Locus 4240

Sequence ID 2R_DroMel_CAF1
Location 14,010,317 – 14,010,407
Length 90
Max. P 0.995535
window6804 window6805

overview

Window 4

Location 14,010,317 – 14,010,407
Length 90
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.66
Mean single sequence MFE -25.22
Consensus MFE -11.98
Energy contribution -12.82
Covariance contribution 0.84
Combinations/Pair 1.22
Mean z-score -2.76
Structure conservation index 0.48
SVM decision value 1.60
SVM RNA-class probability 0.966870
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14010317 90 + 20766785
-UGAGCGU------GCAGGAUU-UUGGGAUAUGUGUA--CA--------UACGAUUUUCUGCAGCGAAUAUAAACAAAGUU-UUAAUGUUUAUAUAGAGCUCAGAGAGA
-(((((.(------((((((..-(((...((((....--))--------)))))..)))))))....(((((((((.....-....)))))))))...)))))...... ( -25.10)
>DroSec_CAF1 40997 90 + 1
-UGAGCGU------GCUGUAUU-UUGGGAUAUACGUA--CA--------UACGAUUUUCUGCAGCGAAUAUAAACAAAGUU-UUAAUGUUUAUAUAGAGCUCAGAGAGA
-.....((------((((((((-....)))))).)))--).--------.....(((((((.(((..(((((((((.....-....)))))))))...)))))))))). ( -23.80)
>DroSim_CAF1 40385 90 + 1
-UGAGCGU------GCAGGAUU-UUGGGAUAUGCGUA--CA--------UACGAUAUUCUGCAGCGAAUAUAAACAAAGUU-UUAAUGUUUAUAUAGAGCUCAGAGAGA
-(((((.(------(((((((.-(((...((((....--))--------))))).))))))))....(((((((((.....-....)))))))))...)))))...... ( -24.50)
>DroEre_CAF1 41517 97 + 1
-UGAGCGU------GCAGGAUU-UUGGGAUAUGUGUA--CAUA--CUCGUACGAUUUUCUGCAGCGAAUAUAAACAAAGUUUUUAAUGUUUAUAUAGAGCUCAGAGAGA
-(((((.(------((((((..-(((.((((((....--))))--.))...)))..)))))))....(((((((((..........)))))))))...)))))...... ( -26.80)
>DroYak_CAF1 41108 103 + 1
GUGAGCGU------GCAGGAUUUUUGGGAUGUGUGUGUGUGUACACAUACACAAUUUGCUGCAGCGAAUAUAAACAAAGUUUUUAAUGUUUAUAUAGAGCUCAGAGAGA
.(((((.(------((((.(..(......((((((((((....)))))))))))..).)))))....(((((((((..........)))))))))...)))))...... ( -31.90)
>DroAna_CAF1 39970 87 + 1
-UGAGUGUUGAUAUAAAAGAUU-UUG-GAUUUCUGGU--CG--------AA-GAAUCGCGCGUGCAAAUAUAAACAAUGUU-UU-AUGUGUAUUUACAGCUCA------
-.((((((.(((......((((-((.-(((.....))--).--------.)-)))))(((((((.((((((.....)))))-))-))))))))).))).))).------ ( -19.20)
>consensus
_UGAGCGU______GCAGGAUU_UUGGGAUAUGUGUA__CA________UACGAUUUUCUGCAGCGAAUAUAAACAAAGUU_UUAAUGUUUAUAUAGAGCUCAGAGAGA
.(((((....................(((....((((((........))))))....))).......(((((((((..........)))))))))...)))))...... (-11.98 = -12.82 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,010,317 – 14,010,407
Length 90
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.66
Mean single sequence MFE -19.17
Consensus MFE -9.83
Energy contribution -11.17
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -3.59
Structure conservation index 0.51
SVM decision value 2.59
SVM RNA-class probability 0.995535
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14010317 90 - 20766785
UCUCUCUGAGCUCUAUAUAAACAUUAA-AACUUUGUUUAUAUUCGCUGCAGAAAAUCGUA--------UG--UACACAUAUCCCAA-AAUCCUGC------ACGCUCA-
.......((((...(((((((((....-.....)))))))))..(.(((((......(((--------((--....))))).....-....))))------)))))).- ( -19.06)
>DroSec_CAF1 40997 90 - 1
UCUCUCUGAGCUCUAUAUAAACAUUAA-AACUUUGUUUAUAUUCGCUGCAGAAAAUCGUA--------UG--UACGUAUAUCCCAA-AAUACAGC------ACGCUCA-
....(((((((...(((((((((....-.....)))))))))..))).)))).....(..--------((--(..((((.......-.)))).))------)..)...- ( -18.30)
>DroSim_CAF1 40385 90 - 1
UCUCUCUGAGCUCUAUAUAAACAUUAA-AACUUUGUUUAUAUUCGCUGCAGAAUAUCGUA--------UG--UACGCAUAUCCCAA-AAUCCUGC------ACGCUCA-
.......((((...(((((((((....-.....)))))))))..(.(((((......(((--------((--....))))).....-....))))------)))))).- ( -19.36)
>DroEre_CAF1 41517 97 - 1
UCUCUCUGAGCUCUAUAUAAACAUUAAAAACUUUGUUUAUAUUCGCUGCAGAAAAUCGUACGAG--UAUG--UACACAUAUCCCAA-AAUCCUGC------ACGCUCA-
....(((((((...(((((((((..........)))))))))..))).)))).........(((--..((--((............-.....)))------)..))).- ( -20.83)
>DroYak_CAF1 41108 103 - 1
UCUCUCUGAGCUCUAUAUAAACAUUAAAAACUUUGUUUAUAUUCGCUGCAGCAAAUUGUGUAUGUGUACACACACACACAUCCCAAAAAUCCUGC------ACGCUCAC
......(((((...(((((((((..........)))))))))..(.(((((.....(((((.((((....)))).)))))...........))))------))))))). ( -25.99)
>DroAna_CAF1 39970 87 - 1
------UGAGCUGUAAAUACACAU-AA-AACAUUGUUUAUAUUUGCACGCGCGAUUC-UU--------CG--ACCAGAAAUC-CAA-AAUCUUUUAUAUCAACACUCA-
------(((((((((((((.(((.-..-.....)))...)))))))).)).(((...-.)--------))--..........-...-...........))).......- ( -11.50)
>consensus
UCUCUCUGAGCUCUAUAUAAACAUUAA_AACUUUGUUUAUAUUCGCUGCAGAAAAUCGUA________UG__UACACAUAUCCCAA_AAUCCUGC______ACGCUCA_
....(((((((...(((((((((..........)))))))))..))).))))......................................................... ( -9.83 = -11.17 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:00 2006