Locus 4289

Sequence ID 3L_DroMel_CAF1
Location 12,561,102 – 12,561,259
Length 157
Max. P 0.865777
window6632 window6633 window6634

overview

Window 2

Location 12,561,102 – 12,561,219
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.02
Mean single sequence MFE -29.35
Consensus MFE -22.24
Energy contribution -22.80
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.95
Structure conservation index 0.76
SVM decision value 0.68
SVM RNA-class probability 0.820653
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12561102 117 + 23771897
AGUGUGUGUGAGCGCCCACACAGUGGGGGGUAGAAAUA---GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAGCAGUUUCAGGAUAUCCUGAACAACAAUUUAA
.(((((.((....)).))))).((..(((((((((((.---((....((((........))))....((((((......))))))...)).)))))....))))))..)).......... ( -30.50)
>DroSec_CAF1 49288 117 + 1
UGUGUGUGUGAGCGCCCACACAGUGGGGGGCAGAAAUA---GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAUUUUCAGGAUAUCCUGAACAACAAUUUAA
((((((.((....)).))))))((((.((((((....(---(((.......)))))))))).)....((((((......))))))....))).((((((....))))))........... ( -32.40)
>DroSim_CAF1 50682 117 + 1
UGUGUGUGUGAGCGCCCACACAGUGAGGGGCAGAAAUA---GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAGUUUCAGGAUAUCCUAAACAACAAUUUAA
..(((.(((..((.(((((...))).)).)).(((((.---((....((((........))))....((((((......))))))...)).)))))(((....)))..))))))...... ( -28.00)
>DroEre_CAF1 50000 110 + 1
----UGUGUGAGCGCCCACACAGUGGGGGGCAGAAAUA---GUAAUAGCAGUACUUUGGCUGCCAAAGCUAUUUAUUAUACUAGCAAAACUGUUUGAGGAUAUCCUGAACAAUUUUU---
----.((((((((.(((........))).))..(((((---((....(((((......)))))....))))))).))))))....((((.(((((.(((....)))))))).)))).--- ( -31.70)
>DroYak_CAF1 50666 113 + 1
----UGUGUGAGCGCCCACACAGUGGGGGGCAGUAAUAAUAAUAAUAGCAGUACUUUGUCUGCAAAACCUAUUUAUUAUAAUAGCAAAACAGUUUUAGGAUAUCCUGAACAAGAAUU---
----..(((..((((((.(.....)..)))).(((((((........((((........)))).........)))))))....))...)))((((.(((....))))))).......--- ( -24.13)
>consensus
_GUGUGUGUGAGCGCCCACACAGUGGGGGGCAGAAAUA___GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAGUUUCAGGAUAUCCUGAACAACAAUUUAA
...........((.(((((...))).)).))................((((........))))....((((((......))))))........((((((....))))))........... (-22.24 = -22.80 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,561,102 – 12,561,219
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.02
Mean single sequence MFE -25.72
Consensus MFE -21.20
Energy contribution -21.92
Covariance contribution 0.72
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.82
SVM decision value 0.85
SVM RNA-class probability 0.865735
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12561102 117 - 23771897
UUAAAUUGUUGUUCAGGAUAUCCUGAAACUGCUUUGCUAUUAUAAUAAAUAGCUUUUGCAGGCAAAGUACUGCUAUUAC---UAUUUCUACCCCCCACUGUGUGGGCGCUCACACACACU
.....((((..((((((....)))))).((((...((((((......))))))....))))))))((((.......)))---)...............(((((((....))))))).... ( -29.50)
>DroSec_CAF1 49288 117 - 1
UUAAAUUGUUGUUCAGGAUAUCCUGAAAAUGUUUUGCUAUUAUAAUAAAUAGCUUUUGCAGGCAAAGUACUGCUAUUAC---UAUUUCUGCCCCCCACUGUGUGGGCGCUCACACACACA
