Locus 5466

Sequence ID 3L_DroMel_CAF1
Location 14,943,841 – 14,943,995
Length 154
Max. P 0.898820
window8647 window8648 window8649

overview

Window 7

Location 14,943,841 – 14,943,955
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.68
Mean single sequence MFE -23.23
Consensus MFE -15.62
Energy contribution -15.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.67
SVM decision value 0.14
SVM RNA-class probability 0.600751
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14943841 114 + 23771897
CAAAAUCACUCACUCCAAGAACCCAAGACCGUCCC-----UUCUGCUGACUCGUUUUUAACGAUCUCGCAGACCCCAAA-AAACAAGAAGGGUCCCCCCUCCAACCCCACCAGUGGAGCU
............(((((..................-----.(((((.((.((((.....))))))..))))).......-......(.((((....)))).)...........))))).. ( -21.50)
>DroSec_CAF1 124213 108 + 1
CAAAAUCACUCACUCCAAGAACCCAAGACCGUCCC-----UUCUGCUGACUCGUUUUUAACGAUCUCGCAGACCCCAAA-AAACAAGAAGGGUCCCCCCUUC------GUCAGUGGAGCU
............(((((.(....)..(((......-----.(((((.((.((((.....))))))..))))).......-......((((((....))))))------)))..))))).. ( -26.70)
>DroSim_CAF1 121980 109 + 1
CAAAAUCACUCACUCCAAGAACCCAAGACCGUCCC-----UACUGCUGACUCGUUUUUAACGAUCUCGCAGACCCCAAAAAAACAAGAAGGGUCCCCCCUUC------GCCAGUGGAGCU
............(((((..................-----..((((.((.((((.....))))))..))))...............((((((....))))))------.....))))).. ( -24.90)
>DroEre_CAF1 119082 96 + 1
CAAAGUCA----CUCCAAGAACCC--GACCGUCCC-----UUC-UUCGACUCGUUUUUAACGAUCUCGCAGACCCCAA--AAACAAGAAGGGUCCCCC----------GCCAGUGGAGCU
........----(((((......(--(...(.(((-----(((-(((((.((((.....))))..)))..........--....)))))))).)...)----------)....))))).. ( -21.13)
>DroYak_CAF1 120044 102 + 1
CAAAAUCA----CUCCAAGAACCC--GACCGUCCCGUCCCUUCUUUUGACUCGUUUUUAACGAUCGCGCCGACCCCAA--AAACAAGAAGGGUCCCCC----------GCCAGUGGAGCU
........----(((((((((...--(((......)))..))))...((.((((.....))))))(((..(((((...--.........)))))...)----------))...))))).. ( -21.90)
>consensus
CAAAAUCACUCACUCCAAGAACCCAAGACCGUCCC_____UUCUGCUGACUCGUUUUUAACGAUCUCGCAGACCCCAAA_AAACAAGAAGGGUCCCCCCU_C______GCCAGUGGAGCU
............(((((..............................((.((((.....)))))).....(((((..............)))))...................))))).. (-15.62 = -15.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,943,841 – 14,943,955
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.68
Mean single sequence MFE -37.70
Consensus MFE -26.28
Energy contribution -27.80
Covariance contribution 1.52
Combinations/Pair 1.15
Mean z-score -2.01
Structure conservation index 0.70
SVM decision value 0.45
SVM RNA-class probability 0.741870
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14943841 114 - 23771897
AGCUCCACUGGUGGGGUUGGAGGGGGGACCCUUCUUGUUU-UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA-----GGGACGGUCUUGGGUUCUUGGAGUGAGUGAUUUUG
.(((((.(((.(((....((((((....))))))((((((-((.(.((((.....)))).).)))))))).))).))).(-----(((((........)))))))))))........... ( -40.50)
>DroSec_CAF1 124213 108 - 1
AGCUCCACUGAC------GAAGGGGGGACCCUUCUUGUUU-UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA-----GGGACGGUCUUGGGUUCUUGGAGUGAGUGAUUUUG
.(((((.(((((------((((((....))))))((((((-((.(.((((.....)))).).)))))))))))))....(-----(((((........)))))))))))........... ( -42.00)
