -31.80)
>DroMoj_CAF1 11767 111 - 1
GCAUGAAUCAACUGGGCA---GCAAGUCGCCUAACCUGCAAUCGCCCAACACGGCUGGCAUGCAG------GUGGCCACACAGAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGA
...(((.....((((((.---....)))(((..(((((((.(((((......))).))..)))))------)))))....)))((((((((((.((......)).)))))))))).))). ( -39.70)
>DroAna_CAF1 15789 117 - 1
GGAUGCAGCAACUGGGCA---GCAAGUCGCCCAAUCUGCAGAGUCCCAACCAGGGCGGCAUGCAGCAGGUGGUGGGCACACAGAUGGGCAUGGUCAACUCGAUGCCCAUGUCCAUAUCGA
((((((((....(((((.---.......)))))..))))...((((((.(((..((........))...))))))).))....((((((((.(......).))))))))))))....... ( -45.20)
>DroPer_CAF1 8765 114 - 1
GGAUGAACCAAUUGGGCA---GCAAAUCCCCAAAUCUGCAGUCGCCCAAUCAGAGCGUCAUGCAGCAGGU---UGCCACACAGAUGGGCAUGGUAAAUUCGAUGCCCAUGUCGAUAUCGA
((...((((..(((((.(---.....).)))))..((((((.(((.(.....).))).).)))))..)))---).))......((((((((.(......).)))))))).(((....))) ( -36.70)
>consensus
GCAUGAAGCAACUGGGCA___GCAAGUCGCCCAAUCUGCAAUCGCCCAACCAGGGCGGCAUGCAGCAGGU_GUGGCCACACAGAUGGGCAUGGUCAACUCAAUGCCCAUGUCCAUAUCGA
..............(((....(((.((((((......................)))))).)))....................((((((((.(......).)))))))))))........ (-22.16 = -22.85 +   0.69)

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 11:02:13 2006