Locus 2458

Sequence ID X_DroMel_CAF1
Location 6,572,438 – 6,572,591
Length 153
Max. P 0.999806
window4013 window4014 window4015

overview

Window 3

Location 6,572,438 – 6,572,558
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.24
Mean single sequence MFE -46.51
Consensus MFE -44.26
Energy contribution -44.82
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.41
Structure conservation index 0.95
SVM decision value 4.13
SVM RNA-class probability 0.999806
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6572438 120 + 22224390
ACUUCAAGCGGUGGAAAGUAUCUGAGCGGCGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGGGCGACAGUGGAACGCGGCUUAUCACCCGCCCACCGCCCCCCUCCC
.......((((((....((((.((((((((........)))))))).))))...(....).)).))))(((..(((((...((((...((((........)))))))))))))...))). ( -46.10)
>DroSec_CAF1 17275 115 + 1
ACUUCAAGCGGUGGAAAGUAUCUGAGCGGCGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGAGCGGCAUUGGAACGCGGCUUAUCACCCGCCCACCGCCCCC-----
.......(((((((........(((((.((((((.(..(((((((........(....)(((....)))....)))))))..).)))))).)))))........)))))))....----- ( -46.09)
>DroSim_CAF1 27850 115 + 1
ACUUCAAGCGGUGGAAAGUAUCUGAGCGGCGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGAGCGGCAUUGGAACGCGGCUUAUCACCCGCCCACCGCCCCC-----
.......(((((((........(((((.((((((.(..(((((((........(....)(((....)))....)))))))..).)))))).)))))........)))))))....----- ( -46.09)
>DroEre_CAF1 16915 115 + 1
ACUUCAAGCGGUGGAAAGUAUGUGAGCGACGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGGGCGGCAGUGGAACGCGGCUUAUCACCCGCCCACCGCCCCC-----
.......(((((((...(..(((((((..(((((.((.(((((((........(....)(((....)))....))))))).)).)))))..))))).))..)..)))))))....----- ( -45.50)
>DroYak_CAF1 26824 115 + 1
ACUUCAAGCGGUGGAAAGUAUCUGAGCGGCGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGGGCGGCAGUGGAACGCGGCUUAUCACCCGCCCACCGCCCCC-----
.......(((((((........(((((.((((((.((.(((((((........(....)(((....)))....))))))).)).)))))).)))))........)))))))....----- ( -48.79)
>consensus
ACUUCAAGCGGUGGAAAGUAUCUGAGCGGCGUUCGACGGCCGCUUAAAUACACAGAAAUCGCAUCCGCGGAACGGGCGGCAGUGGAACGCGGCUUAUCACCCGCCCACCGCCCCC_____
.......(((((((........(((((.((((((.((.(((((((.............((((....))))...))))))).)).)))))).)))))........)))))))......... (-44.26 = -44.82 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,572,438 – 6,572,558
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.24
Mean single sequence MFE -51.60
Consensus MFE -49.02
Energy contribution -49.10
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.95
SVM decision value 3.03
SVM RNA-class probability 0.998207
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6572438 120 - 22224390
GGGAGGGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGUCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGCCGCUCAGAUACUUUCCACCGCUUGAAGU
((((.(((((((((((((((((.....))).)).))))))))).))).))))((((.((.((.......((((((.((((((........)))))).))))))..))))))))....... ( -56.60)
>DroSec_CAF1 17275 115 - 1
-----GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCAAUGCCGCUCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGCCGCUCAGAUACUUUCCACCGCUUGAAGU
-----..((((((((((.(((((...(((.((((((....((((((.....((((((.......))))))......))))))....)))))).)))....)))))))))))))))..... ( -49.70)
>DroSim_CAF1 27850 115 - 1
-----GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCAAUGCCGCUCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGCCGCUCAGAUACUUUCCACCGCUUGAAGU
-----..((((((((((.(((((...(((.((((((....((((((.....((((((.......))))))......))))))....)))))).)))....)))))))))))))))..... ( -49.70)
>DroEre_CAF1 16915 115 - 1
-----GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGUCGCUCACAUACUUUCCACCGCUUGAAGU
-----..((((((((((.(((((...(((.((((((.((.(((((......((((((.......)))))).......))))).)).)))))).)))..))).)).))))))))))..... ( -49.72)
>DroYak_CAF1 26824 115 - 1
-----GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGCCGCUCAGAUACUUUCCACCGCUUGAAGU
-----(((((((((((((((((.....))).)).))))))))).))).(((.((((.((.((.......((((((.((((((........)))))).))))))..))))))))..))).. ( -52.30)
>consensus
_____GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCGGCCGUCGAACGCCGCUCAGAUACUUUCCACCGCUUGAAGU
.......((((((((((.(((((...(((.((((((.((.(((((......((((((.......)))))).......))))).)).)))))).)))....)))))))))))))))..... (-49.02 = -49.10 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,572,478 – 6,572,591
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.64
Mean single sequence MFE -42.08
Consensus MFE -40.20
Energy contribution -39.80
Covariance contribution -0.40
Combinations/Pair 1.12
Mean z-score -1.52
Structure conservation index 0.96
SVM decision value 1.36
SVM RNA-class probability 0.946671
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6572478 113 - 22224390
UGGAGCGGCC-------AGGCAGUGAAAACGGUAAAAAGGGGGAGGGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGUCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.(((((..((-------..((.((....)).))......))...(((.((((((((((((((.....))).)).))))))))).))))))))((.((((((.......))))))...)). ( -44.70)
>DroSec_CAF1 17315 105 - 1
UGGAGCGGCC-------AAGCAGUGAAAACGGUAAAA--------GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCAAUGCCGCUCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.((((((((.-------..((.((....)).))....--------...((((.(((((((((.....))).)).)))).)))))).))))))((.((((((.......))))))...)). ( -35.80)
>DroSim_CAF1 27890 105 - 1
UGGAGCGGGC-------AAGCAGUGAAAAUGGUAAAA--------GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCAAUGCCGCUCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.(((((((((-------..((.((....)).))....--------...((((.(((((((((.....))).)).)))).)))))))))))))((.((((((.......))))))...)). ( -39.30)
>DroEre_CAF1 16955 105 - 1
UGGAACAGCG-------AGGCAGUGAAAACGGUAAAA--------GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.(((((....-------..((.((....)).))....--------(((((((((((((((((.....))).)).))))))))).))))))))((.((((((.......))))))...)). ( -43.80)
>DroYak_CAF1 26864 112 - 1
UGGAACAGUGCGGCGUGCGGCAGUGAAAACGGUAAAA--------GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.(((((..(((.(....).)))((....)).......--------(((((((((((((((((.....))).)).))))))))).))))))))((.((((((.......))))))...)). ( -46.80)
>consensus
UGGAGCGGCC_______AGGCAGUGAAAACGGUAAAA________GGGGGCGGUGGGCGGGUGAUAAGCCGCGUUCCACUGCCGCCCGUUCCGCGGAUGCGAUUUCUGUGUAUUUAAGCG
.(((((.............((.((....)).))............(((((((((((((((((.....))).)).))))))))).))))))))((.((((((.......))))))...)). (-40.20 = -39.80 +  -0.40)

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 10:35:14 2006