Locus 7896

Sequence ID	3L_DroMel_CAF1
Location	21,042,879 – 21,043,027
Length	148
Max. P	0.933427

overview

Window 6

Location	21,042,879 – 21,042,987
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-41.45
Consensus MFE	-32.30
Energy contribution	-32.67
Covariance contribution	0.38
Combinations/Pair	1.11
Mean z-score	-2.23
Structure conservation index	0.78
SVM decision value	1.23
SVM RNA-class probability	0.933427
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21042879 108 + 23771897
UCAAAGCGAAGCGCCGUUCCAGUCUGGGAAUGGGAACCCAUG------------UACAUACAUAUCUACUUGUGUAUGUAUGGAGCUGCCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAG
.....((((.((.(((((((......)))))))((.(((..(------------((((((((((......)))))))))))((((((......))))))...))).))))...)).)).. ( -40.80)
>DroSec_CAF1 98138 117 + 1
UCAAAGCGAAGCGCCGUUCCAGUCUGGGAAUGGGAACCCAUGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG---CCUGGAGCUCUUCAGGGAUUGUGAGUCAGCAG
.....((((..(((.(((((.(((..(..((((....))))..)..)))....((((((((((((....))))))))))))((((---(.....)))))...))))).)))..)).)).. ( -40.50)
>DroSim_CAF1 4367 117 + 1
UCAAAGCGAAGCGCCGUUCCAGUCUGGGAAUGGGAACCCAUGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG---CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAG
.....((((..(((.(((((((((((((........)))).))))))).)).........(((((((((....)))))))))((.---((((((....))))))..)))))..)).)).. ( -40.90)
>DroEre_CAF1 20277 113 + 1
CCAAAGCGAAGCGCCGUUCCAGUCUGGGAAUGGGAUCCCAUGGUUGGGUACAUACUUGUACAUGUGUA----UGUAUGUACGGAG---CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAC
.....((((.((.(((((((......)))))))((((((..((((..((((((((..((((....)))----)))))))))..))---))((((....))))))))))))...)).)).. ( -43.60)
>consensus
UCAAAGCGAAGCGCCGUUCCAGUCUGGGAAUGGGAACCCAUGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG___CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAG
.....((((..(((.(((((((((((((........)))).)))))).........(((((((((........)))))))))......((((((....))))))))).)))..)).)).. (-32.30 = -32.67 +   0.38)

alignment

secondary structure

dotplot

Window 7

Location	21,042,919 – 21,043,027
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.78
Mean single sequence MFE	-34.95
Consensus MFE	-25.27
Energy contribution	-24.78
Covariance contribution	-0.50
Combinations/Pair	1.11
Mean z-score	-2.37
Structure conservation index	0.72
SVM decision value	1.07
SVM RNA-class probability	0.910490
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21042919 108 + 23771897
UG------------UACAUACAUAUCUACUUGUGUAUGUAUGGAGCUGCCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAGAGUUUUGGCUAAGAAAUCUGCUAAAAAUAUAAGCCUCGAU
.(------------((((((((((......)))))))))))(..(((.((((((....))))))((.(....)))((((((.((((.....)))).)))))).........)))..)... ( -35.40)
>DroSec_CAF1 98178 117 + 1
UGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG---CCUGGAGCUCUUCAGGGAUUGUGAGUCAGCAGAGUUUUGGCUAAGAAAUCUGCUAAAAAUAUAAGCCUCGAU
.((((((.(((((.......(((((((((....)))))))))...---((((((....))))))..)))))..))((((((.((((.....)))).)))))).........))))..... ( -36.20)
>DroSim_CAF1 4407 117 + 1
UGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG---CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAGAGUUUUGGCUAAGAAAUCUGCUAAAAAUAUAAGCCUCGAU
.((((.(((.((........(((((((((....)))))))))((.---((((((....))))))..)).)).)))((((((.((((.....)))).)))))).........))))..... ( -35.60)
>DroEre_CAF1 20317 113 + 1
UGGUUGGGUACAUACUUGUACAUGUGUA----UGUAUGUACGGAG---CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCACAGUUUUGGCUAAGAAAUCUGCUAAAAAUAUAAGCCUCGAU
.((((..(((((....))))).(((((.----((....(((((..---((((((....))))))..)))))...))))))).(((((((..(....)..))))))).....))))..... ( -32.60)
>consensus
UGGCUGGGCACAAAUGUAUACAUAUGUACAUGUGUAUGUAUGGAG___CCUGGAGCUCUUCAGGGAUCGUGAGUCAGCAGAGUUUUGGCUAAGAAAUCUGCUAAAAAUAUAAGCCUCGAU
................(((((((((........)))))))))(((...((((((....))))))...........((((((.((((.....)))).))))))............)))... (-25.27 = -24.78 +  -0.50)

alignment

secondary structure

dotplot

Window 8

Location	21,042,919 – 21,043,027
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.78
Mean single sequence MFE	-25.08
Consensus MFE	-16.70
Energy contribution	-16.82
Covariance contribution	0.12
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.67
SVM decision value	0.09
SVM RNA-class probability	0.576420
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21042919 108 - 23771897
AUCGAGGCUUAUAUUUUUAGCAGAUUUCUUAGCCAAAACUCUGCUGACUCACGAUCCCUGAAGAGCUCCAGGCAGCUCCAUACAUACACAAGUAGAUAUGUAUGUA------------CA
...(..(((.......(((((((((((........))).)))))))).........((((........)))).)))..).((((((((..........))))))))------------.. ( -23.00)
>DroSec_CAF1 98178 117 - 1
AUCGAGGCUUAUAUUUUUAGCAGAUUUCUUAGCCAAAACUCUGCUGACUCACAAUCCCUGAAGAGCUCCAGG---CUCCAUACAUACACAUGUACAUAUGUAUACAUUUGUGCCCAGCCA
.....((((.......(((((((((((........))).))))))))..(((((........((((.....)---))).(((((((..........)))))))....)))))...)))). ( -26.10)
>DroSim_CAF1 4407 117 - 1
AUCGAGGCUUAUAUUUUUAGCAGAUUUCUUAGCCAAAACUCUGCUGACUCACGAUCCCUGAAGAGCUCCAGG---CUCCAUACAUACACAUGUACAUAUGUAUACAUUUGUGCCCAGCCA
.....((((.......(((((((((((........))).))))))))..(((((........((((.....)---))).(((((((..........)))))))....)))))...)))). ( -25.80)
>DroEre_CAF1 20317 113 - 1
AUCGAGGCUUAUAUUUUUAGCAGAUUUCUUAGCCAAAACUGUGCUGACUCACGAUCCCUGAAGAGCUCCAGG---CUCCGUACAUACA----UACACAUGUACAAGUAUGUACCCAACCA
...(((.((....(((((((..((((..(((((((....)).))))).....)))).))))))).....)).---))).((((((((.----(((....)))...))))))))....... ( -25.40)
>consensus
AUCGAGGCUUAUAUUUUUAGCAGAUUUCUUAGCCAAAACUCUGCUGACUCACGAUCCCUGAAGAGCUCCAGG___CUCCAUACAUACACAUGUACAUAUGUAUACAUUUGUGCCCAGCCA
...(((..........(((((((((((........))).)))))))).........((((........))))...))).(((((((..........)))))))................. (-16.70 = -16.82 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:52 2006