Locus 3536

Sequence ID 3R_DroMel_CAF1
Location 9,557,472 – 9,557,607
Length 135
Max. P 0.974473
window5683 window5684 window5685 window5686

overview

Window 3

Location 9,557,472 – 9,557,575
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 88.85
Mean single sequence MFE -32.10
Consensus MFE -23.15
Energy contribution -23.65
Covariance contribution 0.50
Combinations/Pair 1.14
Mean z-score -2.90
Structure conservation index 0.72
SVM decision value 1.12
SVM RNA-class probability 0.917947
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557472 103 + 27905053
AAUUCGAUAAUUUGCCCAAGGCAUUAU--CUUGUUGGUUAUAAUUUACCCAAAGGCAGGCCAUAAACUGGCCACAAGGGGGAAACCCGAUUGUUGUUGGCCAGCU
.....(((((..((((...))))))))--)..((((((((.................(((((.....)))))((((.(((....)))..))))...)))))))). ( -34.50)
>DroSec_CAF1 34124 100 + 1
AAUUCGAUAAUUUGCCCAAGGCAUUAU--CUUGUUGGUUAUAAUUUACACAAAGGCAGGCCAUAAACUGGCCACAUAGGGGAAACCUGAUUG---UUGGCCAGCU
.....(((((..((((...))))))))--)..((((((((.................(((((.....)))))(((..(((....)))...))---))))))))). ( -32.10)
>DroEre_CAF1 35781 100 + 1
AAUUCGAUAAUUUGUCCAAGAA-UUAUCUCUGGUUGGUUAUAAUUUACACAACGGCAGGACAUAAACUGGCCACAAGGGGGA-ACCCGAUUG---UUGGCUAGCU
............(((((.(((.-.....))).((((((........)).))))....)))))....(((((((((.(((...-.)))...))---.))))))).. ( -29.50)
>DroYak_CAF1 34396 102 + 1
AAUUCGAUAAUUUGCCCAAGGAUUUAUUUCUGGCUGGUUAUAAUUUACUCAAAGGCAGGCUAUAAACUGGCCACAAGGGGGAAACCCGAUUG---UUGGCCAGCU
......(((((..(((..((((.....)))))))..))))).........................((((((((((.(((....)))..)))---.))))))).. ( -32.30)
>consensus
AAUUCGAUAAUUUGCCCAAGGAAUUAU__CUGGUUGGUUAUAAUUUACACAAAGGCAGGCCAUAAACUGGCCACAAGGGGGAAACCCGAUUG___UUGGCCAGCU
..........((((((....(((((((..((....))..))))))).......)))))).......((((((((((.(((....)))..)))....))))))).. (-23.15 = -23.65 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,557,472 – 9,557,575
Length 103
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 88.85
Mean single sequence MFE -26.24
Consensus MFE -17.71
Energy contribution -18.40
Covariance contribution 0.69
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.521515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557472 103 - 27905053
AGCUGGCCAACAACAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUGGCCUGCCUUUGGGUAAAUUAUAACCAACAAG--AUAAUGCCUUGGGCAAAUUAUCGAAUU
.((((((((.(((.....(((.....))))))))))))))((((((..((((....))))..)))))).......(--((((((((...))))..)))))..... ( -30.10)
>DroSec_CAF1 34124 100 - 1
AGCUGGCCAA---CAAUCAGGUUUCCCCUAUGUGGCCAGUUUAUGGCCUGCCUUUGUGUAAAUUAUAACCAACAAG--AUAAUGCCUUGGGCAAAUUAUCGAAUU
(((((((((.---..((.(((.....))))).)))))))))...((....)).((((..............))))(--((((((((...))))..)))))..... ( -24.94)
>DroEre_CAF1 35781 100 - 1
AGCUAGCCAA---CAAUCGGGU-UCCCCCUUGUGGCCAGUUUAUGUCCUGCCGUUGUGUAAAUUAUAACCAACCAGAGAUAA-UUCUUGGACAAAUUAUCGAAUU
((((.((((.---(((..(((.-...)))))))))).))))..(((((....((((((.....))))))......((((...-.)))))))))............ ( -24.70)
>DroYak_CAF1 34396 102 - 1
AGCUGGCCAA---CAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUAGCCUGCCUUUGAGUAAAUUAUAACCAGCCAGAAAUAAAUCCUUGGGCAAAUUAUCGAAUU
.((((((((.---(((..(((....))).)))))))))))((((((..(((......)))..))))))...(((.((......))....)))............. ( -25.20)
>consensus
AGCUGGCCAA___CAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUGGCCUGCCUUUGUGUAAAUUAUAACCAACAAG__AUAAUGCCUUGGGCAAAUUAUCGAAUU
(((((((((....(((..(((.....))))))))))))))).......((((.(((.((........)))))((((.........))))))))............ (-17.71 = -18.40 +   0.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,557,507 – 9,557,607
