Locus 5734

Sequence ID 3L_DroMel_CAF1
Location 15,608,423 – 15,608,572
Length 149
Max. P 0.969090
window9082 window9083 window9084

overview

Window 2

Location 15,608,423 – 15,608,543
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.92
Mean single sequence MFE -15.00
Consensus MFE -12.50
Energy contribution -12.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.83
SVM decision value 0.80
SVM RNA-class probability 0.855184
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15608423 120 + 23771897
ACAGUAAGACCAAUGCAAUUUGCAAUUACUCUAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAAUCACCCCUCGAUAAAACAA
.............((((((((((((((............................................)))))))))))).))((.......))....................... ( -12.50)
>DroSec_CAF1 31664 119 + 1
ACAGUGAGACCAAUGCAAUUUGCAAUUACUCUAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGA-CCACCCCUCGAUAAAACAA
....((((.....((((((((((((((............................................)))))))))))).))((.......))...-......))))......... ( -15.70)
>DroSim_CAF1 31686 120 + 1
GCAGUAAGACCAAUGCAAUUUGCAAUUAAUCUAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAA
(((..(((.....((((((((((((((............................................)))))))))))).)).)))....)))....................... ( -14.90)
>DroEre_CAF1 31555 120 + 1
ACAGUAAGGCCAAUGCAAUUUGCAAUUACUCCAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAA
.......((....((((((((((((((............................................)))))))))))).))((.......))....))................. ( -14.00)
>DroYak_CAF1 33811 120 + 1
ACAGUAAGGCCAAUGCAAUUUGCAAUUACUCGAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGGACCACCCCUCGAUAAAACAA
.......((((..((((((((((((((............................................)))))))))))).))((.......)).)).))................. ( -17.90)
>consensus
ACAGUAAGACCAAUGCAAUUUGCAAUUACUCUAUAAUUAUACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAA
.............((((((((((((((............................................)))))))))))).))((.......))....................... (-12.50 = -12.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 15,608,463 – 15,608,572
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.29
Mean single sequence MFE -19.16
Consensus MFE -13.30
Energy contribution -13.30
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.69
SVM decision value 0.15
SVM RNA-class probability 0.608870
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15608463 109 + 23771897
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAAUCACCCCUCGAUAAAACAAAUGCAAUUGACCUGCAUUUCAAAUUG-----------CAC
.........((((((..................(((((..((((.....)))).)))))...................(((((((.......)))))))..)))))-----------).. ( -16.10)
>DroSec_CAF1 31704 108 + 1
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGA-CCACCCCUCGAUAAAACAAAUGCAAUUGACCUGCAUUUCAAAUUG-----------CGC
.........((((((..................(((((..((((.....)))).))))).-.................(((((((.......)))))))..)))))-----------).. ( -16.10)
>DroSim_CAF1 31726 109 + 1
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAAAUGCAAUUGACCUGCAUUUCAAAUUG-----------CAC
.........((((((..................(((((..((((.....)))).)))))...................(((((((.......)))))))..)))))-----------).. ( -16.10)
>DroEre_CAF1 31595 120 + 1
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAAAUGCAGUUGACCUGCAUUUCAAAUUGCAGGUGCCGAGCAC
.........((((((..(((......)))..)))))).........(((((((.((((.......................)))).)))(((((((........)))))))...)))).. ( -23.70)
>DroYak_CAF1 33851 120 + 1
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGGACCACCCCUCGAUAAAACAAAUGCAAUUGACCUGCAUUUCAAAUGGCAGGUGCCGAGCAC
.........((((((..(((......)))..)))))).........((((.(((((((((........(((((............)))))))))))))).....(((....))))))).. ( -23.80)
>consensus
ACAACAAAAGCAAUUAAAUUCAACUUAAUCAAAUUGCAAAUUGACAGCUUCAAAUGCAGAACCACCCCUCGAUAAAACAAAUGCAAUUGACCUGCAUUUCAAAUUG___________CAC
.........((((((..(((......)))..))))))...((((..((.((((.((((.......................)))).))))...))...)))).................. (-13.30 = -13.30 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,608,463 – 15,608,572
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.29
Mean single sequence MFE -28.30
Consensus MFE -24.42
Energy contribution -24.34
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.78
Structure conservation index 0.86
SVM decision value 1.64
SVM RNA-class probability 0.969090
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15608463 109 - 23771897
GUG-----------CAAUUUGAAAUGCAGGUCAAUUGCAUUUGUUUUAUCGAGGGGUGAUUCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
..(-----------((.(((.(((((((((...((..(.((((......))))..)..))))))))))).))).)))((((..((((((.((((......)))).))))))....)))). ( -25.70)
>DroSec_CAF1 31704 108 - 1
GCG-----------CAAUUUGAAAUGCAGGUCAAUUGCAUUUGUUUUAUCGAGGGGUGG-UCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
..(-----------((.(((.((((((((..((......((((......))))...)).-.)))))))).))).)))((((..((((((.((((......)))).))))))....)))). ( -27.80)
>DroSim_CAF1 31726 109 - 1
GUG-----------CAAUUUGAAAUGCAGGUCAAUUGCAUUUGUUUUAUCGAGGGGUGGUUCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
..(-----------((.(((.(((((((((...((..(.((((......))))..)..))))))))))).))).)))((((..((((((.((((......)))).))))))....)))). ( -26.00)
>DroEre_CAF1 31595 120 - 1
GUGCUCGGCACCUGCAAUUUGAAAUGCAGGUCAACUGCAUUUGUUUUAUCGAGGGGUGGUUCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
.....((((.((((((........))))))((((.((((...(..(((((....)))))..))))).)))).)))).((((..((((((.((((......)))).))))))....)))). ( -30.20)
>DroYak_CAF1 33851 120 - 1
GUGCUCGGCACCUGCCAUUUGAAAUGCAGGUCAAUUGCAUUUGUUUUAUCGAGGGGUGGUCCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
..((..(((....)))..((.(((((((((...((..(.((((......))))..)..))))))))))).))))...((((..((((((.((((......)))).))))))....)))). ( -31.80)
>consensus
GUG___________CAAUUUGAAAUGCAGGUCAAUUGCAUUUGUUUUAUCGAGGGGUGGUUCUGCAUUUGAAGCUGUCAAUUUGCAAUUUGAUUAAGUUGAAUUUAAUUGCUUUUGUUGU
..............((.(((.(((((((((...((..(.((((......))))..)..))))))))))).))).)).((((..((((((.((((......)))).))))))....)))). (-24.42 = -24.34 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:08 2006