Locus 6858

Sequence ID X_DroMel_CAF1
Location 17,104,063 – 17,104,195
Length 132
Max. P 0.994163
window11223 window11224 window11225 window11226

overview

Window 3

Location 17,104,063 – 17,104,171
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 86.90
Mean single sequence MFE -35.14
Consensus MFE -24.66
Energy contribution -24.09
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -2.23
Structure conservation index 0.70
SVM decision value 0.79
SVM RNA-class probability 0.850784
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17104063 108 + 22224390
UGCACCAAAUGCAUCGAAUUCGGUCUUUUAAUCCG--AUCUGUAAGCAGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAAC-UGCAGCAGUUGAACGCAAUGCAGGUCA
.(((.....)))((((....))))..........(--(((((((.((((......(((.....)))(((((.....))))).)-))).((........))..)))))))). ( -34.20)
>DroSec_CAF1 110839 103 + 1
UGCUCCAAAUGCCUCGAAUUCGGCCUUUUAAUCCG--AUCUGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAACUUGCAGCAG------GCAAUACGGGUCA
.((((....(((((.....((((.........)))--).(((((((.........(((.....)))(((((.....))))).))))))).))------)))....)))).. ( -33.90)
>DroSim_CAF1 101557 103 + 1
UGCUCCAAAUGCUUCGAAUUCGGCCUUUUAAUCCG--AUCUGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAACUUGCAGCAG------GCAAUGCGGGUCA
.((.......)).(((....)))...........(--(((((((.((((((....(((.....)))(((((.....)))))......))).)------))..)))))))). ( -33.90)
>DroEre_CAF1 101736 100 + 1
UGCUCC----GCUUUAAAUUCGGCCUUUUAAUCCGCAGUCUGCGAGCCGCAGGCUGCCAACUUGGCUGGCCAUCUUGGCCAAC-UGCAGCAG------GCAAUGCGGGUCA
.(..((----((.........((((.........((((((((((...))))))))))......))))((((.....))))...-(((.....------)))..))))..). ( -38.56)
>consensus
UGCUCCAAAUGCUUCGAAUUCGGCCUUUUAAUCCG__AUCUGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAAC_UGCAGCAG______GCAAUGCGGGUCA
.((.......)).........(((((.............((((..((........(((.....)))(((((.....)))))....)).)))).............))))). (-24.66 = -24.09 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,104,063 – 17,104,171
Length 108
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 86.90
Mean single sequence MFE -39.10
Consensus MFE -26.73
Energy contribution -27.10
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -2.37
Structure conservation index 0.68
SVM decision value 0.80
SVM RNA-class probability 0.853109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17104063 108 - 22224390
UGACCUGCAUUGCGUUCAACUGCUGCA-GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCUGCUUACAGAU--CGGAUUAAAAGACCGAAUUCGAUGCAUUUGGUGCA
..((((((((((.((((..(((..(((-(((((((.....)))).(((.....)))....))))))...)))..--.((.........)))))).)))))))...)))... ( -38.20)
>DroSec_CAF1 110839 103 - 1
UGACCCGUAUUGC------CUGCUGCAAGUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCAGAU--CGGAUUAAAAGGCCGAAUUCGAGGCAUUUGGAGCA
.(..(((...(((------((.(((((((((((((.....)))).(((.....))).......))))))))).(--(((.........)))).....)))))..)))..). ( -40.40)
>DroSim_CAF1 101557 103 - 1
UGACCCGCAUUGC------CUGCUGCAAGUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCAGAU--CGGAUUAAAAGGCCGAAUUCGAAGCAUUUGGAGCA
.....((((((((------(.(((....(((((((.....)))))))..))).))))))..)))((((.(((((--((((((.........)))))))....)))))))). ( -36.60)
>DroEre_CAF1 101736 100 - 1
UGACCCGCAUUGC------CUGCUGCA-GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGCCUGCGGCUCGCAGACUGCGGAUUAAAAGGCCGAAUUUAAAGC----GGAGCA
.(..((((..(((------(.(((...-(((((((.....)))))))..))).))))((((..((..(((.....)))..))...))))..........))----))..). ( -41.20)
>consensus
UGACCCGCAUUGC______CUGCUGCA_GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCAGAU__CGGAUUAAAAGGCCGAAUUCGAAGCAUUUGGAGCA
.(..(((...(((........(((((....(((((.....)))))(((.....))).....))))).....((...(((.........)))...))...)))..)))..). (-26.73 = -27.10 +   0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,104,101 – 17,104,195
