Locus 5111

Sequence ID X_DroMel_CAF1
Location 13,349,082 – 13,349,220
Length 138
Max. P 0.968510
window8310 window8311 window8312

overview

Window 0

Location 13,349,082 – 13,349,200
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -30.40
Consensus MFE -19.84
Energy contribution -20.77
Covariance contribution 0.92
Combinations/Pair 1.23
Mean z-score -2.24
Structure conservation index 0.65
SVM decision value 0.01
SVM RNA-class probability 0.539718
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13349082 118 - 22224390
CUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGGCAUCUCAAACCGGCGGCGAAUCUGCAUUUGAUGCUCACAGCUUUCAUUGUUUGAUUGGCAACCAUUUGUGAA--AUAUUC
...........(((((((((((..((.((..(((((((((.........))))))).))...)).))..))))))))))).((((((.....(((.(....).))).)))))--)..... ( -34.50)
>DroSec_CAF1 10913 118 - 1
CUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCGGCGUAUCUGCAUUUGAUGCUCACAGCUUUCAUUGUUUGAUUGGCAACCAUUUGUGAA--AUAUUC
...........(((((((((((.((((.((.....)).))))..........((((.....))))....))))))))))).((((((.....(((.(....).))).)))))--)..... ( -31.10)
>DroSim_CAF1 13494 114 - 1
CUAU-GAC-UCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACAG--GGCGAAUCUGCAUUUGAUGCUCACAGCUUUCAUUGUUUGAUUGGCAACCAUUUGUGAA--AUAUUC
....-...-..(((((((((((..........(((((.((....))..))))--)(((....)))....))))))))))).((((((.....(((.(....).))).)))))--)..... ( -29.80)
>DroEre_CAF1 9964 118 - 1
CUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCAGCGAAUCUGCAUUUGAUGCUCGCAGCUUCCAUUGUUUGAUUGGCAGCCAUUUGUGAA--AUAUUC
...((.((....((((((((((..((.((..((((((((...........)))))).))...)).))..))))))))))(((.(((.........))).))).....)).))--...... ( -31.00)
>DroYak_CAF1 16288 118 - 1
CUAUUGACUUCCUGUGAGCAUCCUGUUCACAUCCUGUCGACAUCUCAAACCGGCGGCGAAUCUGCAUUUGAUGCUCACAGCUUCCAUUGUUUGAUUGGCAACCAUUUGUGAA--AUAUUC
...(((((....(((((((.....)))))))....)))))..((.((((..((..((.((((.(((...((.((.....)).))...)))..)))).))..)).)))).)).--...... ( -32.30)
>DroAna_CAF1 12049 97 - 1
-GGAUGCCUUC------ACAUCCUUU--GCAUCCUGAUAGCGCUUCU--------GAUAUUCUGCUGUUGAUGC------CUUUCAUUGUUUGAUUGGCAACCGUUUGUGAACCACAUUC
-(((((.....------.)))))((.--.((..(.(((((((.....--------.......)))))))..(((------(..(((.....)))..))))...)..))..))........ ( -23.70)
>consensus
CUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCGGCGAAUCUGCAUUUGAUGCUCACAGCUUUCAUUGUUUGAUUGGCAACCAUUUGUGAA__AUAUUC
...........(((((((((((.((((.((.....)).))))..........((((.....))))....)))))))))))......(((((.....)))))................... (-19.84 = -20.77 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,349,120 – 13,349,220
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -31.25
Consensus MFE -26.94
Energy contribution -27.25
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.86
SVM decision value 1.63
SVM RNA-class probability 0.968510
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13349120 100 + 22224390
CUGUGAGCAUCAAAUGCAGAUUCGCCGCCGGUUUGAGAUGCCGACAGGAUGUGGACAGGAUGCUCACAGGAAGUCAAUAGACAUAUACACCAUACCCCAA
(((((((((((...(.((.((((...(.((((.......)))).).)))).)).)...)))))))))))...(((....))).................. ( -32.60)
>DroSec_CAF1 10951 99 + 1
CUGUGAGCAUCAAAUGCAGAUACGCCGCCGGUUUGAGAUGUCGACAGGAUGUGGACAGGAUGCUCACAGGAAGUCAAUAGACAUAUACACCAUGCCCC-A
(((((((((((.....(((((.((....)))))))...((((.((.....)).)))).)))))))))))...(((....)))................-. ( -31.40)
>DroSim_CAF1 13532 94 + 1
CUGUGAGCAUCAAAUGCAGAUUCGCC--CUGUUUGAGAUGUCGACAGGAUGUGGACAGGAUGCUCACAGGA-GUC-AUAGACAUAUACACCAUAC-CC-A
(((((((((((...((....((((((--(((((.((....))))))))..))))))).)))))))))))..-(((-...))).............-..-. ( -30.40)
>DroEre_CAF1 10002 100 + 1
CUGCGAGCAUCAAAUGCAGAUUCGCUGCCGGUUUGAGAUGUCGACAGGAUGUGGACAGGAUGCUCACAGGAAGUCAAUAGAUAUACACCACAUAUAUCAA
(((.(((((((....((((.....))))..........((((.((.....)).)))).))))))).)))..........((((((.......)))))).. ( -30.60)
>consensus
CUGUGAGCAUCAAAUGCAGAUUCGCCGCCGGUUUGAGAUGUCGACAGGAUGUGGACAGGAUGCUCACAGGAAGUCAAUAGACAUAUACACCAUACCCC_A
(((((((((((.....(((((.........)))))...((((.((.....)).)))).)))))))))))...(((....))).................. (-26.94 = -27.25 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,349,120 – 13,349,220
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -31.15
Consensus MFE -25.96
Energy contribution -25.65
Covariance contribution -0.31
Combinations/Pair 1.25
Mean z-score -2.14
Structure conservation index 0.83
SVM decision value 1.18
SVM RNA-class probability 0.926735
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13349120 100 - 22224390
UUGGGGUAUGGUGUAUAUGUCUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGGCAUCUCAAACCGGCGGCGAAUCUGCAUUUGAUGCUCACAG
..(((((((((.........))))..)))))(((((((((((..((.((..(((((((((.........))))))).))...)).))..))))))))))) ( -32.20)
>DroSec_CAF1 10951 99 - 1
U-GGGGCAUGGUGUAUAUGUCUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCGGCGUAUCUGCAUUUGAUGCUCACAG
.-.(((((((.....))))))).........(((((((((((.((((.((.....)).))))..........((((.....))))....))))))))))) ( -32.40)
>DroSim_CAF1 13532 94 - 1
U-GG-GUAUGGUGUAUAUGUCUAU-GAC-UCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACAG--GGCGAAUCUGCAUUUGAUGCUCACAG
.-((-((((((.........))))-.))-))(((((((((((..........(((((.((....))..))))--)(((....)))....))))))))))) ( -28.30)
>DroEre_CAF1 10002 100 - 1
UUGAUAUAUGUGGUGUAUAUCUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCAGCGAAUCUGCAUUUGAUGCUCGCAG
..(((((((.....)))))))..........(((((((((((..((.((..((((((((...........)))))).))...)).))..))))))))))) ( -31.70)
>consensus
U_GGGGUAUGGUGUAUAUGUCUAUUGACUUCCUGUGAGCAUCCUGUCCACAUCCUGUCGACAUCUCAAACCGGCGGCGAAUCUGCAUUUGAUGCUCACAG
...(((((((.....))))))).........(((((((((((.((((.((.....)).))))..........((((.....))))....))))))))))) (-25.96 = -25.65 +  -0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:23 2006