Locus 4613

Sequence ID X_DroMel_CAF1
Location 12,071,964 – 12,072,096
Length 132
Max. P 0.981223
window7583 window7584 window7585

overview

Window 3

Location 12,071,964 – 12,072,057
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.45
Mean single sequence MFE -20.96
Consensus MFE -12.26
Energy contribution -13.12
Covariance contribution 0.86
Combinations/Pair 1.05
Mean z-score -2.22
Structure conservation index 0.58
SVM decision value 0.07
SVM RNA-class probability 0.569336
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12071964 93 - 22224390
CCAAACAACAAGAUGUCAUAUCAUC--GGAAUGG-CAGUCUCAUUACGAGACUUUGUUC----------AUCGCCUUUUUGUUCG-UUUCCCUUUU--CGUUGUGUCUU-----------
....(((((..((((......))))--.(((..(-.((((((.....)))))))..)))----------................-..........--.))))).....----------- ( -21.00)
>DroSec_CAF1 7846 95 - 1
CCAAACAACAAGAUGUCAUAUCAUC--GGAAUGG-CAGUCUCAUUACGAGACUUUGUUC----------AUCGCCUUUUUGUUCG-CUUCCCUUUUUUUGUUGUGUCUU-----------
....(((((((((((......))))--.(((..(-.((((((.....)))))))..)))----------................-...........))))))).....----------- ( -22.50)
>DroSim_CAF1 7835 95 - 1
CCAAACAACAAGAUGUCAUAUCAUC--GGAAUGG-CAGUCUCAUUACAAAACUUUGUUC----------AUCUCCUUUUUGUUCC-CUUCCCUUUUUCUGUUGUGUCUU-----------
....((((((.((((......))))--((((..(-.((.......((((....))))..----------.....))..)..))))-............)))))).....----------- ( -15.04)
>DroEre_CAF1 7367 93 - 1
CCAAACAACAAGAUGUCAUAUCAUC--GGAAUGG-CAGUCUCAUUACGAGACUUUGUUC----------AUCGCCUUUUUGUUCG-UUUCCCUUUU--UGUUGUGUCUU-----------
....(((((((((((......))))--.(((..(-.((((((.....)))))))..)))----------................-.........)--)))))).....----------- ( -22.50)
>DroYak_CAF1 8249 91 - 1
CCAAACAACAAGAUGUCAUAUCAUC--GGAAUGG-CAGUCUCAUUACGAGACUUUGUUC----------GUCGCCUUUUUGUUCG-UUUCCCUUUU--UGUUG--UCUU-----------
....(((((((((((......))))--.(((..(-.((((((.....)))))))..)))----------................-.........)--)))))--)...----------- ( -21.90)
>DroAna_CAF1 8253 120 - 1
CCGAACAACAAGAUGUCAUAUCAUCUCCGAAUGGUUACUCUCAUUACGGGACUUUGUUGCCUCCUUUUGUUGGCCAUUUUGUUUCAUUUCUGUUUUGUUGUUGUUUUCUUCGUUACUCUC
..(((((((((((((......)))).((((((((......))))).)))(((...((.(((..(....)..))).))...)))..............))))))))).............. ( -22.80)
>consensus
CCAAACAACAAGAUGUCAUAUCAUC__GGAAUGG_CAGUCUCAUUACGAGACUUUGUUC__________AUCGCCUUUUUGUUCG_UUUCCCUUUU__UGUUGUGUCUU___________
....((((((.((((......))))...(((..(..((((((.....)))))))..))).......................................))))))................ (-12.26 = -13.12 +   0.86)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,071,990 – 12,072,096
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 94.06
Mean single sequence MFE -30.48
Consensus MFE -26.66
Energy contribution -26.06
Covariance contribution -0.60
Combinations/Pair 1.16
Mean z-score -1.81
Structure conservation index 0.87
SVM decision value 1.88
SVM RNA-class probability 0.981223
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12071990 106 + 22224390
AAAAAGGCGAUGAACAAAGUCUCGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUCGACUGGAGGACUCAAGGACCGAAUGGAGCCA
.....(((.........((((((.....)))))).((((((.((((......))))..(((.(((((((((.((.....)).)))))))))))).)))))).))). ( -35.70)
>DroSec_CAF1 7874 106 + 1
