Locus 2622

Sequence ID 3L_DroMel_CAF1
Location 7,233,824 – 7,233,980
Length 156
Max. P 0.964991
window4109 window4110 window4111

overview

Window 9

Location 7,233,824 – 7,233,940
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.56
Mean single sequence MFE -20.96
Consensus MFE -16.58
Energy contribution -16.58
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.79
SVM decision value 0.11
SVM RNA-class probability 0.587315
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7233824 116 - 23771897
AAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAUACAUUAACUUUAUAUACAAAUAUACAAUGG-GGAGAAAA-
..........(....).(((((--.........(((.....)))....((((.(((......))).))))....................................))))-).......- ( -18.90)
>DroSec_CAF1 15396 113 - 1
AAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAUACAAUAACUUUAUAAACAAAUAUACAAUGG-GGGGA----
..........(....).(((..--(((((....(((.....)))....((((.(((......))).))))....................................))))-)))).---- ( -20.10)
>DroSim_CAF1 15357 113 - 1
AAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAUACAAUAACUCUAUAAACAAAUAUACAAUGG-GGGAG----
..........(((.........--.........(((.....)))....((((.(((......))).))))..)))............((((((.............))))-))...---- ( -20.02)
>DroEre_CAF1 15809 117 - 1
AAUUAUAAAAGGCAACACCCCU--CUCAUAAAUCGCUGUCUGCGUUUUGCCGCCAAAAGACCUUGGCGGCCAGCCAAAAUACAUUAACUUUAUAUACUCGUAUACAAAUG-ACCGACAAC
..........(((.........--.....(((.(((.....))).)))((((((((......))))))))..)))......((((.....(((((....)))))..))))-......... ( -24.40)
>DroYak_CAF1 16848 111 - 1
AAUUAUAAAAGGCAACACCCCUCUCUCAUAAAUCGCUGUCUGCGUUUUGCCGCCAAAAGACCUUGACGGCCAGCCAAAAUACAA-AACUUUAUACA--------CAAAUGUAUAGACAAC
..........(((................(((.(((.....))).)))((((.(((......))).))))..))).........-...((((((((--------....)))))))).... ( -21.40)
>consensus
AAUUAUAAAAGGCAACACCCAU__CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAUACAAUAACUUUAUAAACAAAUAUACAAUGG_GGAGA_AA_
..........(((....................(((.....)))....((((.(((......))).))))..)))............................................. (-16.58 = -16.58 +   0.00)

