Locus 1543

Sequence ID X_DroMel_CAF1
Location 4,452,025 – 4,452,168
Length 143
Max. P 0.990510
window2526 window2527 window2528

overview

Window 6

Location 4,452,025 – 4,452,128
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.29
Mean single sequence MFE -27.74
Consensus MFE -17.72
Energy contribution -17.76
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -2.74
Structure conservation index 0.64
SVM decision value 0.70
SVM RNA-class probability 0.826810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4452025 103 + 22224390
-------UCACCAUU------AUAGAG----AGAGUAUCUCAGCUCCCCUUCCCCUAAAUGGAAACCACCAUGUUUUUGGGGCCAAAUCCCCAUCACGGAUAGUUUUUCCGGAUACACAA
-------...(((((------.(((.(----(((((......))))....))..)))))))).........(((....((((......))))(((.((((.......)))))))..))). ( -21.90)
>DroSec_CAF1 53494 107 + 1
-------CCACCAUU------AUAGAGAGAGAGAGUAUCUCAGCUCCCCUUCCCCUAAAUGGAAGCCCCUCUGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAA
-------...(((((------.(((.(..((.((((......))))..))..).))))))))..(((((.........))))).........(((.((((.......)))))))...... ( -29.40)
>DroSim_CAF1 54831 105 + 1
-------CCACCAUU------AUAGAGA--GAGAGUAUCUCAGCUCCCCUUCCCCUAAAUGGAAGCCCCUCUGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAA
-------........------...(.((--(((((((((((((.....(((((.......))))).....)))....(((((......)))))....))))))))))))).......... ( -27.50)
>DroEre_CAF1 55475 107 + 1
CUGUCAUCCACCAUU------AUAGAG----AGAGUAUCUCGACUCCUCUUCCCCUAAAUGGAAACCCC--UGUU-UUGGGGCCAAAUUCCCAUCACGGAUACUUUUUCCGGAUACACAA
.(((.((((.(((((------..((((----.((((......)))))))).......)))))......(--(((.-.(((((......)))))..))))...........)))))))... ( -27.90)
>DroYak_CAF1 54201 114 + 1
CUGUCAUCCACCAUUAUGAUUAUGGAG----AGAGUAUCUCAGCUCCUCUUCCCCUAAAUGGAAACCCC--UGUUUUUGGGGCCGAAUCGCCAUCACGGAUACUUUUUCCGGAUACACAA
.(((.((((..(.....).....((((----(((((((((..((...((..((((.((((((......)--)))))..))))..))...))......))))))))))))))))))))... ( -32.00)
>consensus
_______CCACCAUU______AUAGAG____AGAGUAUCUCAGCUCCCCUUCCCCUAAAUGGAAACCCC__UGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAA
..................................(((((..........((((.......)))).............(((((......)))))...((((.......))))))))).... (-17.72 = -17.76 +   0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,452,048 – 4,452,168
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.82
Mean single sequence MFE -25.15
Consensus MFE -20.98
Energy contribution -21.18
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -2.27
Structure conservation index 0.83
SVM decision value 2.22
SVM RNA-class probability 0.990510
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4452048 120 + 22224390
CAGCUCCCCUUCCCCUAAAUGGAAACCACCAUGUUUUUGGGGCCAAAUCCCCAUCACGGAUAGUUUUUCCGGAUACACAACUUGCAUUCCACUUUAGCUGUUUACUUAGCACUCCACAGA
..(((.........((((((((((..............((((......))))(((.((((.......)))))))............))))).)))))..........))).......... ( -23.71)
>DroSec_CAF1 53521 120 + 1
CAGCUCCCCUUCCCCUAAAUGGAAGCCCCUCUGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAACUUGCAUUCCACUUUAGCUGUUUACUCAGCACUCCACAGA
...............((((((((((((((.........))))).........(((.((((.......)))))))............))))).))))((((......)))).......... ( -27.80)
>DroSim_CAF1 54856 120 + 1
