Locus 4647

Sequence ID 3R_DroMel_CAF1
Location 12,234,802 – 12,234,896
Length 94
Max. P 0.819498
window7636 window7637

overview

Window 6

Location 12,234,802 – 12,234,896
Length 94
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.66
Mean single sequence MFE -31.75
Consensus MFE -19.47
Energy contribution -20.33
Covariance contribution 0.86
Combinations/Pair 1.07
Mean z-score -2.16
Structure conservation index 0.61
SVM decision value 0.65
SVM RNA-class probability 0.812768
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12234802 94 + 27905053
GUGGCU------------GUUGCUUUAGCCA--ACAUAUUUAUCC---------U-CCGCCCUGCCCUGCUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
.(((((------------(......))))))--(((...((((.(---------(-(.(((((((.(((((((.............)))))))..))))))).).)).))))...))) ( -37.72)
>DroSec_CAF1 48586 94 + 1
GUGGCU------------GUUGCUUUAGCCA--ACAUAUUUAUCC---------U-CCGCCCUGCCCUGCUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
.(((((------------(......))))))--(((...((((.(---------(-(.(((((((.(((((((.............)))))))..))))))).).)).))))...))) ( -37.72)
>DroSim_CAF1 48291 94 + 1
GCGGCU------------GUUGCUUUAGCCA--ACAUAUUUAUCC---------U-CCGCCCUGCCCUGCUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
..((((------------(......))))).--(((...((((.(---------(-(.(((((((.(((((((.............)))))))..))))))).).)).))))...))) ( -37.12)
>DroEre_CAF1 49989 106 + 1
GUUGCUGUAGCUGUAGCUGUAGCUGUAGCCA--ACAUAUUUAUCC---------U-CCGCCCUGCCCUGUUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
(((((((((((((......))))))))).))--))....((((.(---------(-(.(((((((.(((((((.............)))))))..))))))).).)).))))...... ( -38.32)
>DroYak_CAF1 50032 88 + 1
G------------------UAGCUGUAGCCA--ACAUAUUUAUCC---------A-CCGCCCUGCCCGACUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
.------------------..((....))..--(((((((..((.---------.-(.(((((((..(.((((..((........))..))))).))))))).)..))..)))).))) ( -23.90)
>DroAna_CAF1 48858 94 + 1
GA------------------------AGCCAAAACAUUUUUAUCCAGUCCAGUCUCCCGCCAGUCCUCCCUCCAUCCUGAUCAAUGGCAGCAGCCGCGGGGCCACAAAAUGAUAUUGU
..------------------------.......(((....((((..........(((((((((.............)))......(((....))))))))).........)))).))) ( -15.73)
>consensus
GUGGCU____________GUUGCUUUAGCCA__ACAUAUUUAUCC_________U_CCGCCCUGCCCUGCUGCAUCCUGAUCAAUGGCAGCAGCCGCAGGGCCGCAGAAUGAUAUUGU
..........................................................(((((((...(((((..((........))..))))).)))))))................ (-19.47 = -20.33 +   0.86)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,234,802 – 12,234,896
Length 94
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 80.66
Mean single sequence MFE -35.48
Consensus MFE -20.64
Energy contribution -21.39
Covariance contribution 0.75
Combinations/Pair 1.11
Mean z-score -2.33
Structure conservation index 0.58
SVM decision value 0.68
SVM RNA-class probability 0.819498
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12234802 94 - 27905053
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAGCAGGGCAGGGCGG-A---------GGAUAAAUAUGU--UGGCUAAAGCAAC------------AGCCAC
........(((((.(.(((((((..(((((((.(((......)))))))))).))))))).)-)---------))))........--(((((........------------))))). ( -38.50)
>DroSec_CAF1 48586 94 - 1
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAGCAGGGCAGGGCGG-A---------GGAUAAAUAUGU--UGGCUAAAGCAAC------------AGCCAC
........(((((.(.(((((((..(((((((.(((......)))))))))).))))))).)-)---------))))........--(((((........------------))))). ( -38.50)
>DroSim_CAF1 48291 94 - 1
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAGCAGGGCAGGGCGG-A---------GGAUAAAUAUGU--UGGCUAAAGCAAC------------AGCCGC
........(((((.(.(((((((..(((((((.(((......)))))))))).))))))).)-)---------))))........--.((((........------------)))).. ( -37.90)
>DroEre_CAF1 49989 106 - 1
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAACAGGGCAGGGCGG-A---------GGAUAAAUAUGU--UGGCUACAGCUACAGCUACAGCUACAGCAAC
....((((.((((((.((((((..(((.(((........))).).))..))))))...))))-)---------)))))....(((--(((((..(((....)))..)))..))))).. ( -38.10)
>DroYak_CAF1 50032 88 - 1
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAGUCGGGCAGGGCGG-U---------GGAUAAAUAUGU--UGGCUACAGCUA------------------C
.((((((...((..(.(((((((((((((..((........))..))))))..))))))).)-.---------.)).....))))--))((....))..------------------. ( -37.40)
>DroAna_CAF1 48858 94 - 1
ACAAUAUCAUUUUGUGGCCCCGCGGCUGCUGCCAUUGAUCAGGAUGGAGGGAGGACUGGCGGGAGACUGGACUGGAUAAAAAUGUUUUGGCU------------------------UC
.(((...(((((((..(((....)))..)..(((((......)))))........(..((((....)))..)..)...))))))..)))...------------------------.. ( -22.50)
>consensus
ACAAUAUCAUUCUGCGGCCCUGCGGCUGCUGCCAUUGAUCAGGAUGCAGCAGGGCAGGGCGG_A_________GGAUAAAUAUGU__UGGCUAAAGCAAC____________AGCCAC
....((((......(.(((((((.(((((..((........))..)))))...))))))).)............))))........................................ (-20.64 = -21.39 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:31 2006