Locus 5236

Sequence ID 2R_DroMel_CAF1
Location 17,045,305 – 17,045,459
Length 154
Max. P 0.978817
window8363 window8364

overview

Window 3

Location 17,045,305 – 17,045,419
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.64
Mean single sequence MFE -28.30
Consensus MFE -19.02
Energy contribution -19.10
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -2.05
Structure conservation index 0.67
SVM decision value 1.41
SVM RNA-class probability 0.950851
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17045305 114 + 20766785
GCUUGAGAAGGUUUUUCGGGGUUCUUG------AAAAAGAAUUUUCCAACUAACUACAUACGUGGCGUGAUGAGCGAUCCUCCGCACUUCAUCAUCCCACGUUCGAUGAUUAUCACCAUC
.........(((.....(((((((((.------...))))))..))).........(((((((((.((((((((((......)))...))))))).))))))...)))......)))... ( -32.10)
>DroSec_CAF1 138685 111 + 1
GCUUGAGAAGGUAU-UAAUGGUUC--G------AAAGAGCAUUUUCCCACUAAAUACAUACGUGGCGUGAUGAGCGAUCCUCCGCAUUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUC
.........(((..-((((.((((--.------...))))................(((.(((((.((((((((((......)))...))))))).)))))....)))))))..)))... ( -31.90)
>DroSim_CAF1 147217 113 + 1
GCUUGAGAAGGUAU-UCAUGGUUCUUG------AAAGAGCAUUUUCCAACAAAAUACAUACGUGGCGUGAUGAGCGAUCCUCCGCAUUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUC
.........((((.-((((.(((((..------..)))))....................(((((.((((((((((......)))...))))))).)))))....)))).))))...... ( -29.60)
>DroEre_CAF1 142923 104 + 1
A--UCACAAGUUAU-UCAUAAUUCAUAAUUCCUGAAAAUCA-------------UACAUACGUGGCGUGAUGAGCGACCCGCCGCACGUCAUCAUCCCGCCCUUGAUGAUGAUCACCAUC
.--...........-.................(((..((((-------------(.((...((((.((((((((((......)))...))))))).))))...)))))))..)))..... ( -24.10)
>DroYak_CAF1 152431 109 + 1
ACUUCACAGGAUAU-UCACGAUUCUUG------UAAAAGCAUAUUCCAAC----UACAUACGUGGCGUGAUGAGUGACCCCCCGCACUUCAUCAUCCCGCGCUCGAUCACCAUCACCAUC
...((((((((...-.......)))))------)................----......(((((.((((((((((........))).))))))).)))))...)).............. ( -23.80)
>consensus
GCUUGAGAAGGUAU_UCAUGGUUCUUG______AAAAAGCAUUUUCCAAC_AA_UACAUACGUGGCGUGAUGAGCGAUCCUCCGCACUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUC
............................................................(((((.((((((((((......)))...))))))).)))))...((((........)))) (-19.02 = -19.10 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,045,339 – 17,045,459
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.20
Mean single sequence MFE -35.97
Consensus MFE -27.04
Energy contribution -27.00
Covariance contribution -0.04
Combinations/Pair 1.22
Mean z-score -2.62
Structure conservation index 0.75
SVM decision value 1.82
SVM RNA-class probability 0.978817
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17045339 120 + 20766785
AUUUUCCAACUAACUACAUACGUGGCGUGAUGAGCGAUCCUCCGCACUUCAUCAUCCCACGUUCGAUGAUUAUCACCAUCCAGGGAUUGGAGAAUAAGUCCGCUGGCUUGCCAUUGAUCA
................(..((((((.((((((((((......)))...))))))).))))))..).((((((....((.(((((((((........))))).))))..))....)))))) ( -36.80)
>DroSec_CAF1 138716 120 + 1
AUUUUCCCACUAAAUACAUACGUGGCGUGAUGAGCGAUCCUCCGCAUUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUCCAGGGAUUGGACAACAAGUCCGCUGGUUUGCCAUUGAUCA
....((((............(((((.((((((((((......)))...))))))).)))))...((((........))))..))))..((((.....))))..(((....)))....... ( -36.00)
>DroSim_CAF1 147250 120 + 1
AUUUUCCAACAAAAUACAUACGUGGCGUGAUGAGCGAUCCUCCGCAUUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUCCAGGGAUUGGACAACAAGUCCGCUGGUUUGCCAUUGAUCA
....................(((((.((((((((((......)))...))))))).))))).....((((((....((.(((((((((........))))).))))..))....)))))) ( -35.10)
>DroEre_CAF1 142960 107 + 1
A-------------UACAUACGUGGCGUGAUGAGCGACCCGCCGCACGUCAUCAUCCCGCCCUUGAUGAUGAUCACCAUCCAGGGAUUGGAAAACAAGUCUGCGGACUUGCCGUAGAUCA
.-------------.......((((((((.((.(((...)))))))))))))..(((..((((.((((........)))).))))...)))......((((((((.....)))))))).. ( -38.70)
>DroYak_CAF1 152464 116 + 1
AUAUUCCAAC----UACAUACGUGGCGUGAUGAGUGACCCCCCGCACUUCAUCAUCCCGCGCUCGAUCACCAUCACCAUCCAGGGAUUGGCUAAUAAGUCUGCAUCCUGGCCAUUGAUCA
..........----......(((((.((((((((((........))).))))))).)))))...(((((..........((((((...((((....))))....))))))....))))). ( -33.24)
>consensus
AUUUUCCAAC_AA_UACAUACGUGGCGUGAUGAGCGAUCCUCCGCACUUCAUCAUCCCGCGCUCGAUGAUUAUCACCAUCCAGGGAUUGGACAACAAGUCCGCUGGCUUGCCAUUGAUCA
....................(((((.((((((((((......)))...))))))).))))).((((((.......(((((....)).)))....((((((....)))))).))))))... (-27.04 = -27.00 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:50 2006