Locus 1948

Sequence ID X_DroMel_CAF1
Location 5,319,373 – 5,319,586
Length 213
Max. P 0.938296
window3165 window3166 window3167 window3168

overview

Window 5

Location 5,319,373 – 5,319,493
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.18
Mean single sequence MFE -36.83
Consensus MFE -31.29
Energy contribution -31.30
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 0.11
SVM RNA-class probability 0.588161
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5319373 120 + 22224390
GGUGUUGGGGGGCUAGAGAAAAUCCACCUUGGCCAGAGGCCAUCCAGCUAUUAUUGCUGAUGCCUUUUUAUUUUAAUUCCCAAAUCGAAAAAGUUUCGCCUUGGCGAUUAGGCGAGUAAA
(((.((((((((((((.(........).))))))((((((.(((.(((.......))))))))))))..........)))))))))........(((((((........))))))).... ( -37.20)
>DroSim_CAF1 47284 118 + 1
GGGGU--GGGGGCCAGAGAAAAUCCUACUUGGCCAGAGGCCAUCCAGCUAUUAUUGCUGAUGCCUUUUUAUUUUAAUUCCCAAAUCGAAAAAGUUUCGCCCUGGCGAUUAGGCGAGUAAA
((..(--((((((((.((......))...)))))((((((.(((.(((.......))))))))))))...........))))..))........((((((..........)))))).... ( -36.60)
>DroEre_CAF1 58460 118 + 1
GUGGA--GGGGGCUAGAGUAAAUCCUCCCUGGCCAGAGGCCAUUUAGCUAUUAUUGCUGAUGCCUUUUUAUUUUAAUUCCCAAAUCGAAAAAGUUUCGCCUUGGCGAUUAGGCAAGUAAA
..(((--(((.((....))...))))))((.(((((((((...(((((.......))))).))))))......(((((.((((..((((.....))))..)))).)))))))).)).... ( -36.70)
>consensus
GGGGU__GGGGGCUAGAGAAAAUCCUCCUUGGCCAGAGGCCAUCCAGCUAUUAUUGCUGAUGCCUUUUUAUUUUAAUUCCCAAAUCGAAAAAGUUUCGCCUUGGCGAUUAGGCGAGUAAA
.......(((((((((............))))))((((((.(((.(((.......))))))))))))...........))).............(((((((........))))))).... (-31.29 = -31.30 +   0.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,319,413 – 5,319,533
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -30.37
Consensus MFE -30.58
Energy contribution -30.03
Covariance contribution -0.55
Combinations/Pair 1.12
Mean z-score -1.92
Structure conservation index 1.01
SVM decision value 1.27
SVM RNA-class probability 0.938296
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5319413 120 - 22224390
UUUCCGCAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUGGGAAUUAAAAUAAAAAGGCAUCAGCAAUAAUAGCUGGAUG
......(((((((((((((((((((.....))))))((((((...((((((........)))))))))))).....)))))))).............((....))......))))).... ( -32.00)
>DroSim_CAF1 47322 118 - 1
--UGCACAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAGGGCGAAACUUUUUCGAUUUGGGAAUUAAAAUAAAAAGGCAUCAGCAAUAAUAGCUGGAUG
--....(((((((((((((((((((.....))))))((((((...((((((........)))))))))))).....)))))))).............((....))......))))).... ( -32.30)
>DroEre_CAF1 58498 120 - 1
UUUGCACGGCUUUUCCAAGAAGCGCUUAAAGCGUUUAGAGUUUACUUGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUGGGAAUUAAAAUAAAAAGGCAUCAGCAAUAAUAGCUAAAUG
.......((((((((((((((((((.....))))))((((((...((((((........)))))))))))).....)))))))).............((....))......))))..... ( -26.80)
>consensus
UUUGCACAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUGGGAAUUAAAAUAAAAAGGCAUCAGCAAUAAUAGCUGGAUG
......(((((((((((((((((((.....))))))((((((...((((((........)))))))))))).....)))))))).............((....))......))))).... (-30.58 = -30.03 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,319,453 – 5,319,546
Length 93
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.77
Mean single sequence MFE -21.10
Consensus MFE -17.66
Energy contribution -17.00
Covariance contribution -0.66
Combinations/Pair 1.17
Mean z-score -0.58
Structure conservation index 0.84
SVM decision value 0.15
SVM RNA-class probability 0.606295
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5319453 93 - 22224390
UUAGCCC---------------------------ACCGAUUUUCCGCAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUG
...(((.---------------------------..(((((....((............((((((.....)))))).(((....)))))..)))))....)))................. ( -19.70)
>DroSim_CAF1 47362 80 - 1
UU----------------------------------------UGCACAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAGGGCGAAACUUUUUCGAUUUG
..----------------------------------------.................((((((.....))))))((((((...((((((........))))))))))))......... ( -17.70)
>DroEre_CAF1 58538 120 - 1
UUUGCCCAGUCCCGAAUUCGUCGCCAAAUUUGCCAACGAUUUUGCACGGCUUUUCCAAGAAGCGCUUAAAGCGUUUAGAGUUUACUUGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUG
............((((....(((((....(((....(((((..(((.(....(((....((((((.....)))))).)))....).)))..))))).))))))))......))))..... ( -25.90)
>consensus
UU_GCCC___________________________A_CGAUUUUGCACAGCUUUUCCAAGAAACGCUUAAAGCGUUUAGAGUUUACUCGCCUAAUCGCCAAGGCGAAACUUUUUCGAUUUG
...........................................................((((((.....))))))((((((...((((((........))))))))))))......... (-17.66 = -17.00 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,319,493 – 5,319,586
Length 93
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.77
Mean single sequence MFE -23.80
Consensus MFE -15.55
Energy contribution -15.33
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -1.26
Structure conservation index 0.65
SVM decision value 0.17
SVM RNA-class probability 0.615674
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5319493 93 + 22224390
CUCUAAACGCUUUAAGCGUUUCUUGGAAAAGCUGCGGAAAAUCGGU---------------------------GGGCUAAAGCGUAUGUGAAAUACUAAUUUAACAUGUCUGAGAAGUUU
(((...((((((((.((....(((....)))(..(.(.....).).---------------------------.)))))))))))((((.((((....)))).))))....)))...... ( -21.20)
>DroSim_CAF1 47402 80 + 1
CUCUAAACGCUUUAAGCGUUUCUUGGAAAAGCUGUGCA----------------------------------------AAAGCGUAUGUGAAAUACUAAUUUAACAUGUCUGAGAACUUU
.....(((((.....)))))(((..((...(((.....----------------------------------------..))).(((((.((((....)))).)))))))..)))..... ( -17.40)
>DroEre_CAF1 58578 120 + 1
CUCUAAACGCUUUAAGCGCUUCUUGGAAAAGCCGUGCAAAAUCGUUGGCAAAUUUGGCGACGAAUUCGGGACUGGGCAAAGGCGUAUGUGAAAUACUAAUUUAACAUGUCUGAGAAGUUU
........((.....))((((((..((...(((.(((....((((((.((....)).))))))..(((....))))))..))).(((((.((((....)))).)))))))..)))))).. ( -32.80)
>consensus
CUCUAAACGCUUUAAGCGUUUCUUGGAAAAGCUGUGCAAAAUCG_U___________________________GGGC_AAAGCGUAUGUGAAAUACUAAUUUAACAUGUCUGAGAAGUUU
.......(((.....)))(((((..((...(((...............................................))).(((((.((((....)))).)))))))..)))))... (-15.55 = -15.33 +  -0.22)

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 10:22:35 2006