Locus 4060

Sequence ID 3L_DroMel_CAF1
Location 11,836,962 – 11,837,052
Length 90
Max. P 0.869504
window6323 window6324

overview

Window 3

Location 11,836,962 – 11,837,052
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 81.88
Mean single sequence MFE -44.10
Consensus MFE -26.80
Energy contribution -26.92
Covariance contribution 0.12
Combinations/Pair 1.29
Mean z-score -2.22
Structure conservation index 0.61
SVM decision value 0.35
SVM RNA-class probability 0.699508
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11836962 90 + 23771897
GUCGAUGGGAGCCGGCAGCAGUGCUGUGGGUAUCACCAUGAUAGGCAUCAUGGCCGGCGGAGCCGAGGAUGUCGUUGAU------CCGCCGGCUGC
(((.(((((((((.(((((...))))).))).)).))))....))).....((((((((((..(((.(....).))).)------))))))))).. ( -44.40)
>DroSec_CAF1 14306 90 + 1
GUCGAUGGAUGCCGGCAGCAGUGCUGUGGGUAUCACCAUGAUGGGCAUCAUGGCCGGCGGAGCCGAGGAUGCCGUUGAU------CCGCCGGCUGC
...((((((((((.(((((...))))).)))))).((.....)).))))..((((((((((..(((.(....).))).)------))))))))).. ( -47.80)
>DroSim_CAF1 13845 90 + 1
GUCGAUGGGUGCCGGCAGCAGUGCUGUGGGUAUCACCAUGAUGGGCAUCAUGGCCGGCGGAGCCGAGGAUGCCGUUGAU------CCGCCGGCUGC
...((((((((((.(((((...))))).)))))).((.....)).))))..((((((((((..(((.(....).))).)------))))))))).. ( -47.20)
>DroEre_CAF1 13685 90 + 1
GUCUAUGGCAGCCGGCAGAAGUGCUGUGGGUAUCACCAUGAUGGGCAUCAUGGCCGGCGGAGCCGAGGAUGACGCUGAU------CCGCCGGCUGC
.......(((((((((....((.((((.((.....(((((((....))))))))).)))).))...((((.......))------))))))))))) ( -40.70)
>DroYak_CAF1 14461 90 + 1
GUCGAUGGGAGCCGGCAGAAGAGCUGUGGGUAUCACCAUGAUGGGCAUCAUGGCCGGCGCAGCCGAGGAUGCCGUUGCU------CCGCCGGCUGC
((((...((.(((.((((.....)))).))).)).(((((((....))))))).))))(((((((.(((.((....)))------))..))))))) ( -43.20)
>DroMoj_CAF1 31808 93 + 1
CGCUCCGGGC---GCCAGCAGCGCUGUCGGUAUGACCAUUAUGGGCAACAUUGUUGGCGCCGCUGCCGUUGCCGGCUGUGUGUUGCUGCCGCACGG
....(((.((---(.(((((((((.(((((((((.((.....)).))........((((....))))..)))))))...))))))))).))).))) ( -41.30)
>consensus
GUCGAUGGGAGCCGGCAGCAGUGCUGUGGGUAUCACCAUGAUGGGCAUCAUGGCCGGCGGAGCCGAGGAUGCCGUUGAU______CCGCCGGCUGC
((((.(((..(((.((((.....)))).)))............((((((.....((((...))))..))))))............))).))))... (-26.80 = -26.92 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,836,962 – 11,837,052
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 81.88
Mean single sequence MFE -38.67
Consensus MFE -25.64
Energy contribution -26.45
Covariance contribution 0.81
Combinations/Pair 1.14
Mean z-score -2.66
Structure conservation index 0.66
SVM decision value 0.86
SVM RNA-class probability 0.869504
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11836962 90 - 23771897
GCAGCCGGCGG------AUCAACGACAUCCUCGGCUCCGCCGGCCAUGAUGCCUAUCAUGGUGAUACCCACAGCACUGCUGCCGGCUCCCAUCGAC
(((((((((((------(....(((.....)))..)))))))((((((((....))))))))...............))))).............. ( -33.40)
>DroSec_CAF1 14306 90 - 1
GCAGCCGGCGG------AUCAACGGCAUCCUCGGCUCCGCCGGCCAUGAUGCCCAUCAUGGUGAUACCCACAGCACUGCUGCCGGCAUCCAUCGAC
...((((((((------.......((.....((((...))))((((((((....))))))))..........))....)))))))).......... ( -35.60)
>DroSim_CAF1 13845 90 - 1
GCAGCCGGCGG------AUCAACGGCAUCCUCGGCUCCGCCGGCCAUGAUGCCCAUCAUGGUGAUACCCACAGCACUGCUGCCGGCACCCAUCGAC
...((((((((------.......((.....((((...))))((((((((....))))))))..........))....)))))))).......... ( -35.60)
>DroEre_CAF1 13685 90 - 1
GCAGCCGGCGG------AUCAGCGUCAUCCUCGGCUCCGCCGGCCAUGAUGCCCAUCAUGGUGAUACCCACAGCACUUCUGCCGGCUGCCAUAGAC
(((((((((((------(...((........((((...))))((((((((....))))))))..........))...))))))))))))....... ( -44.40)
>DroYak_CAF1 14461 90 - 1
GCAGCCGGCGG------AGCAACGGCAUCCUCGGCUGCGCCGGCCAUGAUGCCCAUCAUGGUGAUACCCACAGCUCUUCUGCCGGCUCCCAUCGAC
((((((((.((------(((....)).)))))))))))((((((((((((....))))))(((.....))).........)))))).......... ( -42.80)
>DroMoj_CAF1 31808 93 - 1
CCGUGCGGCAGCAACACACAGCCGGCAACGGCAGCGGCGCCAACAAUGUUGCCCAUAAUGGUCAUACCGACAGCGCUGCUGGC---GCCCGGAGCG
(((.(((.(((((.(.....((((....)))).((((((.((....)).)))).......(((.....))).))).))))).)---)).))).... ( -40.20)
>consensus
GCAGCCGGCGG______AUCAACGGCAUCCUCGGCUCCGCCGGCCAUGAUGCCCAUCAUGGUGAUACCCACAGCACUGCUGCCGGCUCCCAUCGAC
...((((((((............((((((.(((((...)))))....)))))).......(((.....))).......)))))))).......... (-25.64 = -26.45 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:35 2006