Length 94
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -33.02
Consensus MFE -20.66
Energy contribution -22.10
Covariance contribution 1.44
Combinations/Pair 1.16
Mean z-score -2.52
Structure conservation index 0.63
SVM decision value 2.04
SVM RNA-class probability 0.986395
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17104101 94 + 22224390
UGUAAGCAGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAAC-UGCAGCAGUUGAACGCAAUGCAGGUCAAUUGCUACGUUAAGUGCAUUGGCC
........(((((.(((..((((((((((((.....)))))..-.(.(((((((((..((...))...))))))))).)))))))))))))))). ( -34.10)
>DroSec_CAF1 110877 89 + 1
UGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAACUUGCAGCAG------GCAAUACGGGUCAAUUGCUGCGUUAAGUGCAUUGGCU
........(((((.(((..((((((((((((.....)))))....(((((((------((.......)))...))))))))))))))))))))). ( -33.80)
>DroSim_CAF1 101595 89 + 1
UGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAACUUGCAGCAG------GCAAUGCGGGUCAAUUGCUGCGUUAAGUGCAUUGGCU
........(((((.(((..((((((((((((.....)))))....(((((((------((.......)))...))))))))))))))))))))). ( -33.80)
>DroEre_CAF1 101772 88 + 1
UGCGAGCCGCAGGCUGCCAACUUGGCUGGCCAUCUUGGCCAAC-UGCAGCAG------GCAAUGCGGGUCAAUUGCAGAGCUGAGUGCAUUGCCA
.....((.((((...(((.....)))(((((.....))))).)-))).)).(------(((((((((.((.......)).))....)))))))). ( -37.70)
>DroYak_CAF1 106476 71 + 1
----AUCUGCAAGCUGCUAACUU-------------GGCCAAC-UGUAGUUG------GCAAUGCGGGUCAAUUGCAGAGUUGAGUGCAUUGGCA
----.(((((((...(((..(..-------------.((((((-....))))------))...)..)))...)))))))((..(.....)..)). ( -25.70)
>consensus
UGCAAGCCGCUAACUGCCAACUUGGCUGGCCAUCUUGGCCAAC_UGCAGCAG______GCAAUGCGGGUCAAUUGCUGCGUUAAGUGCAUUGGCA
........(((((.(((..((((((((((((.....))))).................(((((........)))))...))))))))))))))). (-20.66 = -22.10 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,104,101 – 17,104,195
Length 94
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 78.81
Mean single sequence MFE -32.32
Consensus MFE -18.36
Energy contribution -19.88
Covariance contribution 1.52
Combinations/Pair 1.17
Mean z-score -2.82
Structure conservation index 0.57
SVM decision value 2.46
SVM RNA-class probability 0.994163
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17104101 94 - 22224390
GGCCAAUGCACUUAACGUAGCAAUUGACCUGCAUUGCGUUCAACUGCUGCA-GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCUGCUUACA
(((.............((((((.((((..(((...))).)))).)))))).-..(((((.....))))))))..((.(((((....))))).)). ( -34.50)
>DroSec_CAF1 110877 89 - 1
AGCCAAUGCACUUAACGCAGCAAUUGACCCGUAUUGC------CUGCUGCAAGUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCA
......(((.......)))((((.....(((((((((------(.(((....(((((((.....)))))))..))).))))))..)))).)))). ( -32.80)
>DroSim_CAF1 101595 89 - 1
AGCCAAUGCACUUAACGCAGCAAUUGACCCGCAUUGC------CUGCUGCAAGUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCA
......(((.......)))((((.....(((((((((------(.(((....(((((((.....)))))))..))).))))))..)))).)))). ( -34.20)
>DroEre_CAF1 101772 88 - 1
UGGCAAUGCACUCAGCUCUGCAAUUGACCCGCAUUGC------CUGCUGCA-GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGCCUGCGGCUCGCA
.((((((((..((((........))))...)))))))------).((((((-(.(((((.....)))))(((.....)))...)))))))..... ( -39.70)
>DroYak_CAF1 106476 71 - 1
UGCCAAUGCACUCAACUCUGCAAUUGACCCGCAUUGC------CAACUACA-GUUGGCC-------------AAGUUAGCAGCUUGCAGAU----
(((....)))......((((((((((.(..((...((------((((....-)))))).-------------..))..)))).))))))).---- ( -20.40)
>consensus
AGCCAAUGCACUUAACGCAGCAAUUGACCCGCAUUGC______CUGCUGCA_GUUGGCCAAGAUGGCCAGCCAAGUUGGCAGUUAGCGGCUUGCA
...((((((..((((........))))...)))))).........(((((....(((((.....)))))(((.....))).....)))))..... (-18.36 = -19.88 +   1.52)

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 12:24:35 2006