Length 100
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 89.92
Mean single sequence MFE -35.02
Consensus MFE -28.06
Energy contribution -28.50
Covariance contribution 0.44
Combinations/Pair 1.13
Mean z-score -2.99
Structure conservation index 0.80
SVM decision value 1.73
SVM RNA-class probability 0.974473
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557507 100 + 27905053
UUAUAAUUUACCCAAAGGCAGGCCAUAAACUGGCCACAAGGGGGAAACCCGAUUGUUGUUGGCCAGCUGUUUUGGCCAAAUUGA----UGUACCUUGCCUGGCC
...........(((..(((((((((.....)))))((((.(((....)))..))))..((((((((.....)))))))).....----.......))))))).. ( -36.50)
>DroSec_CAF1 34159 101 + 1
UUAUAAUUUACACAAAGGCAGGCCAUAAACUGGCCACAUAGGGGAAACCUGAUUG---UUGGCCAGCUGUUUUGGCCAAAUUGAACUAUGUACCUGGCCUGGCC
...............((((.(((((.....)))))((((((((....))......---((((((((.....))))))))......)))))).....)))).... ( -36.70)
>DroEre_CAF1 35817 100 + 1
UUAUAAUUUACACAACGGCAGGACAUAAACUGGCCACAAGGGGGA-ACCCGAUUG---UUGGCUAGCUGUUUCGGCCAAAUUGAACUAUGUACCUGGCCUGGCU
................(((((((((((..(((((((((.(((...-.)))...))---.)))))))....(((((.....))))).))))).))).)))..... ( -30.90)
>DroYak_CAF1 34433 101 + 1
UUAUAAUUUACUCAAAGGCAGGCUAUAAACUGGCCACAAGGGGGAAACCCGAUUG---UUGGCCAGCUGUUUCGGCCAAAUUGAACUAUGUACCUUGCCUGGCU
...............(((((((.((((..((((((((((.(((....)))..)))---.)))))))....(((((.....)))))...)))).))))))).... ( -36.00)
>consensus
UUAUAAUUUACACAAAGGCAGGCCAUAAACUGGCCACAAGGGGGAAACCCGAUUG___UUGGCCAGCUGUUUCGGCCAAAUUGAACUAUGUACCUGGCCUGGCC
...............((((.(((((.....)))))(((..(((....)))........((((((((.....)))))))).........))).....)))).... (-28.06 = -28.50 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,557,507 – 9,557,607
Length 100
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 89.92
Mean single sequence MFE -32.67
Consensus MFE -24.88
Energy contribution -26.25
Covariance contribution 1.38
Combinations/Pair 1.03
Mean z-score -2.51
Structure conservation index 0.76
SVM decision value 1.06
SVM RNA-class probability 0.909344
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557507 100 - 27905053
GGCCAGGCAAGGUACA----UCAAUUUGGCCAAAACAGCUGGCCAACAACAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUGGCCUGCCUUUGGGUAAAUUAUAA
((((((((.((((...----...)))).))).....(((((((((.(((.....(((.....)))))))))))))))..)))))((((....))))........ ( -36.00)
>DroSec_CAF1 34159 101 - 1
GGCCAGGCCAGGUACAUAGUUCAAUUUGGCCAAAACAGCUGGCCAA---CAAUCAGGUUUCCCCUAUGUGGCCAGUUUAUGGCCUGCCUUUGUGUAAAUUAUAA
(((((((((((((..........)))))))).....(((((((((.---..((.(((.....))))).)))))))))..))))).................... ( -36.60)
>DroEre_CAF1 35817 100 - 1
AGCCAGGCCAGGUACAUAGUUCAAUUUGGCCGAAACAGCUAGCCAA---CAAUCGGGU-UCCCCCUUGUGGCCAGUUUAUGUCCUGCCGUUGUGUAAAUUAUAA
.....(((.(((.((((((......(((((((........((((..---......)))-)........))))))).))))))))))))................ ( -26.49)
>DroYak_CAF1 34433 101 - 1
AGCCAGGCAAGGUACAUAGUUCAAUUUGGCCGAAACAGCUGGCCAA---CAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUAGCCUGCCUUUGAGUAAAUUAUAA
((.(((((..(((.((..........))))).....(((((((((.---(((..(((....))).))))))))))))....))))).))............... ( -31.60)
>consensus
AGCCAGGCAAGGUACAUAGUUCAAUUUGGCCAAAACAGCUGGCCAA___CAAUCGGGUUUCCCCCUUGUGGCCAGUUUAUGGCCUGCCUUUGUGUAAAUUAUAA
(((.(((((((((.((..........))))).....(((((((((....(((..(((.....)))))))))))))))..)))))))))................ (-24.88 = -26.25 +   1.38)

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 11:03:40 2006