Locus 2119

Sequence ID 3R_DroMel_CAF1
Location 6,053,158 – 6,053,281
Length 123
Max. P 0.984249
window3463 window3464 window3465

overview

Window 3

Location 6,053,158 – 6,053,263
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.50
Mean single sequence MFE -33.98
Consensus MFE -20.61
Energy contribution -21.20
Covariance contribution 0.59
Combinations/Pair 1.12
Mean z-score -2.09
Structure conservation index 0.61
SVM decision value 1.97
SVM RNA-class probability 0.984249
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6053158 105 + 27905053
ACACACACGUGAGGUGGU-------ACCU-CUU-UUGGCCAUGGCUGAUAUGGCGAG------CUAUUGUUGGUGCCAUUGUUGCUGCAUUGUACGAGUGUGAUUCAUGUCAUGCUCUCA
(((..((.(..(((((((-------(((.-...-...((((((.....)))))).((------(....)))))))))))).)..)))...)))..(((((((((....)))))))))... ( -34.20)
>DroSec_CAF1 59060 92 + 1
-CACACACGUGAGAUGGU-------UCCU-CUU-UUGGCCAUGGCUGAUAUGGCCAG------CUAUU------------GUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA
-.......(((.((((..-------....-...-..(((((((.....)))))))((------(....------------...))).)))).)))(((((((((....)))))))))... ( -31.40)
>DroSim_CAF1 60386 93 + 1
-CACACACGUGAGGUAGU-------GCCU-CUUUUUGGCCAUGGCUGAUAUGGCCAG------CUAUU------------GUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA
-.......(((..(((((-------..(.-.(..(((((((((.....)))))))))------..)..------------)..)))))....)))(((((((((....)))))))))... ( -34.30)
>DroEre_CAF1 59475 101 + 1
----ACGCCUCAUGUGAU-------GCCC-CUU-UUGGCCAUGGCUGAUAUGGCCAG------CCAUUGUUGCUGCCAUUGUUGCUGCAGUGUACGAGUGUGAUUCAUGUCACGCUCUCA
----..((.((....)).-------))..-...-(((((((((.....)))))))))------.((((((.((.((....)).)).))))))...(((((((((....)))))))))... ( -36.10)
>DroYak_CAF1 61648 105 + 1
ACACACACAUGAGGUGAU-------GCCU-CUU-UUGGCCAUGACUGAUAUGGCCAG------CUAUUGUUGCUGCCAUUGUUGCUGCAGUGCACGAGUGUGAUUCAUGUCACGCUCUCA
..........((((....-------.)))-)..-.((((((((.....))))))))(------(.(((((.((.((....)).)).)))))))..(((((((((....)))))))))... ( -38.90)
>DroAna_CAF1 53014 109 + 1
A--CCCACGGCAACUGCCCGCCCACCCAUCGUU-AUGGCCGUGUUUUGGAUGUGCAGAGGUGCCACUUUUUGCUGCCAUUGUUG--------UUUGAGUAUGAUUCAUGUCACGCUCGCA
.--...(((((((((((.((.(((..(((.((.-...)).)))...))).)).)))).(((((........)).))).))))))--------)..(((..((((....))))..)))... ( -29.00)
>consensus
_CACACACGUGAGGUGGU_______GCCU_CUU_UUGGCCAUGGCUGAUAUGGCCAG______CUAUUGUUGCUGCCAUUGUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA
...................................((((((((.....)))))))).......................................(((((((((....)))))))))... (-20.61 = -21.20 +   0.59)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,053,189 – 6,053,281
Length 92
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 78.98
Mean single sequence MFE -29.05
Consensus MFE -19.55
Energy contribution -19.97
Covariance contribution 0.42
Combinations/Pair 1.18
Mean z-score -2.07
Structure conservation index 0.67
SVM decision value 1.18
SVM RNA-class probability 0.927689
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6053189 92 + 27905053
AUGGCUGAUAUGGCGAG------CUAUUGUUGGUGCCAUUGUUGCUGCAUUGUACGAGUGUGAUUCAUGUCAUGCUCUCA--CACUCGACCAGCGAAAAG
.(((((.........))------)))((((((((..((.(((....))).))..(((((((((..(((...)))...)))--)))))))))))))).... ( -28.40)
>DroSec_CAF1 59090 80 + 1
AUGGCUGAUAUGGCCAG------CUAUU------------GUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA--CACUCGACCAGCGAAAAG
(((((((.......)))------)))).------------.((((((...(((..(((((((((....)))))))))..)--))......)))))).... ( -27.10)
