Locus 2939

Sequence ID	X_DroMel_CAF1
Location	7,872,196 – 7,872,338
Length	142
Max. P	0.929864

overview

Window 0

Location	7,872,196 – 7,872,311
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.20
Mean single sequence MFE	-34.90
Consensus MFE	-21.29
Energy contribution	-22.58
Covariance contribution	1.29
Combinations/Pair	1.08
Mean z-score	-2.08
Structure conservation index	0.61
SVM decision value	0.95
SVM RNA-class probability	0.888306
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7872196 115 + 22224390
---GGGAUCAUGGGACAUGGUAGAUGG-GCUACCAACAGCCAGGAGCUUACCACAUGCAC-CCAUGUGUUUCUUUCACAAAAAGGGGAAUCCUCUAGUCGCCCCAUUCGAUUCCCUAUUA
---(((((((((((.(.((((.(.(((-....))).).))))((((.....((((((...-.))))))(..((((.....))))..)....))))....).)))))..))))))...... ( -33.70)
>DroSec_CAF1 3925 116 + 1
---GGGAUCAUGGGACAUGGUAGAUGGGGCUACCAGCAGCCAGGAGCUUACCACAUGCACCCCAUGUGUUUCUUUCACAA-AAGGGGAAUCCCCCAGUCGCCUCAUUCCAUUCCCUGUUA
---((((..((((((...(((...(((((......(((....((......))...))).((((.((((.......)))).-..))))....)))))...)))...))))))))))..... ( -39.50)
>DroSim_CAF1 3915 114 + 1
---GGGAUCAUGGGACAUGGUAGAUGG-GCUACCAGCAGCCAGGAGCUUACCACAUGCAC-CCAUGUGUUUCUUUCACAA-AAGGGGAAUCCCCCAGUCGCCUCGUUCCAUUCCCUGUUA
---((((..(((((((.((((.(.(((-....))).).))))(..((....((((((...-.))))))............-..((((....))))....))..))))))))))))..... ( -40.80)
>DroEre_CAF1 3950 88 + 1
---GGGACCAUGGGACAUGGUAGAUGG-GCUUCCAGCAGCCAGGAGCUUACCACAUGCAC-CCAUGUGUUACUUUUCCA--------------------------UUCCAU-CCCUUUAA
---((((..((((((...(((((.(((-(((.((........)))))))).((((((...-.))))))))))).)))))--------------------------)....)-)))..... ( -26.60)
>DroYak_CAF1 5295 94 + 1
GUGGGGAUCAUGGGACAUGGUAGAUGG-GCUACCAGCAGCCAGGAGCUUACCACAUGCAC-CCAUGUGUUUCCUUUACAA-AAGGA-------------------UUC----CCCUUUAA
..(((((.((((((...((((((....-.))))))(((....((......))...))).)-)))))....(((((.....-)))))-------------------.))----)))..... ( -33.90)
>consensus
___GGGAUCAUGGGACAUGGUAGAUGG_GCUACCAGCAGCCAGGAGCUUACCACAUGCAC_CCAUGUGUUUCUUUCACAA_AAGGGGAAUCC_C_AGUCGCC_C_UUCCAUUCCCUGUUA
...(((....(((....((((((......))))))....)))((((.....((((((.....))))))...............((((....))))..........))))...)))..... (-21.29 = -22.58 +   1.29)

alignment

secondary structure

dotplot

Window 1

Location	7,872,232 – 7,872,338
Length	106
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-18.01
Consensus MFE	-12.87
Energy contribution	-13.56
Covariance contribution	0.69
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.71
SVM decision value	1.20
SVM RNA-class probability	0.929864
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7872232 106 + 22224390
CAGGAGCUUACCACAUGCAC-CCAUGUGUUUCUUUCACAAAAAGGGGAAUCCUCUAGUCGCCCCAUUCGAUUCCCUAUUAAUCCAACCCUAUCAGUACCUUCACGCU
.(((.(((...((((((...-.))))))...............((((((((.................)))))))).................))).)))....... ( -19.53)
>DroSec_CAF1 3962 105 + 1
CAGGAGCUUACCACAUGCACCCCAUGUGUUUCUUUCACAA-AAGGGGAAUCCCCCAGUCGCCUCAUUCCAUUCCCUGUUAAUCCAACCCUAUCAGU-CCUUCACGCU
((((.......((((((.....))))))............-..((((....))))..................))))...................-.......... ( -18.20)
>DroSim_CAF1 3951 104 + 1
CAGGAGCUUACCACAUGCAC-CCAUGUGUUUCUUUCACAA-AAGGGGAAUCCCCCAGUCGCCUCGUUCCAUUCCCUGUUAAUCCAACCCUAUCAGU-CCUUCACGCU
..(((((....((((((...-.))))))............-..((((....)))).........)))))...........................-.......... ( -20.90)
>DroYak_CAF1 5334 81 + 1
CAGGAGCUUACCACAUGCAC-CCAUGUGUUUCCUUUACAA-AAGGA-------------------UUC----CCCUUUAAAUCCAACUCUAUCAGU-CCUUCAAUCA
.((((......((((((...-.))))))............-..(((-------------------((.----.......)))))...........)-)))....... ( -13.40)
>consensus
CAGGAGCUUACCACAUGCAC_CCAUGUGUUUCUUUCACAA_AAGGGGAAUCCCCCAGUCGCCUCAUUCCAUUCCCUGUUAAUCCAACCCUAUCAGU_CCUUCACGCU
.(((.(((...((((((.....))))))...............(((((((...................))))))).................))).)))....... (-12.87 = -13.56 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:12 2006