Locus 4013

Sequence ID 2L_DroMel_CAF1
Location 11,660,468 – 11,660,565
Length 97
Max. P 0.658289
window6325 window6326

overview

Window 5

Location 11,660,468 – 11,660,565
Length 97
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -17.62
Consensus MFE -10.90
Energy contribution -12.35
Covariance contribution 1.45
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.62
SVM decision value 0.23
SVM RNA-class probability 0.643361
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11660468 97 + 22407834
UUUAUUUUGC-----UAUUUUCCUGGCUUUUGUACUCCACCUUGGCUUAUUAUGCCAUCAGCGGCGUCUACUAGCUCGGAUAUUCCAUCUCAGAUAUUUUUA-----
..........-----.....(((.((((..((.((.((.(..((((.......))))...).)).)).))..)))).)))......................----- ( -18.70)
>DroSec_CAF1 121783 94 + 1
UUUAUUUCAC-----UAUUUUCCCAGCUUUUGUACUCCUCCUUGGCUUAUUAUGCCAUCAGCGGCGUG---UAGCUCUGAUAUUCCAUCUCAGAUAUUUUUA-----
..........-----..........(((....(((.((.(..((((.......))))...).)).)))---.)))(((((.........)))))........----- ( -15.10)
>DroSim_CAF1 119609 94 + 1
UUUAUUUCAC-----UAUUUUUCCAGCUUUUGUACUCCUCCUUGGCUUAUUAUGCCAUCAGCGGCGUC---UAGCUCGGAUAUUCCAUCUCAGAUAUUUUUA-----
..........-----......(((((((...(.((.((.(..((((.......))))...).)).)))---.)))).)))......................----- ( -16.60)
>DroEre_CAF1 143306 94 + 1
UUUAUUUUAC-----UAUUUUCCCAGCUUUUGUACUCCUCCUUGGCUUAUUAUGCCAUCAGUGGCGUC---UAGCUCGGAUAUUCCAUCUCAGAUAUUUUUA-----
..........-----.....(((.((((...(.((.((.(..((((.......))))...).)).)))---.)))).)))......................----- ( -17.50)
>DroYak_CAF1 117531 99 + 1
UUUAUUUUACCAUAGUAUUUUCCCAGCUUUUGUACUCCUCCUUGGCUUAUUAUGCCAACAGCGGCGUC---UAGCUCGGAUAUUCCAUCUGAGAUAUUUUUA-----
..(((((((...........(((.((((...(.((.((.(.(((((.......)))))..).)).)))---.)))).))).........)))))))......----- ( -19.05)
>DroAna_CAF1 127619 88 + 1
UUUAUUUCAU-----UAU-----------UUGUCCUCCGCUCUGGCUUAUUAUGCCAUCAGUCGAGCC---UGACUGGGGUAUUCUUUCUCAGGAAUGUCUACAUGC
.......(((-----(..-----------.....(((.(((.((((.......))))..))).)))((---(((..(((.....)))..)))))))))......... ( -18.80)
>consensus
UUUAUUUCAC_____UAUUUUCCCAGCUUUUGUACUCCUCCUUGGCUUAUUAUGCCAUCAGCGGCGUC___UAGCUCGGAUAUUCCAUCUCAGAUAUUUUUA_____
....................(((.((((.....((.((.(..((((.......))))...).)).)).....)))).)))........................... (-10.90 = -12.35 +   1.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,660,468 – 11,660,565
Length 97
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.83
Mean single sequence MFE -19.24
Consensus MFE -12.17
Energy contribution -14.03
Covariance contribution 1.86
Combinations/Pair 1.06
Mean z-score -1.95
Structure conservation index 0.63
SVM decision value 0.26
SVM RNA-class probability 0.658289
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11660468 97 - 22407834
-----UAAAAAUAUCUGAGAUGGAAUAUCCGAGCUAGUAGACGCCGCUGAUGGCAUAAUAAGCCAAGGUGGAGUACAAAAGCCAGGAAAAUA-----GCAAAAUAAA
-----........(((.....)))...(((..(((.....((.(((((..((((.......)))).))))).)).....)))..))).....-----.......... ( -22.50)
>DroSec_CAF1 121783 94 - 1
-----UAAAAAUAUCUGAGAUGGAAUAUCAGAGCUA---CACGCCGCUGAUGGCAUAAUAAGCCAAGGAGGAGUACAAAAGCUGGGAAAAUA-----GUGAAAUAAA
-----........(((((.........)))))....---(((.((.((..((((.......)))).)).))(((......))).........-----)))....... ( -16.50)
>DroSim_CAF1 119609 94 - 1
-----UAAAAAUAUCUGAGAUGGAAUAUCCGAGCUA---GACGCCGCUGAUGGCAUAAUAAGCCAAGGAGGAGUACAAAAGCUGGAAAAAUA-----GUGAAAUAAA
-----........(((.....)))...(((.((((.---.((.((.((..((((.......)))).)).)).)).....)))))))......-----.......... ( -18.10)
>DroEre_CAF1 143306 94 - 1
-----UAAAAAUAUCUGAGAUGGAAUAUCCGAGCUA---GACGCCACUGAUGGCAUAAUAAGCCAAGGAGGAGUACAAAAGCUGGGAAAAUA-----GUAAAAUAAA
-----........(((.....)))...(((.((((.---.((.((.((..((((.......)))).)).)).)).....)))).))).....-----.......... ( -20.30)
>DroYak_CAF1 117531 99 - 1
-----UAAAAAUAUCUCAGAUGGAAUAUCCGAGCUA---GACGCCGCUGUUGGCAUAAUAAGCCAAGGAGGAGUACAAAAGCUGGGAAAAUACUAUGGUAAAAUAAA
-----......((((..((.((.....(((.((((.---.((.((.((.(((((.......))))))).)).)).....)))).)))...))))..))))....... ( -21.70)
>DroAna_CAF1 127619 88 - 1
GCAUGUAGACAUUCCUGAGAAAGAAUACCCCAGUCA---GGCUCGACUGAUGGCAUAAUAAGCCAGAGCGGAGGACAA-----------AUA-----AUGAAAUAAA
.(((.......((((...............(((((.---.....))))).((((.......))))....)))).....-----------...-----)))....... ( -16.36)
>consensus
_____UAAAAAUAUCUGAGAUGGAAUAUCCGAGCUA___GACGCCGCUGAUGGCAUAAUAAGCCAAGGAGGAGUACAAAAGCUGGGAAAAUA_____GUAAAAUAAA
...........................(((.((((.....((.((.((..((((.......)))).)).)).)).....)))).))).................... (-12.17 = -14.03 +   1.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:09 2006