>DroSim_CAF1 60417 80 + 1
AUGGCUGAUAUGGCCAG------CUAUU------------GUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA--CACUCGACCAGCGAAAAG
(((((((.......)))------)))).------------.((((((...(((..(((((((((....)))))))))..)--))......)))))).... ( -27.10)
>DroEre_CAF1 59502 92 + 1
AUGGCUGAUAUGGCCAG------CCAUUGUUGCUGCCAUUGUUGCUGCAGUGUACGAGUGUGAUUCAUGUCACGCUCUCA--CACUCGACCAGCGAAAAG
(((((((.......)))------))))..((((((.....((((....(((((..(((((((((....)))))))))..)--)))))))))))))).... ( -35.10)
>DroYak_CAF1 61679 92 + 1
AUGACUGAUAUGGCCAG------CUAUUGUUGCUGCCAUUGUUGCUGCAGUGCACGAGUGUGAUUCAUGUCACGCUCUCA--CACUCGACCAGCGAAAAG
..(((....(((((.((------(.......)))))))).)))((((.((((...(((((((((....)))))))))...--))))....))))...... ( -32.50)
>DroAna_CAF1 53051 92 + 1
GUGUUUUGGAUGUGCAGAGGUGCCACUUUUUGCUGCCAUUGUUG--------UUUGAGUAUGAUUCAUGUCACGCUCGCAAGCACUCGCCCUGCAAAAAG
.(((...((..((((...(((((........)).)))....(((--------(..(((..((((....))))..)))))))))))...))..)))..... ( -24.10)
>consensus
AUGGCUGAUAUGGCCAG______CUAUUGUUGCUGCCAUUGUUGCUGCAUUGUACGAGUGUGAUUCAUGUCACGCUCUCA__CACUCGACCAGCGAAAAG
.(((((.....))))).........................((((((........(((((((((....)))))))))((........)).)))))).... (-19.55 = -19.97 +   0.42)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,053,189 – 6,053,281
Length 92
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 78.98
Mean single sequence MFE -27.46
Consensus MFE -12.16
Energy contribution -12.83
Covariance contribution 0.67
Combinations/Pair 1.17
Mean z-score -2.32
Structure conservation index 0.44
SVM decision value 0.19
SVM RNA-class probability 0.625152
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6053189 92 - 27905053
CUUUUCGCUGGUCGAGUG--UGAGAGCAUGACAUGAAUCACACUCGUACAAUGCAGCAACAAUGGCACCAACAAUAG------CUCGCCAUAUCAGCCAU
......((((((((((((--(((...(((...)))..))))))))).))............(((((...........------...)))))..))))... ( -27.14)
>DroSec_CAF1 59090 80 - 1
CUUUUCGCUGGUCGAGUG--UGAGAGCGUGACAUGAAUCACACUCGUACAAUGCAGCAAC------------AAUAG------CUGGCCAUAUCAGCCAU
......((((((((((((--(((...(((...)))..))))))))).))....((((...------------....)------))).......))))... ( -26.40)
>DroSim_CAF1 60417 80 - 1
CUUUUCGCUGGUCGAGUG--UGAGAGCGUGACAUGAAUCACACUCGUACAAUGCAGCAAC------------AAUAG------CUGGCCAUAUCAGCCAU
......((((((((((((--(((...(((...)))..))))))))).))....((((...------------....)------))).......))))... ( -26.40)
>DroEre_CAF1 59502 92 - 1
CUUUUCGCUGGUCGAGUG--UGAGAGCGUGACAUGAAUCACACUCGUACACUGCAGCAACAAUGGCAGCAACAAUGG------CUGGCCAUAUCAGCCAU
......((((((..((((--((.(((.((((......)))).))).)))))).........((((((((.......)------)).)))))))))))... ( -31.90)
>DroYak_CAF1 61679 92 - 1
CUUUUCGCUGGUCGAGUG--UGAGAGCGUGACAUGAAUCACACUCGUGCACUGCAGCAACAAUGGCAGCAACAAUAG------CUGGCCAUAUCAGUCAU
......((((((((((((--(((...(((...)))..)))))))))(((......)))...((((((((.......)------)).)))))))))))... ( -30.60)
>DroAna_CAF1 53051 92 - 1
CUUUUUGCAGGGCGAGUGCUUGCGAGCGUGACAUGAAUCAUACUCAAA--------CAACAAUGGCAGCAAAAAGUGGCACCUCUGCACAUCCAAAACAC
.....(((((((...(((((((((((..(((......)))..)))...--------((....))...)))......))))))))))))............ ( -22.30)
>consensus
CUUUUCGCUGGUCGAGUG__UGAGAGCGUGACAUGAAUCACACUCGUACAAUGCAGCAACAAUGGCAGCAACAAUAG______CUGGCCAUAUCAGCCAU
......((((.(((......)))(((.((((......)))).)))........))))...........................((((.......)))). (-12.16 = -12.83 +   0.67)

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 10:27:54 2006