AAAAAGGCGAUGAACAAAGUCUCGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUCGACUGGAGGACUCAAGGACCAAAAGGAGCCA
.....(((.........((((((.....)))))).....(((((((......))))(((.(.(((((((((.((.....)).))))))))).).)))..)))))). ( -33.30)
>DroSim_CAF1 7863 106 + 1
AAAAAGGAGAUGAACAAAGUUUUGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUAGAUUGGAGGACUCAAGGACCAAAAGGAGCCA
.....((..........((((((.....))))))....((((((((......))))(((.(.(((((((((.((.....)).))))))))).).)))..)))))). ( -26.10)
>DroEre_CAF1 7393 106 + 1
AAAAAGGCGAUGAACAAAGUCUCGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUCGACUGGCGGACUCGAGGACCAAAGACAACCA
.....((.((((.....((((((.....))))))..))))))((((......))))..(((((((.(((((..((((.........)))))))))..))))))).. ( -30.10)
>DroYak_CAF1 8273 106 + 1
AAAAAGGCGACGAACAAAGUCUCGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUCGACUGGAGGGCUCAAGGACCAAAAAGAACCA
.....((...(((((((((((((.....))))))........((((......))))...)))))))(((((.(((.....))).......)))))........)). ( -27.20)
>consensus
AAAAAGGCGAUGAACAAAGUCUCGUAAUGAGACUGCCAUUCCGAUGAUAUGACAUCUUGUUGUUUGGGUCCACUCGACUGGAGGACUCAAGGACCAAAAGGAGCCA
.....((.((((.....((((((.....))))))..))))))((((......))))(((.(.(((((((((.((.....)).))))))))).).)))......... (-26.66 = -26.06 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,071,990 – 12,072,096
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 94.06
Mean single sequence MFE -27.34
Consensus MFE -23.54
Energy contribution -24.06
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.36
Structure conservation index 0.86
SVM decision value 0.43
SVM RNA-class probability 0.731347
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12071990 106 - 22224390
UGGCUCCAUUCGGUCCUUGAGUCCUCCAGUCGAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACGAGACUUUGUUCAUCGCCUUUUU
(((.(((((((((..((.((....)).))))))))))).)))........((((......)))).(((..(.((((((.....)))))))..)))........... ( -32.10)
>DroSec_CAF1 7874 106 - 1
UGGCUCCUUUUGGUCCUUGAGUCCUCCAGUCGAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACGAGACUUUGUUCAUCGCCUUUUU
.(((.......(((((((((.(.....).))))..)))))..........((((......)))).(((..(.((((((.....)))))))..)))...)))..... ( -28.80)
>DroSim_CAF1 7863 106 - 1
UGGCUCCUUUUGGUCCUUGAGUCCUCCAAUCUAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACAAAACUUUGUUCAUCUCCUUUUU
.((((((......((((((.((((...........)))).))).......((((......)))))))..)).)))).............................. ( -18.60)
>DroEre_CAF1 7393 106 - 1
UGGUUGUCUUUGGUCCUCGAGUCCGCCAGUCGAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACGAGACUUUGUUCAUCGCCUUUUU
..(((((.((.(((((((((.(.....).))))..))))).)))))))..((((......)))).(((..(.((((((.....)))))))..)))........... ( -31.70)
>DroYak_CAF1 8273 106 - 1
UGGUUCUUUUUGGUCCUUGAGCCCUCCAGUCGAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACGAGACUUUGUUCGUCGCCUUUUU
.(((...(((.(((((((((.(......)))))..))))).)))......((((......)))).(((..(.((((((.....)))))))..)))...)))..... ( -25.50)
>consensus
UGGCUCCUUUUGGUCCUUGAGUCCUCCAGUCGAGUGGACCCAAACAACAAGAUGUCAUAUCAUCGGAAUGGCAGUCUCAUUACGAGACUUUGUUCAUCGCCUUUUU
.(((.......(((((((((.........))))..)))))..........((((......)))).(((..(.((((((.....)))))))..)))...)))..... (-23.54 = -24.06 +   0.52)

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 11:29:26 2006