...........((((((....))))))..(((...((((((......))))))....)))(((((((((.((....)).---))))).))))......(((((((....))))))).... ( -27.70)
>DroSim_CAF1 50682 117 - 1
UUAAAUUGUUGUUUAGGAUAUCCUGAAACUGUUUUGCUAUUAUAAUAAAUAGCUUUUGCAGGCAAAGUACUGCUAUUAC---UAUUUCUGCCCCUCACUGUGUGGGCGCUCACACACACA
...........((((((....)))))).((((...((((((......))))))....))))((..((((.......)))---)......(((((.......).))))))........... ( -25.70)
>DroEre_CAF1 50000 110 - 1
---AAAAAUUGUUCAGGAUAUCCUCAAACAGUUUUGCUAGUAUAAUAAAUAGCUUUGGCAGCCAAAGUACUGCUAUUAC---UAUUUCUGCCCCCCACUGUGUGGGCGCUCACACA----
---.(((((((((.(((....)))..)))))))))((((..........))))...(((((....((((.......)))---)....))))).......((((((....)))))).---- ( -27.10)
>DroYak_CAF1 50666 113 - 1
---AAUUCUUGUUCAGGAUAUCCUAAAACUGUUUUGCUAUUAUAAUAAAUAGGUUUUGCAGACAAAGUACUGCUAUUAUUAUUAUUACUGCCCCCCACUGUGUGGGCGCUCACACA----
---...........(((....)))...........((....(((((((.(((.....((((........))))..))))))))))....))........((((((....)))))).---- ( -18.60)
>consensus
UUAAAUUGUUGUUCAGGAUAUCCUGAAACUGUUUUGCUAUUAUAAUAAAUAGCUUUUGCAGGCAAAGUACUGCUAUUAC___UAUUUCUGCCCCCCACUGUGUGGGCGCUCACACACAC_
...........((((((....))))))........((((((......))))))....((((........)))).........................(((((((....))))))).... (-21.20 = -21.92 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,561,140 – 12,561,259
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 86.83
Mean single sequence MFE -20.81
Consensus MFE -15.07
Energy contribution -15.82
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.72
SVM decision value 0.85
SVM RNA-class probability 0.865777
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12561140 119 + 23771897
GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAGCAGUUUCAGGAUAUCCUGAACAACAAUUUAAAAAUUUCAACAGCUUAGUAAUUUAUAAAAUAAGAUAAUAC
...((((...((((..((((((....((((((......))))))...)))).((((((....))))))......................))..))))..))))............... ( -23.50)
>DroSec_CAF1 49326 119 + 1
GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAUUUUCAGGAUAUCCUGAACAACAAUUUAAAAAUUUCAAUAACUCAGUAAUUUAUAAAAUAAGAGAACAU
......((((........))))....((((((......))))))........((((((....)))))).......................(((.................)))..... ( -19.03)
>DroSim_CAF1 50720 119 + 1
GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAGUUUCAGGAUAUCCUAAACAACAAUUUAAAAAUUUCAACAGCUUAGUACUUUAAUAAAUAAGAGAAUAU
....(((.((((((..((.((.....((((((......))))))......((((.(((....)))))))...................))))..)))))))))................ ( -21.10)
>DroEre_CAF1 50034 114 + 1
GUAAUAGCAGUACUUUGGCUGCCAAAGCUAUUUAUUAUACUAGCAAAACUGUUUGAGGAUAUCCUGAACAAUUUUU---AAAUCUCCACAGCUAAGUAAUUUAUAAAA--AUUUCACAU
...((((...(((((.(((((.....((((..........))))((((.(((((.(((....)))))))).)))).---.........))))))))))..))))....--......... ( -19.60)
>consensus
GUAAUAGCAGUACUUUGCCUGCAAAAGCUAUUUAUUAUAAUAGCAAAACAGUUUCAGGAUAUCCUGAACAACAAUUUAAAAAUUUCAACAGCUUAGUAAUUUAUAAAAUAAGAGAACAU
......((((........))))....((((((......))))))........((((((....))))))................................................... (-15.07 = -15.82 +   0.75)

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 11:18:41 2006