Locus 1709

Sequence ID 2L_DroMel_CAF1
Location 4,694,488 – 4,694,594
Length 106
Max. P 0.722408
window2742 window2743

overview

Window 2

Location 4,694,488 – 4,694,594
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 82.00
Mean single sequence MFE -15.88
Consensus MFE -10.80
Energy contribution -10.68
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.68
SVM decision value 0.40
SVM RNA-class probability 0.722408
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4694488 106 + 22407834
CAAGGAAUACAUAUUUAUUUAUGCACAGAAUUUUUCUCUGUAUUCCCAAAAGGGGAAAUAAACAUCAGACCAACACAGAAUUCCACUCAAAACAAUUAUGAAUGAA
...(((((.((((......)))).(((((.......))))).(((((.....)))))......................)))))...................... ( -16.40)
>DroSec_CAF1 124013 106 + 1
GAAGAAAUACAUAUUUAUUUAUGCACACAAUUUUUCUCUGUAUUCCCGAAAGGGGAAAUAAGCAUCAGACCAACACAGAAUUCCACUCAAAACAAUUAUGAAUGAA
((((((...((((......)))).......))))))(((((.(((((....)))))...........(.....))))))....((.(((.........))).)).. ( -14.60)
>DroSim_CAF1 116902 106 + 1
AAAGAAAUACAUAUUUAUUUAUGCACACAAUUUUUCUCUGUAUUCCCGAAAGGGGAAAUAAACAUCAGACCAACACAGAAUUCCACUCAAAACAAUUAUGAAUGAA
.............((((((((((.............(((((.(((((....)))))......(....)......))))).................)))))))))) ( -14.11)
>DroEre_CAF1 127862 85 + 1
---------------------UGCACAGCAUUUCGCUGUGUAUUCCCGAAAGUGGAAAUAAACAUCAGGCCAACACACAAUUUCACUCAAAACAAUUAUGAAUGAA
---------------------((((((((.....))))))))(((((....).))))........................((((.(((.........))).)))) ( -19.50)
>DroYak_CAF1 128617 85 + 1
---------------------CGUACAGAAUUUUUCUCUGUAUUCCCGAAAGGGGAAAUAAACAUCAGGCCAACACAGAAUUCCACUCAAAACAAUUAUGAAUGAA
---------------------..((((((.......))))))(((((....)))))...........................((.(((.........))).)).. ( -14.80)
>consensus
_AAG_AAUACAUAUUUAUUUAUGCACAGAAUUUUUCUCUGUAUUCCCGAAAGGGGAAAUAAACAUCAGACCAACACAGAAUUCCACUCAAAACAAUUAUGAAUGAA
....................................(((((.(((((....)))))...........(.....))))))....((.(((.........))).)).. (-10.80 = -10.68 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,694,488 – 4,694,594
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 82.00
Mean single sequence MFE -21.77
Consensus MFE -18.70
Energy contribution -17.82
Covariance contribution -0.88
Combinations/Pair 1.18
Mean z-score -1.53
Structure conservation index 0.86
SVM decision value 0.25
SVM RNA-class probability 0.651857
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4694488 106 - 22407834
UUCAUUCAUAAUUGUUUUGAGUGGAAUUCUGUGUUGGUCUGAUGUUUAUUUCCCCUUUUGGGAAUACAGAGAAAAAUUCUGUGCAUAAAUAAAUAUGUAUUCCUUG
((((((((.........)))))))).(((((((((.....((........))(((....)))))))))))).........(((((((......)))))))...... ( -22.90)
>DroSec_CAF1 124013 106 - 1
UUCAUUCAUAAUUGUUUUGAGUGGAAUUCUGUGUUGGUCUGAUGCUUAUUUCCCCUUUCGGGAAUACAGAGAAAAAUUGUGUGCAUAAAUAAAUAUGUAUUUCUUC
((((((((.........)))))))).((((((((((((.....)))......(((....)))))))))))).........(((((((......)))))))...... ( -22.40)
>DroSim_CAF1 116902 106 - 1
UUCAUUCAUAAUUGUUUUGAGUGGAAUUCUGUGUUGGUCUGAUGUUUAUUUCCCCUUUCGGGAAUACAGAGAAAAAUUGUGUGCAUAAAUAAAUAUGUAUUUCUUU
((((((((.........)))))))).(((((((((.....((........))(((....)))))))))))).........(((((((......)))))))...... ( -22.30)
>DroEre_CAF1 127862 85 - 1
UUCAUUCAUAAUUGUUUUGAGUGAAAUUGUGUGUUGGCCUGAUGUUUAUUUCCACUUUCGGGAAUACACAGCGAAAUGCUGUGCA---------------------
((((((((.........))))))))..(((((((...(((((.((........))..))))).)))))))(((........))).--------------------- ( -21.40)
>DroYak_CAF1 128617 85 - 1
UUCAUUCAUAAUUGUUUUGAGUGGAAUUCUGUGUUGGCCUGAUGUUUAUUUCCCCUUUCGGGAAUACAGAGAAAAAUUCUGUACG---------------------
((((((((.........)))))))).((((((((...(((((...............))))).))))))))..............--------------------- ( -19.86)
>consensus
UUCAUUCAUAAUUGUUUUGAGUGGAAUUCUGUGUUGGUCUGAUGUUUAUUUCCCCUUUCGGGAAUACAGAGAAAAAUUCUGUGCAUAAAUAAAUAUGUAUU_CUU_
((((((((.........)))))))).(((((((((..(((((...............))))))))))))))................................... (-18.70 = -17.82 +  -0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:08 2006