>DroSim_CAF1 121980 109 - 1
AGCUCCACUGGC------GAAGGGGGGACCCUUCUUGUUUUUUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGUA-----GGGACGGUCUUGGGUUCUUGGAGUGAGUGAUUUUG
.(((((.(((((------((((((....))))))((((((((..(.((((.....)))).).)))))))))))))....(-----(((((........)))))))))))........... ( -40.30)
>DroEre_CAF1 119082 96 - 1
AGCUCCACUGGC----------GGGGGACCCUUCUUGUUU--UUGGGGUCUGCGAGAUCGUUAAAAACGAGUCGAA-GAA-----GGGACGGUC--GGGUUCUUGGAG----UGACUUUG
.(((((((((((----------.(....((((((((((((--((((((((.....)))).))))))))......))-)))-----))).).)))--)).....)))))----)....... ( -32.20)
>DroYak_CAF1 120044 102 - 1
AGCUCCACUGGC----------GGGGGACCCUUCUUGUUU--UUGGGGUCGGCGCGAUCGUUAAAAACGAGUCAAAAGAAGGGACGGGACGGUC--GGGUUCUUGGAG----UGAUUUUG
.((((((.....----------..(((((((..(((((((--(((((((((...))))).)))))))))))...........(((......)))--))))))))))))----)....... ( -33.51)
>consensus
AGCUCCACUGGC______G_AGGGGGGACCCUUCUUGUUU_UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA_____GGGACGGUCUUGGGUUCUUGGAGUGAGUGAUUUUG
.(((((((((((......((((((....))))))((((((....(.(((((...))))).)...)))))))))))..........(((((........)))))))))))........... (-26.28 = -27.80 +   1.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,943,876 – 14,943,995
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -37.75
Consensus MFE -25.81
Energy contribution -27.25
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -2.03
Structure conservation index 0.68
SVM decision value 1.00
SVM RNA-class probability 0.898820
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14943876 119 - 23771897
GGUGAGUAAGUGCCUGUGCCUUGCACUCGGAAUGCACAUAAGCUCCACUGGUGGGGUUGGAGGGGGGACCCUUCUUGUUU-UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA
.....(((((.((....))))))).(((((((.(((....(((((((....)))))))((((((....)))))).))).)-)))))).(((((....((((.....))))....))))). ( -46.90)
>DroSec_CAF1 124248 99 - 1
G--------------GUGCCUUGCAUUCUGAAUGCACAUAAGCUCCACUGAC------GAAGGGGGGACCCUUCUUGUUU-UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA
(--------------(.((..(((((.....))))).....)).)).(((((------((((((....))))))((((((-((.(.((((.....)))).).)))))))))))))..... ( -37.60)
>DroSim_CAF1 122015 100 - 1
G--------------GUGCCUUGCAUUCGGAAUGCACAUAAGCUCCACUGGC------GAAGGGGGGACCCUUCUUGUUUUUUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGUA
(--------------(.((..(((((.....))))).....)).)).(((((------((((((....))))))((((((((..(.((((.....)))).).)))))))))))))..... ( -36.00)
>DroYak_CAF1 120078 107 - 1
-GUGAGCGAGUGCCUGUGUCUUAUAUUCAGAAUGCACAUAAGCUCCACUGGC----------GGGGGACCCUUCUUGUUU--UUGGGGUCGGCGCGAUCGUUAAAAACGAGUCAAAAGAA
-((.(((((((((((((((.((........)).)))))...((((((..(((----------(((((....)))))))).--.)))))).)))))..)))))....))............ ( -30.50)
>consensus
G______________GUGCCUUGCAUUCGGAAUGCACAUAAGCUCCACUGGC______GAAGGGGGGACCCUUCUUGUUU_UUUGGGGUCUGCGAGAUCGUUAAAAACGAGUCAGCAGAA
...............((((.((........)).))))....((((((...........((((((....)))))).........))))))((((....((((.....))))....)))).. (-25.81 = -27.25 +   1.44)

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 11:51:05 2006