Locus 6408

Sequence ID 3R_DroMel_CAF1
Location 16,784,692 – 16,784,823
Length 131
Max. P 0.986276
window10448 window10449 window10450

overview

Window 8

Location 16,784,692 – 16,784,794
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.46
Mean single sequence MFE -20.20
Consensus MFE -10.70
Energy contribution -13.58
Covariance contribution 2.88
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.53
SVM decision value 2.04
SVM RNA-class probability 0.986276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16784692 102 + 27905053
UGGCCUCUCCAU--------UGCCAUGUGCCGUUAUUCGGCAUCCUGGAAACUGCAGCUCGCCUGCA-UUUCCAUAC-ACACACUCGCUUCCAUUGUCC--------ACUUCCACACAAU
((((........--------.)))).((((((.....))))))..((((((.(((((.....)))))-))))))...-.....................--------............. ( -23.50)
>DroSec_CAF1 17246 101 + 1
UGGCCUCUCCAU-------UUGCCAUGUGCCGUUAUUCGGCAUCCUGGAAACUGCAGCUCGCCUGCA-UUUCCAUAC-A--CACUCGCUUCCAUUGUCC--------ACUUCCACACAAU
((((........-------..)))).((((((.....))))))..((((((.(((((.....)))))-))))))...-.--..................--------............. ( -23.40)
>DroEre_CAF1 13174 103 + 1
UGGUCUCUCCAU-------UUGCCAUGUGCCGUUAUUCGGCAUCCUGGAAACUGCAGCUCGCCUGCA-UUUCCAUAC-ACACACUCGCUUCCAUUGUCC--------ACUUCCACACAAU
(((.(.......-------..((...((((((.....))))))..((((((.(((((.....)))))-))))))...-........)).......).))--------)............ ( -23.59)
>DroWil_CAF1 10453 108 + 1
GAGUCUCUCUAUGAUUCGUGUGUCAUGUGCCGUUAUUUCGCAUCUUGCCA--------UGGCCUGCAGUUUCCAGUCUGUUUGCAUGCUUCCAUGUUCCUACAUAUCCCUUCC----AAU
(((((.......)))))(((((.((((.((.........((.....))..--------..((..((((........))))..))..))...))))....))))).........----... ( -18.60)
>DroYak_CAF1 2 77 + 1
---------------------------------UAUUCGGCAUCCUGGAAACUGCAGCUCGCCUGCA-UUUCCAUAC-ACACACUCGCUUCCAUCGUCC--------ACUUCCACAAAAU
---------------------------------............((((((.(((((.....)))))-))))))...-.....................--------............. ( -11.90)
>consensus
UGGCCUCUCCAU________UGCCAUGUGCCGUUAUUCGGCAUCCUGGAAACUGCAGCUCGCCUGCA_UUUCCAUAC_ACACACUCGCUUCCAUUGUCC________ACUUCCACACAAU
..........................((((((.....))))))..((((((.(((((.....))))).)))))).............................................. (-10.70 = -13.58 +   2.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,784,724 – 16,784,823
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 97.98
Mean single sequence MFE -22.40
Consensus MFE -21.55
Energy contribution -21.80
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.96
SVM decision value 1.33
SVM RNA-class probability 0.943032
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16784724 99 + 27905053
CAUCCUGGAAACUGCAGCUCGCCUGCAUUUCCAUACACACACUCGCUUCCAUUGUCCACUUCCACACAAUUUCCCGUGACUCCGUGGCCUUCCAGCGGU
.....((((((.(((((.....))))))))))).........(((((......(.((((.....(((........))).....)))).)....))))). ( -22.90)
>DroSec_CAF1 17279 97 + 1
CAUCCUGGAAACUGCAGCUCGCCUGCAUUUCCAUACA--CACUCGCUUCCAUUGUCCACUUCCACACAAUUUCCCGUGACUCCGUGGCCUUCCAGCGGU
.....((((((.(((((.....)))))))))))....--...(((((......(.((((.....(((........))).....)))).)....))))). ( -22.90)
>DroEre_CAF1 13207 99 + 1
CAUCCUGGAAACUGCAGCUCGCCUGCAUUUCCAUACACACACUCGCUUCCAUUGUCCACUUCCACACAAUUUCCCGUGACUCCGUGGCCUUCCAGCGGU
.....((((((.(((((.....))))))))))).........(((((......(.((((.....(((........))).....)))).)....))))). ( -22.90)
>DroYak_CAF1 9 99 + 1
CAUCCUGGAAACUGCAGCUCGCCUGCAUUUCCAUACACACACUCGCUUCCAUCGUCCACUUCCACAAAAUUUCCCGUGACUCCGUGGCCUUCCAGCGGU
.....((((((.(((((.....))))))))))).........(((((......(.((((...(((..........))).....))))).....))))). ( -20.90)
>consensus
CAUCCUGGAAACUGCAGCUCGCCUGCAUUUCCAUACACACACUCGCUUCCAUUGUCCACUUCCACACAAUUUCCCGUGACUCCGUGGCCUUCCAGCGGU
.....((((((.(((((.....))))))))))).........(((((......(.((((.....(((........))).....)))).)....))))). (-21.55 = -21.80 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,784,724 – 16,784,823
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 97.98
Mean single sequence MFE -33.52
Consensus MFE -30.61
Energy contribution -30.92
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.76
Structure conservation index 0.91
SVM decision value 1.13
SVM RNA-class probability 0.920215
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16784724 99 - 27905053
ACCGCUGGAAGGCCACGGAGUCACGGGAAAUUGUGUGGAAGUGGACAAUGGAAGCGAGUGUGUGUAUGGAAAUGCAGGCGAGCUGCAGUUUCCAGGAUG
.(((.(((....)))))).(((...(((((((((.((........)).....(((...(((.(((((....))))).))).))))))))))))..))). ( -33.40)
>DroSec_CAF1 17279 97 - 1
ACCGCUGGAAGGCCACGGAGUCACGGGAAAUUGUGUGGAAGUGGACAAUGGAAGCGAGUG--UGUAUGGAAAUGCAGGCGAGCUGCAGUUUCCAGGAUG
.(((.(((....)))))).(((...(((((((((.((........)).....(((..((.--(((((....))))).))..))))))))))))..))). ( -33.90)
>DroEre_CAF1 13207 99 - 1
ACCGCUGGAAGGCCACGGAGUCACGGGAAAUUGUGUGGAAGUGGACAAUGGAAGCGAGUGUGUGUAUGGAAAUGCAGGCGAGCUGCAGUUUCCAGGAUG
.(((.(((....)))))).(((...(((((((((.((........)).....(((...(((.(((((....))))).))).))))))))))))..))). ( -33.40)
>DroYak_CAF1 9 99 - 1
ACCGCUGGAAGGCCACGGAGUCACGGGAAAUUUUGUGGAAGUGGACGAUGGAAGCGAGUGUGUGUAUGGAAAUGCAGGCGAGCUGCAGUUUCCAGGAUG
.(((((......(((((((((........))))))))).)))))....(((((((.(((((.(((((....))))).))..)))...)))))))..... ( -33.40)
>consensus
ACCGCUGGAAGGCCACGGAGUCACGGGAAAUUGUGUGGAAGUGGACAAUGGAAGCGAGUGUGUGUAUGGAAAUGCAGGCGAGCUGCAGUUUCCAGGAUG
.(((.(((....)))))).(((...(((((((((.((........)).....(((...(((.(((((....))))).))).))))))))))))..))). (-30.61 = -30.92 +   0.31)

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 12:20:50 2006