alignment

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secondary structure

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Window 0

Location 7,233,862 – 7,233,980
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.76
Mean single sequence MFE -33.52
Consensus MFE -28.68
Energy contribution -28.52
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.34
Structure conservation index 0.86
SVM decision value 0.35
SVM RNA-class probability 0.698724
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7233862 118 + 23771897
AUUUUGGCUGGCCGUCAAGGUCUUUUGGCGGCGAAACGCAGACAGCGAUUUAUGAG--AUGGGUGUUGCCUUUUAUAAUUUGGCCAACCAACUUGAUGUUGUAUAUUAUUUGCUUUUGCU
...((((((.(((((((((....)))))))))((((.((((.((.(.(((.....)--)).).)))))).)))).......)))))).((((.....))))..........((....)). ( -32.90)
>DroSec_CAF1 15431 118 + 1
AUUUUGGCUGGCCGUCAAGGUCUUUUGGCGGCGAAACGCAGACAGCGAUUUAUGAG--AUGGGUGUUGCCUUUUAUAAUUUGGCCAACCAACUUGAUGUUGUAUAUUAUUUGCUCUUGCU
...((((((.(((((((((....)))))))))((((.((((.((.(.(((.....)--)).).)))))).)))).......)))))).((((.....))))..........((....)). ( -32.90)
>DroSim_CAF1 15392 118 + 1
AUUUUGGCUGGCCGUCAAGGUCUUUUGGCGGCGAAACGCAGACAGCGAUUUAUGAG--AUGGGUGUUGCCUUUUAUAAUUUGGCCAACUAACUUGAUGUUGUAUAUUAUUUGCUUUUGCU
.....(..(.(((((((((....))))))))).)..)(((((.(((((..((..(.--((((((((((((...........)).))))..)))).)).)..))......)))))))))). ( -31.20)
>DroEre_CAF1 15848 115 + 1
AUUUUGGCUGGCCGCCAAGGUCUUUUGGCGGCAAAACGCAGACAGCGAUUUAUGAG--AGGGGUGUUGCCUUUUAUAAUUUGGCCAAA---GCUGAUGUUGUAUAAUAUUUGCCUUUGCU
..(((((((.(((((((((....)))))))))....(((.....)))..(((((((--(((.......))))))))))...)))))))---((.((((((....)))))).))....... ( -39.70)
>DroYak_CAF1 16879 117 + 1
AUUUUGGCUGGCCGUCAAGGUCUUUUGGCGGCAAAACGCAGACAGCGAUUUAUGAGAGAGGGGUGUUGCCUUUUAUAAUUUGGCCAAC---GUUGAUGUUGUAUAAUAUUUGCCUUUGCU
...((((((.(((((((((....)))))))))....(((.....)))..(((((((((.(........))))))))))...)))))).---((.((((((....)))))).))....... ( -30.90)
>consensus
AUUUUGGCUGGCCGUCAAGGUCUUUUGGCGGCGAAACGCAGACAGCGAUUUAUGAG__AUGGGUGUUGCCUUUUAUAAUUUGGCCAAC_AACUUGAUGUUGUAUAUUAUUUGCUUUUGCU
...((((((.(((((((((....)))))))))....(((.....)))..(((((((....(((.....))))))))))...))))))........................((....)). (-28.68 = -28.52 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,233,862 – 7,233,980
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.76
Mean single sequence MFE -26.27
Consensus MFE -21.12
Energy contribution -21.16
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.23
Structure conservation index 0.80
SVM decision value 1.57
SVM RNA-class probability 0.964991
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7233862 118 - 23771897
AGCAAAAGCAAAUAAUAUACAACAUCAAGUUGGUUGGCCAAAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAU
.((....))....................((((((((((...........(....)......--........(((..(((((((......)))....))))..))).))))))))))... ( -28.10)
>DroSec_CAF1 15431 118 - 1
AGCAAGAGCAAAUAAUAUACAACAUCAAGUUGGUUGGCCAAAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAU
.((....))....................((((((((((...........(....)......--........(((..(((((((......)))....))))..))).))))))))))... ( -28.10)
>DroSim_CAF1 15392 118 - 1
AGCAAAAGCAAAUAAUAUACAACAUCAAGUUAGUUGGCCAAAUUAUAAAAGGCAACACCCAU--CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAU
.((....)).......................(((((((...........(....)......--........(((..(((((((......)))....))))..))).)))))))...... ( -22.30)
>DroEre_CAF1 15848 115 - 1
AGCAAAGGCAAAUAUUAUACAACAUCAGC---UUUGGCCAAAUUAUAAAAGGCAACACCCCU--CUCAUAAAUCGCUGUCUGCGUUUUGCCGCCAAAAGACCUUGGCGGCCAGCCAAAAU
.((.(((((..................))---))).))............(((.........--.....(((.(((.....))).)))((((((((......))))))))..)))..... ( -28.67)
>DroYak_CAF1 16879 117 - 1
AGCAAAGGCAAAUAUUAUACAACAUCAAC---GUUGGCCAAAUUAUAAAAGGCAACACCCCUCUCUCAUAAAUCGCUGUCUGCGUUUUGCCGCCAAAAGACCUUGACGGCCAGCCAAAAU
......(((.....((((.((((......---))))(((...........)))..............))))...((((((...(((((........)))))...))))))..)))..... ( -24.20)
>consensus
AGCAAAAGCAAAUAAUAUACAACAUCAAGUU_GUUGGCCAAAUUAUAAAAGGCAACACCCAU__CUCAUAAAUCGCUGUCUGCGUUUCGCCGCCAAAAGACCUUGACGGCCAGCCAAAAU
.((....)).......................(((((((...........(....)................(((..(((((((......)))....))))..))).)))))))...... (-21.12 = -21.16 +   0.04)

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 10:37:48 2006