CAGCUCCCCUUCCCCUAAAUGGAAGCCCCUCUGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAACUUGCAUUCCACUUUAGCUGUUUACUCAGCACUCCACAGA
...............((((((((((((((.........))))).........(((.((((.......)))))))............))))).))))((((......)))).......... ( -27.80)
>DroEre_CAF1 55505 117 + 1
CGACUCCUCUUCCCCUAAAUGGAAACCCC--UGUU-UUGGGGCCAAAUUCCCAUCACGGAUACUUUUUCCGGAUACACAACUUGCAUUCCACUUUAGCUGUUUACUUUGCACUCCACAGA
..............((((((((((.((((--....-..))))..........(((.((((.......)))))))............))))).)))))((((..............)))). ( -23.04)
>DroYak_CAF1 54237 118 + 1
CAGCUCCUCUUCCCCUAAAUGGAAACCCC--UGUUUUUGGGGCCGAAUCGCCAUCACGGAUACUUUUUCCGGAUACACAACUUGCACUCCACUUUAGCUGUUUACUUAGCACUCCACAGA
..((...((..((((.((((((......)--)))))..))))..))......(((.((((.......))))))).........))...........((((......)))).......... ( -23.40)
>consensus
CAGCUCCCCUUCCCCUAAAUGGAAACCCC__UGUUUUUGGGGCCAAAUCCCCAUCACGGAUACUUUUUCCGGAUACACAACUUGCAUUCCACUUUAGCUGUUUACUUAGCACUCCACAGA
...............(((((((((.......(((....((((......))))(((.((((.......)))))))..))).......))))).))))((((......)))).......... (-20.98 = -21.18 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,452,048 – 4,452,168
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.82
Mean single sequence MFE -33.56
Consensus MFE -28.52
Energy contribution -28.36
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.37
Structure conservation index 0.85
SVM decision value 0.37
SVM RNA-class probability 0.707888
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4452048 120 - 22224390
UCUGUGGAGUGCUAAGUAAACAGCUAAAGUGGAAUGCAAGUUGUGUAUCCGGAAAAACUAUCCGUGAUGGGGAUUUGGCCCCAAAAACAUGGUGGUUUCCAUUUAGGGGAAGGGGAGCUG
....................(((((.....(((.((((.....)))))))((((..((((.(((((.(((((......)))))....)))))))))))))...............))))) ( -31.80)
>DroSec_CAF1 53521 120 - 1
UCUGUGGAGUGCUGAGUAAACAGCUAAAGUGGAAUGCAAGUUGUGUAUCCGGAAAAAGUAUCCGUGAUGGGGAUUUGGCCCCAAAAACAGAGGGGCUUCCAUUUAGGGGAAGGGGAGCUG
((((((((..((((......)))).....((((.((((.....)))))))).........)))....(((((......)))))...)))))..(((((((.(((....))).))))))). ( -37.00)
>DroSim_CAF1 54856 120 - 1
UCUGUGGAGUGCUGAGUAAACAGCUAAAGUGGAAUGCAAGUUGUGUAUCCGGAAAAAGUAUCCGUGAUGGGGAUUUGGCCCCAAAAACAGAGGGGCUUCCAUUUAGGGGAAGGGGAGCUG
((((((((..((((......)))).....((((.((((.....)))))))).........)))....(((((......)))))...)))))..(((((((.(((....))).))))))). ( -37.00)
>DroEre_CAF1 55505 117 - 1
UCUGUGGAGUGCAAAGUAAACAGCUAAAGUGGAAUGCAAGUUGUGUAUCCGGAAAAAGUAUCCGUGAUGGGAAUUUGGCCCCAA-AACA--GGGGUUUCCAUUUAGGGGAAGAGGAGUCG
.((((..(.(....).)..))))((.((((((((..((((((.(.((((((((.......)))).)))).)))))))(((((..-....--))))))))))))).))............. ( -31.90)
>DroYak_CAF1 54237 118 - 1
UCUGUGGAGUGCUAAGUAAACAGCUAAAGUGGAGUGCAAGUUGUGUAUCCGGAAAAAGUAUCCGUGAUGGCGAUUCGGCCCCAAAAACA--GGGGUUUCCAUUUAGGGGAAGAGGAGCUG
.((((..(.(....).)..))))((.((((((((..(.((((((.((((((((.......)))).)))))))))).)(((((.......--))))))))))))).))............. ( -30.10)
>consensus
UCUGUGGAGUGCUAAGUAAACAGCUAAAGUGGAAUGCAAGUUGUGUAUCCGGAAAAAGUAUCCGUGAUGGGGAUUUGGCCCCAAAAACA__GGGGUUUCCAUUUAGGGGAAGGGGAGCUG
.((((....(((...))).))))((.((((((((..((((((.(.((((((((.......)))).))))).))))))(((((.........))))))))))))).))............. (-28.52 = -28.36 +  -0.16)

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 10:12:59 2006